{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# 1. Get data & packages" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Data was downloaded from Globus (globus.org). It was sent in two zipped files, one from each lane, containing separate files for each sample (demultiplexed). \n", "\n", "I then checked that the md5 values were the same using `md5 [filename].tar.gz >> [filename].md5` (this appened the new value in the .md5 file, so I could compare). \n", "\n", "### A note on data accessibility & my working environment\n", "\n", "I originally downloaded data to Ostrich, thinking that I could work on that computer remotely using Remote Desktop and Jupyter Notebook. However, my internet connection is too slow to work productively that way. I therefore also downloaded the data to my external hard drive, and worked locally. This also allows me to use all the packages that I had installed on my personal computer in 2018 (which is helpful). \n", "\n", "Canonical versions of the data is saved to Owl/Nightengales in the zipped format here: [nightingales/O_lurida/2020-04-21_QuantSeq-data/](http://owl.fish.washington.edu/nightingales/O_lurida/2020-04-21_QuantSeq-data/) and as individual fastq/sample here [nightingales/O_lurida/](http://owl.fish.washington.edu/nightingales/O_lurida/), and to Gannet as individual fastq/sample here [Atumefaciens/20200426_olur_fastqc_quantseq/](https://gannet.fish.washington.edu/Atumefaciens/20200426_olur_fastqc_quantseq/). \n", "\n", "Sam also ran MultiQC on my samples; check out his [notebook entry](https://robertslab.github.io/sams-notebook/2020/04/26/FastQC-MultiQC-Laura-Spencer's-QuantSeq-Data.html), and the [MultiQC report](https://gannet.fish.washington.edu/Atumefaciens/20200426_olur_fastqc_quantseq/multiqc_report.html)." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Create path variables, i.e. shortcuts to certain directories \n", "\n", "To start, create some variables for commonly accessed paths. NOTE: many of the steps in this workflow require the me to be located within a specific directory to access files. So, while I try to use these path variables, I often have to hard-code my paths. " ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [], "source": [ "# create path variable to raw data, saved on my external hard drive \n", "workingdir = \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/\"" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Bumblebee/O.lurida_QuantSeq-2020\n" ] } ], "source": [ "cd {workingdir}" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "# create path variable to fastqc directory \n", "fastqc = \"/Applications/bioinformatics/FastQC/\"" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "FastQC v0.11.8\r\n" ] } ], "source": [ "# test fqstqc \n", "! {fastqc}fastqc --version" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### I installed MultiQC using git clone via the following: \n", "\n", " git clone https://github.com/ewels/MultiQC.git\n", " cd MultiQC\n", " pip install ." ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "multiqc, version 1.9.dev0\r\n" ] } ], "source": [ "# test multiqc \n", "! multiqc --version" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Install Cutadapt \n", "\n", "The [Cutadapt program](https://cutadapt.readthedocs.io/en/stable/installation.html) is used in the tagseq processing pipeline. I installed `cutadapt` using `python3 -m pip install --user --upgrade cutadapt`. During install, I received this warning: \n", "\n", " WARNING: The script cutadapt is installed in '/Users/laura/.local/bin' which is not on PATH.\n", " Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.\n", " \n", "So, I added that path to my PATH using the following in Terminal: \n", "`PATH=$PATH:/Users/laura/.local/bin`\n", "\n", "For some reason Jupyter Notebook doesn't recognize `cutadapt`, even though I can access it via the Terminal. " ] }, { "cell_type": "code", "execution_count": 109, "metadata": {}, "outputs": [], "source": [ "# Try to add the path here \n", "! PATH=$PATH:/Users/laura/.local/bin" ] }, { "cell_type": "code", "execution_count": 113, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/bin/sh: cutadapt: command not found\r\n" ] } ], "source": [ "# Still doesn't work \n", "! cutadapt --version" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "2.10\r\n" ] } ], "source": [ "# Hard coding the cutadapt path works, though \n", "! /Users/laura/.local/bin/cutadapt --version" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "usage: fastq_quality_filter [-h] [-v] [-q N] [-p N] [-z] [-i INFILE] [-o OUTFILE]\r\n", "Part of FASTX Toolkit 0.0.14 by A. Gordon (assafgordon@gmail.com)\r\n", "\r\n", " [-h] = This helpful help screen.\r\n", " [-q N] = Minimum quality score to keep.\r\n", " [-p N] = Minimum percent of bases that must have [-q] quality.\r\n", " [-z] = Compress output with GZIP.\r\n", " [-i INFILE] = FASTA/Q input file. default is STDIN.\r\n", " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\r\n", " [-v] = Verbose - report number of sequences.\r\n", " If [-o] is specified, report will be printed to STDOUT.\r\n", " If [-o] is not specified (and output goes to STDOUT),\r\n", " report will be printed to STDERR.\r\n", "\r\n" ] } ], "source": [ "# test fastq_quality_filter (see if it's correctly added to my PATH)\n", "! fastq_quality_filter -h" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Unpack raw data \n", "\n", "Currently, the data is still zipped (that's how it arrived via Globus). I need to thus tar/gunzip the lane files, before I can gunzip the individual library files. " ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Bumblebee/O.lurida_QuantSeq-2020/raw-data\n" ] } ], "source": [ "cd raw-data/" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[31mBatch1_69plex_lane1.md5\u001b[m\u001b[m* \u001b[31mkey\u001b[m\u001b[m*\r\n", "\u001b[31mBatch1_69plex_lane1.tar.gz\u001b[m\u001b[m* \u001b[31mquantseq2020_key.csv\u001b[m\u001b[m*\r\n", "\u001b[31mBatch2_77plex_lane2_md5\u001b[m\u001b[m* \u001b[31mquantseq2020_key.xlsx\u001b[m\u001b[m*\r\n", "\u001b[31mBatch2_77plex_lane2_tar.gz\u001b[m\u001b[m* \u001b[30m\u001b[43mtest-batch\u001b[m\u001b[m/\r\n" ] } ], "source": [ "ls" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "a856ffbe2bf102b07ee78607946a463b Batch1_69plex_lane1.tar.gz\n", "MD5 (Batch1_69plex_lane1.tar.gz) = a856ffbe2bf102b07ee78607946a463b\n" ] } ], "source": [ "# check md5's for batch1.tar.gz compared to md5 that seq. facility sent \n", "! cat Batch1_69plex_lane1.md5\n", "! md5 Batch1_69plex_lane1.tar.gz" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "56decbd72a38b6076de6a421cfddf9c5 Batch2_77plex_lane2_tar.gz\n", "MD5 (Batch2_77plex_lane2_tar.gz) = 56decbd72a38b6076de6a421cfddf9c5\n" ] } ], "source": [ "# check md5's for batch2.tar.gz compared to md5 that seq. facility sent\n", "! cat Batch2_77plex_lane2_md5\n", "! md5 Batch2_77plex_lane2_tar.gz" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [], "source": [ "# extract batch/lane 1 data \n", "! gunzip -c Batch1_69plex_lane1.tar.gz | tar xopf -" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [], "source": [ "# extract batch/lane 2 data \n", "! gunzip -c Batch2_77plex_lane2_tar.gz | tar xopf -" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[31mBatch1_69plex_lane1.md5\u001b[m\u001b[m \u001b[31mBatch2_77plex_lane2_tar.gz\u001b[m\u001b[m\r\n", "\u001b[31mBatch1_69plex_lane1.tar.gz\u001b[m\u001b[m \u001b[31mkey\u001b[m\u001b[m\r\n", "\u001b[30m\u001b[43mBatch1_69plex_lane1_done\u001b[m\u001b[m \u001b[31mquantseq2020_key.csv\u001b[m\u001b[m\r\n", "\u001b[30m\u001b[43mBatch2_77plex_lane2_done\u001b[m\u001b[m \u001b[31mquantseq2020_key.xlsx\u001b[m\u001b[m\r\n", "\u001b[31mBatch2_77plex_lane2_md5\u001b[m\u001b[m \u001b[30m\u001b[43mtest-batch\u001b[m\u001b[m\r\n" ] } ], "source": [ "# check out resulting file structure \n", "! ls" ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[31m137_S63_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m314_S49_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m139_S54_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m315_S26_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m140_S64_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m316_S9_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m141_S61_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m317_S33_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m156_S66_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m318_S6_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m159_S68_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m319_S52_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m161_S57_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m321_S29_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m162_S62_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m322_S8_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m168_S67_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m323_S39_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m169_S65_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m324_S47_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m171_S58_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m325_S13_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m172_S59_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m326_S38_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m181_S69_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m327_S37_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m183_S56_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m328_S12_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m184_S55_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m329_S46_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m185_S60_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m331_S53_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m291_S42_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m332_S48_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m292_S32_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m333_S30_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m293_S11_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m334_S50_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m294_S7_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m335_S31_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m295_S41_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m336_S51_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m296_S40_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m337_S35_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m298_S25_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m338_S4_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m299_S21_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m339_S10_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m301_S22_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m341_S19_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m302_S15_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m342_S23_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m303_S17_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m343_S14_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m304_S24_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m344_S27_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m305_S1_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m345_S16_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m306_S44_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m346_S18_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m307_S45_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m347_S43_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m308_S5_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m348_S3_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m309_S20_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31m349_S34_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n", "\u001b[31m311_S2_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[30m\u001b[43mReports\u001b[m\u001b[m\r\n", "\u001b[31m312_S28_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[30m\u001b[43mStats\u001b[m\u001b[m\r\n", "\u001b[31m313_S36_L001_R1_001.fastq.gz\u001b[m\u001b[m \u001b[31mUndetermined_S0_L001_R1_001.fastq.gz\u001b[m\u001b[m\r\n" ] } ], "source": [ "! ls Batch1_69plex_lane1_done/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Move to each batch's directory containing demultiplexed library files, and gunzip all fastq files in that folder" ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Bumblebee/O.lurida_QuantSeq-2020/raw-data/Batch1_69plex_lane1_done\n" ] } ], "source": [ "cd Batch1_69plex_lane1_done/" ] }, { "cell_type": "code", "execution_count": 27, "metadata": {}, "outputs": [], "source": [ "! gunzip *.fastq.gz" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Bumblebee/O.lurida_QuantSeq-2020/raw-data/Batch2_77plex_lane2_done\n" ] } ], "source": [ "cd ../Batch2_77plex_lane2_done/" ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [], "source": [ "! gunzip *.fastq.gz " ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[31m34_S68_L002_R1_001.fastq\u001b[m\u001b[m \u001b[31m482_S25_L002_R1_001.fastq\u001b[m\u001b[m\r\n", "\u001b[31m35_S72_L002_R1_001.fastq\u001b[m\u001b[m \u001b[31m483_S7_L002_R1_001.fastq\u001b[m\u001b[m\r\n", "\u001b[31m37_S70_L002_R1_001.fastq\u001b[m\u001b[m \u001b[31m484_S43_L002_R1_001.fastq\u001b[m\u001b[m\r\n", "\u001b[31m39_S52_L002_R1_001.fastq\u001b[m\u001b[m \u001b[31m485_S21_L002_R1_001.fastq\u001b[m\u001b[m\r\n", "\u001b[31m401_S10_L002_R1_001.fastq\u001b[m\u001b[m \u001b[31m487_S6_L002_R1_001.fastq\u001b[m\u001b[m\r\n", "\u001b[31m402_S5_L002_R1_001.fastq\u001b[m\u001b[m 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Initial QC " ] }, { "cell_type": "code", "execution_count": 45, "metadata": {}, "outputs": [], "source": [ "! mkdir {workingdir}qc-processing/fastqc/" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [], "source": [ "! mkdir {workingdir}qc-processing/fastqc/untrimmed/" ] }, { "cell_type": "code", "execution_count": 49, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Started analysis of 506_S47_L002_R1_001.fastq\n", "Approx 5% complete for 506_S47_L002_R1_001.fastq\n", "Approx 10% complete for 506_S47_L002_R1_001.fastq\n", "Approx 15% complete for 506_S47_L002_R1_001.fastq\n", "Approx 20% complete for 506_S47_L002_R1_001.fastq\n", "Approx 25% complete for 506_S47_L002_R1_001.fastq\n", "Approx 30% complete for 506_S47_L002_R1_001.fastq\n", "Approx 35% complete for 506_S47_L002_R1_001.fastq\n", "Approx 40% complete for 506_S47_L002_R1_001.fastq\n", "Approx 45% complete for 506_S47_L002_R1_001.fastq\n", "Approx 50% complete for 506_S47_L002_R1_001.fastq\n", "Approx 55% complete for 506_S47_L002_R1_001.fastq\n", "Approx 60% complete for 506_S47_L002_R1_001.fastq\n", "Approx 65% complete for 506_S47_L002_R1_001.fastq\n", "Approx 70% complete for 506_S47_L002_R1_001.fastq\n", "Approx 75% complete for 506_S47_L002_R1_001.fastq\n", "Approx 80% complete for 506_S47_L002_R1_001.fastq\n", "Approx 85% complete for 506_S47_L002_R1_001.fastq\n", "Approx 90% complete for 506_S47_L002_R1_001.fastq\n", "Approx 95% complete for 506_S47_L002_R1_001.fastq\n", "Analysis complete for 506_S47_L002_R1_001.fastq\n" ] } ], "source": [ "# test fastqc on one sample file \n", "! {fastqc}fastqc \\\n", "506_S47_L002_R1_001.fastq \\\n", "--outdir ../fastqc/untrimmed/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Run fastqc on all .fastq files in Batch/Lane2, the larval data (current directory) " ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [], "source": [ "! {fastqc}fastqc \\\n", "*.fastq \\\n", "--outdir {workingdir}qc-processing/fastqc/untrimmed/ \\\n", "--quiet" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[31m34_S68_L002_R1_001_fastqc.html\u001b[m\u001b[m \u001b[31m481_S57_L002_R1_001_fastqc.html\u001b[m\u001b[m\r\n", "\u001b[31m34_S68_L002_R1_001_fastqc.zip\u001b[m\u001b[m \u001b[31m481_S57_L002_R1_001_fastqc.zip\u001b[m\u001b[m\r\n", "\u001b[31m35_S72_L002_R1_001_fastqc.html\u001b[m\u001b[m \u001b[31m482_S25_L002_R1_001_fastqc.html\u001b[m\u001b[m\r\n", "\u001b[31m35_S72_L002_R1_001_fastqc.zip\u001b[m\u001b[m \u001b[31m482_S25_L002_R1_001_fastqc.zip\u001b[m\u001b[m\r\n", "\u001b[31m37_S70_L002_R1_001_fastqc.html\u001b[m\u001b[m \u001b[31m483_S7_L002_R1_001_fastqc.html\u001b[m\u001b[m\r\n", "\u001b[31m37_S70_L002_R1_001_fastqc.zip\u001b[m\u001b[m \u001b[31m483_S7_L002_R1_001_fastqc.zip\u001b[m\u001b[m\r\n", 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"source": [ "# check out resulting fastqc files. \n", "! ls {workingdir}qc-processing/fastqc/untrimmed/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Run fastqc on all fastq files in Batch/Lane 1, the adult ctenidia+juvenile samples " ] }, { "cell_type": "code", "execution_count": 34, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Bumblebee/O.lurida_QuantSeq-2020/raw-data/Batch1_69plex_lane1_done\n" ] } ], "source": [ "cd {workingdir}raw-data/Batch1_69plex_lane1_done/" ] }, { "cell_type": "code", "execution_count": 35, "metadata": {}, "outputs": [], "source": [ "! {fastqc}fastqc \\\n", "*.fastq \\\n", "--outdir {workingdir}qc-processing/fastqc/untrimmed/ \\\n", "--quiet" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Generate a MultiQC report on all untrimmed data files " ] }, { "cell_type": "code", "execution_count": 36, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;30m[INFO ]\u001b[0m multiqc : This is MultiQC v1.9.dev0\n", "\u001b[1;30m[INFO ]\u001b[0m multiqc : Template : default\n", "\u001b[1;30m[INFO ]\u001b[0m multiqc : Searching : /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/fastqc/untrimmed\n", "\u001b[1;30m[INFO ]\u001b[0m fastqc : Found 148 reports\n", "\u001b[1;30m[INFO ]\u001b[0m multiqc : Compressing plot data\n", "\u001b[1;30m[INFO ]\u001b[0m multiqc : Report : ../../qc-processing/fastqc/untrimmed/multiqc_report_untrimmed.html\n", "\u001b[1;30m[INFO ]\u001b[0m multiqc : Data : ../../qc-processing/fastqc/untrimmed/multiqc_report_untrimmed_data\n", "\u001b[1;30m[INFO ]\u001b[0m multiqc : MultiQC complete\n" ] } ], "source": [ "! multiqc {workingdir}qc-processing/fastqc/untrimmed/ \\\n", "--filename {workingdir}qc-processing/fastqc/untrimmed/multiqc_report_untrimmed.html" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Inspect MultiQC report" ] }, { "cell_type": "code", "execution_count": 38, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", " \n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "MultiQC Report\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", " \n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
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        \n", " MultiQC: Summarize analysis results for multiple tools and samples in a single report
        \n", " Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        \n", " Bioinformatics (2016)
        \n", " doi: 10.1093/bioinformatics/btw354
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        MultiQC is published in Bioinformatics:

        \n", "
        \n", " MultiQC: Summarize analysis results for multiple tools and samples in a single report
        \n", " Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        \n", " Bioinformatics (2016)
        \n", " doi: 10.1093/bioinformatics/btw354
        \n", " PMID: 27312411\n", "
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        \n", " A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.\n", "

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         Loading report..
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        Report generated on 2020-05-19, 13:34 based on data in:\n", " /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/fastqc/untrimmed\n", " \n", "

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        \n", "\n", "
        \n", " \n", " \n", " \n", " Welcome! Not sure where to start?  \n", " Watch a tutorial video\n", "   (6:06)\n", "
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        General Statistics

        \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " Showing 148/148 rows and 3/5 columns.\n", " \n", "
        \n", "
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        Sample Name% Dups% GCLength% FailedM Seqs
        137_S63_L001_R1_001
        45.9%
        35%
        100 bp
        27%
        6.4
        139_S54_L001_R1_001
        34.8%
        35%
        100 bp
        27%
        2.3
        140_S64_L001_R1_001
        46.4%
        35%
        100 bp
        27%
        5.9
        141_S61_L001_R1_001
        35.0%
        35%
        100 bp
        27%
        2.0
        156_S66_L001_R1_001
        56.4%
        33%
        100 bp
        36%
        5.2
        159_S68_L001_R1_001
        57.8%
        33%
        100 bp
        36%
        9.2
        161_S57_L001_R1_001
        45.3%
        35%
        100 bp
        27%
        6.9
        162_S62_L001_R1_001
        46.3%
        33%
        100 bp
        27%
        6.3
        168_S67_L001_R1_001
        45.2%
        34%
        100 bp
        27%
        3.1
        169_S65_L001_R1_001
        53.4%
        34%
        100 bp
        36%
        11.1
        171_S58_L001_R1_001
        51.2%
        34%
        100 bp
        36%
        8.3
        172_S59_L001_R1_001
        41.4%
        35%
        100 bp
        27%
        5.0
        181_S69_L001_R1_001
        53.5%
        33%
        100 bp
        27%
        2.7
        183_S56_L001_R1_001
        44.6%
        35%
        100 bp
        27%
        9.6
        184_S55_L001_R1_001
        39.1%
        36%
        100 bp
        27%
        3.4
        185_S60_L001_R1_001
        43.8%
        35%
        100 bp
        27%
        2.2
        291_S42_L001_R1_001
        41.5%
        35%
        100 bp
        18%
        7.3
        292_S32_L001_R1_001
        33.4%
        39%
        100 bp
        18%
        5.3
        293_S11_L001_R1_001
        36.4%
        38%
        100 bp
        18%
        5.1
        294_S7_L001_R1_001
        43.2%
        36%
        100 bp
        18%
        7.4
        295_S41_L001_R1_001
        38.3%
        36%
        100 bp
        18%
        9.9
        296_S40_L001_R1_001
        38.3%
        35%
        100 bp
        18%
        12.1
        298_S25_L001_R1_001
        33.3%
        36%
        100 bp
        18%
        6.6
        299_S21_L001_R1_001
        34.4%
        38%
        100 bp
        18%
        9.8
        301_S22_L001_R1_001
        36.9%
        35%
        100 bp
        18%
        7.4
        302_S15_L001_R1_001
        32.8%
        36%
        100 bp
        18%
        10.2
        303_S17_L001_R1_001
        36.2%
        35%
        100 bp
        18%
        7.8
        304_S24_L001_R1_001
        33.4%
        37%
        100 bp
        18%
        9.0
        305_S1_L001_R1_001
        37.9%
        36%
        100 bp
        18%
        6.2
        306_S44_L001_R1_001
        44.0%
        34%
        100 bp
        18%
        8.0
        307_S45_L001_R1_001
        44.2%
        35%
        100 bp
        18%
        7.5
        308_S5_L001_R1_001
        47.3%
        36%
        100 bp
        18%
        8.2
        309_S20_L001_R1_001
        37.3%
        36%
        100 bp
        18%
        8.6
        311_S2_L001_R1_001
        36.2%
        36%
        100 bp
        18%
        7.1
        312_S28_L001_R1_001
        38.1%
        36%
        100 bp
        27%
        7.1
        313_S36_L001_R1_001
        41.1%
        36%
        100 bp
        18%
        7.0
        314_S49_L001_R1_001
        54.1%
        37%
        100 bp
        36%
        5.4
        315_S26_L001_R1_001
        35.9%
        36%
        100 bp
        18%
        9.0
        316_S9_L001_R1_001
        37.6%
        36%
        100 bp
        18%
        9.8
        317_S33_L001_R1_001
        32.4%
        37%
        100 bp
        18%
        5.9
        318_S6_L001_R1_001
        38.3%
        35%
        100 bp
        18%
        6.3
        319_S52_L001_R1_001
        57.0%
        35%
        100 bp
        27%
        8.0
        321_S29_L001_R1_001
        32.5%
        36%
        100 bp
        18%
        6.2
        322_S8_L001_R1_001
        39.0%
        36%
        100 bp
        18%
        7.6
        323_S39_L001_R1_001
        34.1%
        36%
        100 bp
        18%
        10.2
        324_S47_L001_R1_001
        43.3%
        35%
        100 bp
        18%
        8.5
        325_S13_L001_R1_001
        32.6%
        35%
        100 bp
        18%
        7.9
        326_S38_L001_R1_001
        41.4%
        35%
        100 bp
        18%
        9.1
        327_S37_L001_R1_001
        37.6%
        36%
        100 bp
        18%
        5.9
        328_S12_L001_R1_001
        31.3%
        38%
        100 bp
        18%
        12.9
        329_S46_L001_R1_001
        43.7%
        35%
        100 bp
        18%
        8.5
        331_S53_L001_R1_001
        56.5%
        39%
        100 bp
        36%
        6.9
        332_S48_L001_R1_001
        47.0%
        35%
        100 bp
        18%
        5.6
        333_S30_L001_R1_001
        36.5%
        35%
        100 bp
        18%
        5.4
        334_S50_L001_R1_001
        54.6%
        36%
        100 bp
        36%
        5.8
        335_S31_L001_R1_001
        35.5%
        36%
        100 bp
        18%
        5.4
        336_S51_L001_R1_001
        53.8%
        35%
        100 bp
        27%
        7.8
        337_S35_L001_R1_001
        45.0%
        35%
        100 bp
        18%
        10.8
        338_S4_L001_R1_001
        40.5%
        35%
        100 bp
        18%
        6.5
        339_S10_L001_R1_001
        43.2%
        36%
        100 bp
        18%
        7.4
        341_S19_L001_R1_001
        36.3%
        37%
        100 bp
        18%
        5.7
        342_S23_L001_R1_001
        40.9%
        36%
        100 bp
        18%
        8.9
        343_S14_L001_R1_001
        32.3%
        37%
        100 bp
        27%
        7.9
        344_S27_L001_R1_001
        47.1%
        38%
        100 bp
        18%
        11.1
        345_S16_L001_R1_001
        28.4%
        35%
        100 bp
        18%
        5.8
        346_S18_L001_R1_001
        33.4%
        37%
        100 bp
        18%
        5.9
        347_S43_L001_R1_001
        41.5%
        34%
        100 bp
        9%
        6.7
        348_S3_L001_R1_001
        42.1%
        36%
        100 bp
        18%
        7.3
        349_S34_L001_R1_001
        32.6%
        37%
        100 bp
        18%
        5.9
        34_S68_L002_R1_001
        74.4%
        37%
        100 bp
        36%
        6.9
        35_S72_L002_R1_001
        69.7%
        48%
        100 bp
        36%
        2.7
        37_S70_L002_R1_001
        83.3%
        39%
        100 bp
        45%
        7.6
        39_S52_L002_R1_001
        45.7%
        36%
        100 bp
        27%
        6.0
        401_S10_L002_R1_001
        65.3%
        38%
        100 bp
        18%
        4.1
        402_S5_L002_R1_001
        46.0%
        37%
        100 bp
        18%
        5.8
        403_S30_L002_R1_001
        38.8%
        36%
        100 bp
        27%
        6.8
        404_S42_L002_R1_001
        54.7%
        35%
        100 bp
        36%
        7.0
        411_S9_L002_R1_001
        49.1%
        35%
        100 bp
        27%
        6.6
        412_S74_L002_R1_001
        90.7%
        40%
        100 bp
        45%
        7.1
        413_S38_L002_R1_001
        49.3%
        35%
        100 bp
        27%
        6.4
        414_S49_L002_R1_001
        37.2%
        39%
        100 bp
        18%
        5.6
        41_S62_L002_R1_001
        72.6%
        37%
        100 bp
        36%
        8.3
        421_S22_L002_R1_001
        40.3%
        37%
        100 bp
        27%
        7.6
        431b_S8_L002_R1_001
        54.4%
        37%
        100 bp
        36%
        6.4
        432_S75_L002_R1_001
        91.1%
        43%
        100 bp
        27%
        6.0
        434_S55_L002_R1_001
        56.8%
        33%
        100 bp
        36%
        7.1
        43_S46_L002_R1_001
        44.6%
        36%
        100 bp
        18%
        7.3
        441_S73_L002_R1_001
        90.6%
        45%
        100 bp
        45%
        9.2
        442b_S60_L002_R1_001
        57.5%
        35%
        100 bp
        27%
        5.4
        443_S36_L002_R1_001
        53.6%
        34%
        100 bp
        36%
        6.2
        444_S34_L002_R1_001
        55.5%
        32%
        100 bp
        27%
        8.1
        445_S45_L002_R1_001
        40.3%
        36%
        100 bp
        27%
        6.6
        44_S71_L002_R1_001
        66.3%
        51%
        100 bp
        27%
        1.4
        451_S28_L002_R1_001
        47.0%
        35%
        100 bp
        18%
        9.1
        452b_S2_L002_R1_001
        51.2%
        37%
        100 bp
        36%
        5.6
        453_S12_L002_R1_001
        40.2%
        36%
        100 bp
        27%
        5.3
        45_S63_L002_R1_001
        67.6%
        36%
        100 bp
        27%
        7.2
        461b_S31_L002_R1_001
        46.6%
        34%
        100 bp
        27%
        4.6
        462b_S64_L002_R1_001
        57.8%
        34%
        100 bp
        36%
        10.2
        46_S66_L002_R1_001
        74.5%
        36%
        100 bp
        36%
        7.6
        471b_S51_L002_R1_001
        46.8%
        35%
        100 bp
        27%
        6.4
        472b_S48_L002_R1_001
        46.6%
        35%
        100 bp
        27%
        6.3
        473_S20_L002_R1_001
        46.6%
        35%
        100 bp
        18%
        6.6
        474_S14_L002_R1_001
        50.0%
        34%
        100 bp
        27%
        8.5
        475_S16_L002_R1_001
        48.1%
        34%
        100 bp
        18%
        7.4
        476_S17_L002_R1_001
        49.8%
        31%
        100 bp
        18%
        4.7
        477_S37_L002_R1_001
        44.1%
        37%
        100 bp
        27%
        6.6
        47_S58_L002_R1_001
        49.9%
        36%
        100 bp
        27%
        5.5
        481_S57_L002_R1_001
        49.4%
        35%
        100 bp
        27%
        7.7
        482_S25_L002_R1_001
        52.8%
        32%
        100 bp
        27%
        5.4
        483_S7_L002_R1_001
        52.6%
        36%
        100 bp
        36%
        6.1
        484_S43_L002_R1_001
        46.7%
        37%
        100 bp
        27%
        5.2
        485_S21_L002_R1_001
        42.9%
        36%
        100 bp
        27%
        7.1
        487_S6_L002_R1_001
        49.3%
        36%
        100 bp
        18%
        7.4
        488_S26_L002_R1_001
        52.2%
        31%
        100 bp
        27%
        6.9
        489_S35_L002_R1_001
        42.2%
        38%
        100 bp
        27%
        7.4
        490_S19_L002_R1_001
        40.6%
        36%
        100 bp
        27%
        6.0
        491_S50_L002_R1_001
        55.0%
        32%
        100 bp
        27%
        6.5
        492_S40_L002_R1_001
        53.9%
        33%
        100 bp
        27%
        8.0
        506_S47_L002_R1_001
        60.9%
        32%
        100 bp
        27%
        5.9
        513_S56_L002_R1_001
        41.6%
        35%
        100 bp
        18%
        6.4
        521_S65_L002_R1_001
        73.3%
        35%
        100 bp
        36%
        11.8
        522_S1_L002_R1_001
        56.0%
        34%
        100 bp
        36%
        5.9
        523_S4_L002_R1_001
        58.6%
        35%
        100 bp
        36%
        7.1
        524_S11_L002_R1_001
        49.5%
        34%
        100 bp
        18%
        6.2
        525_S18_L002_R1_001
        36.7%
        37%
        100 bp
        18%
        5.5
        526_S15_L002_R1_001
        41.2%
        36%
        100 bp
        27%
        5.3
        527_S39_L002_R1_001
        51.0%
        35%
        100 bp
        36%
        8.0
        528_S27_L002_R1_001
        45.4%
        34%
        100 bp
        18%
        8.8
        529_S53_L002_R1_001
        58.5%
        32%
        100 bp
        27%
        7.0
        531_S44_L002_R1_001
        39.9%
        37%
        100 bp
        18%
        5.1
        532_S33_L002_R1_001
        48.3%
        34%
        100 bp
        18%
        5.1
        533_S61_L002_R1_001
        50.0%
        36%
        100 bp
        18%
        5.4
        541_S41_L002_R1_001
        55.3%
        35%
        100 bp
        36%
        7.2
        542_S3_L002_R1_001
        65.0%
        34%
        100 bp
        36%
        6.3
        543_S29_L002_R1_001
        39.5%
        34%
        100 bp
        18%
        4.0
        551_S24_L002_R1_001
        47.6%
        34%
        100 bp
        18%
        7.6
        552b_S54_L002_R1_001
        49.5%
        35%
        100 bp
        27%
        4.4
        553_S23_L002_R1_001
        37.2%
        36%
        100 bp
        27%
        4.9
        554_S13_L002_R1_001
        41.5%
        37%
        100 bp
        27%
        8.1
        561_S69_L002_R1_001
        85.9%
        34%
        100 bp
        45%
        6.4
        562_S77_L002_R1_001
        74.7%
        39%
        100 bp
        36%
        16.1
        563_S59_L002_R1_001
        65.4%
        34%
        100 bp
        45%
        8.3
        564_S32_L002_R1_001
        40.2%
        36%
        100 bp
        27%
        4.6
        565_S67_L002_R1_001
        74.7%
        40%
        100 bp
        18%
        5.6
        571_S76_L002_R1_001
        79.1%
        36%
        100 bp
        45%
        1.4
        Undetermined_S0_L001_R1_001
        56.3%
        37%
        100 bp
        18%
        11.0
        Undetermined_S0_L002_R1_001
        70.4%
        39%
        100 bp
        18%
        13.6
        \n", " \n", "
        \n", "
        \n", "
        \n", "
        \n", " \n", "

        General Statistics: Columns

        \n", "
        \n", "
        \n", "

        Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

        \n", "

        \n", " \n", " \n", "

        \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
        SortVisibleGroupColumnDescriptionIDScale
        ||\n", " \n", " FastQC% Dups% Duplicate Readspercent_duplicatesNone
        ||\n", " \n", " FastQC% GCAverage % GC Contentpercent_gcNone
        ||\n", " \n", " FastQCLengthAverage Sequence Length (bp)avg_sequence_lengthNone
        ||\n", " \n", " FastQC% FailedPercentage of modules failed in FastQC report (includes those not plotted here)percent_failsNone
        ||\n", " \n", " FastQCM SeqsTotal Sequences (millions)total_sequencesread_count
        \n", "
        \n", "
        \n", "
        \n", "
        \n", "\n", "\n", " \n", "\n", "\n", " \n", "
        \n", "

        FastQC

        \n", "

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        \n", " \n", " \n", " \n", " \n", "
        \n", " \n", "

        \n", " Sequence Counts\n", " \n", " \n", " \n", "

        \n", " \n", "

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        \n", " \n", " \n", "
        \n", "

        This plot show the total number of reads, broken down into unique and duplicate\n", "if possible (only more recent versions of FastQC give duplicate info).

        \n", "

        You can read more about duplicate calculation in the\n", "FastQC documentation.\n", "A small part has been copied here for convenience:

        \n", "

        Only sequences which first appear in the first 100,000 sequences\n", "in each file are analysed. This should be enough to get a good impression\n", "for the duplication levels in the whole file. Each sequence is tracked to\n", "the end of the file to give a representative count of the overall duplication level.

        \n", "

        The duplication detection requires an exact sequence match over the whole length of\n", "the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        \n", "
        \n", " \n", "

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        \n", " \n", " \n", "
        \n", " \n", "
        \n", "
        \n", " \n", " \n", " \n", " \n", "
        \n", " \n", "

        \n", " Sequence Quality Histograms\n", " \n", " \n", " \n", "

        \n", " \n", "

        The mean quality value across each base position in the read.

        \n", " \n", " \n", "
        \n", "

        To enable multiple samples to be plotted on the same graph, only the mean quality\n", "scores are plotted (unlike the box plots seen in FastQC reports).

        \n", "

        Taken from the FastQC help:

        \n", "

        The y-axis on the graph shows the quality scores. The higher the score, the better\n", "the base call. The background of the graph divides the y axis into very good quality\n", "calls (green), calls of reasonable quality (orange), and calls of poor quality (red).\n", "The quality of calls on most platforms will degrade as the run progresses, so it is\n", "common to see base calls falling into the orange area towards the end of a read.

        \n", "
        \n", " \n", "

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        \n", " \n", "
        \n", "
        \n", " \n", " \n", " \n", " \n", "
        \n", " \n", "

        \n", " Per Sequence Quality Scores\n", " \n", " \n", " \n", "

        \n", " \n", "

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        \n", " \n", " \n", "
        \n", "

        From the FastQC help:

        \n", "

        The per sequence quality score report allows you to see if a subset of your\n", "sequences have universally low quality values. It is often the case that a\n", "subset of sequences will have universally poor quality, however these should\n", "represent only a small percentage of the total sequences.

        \n", "
        \n", " \n", "

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        \n", " \n", "
        \n", "
        \n", " \n", " \n", " \n", " \n", "
        \n", " \n", "

        \n", " Per Base Sequence Content\n", " \n", " \n", " \n", "

        \n", " \n", "

        The proportion of each base position for which each of the four normal DNA bases has been called.

        \n", " \n", " \n", "
        \n", "

        To enable multiple samples to be shown in a single plot, the base composition data\n", "is shown as a heatmap. The colours represent the balance between the four bases:\n", "an even distribution should give an even muddy brown colour. Hover over the plot\n", "to see the percentage of the four bases under the cursor.

        \n", "

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        \n", "

        From the FastQC help:

        \n", "

        Per Base Sequence Content plots out the proportion of each base position in a\n", "file for which each of the four normal DNA bases has been called.

        \n", "

        In a random library you would expect that there would be little to no difference\n", "between the different bases of a sequence run, so the lines in this plot should\n", "run parallel with each other. The relative amount of each base should reflect\n", "the overall amount of these bases in your genome, but in any case they should\n", "not be hugely imbalanced from each other.

        \n", "

        It's worth noting that some types of library will always produce biased sequence\n", "composition, normally at the start of the read. Libraries produced by priming\n", "using random hexamers (including nearly all RNA-Seq libraries) and those which\n", "were fragmented using transposases inherit an intrinsic bias in the positions\n", "at which reads start. This bias does not concern an absolute sequence, but instead\n", "provides enrichement of a number of different K-mers at the 5' end of the reads.\n", "Whilst this is a true technical bias, it isn't something which can be corrected\n", "by trimming and in most cases doesn't seem to adversely affect the downstream\n", "analysis.

        \n", "
        \n", " \n", "
        \n", "
        \n", "
        \n", " \n", " Click a sample row to see a line plot for that dataset.\n", "
        \n", "
        Rollover for sample name
        \n", " \n", "
        \n", " Position: -\n", "
        %T: -
        \n", "
        %C: -
        \n", "
        %A: -
        \n", "
        %G: -
        \n", "
        \n", "
        \n", "
        \n", " \n", "
        \n", "
        \n", "
        \n", "
        \n", " \n", " \n", "
        \n", "
        \n", " \n", " \n", " \n", " \n", "
        \n", " \n", "

        \n", " Per Sequence GC Content\n", " \n", " \n", " \n", "

        \n", " \n", "

        The average GC content of reads. Normal random library typically have a\n", " roughly normal distribution of GC content.

        \n", " \n", " \n", "
        \n", "

        From the FastQC help:

        \n", "

        This module measures the GC content across the whole length of each sequence\n", "in a file and compares it to a modelled normal distribution of GC content.

        \n", "

        In a normal random library you would expect to see a roughly normal distribution\n", "of GC content where the central peak corresponds to the overall GC content of\n", "the underlying genome. Since we don't know the the GC content of the genome the\n", "modal GC content is calculated from the observed data and used to build a\n", "reference distribution.

        \n", "

        An unusually shaped distribution could indicate a contaminated library or\n", "some other kinds of biased subset. A normal distribution which is shifted\n", "indicates some systematic bias which is independent of base position. If there\n", "is a systematic bias which creates a shifted normal distribution then this won't\n", "be flagged as an error by the module since it doesn't know what your genome's\n", "GC content should be.

        \n", "
        \n", " \n", "

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        \n", "\n", "\n", "
        \n", "\n", "
        \n", " \n", "
        \n", "
        \n", " \n", " \n", " \n", " \n", "
        \n", " \n", "

        \n", " Per Base N Content\n", " \n", " \n", " \n", "

        \n", " \n", "

        The percentage of base calls at each position for which an N was called.

        \n", " \n", " \n", "
        \n", "

        From the FastQC help:

        \n", "

        If a sequencer is unable to make a base call with sufficient confidence then it will\n", "normally substitute an N rather than a conventional base call. This graph shows the\n", "percentage of base calls at each position for which an N was called.

        \n", "

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially\n", "nearer the end of a sequence. However, if this proportion rises above a few percent\n", "it suggests that the analysis pipeline was unable to interpret the data well enough to\n", "make valid base calls.

        \n", "
        \n", " \n", "

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        \n", " \n", "
        \n", "
        \n", " \n", " \n", " \n", " \n", "
        \n", " \n", "

        \n", " Sequence Length Distribution\n", " \n", "

        \n", " \n", "
        All samples have sequences of a single length (100bp).
        \n", " \n", " \n", "
        \n", " \n", "
        \n", "
        \n", " \n", " \n", " \n", " \n", "
        \n", " \n", "

        \n", " Sequence Duplication Levels\n", " \n", " \n", " \n", "

        \n", " \n", "

        The relative level of duplication found for every sequence.

        \n", " \n", " \n", "
        \n", "

        From the FastQC Help:

        \n", "

        In a diverse library most sequences will occur only once in the final set.\n", "A low level of duplication may indicate a very high level of coverage of the\n", "target sequence, but a high level of duplication is more likely to indicate\n", "some kind of enrichment bias (eg PCR over amplification). This graph shows\n", "the degree of duplication for every sequence in a library: the relative\n", "number of sequences with different degrees of duplication.

        \n", "

        Only sequences which first appear in the first 100,000 sequences\n", "in each file are analysed. This should be enough to get a good impression\n", "for the duplication levels in the whole file. Each sequence is tracked to\n", "the end of the file to give a representative count of the overall duplication level.

        \n", "

        The duplication detection requires an exact sequence match over the whole length of\n", "the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        \n", "

        In a properly diverse library most sequences should fall into the far left of the\n", "plot in both the red and blue lines. A general level of enrichment, indicating broad\n", "oversequencing in the library will tend to flatten the lines, lowering the low end\n", "and generally raising other categories. More specific enrichments of subsets, or\n", "the presence of low complexity contaminants will tend to produce spikes towards the\n", "right of the plot.

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        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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        \n", " Overrepresented sequences\n", " \n", " \n", " \n", "

        \n", " \n", "

        The total amount of overrepresented sequences found in each library.

        \n", " \n", " \n", "
        \n", "

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be\n", "possible to show this for all samples in a MultiQC report, so instead this plot shows\n", "the number of sequences categorized as over represented.

        \n", "

        Sometimes, a single sequence may account for a large number of reads in a dataset.\n", "To show this, the bars are split into two: the first shows the overrepresented reads\n", "that come from the single most common sequence. The second shows the total count\n", "from all remaining overrepresented sequences.

        \n", "

        From the FastQC Help:

        \n", "

        A normal high-throughput library will contain a diverse set of sequences, with no\n", "individual sequence making up a tiny fraction of the whole. Finding that a single\n", "sequence is very overrepresented in the set either means that it is highly biologically\n", "significant, or indicates that the library is contaminated, or not as diverse as you expected.

        \n", "

        FastQC lists all of the sequences which make up more than 0.1% of the total.\n", "To conserve memory only sequences which appear in the first 100,000 sequences are tracked\n", "to the end of the file. It is therefore possible that a sequence which is overrepresented\n", "but doesn't appear at the start of the file for some reason could be missed by this module.

        \n", "
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        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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        \n", " \n", "

        \n", " Adapter Content\n", " \n", " \n", " \n", "

        \n", " \n", "

        The cumulative percentage count of the proportion of your\n", " library which has seen each of the adapter sequences at each position.

        \n", " \n", " \n", "
        \n", "

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        \n", "

        There may be several lines per sample, as one is shown for each adapter\n", "detected in the file.

        \n", "

        From the FastQC Help:

        \n", "

        The plot shows a cumulative percentage count of the proportion\n", "of your library which has seen each of the adapter sequences at each position.\n", "Once a sequence has been seen in a read it is counted as being present\n", "right through to the end of the read so the percentages you see will only\n", "increase as the read length goes on.

        \n", "
        \n", " \n", "

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        \n", " \n", "
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        \n", " \n", "

        \n", " Status Checks\n", " \n", " \n", " \n", "

        \n", " \n", "

        Status for each FastQC section showing whether results seem entirely normal (green),\n", "slightly abnormal (orange) or very unusual (red).

        \n", " \n", " \n", "
        \n", "

        FastQC assigns a status for each section of the report.\n", "These give a quick evaluation of whether the results of the analysis seem\n", "entirely normal (green), slightly abnormal (orange) or very unusual (red).

        \n", "

        It is important to stress that although the analysis results appear to give a pass/fail result,\n", "these evaluations must be taken in the context of what you expect from your library.\n", "A 'normal' sample as far as FastQC is concerned is random and diverse.\n", "Some experiments may be expected to produce libraries which are biased in particular ways.\n", "You should treat the summary evaluations therefore as pointers to where you should concentrate\n", "your attention and understand why your library may not look random and diverse.

        \n", "

        Specific guidance on how to interpret the output of each module can be found in the relevant\n", "report section, or in the FastQC help.

        \n", "

        In this heatmap, we summarise all of these into a single heatmap for a quick overview.\n", "Note that not all FastQC sections have plots in MultiQC reports, but all status checks\n", "are shown in this heatmap.

        \n", "
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        loading..
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        \n", " \n", " \n", " \n", " \n", " MultiQC v1.9.dev0\n", " \n", " - Written by Phil Ewels,\n", " available on GitHub.\n", "

        \n", "

        \n", " This report uses HighCharts,\n", " jQuery,\n", " jQuery UI,\n", " Bootstrap,\n", " FileSaver.js and\n", " clipboard.js.\n", "

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        Plot Table Data

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        \n", " Please select two table columns.\n", "
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        Regex Help

        \n", "
        \n", "
        \n", "

        Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.

        \n", "
        \n", "
        \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
        \n", "
        \n", " \n", "
        \n",
       "samp_1\n",
       "samp_1_edited\n",
       "samp_2\n",
       "samp_2_edited\n",
       "samp_3\n",
       "samp_3_edited\n",
       "prepended_samp_1\n",
       "tmp_samp_1_edited\n",
       "tmpp_samp_1_edited\n",
       "tmppp_samp_1_edited\n",
       "#samp_1_edited.tmp\n",
       "samp_11\n",
       "samp_11111\n",
       "
        \n", "

        See regex101.com for a more heavy duty testing suite.

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        \n", "\n", "\n", "\n" ], "text/plain": [ "" ] }, "execution_count": 38, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import IPython\n", "IPython.display.HTML(filename='/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/fastqc/untrimmed/multiqc_report_untrimmed.html')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# 3. Trim & filter\n", "\n", "### What adapters do I need to trim off? \n", "\n", "According to the QuantSeq FAQ section [\"1.13 What sequence should be trimmed?\"](https://www.lexogen.com/quantseq-3mrna-sequencing/#c873a9746c24c41e7): \n", "\n", "_The reads should be trimmed to remove adapter sequences, poly(A) / poly(T) sequences, and low quality nucleotides. Reads that are too short (i.e., <20 nt) or have generally low quality scores should be removed from the set._\n", "\n", "_As second strand synthesis is based on random priming, there may be a higher proportion of errors at the first nucleotides of the insert due to non-specific hybridization of the random primer to the cDNA template. For QuantSeq FWD data we therefore recommend using an aligner that can perform soft-clipping of the read ends (e.g., STAR aligner) during alignment, or increasing the number of allowed mismatches to 14. Alternatively, trimming the first 12 nt of Read 1 can be performed prior to alignment when using a more stringent aligner (e.g., HISAT2). While trimming the read can decrease the number of reads of suitable length for alignment, the absolute number of mapping reads may increase due to the improved read quality._\n", "\n", "As a reminder, here is how the QuantSeq libraries were generated: \n", "![read_orientation_schematic](https://github.com/fish546-2018/laura-quantseq/blob/master/references/QuantSeq_library_generation_schematic.png?raw=true)\n", "\n", "It looks like I added Illumina sequencing adapters (green) during library prep. This is confirmed in the protocol, which states that during the **First Strand cDNA Synthesis (reverse transcription) step**, \"An oligodT primer containing an Illumina-compatible sequence at its 5’ end is hybridized to the RNA and reverse transcription is performed.\" It's not clear what the Illumina-compatible sequence is. The manual does state the following \n", "\n", "Adapter sequence according to the manual: \n", "\"Read 1: Multiplexing Read 1 Sequencing Primer (not supplied): 5’ ACACTCTTTCCCTACACGACGCTCTTCCGATCT 3’\"\n", "\n", "### Universal Illumina Adapter sequence (according to fastqc) \n", "\n", "The following adapter sequences are listed in the 'FastQC/Configuration/adapter_list.txt' file: \n", " - Illumina Universal Adapter\t\t\t\t\tAGATCGGAAGAG \n", " - Illumina Small RNA 3' Adapter\t\t\t\tTGGAATTCTCGG \n", " - Illumina Small RNA 5' Adapter\t\t\t\tGATCGTCGGACT \n", " - Nextera Transposase Sequence\t\t\t\t CTGTCTCTTATA \n", " - SOLID Small RNA Adapter\t\t\t\t\t\tCGCCTTGGCCGT \n", "\n", "### Explore data: do I need to remove indices? \n", "\n", "Each entry in a FASTQ file consists of four lines:\n", " 1. Sequence identifier \n", " 2. Sequence \n", " 3. Quality score identifier line (consisting only of a +) \n", " 4. Quality score \n", " \n", "First, I will check out a few fastq files - do reads all have the index number included in the sequence, or have those been omitted? " ] }, { "cell_type": "code", "execution_count": 41, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "@A01125:63:HLYCLDRXX:2:2101:3495:1031 1:N:0:GACATC\r\n", "GCGCAAATTACCCACTCCTGGCACGGGGAGGTAGTGACGAAAAATAACAATACGGGACTCCTTCGAGGCCCCGTAATTGGAATGAGTACACTTTAAATCC\r\n", "+\r\n", "FFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF\r\n", "@A01125:63:HLYCLDRXX:2:2101:5900:1031 1:N:0:GACATC\r\n", "GGAGAATTCAAAACTGGAGACACCGCTTTGCACATTGCAATAAAACGGAACTACACGGAAGTGGTGGGACTACTTTTGAAGGCCGGAAGAGCACACGTCT\r\n", "+\r\n", "FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\r\n", "@A01125:63:HLYCLDRXX:2:2101:5954:1031 1:N:0:GACATC\r\n", "AGCAGGCCAGGGTATTGAAAATGTAATCGTTTATTAGATATAATAAAGCTTTATAATATCTGTTTCATTCTTGAATTTGAATAAAATTTTTGAATTGTAA\r\n" ] } ], "source": [ "# Sample 34 index is GACATC. \n", "! head -n 10 {workingdir}/raw-data/Batch2_77plex_lane2_done/34_S68_L002_R1_001.fastq" ] }, { "cell_type": "code", "execution_count": 42, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "@A01125:63:HLYCLDRXX:1:2101:3540:1016 1:N:0:GTCAGG\r\n", "TCCTTGTCCAGTCATATATTTCCTCTTTCGATCATTTTCTTATCAATCATTACAAAAAAAAAAAAAAAAAAAGATCGGAAGAGCACACGTCTGAACACCA\r\n", "+\r\n", "FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFF:F:FFFF,F:FFF,,FFFF,,FFF\r\n", "@A01125:63:HLYCLDRXX:1:2101:3992:1016 1:N:0:GTCAGG\r\n", "GTAGTGATTTGAGTTCAGACCGGCGCAAGCCAGGTCGGTTTCTATCTTCTTTTATAATATTCTTTTGGCATGTACGAAAGGACCGTTAAAAGAGGAAGTT\r\n", "+\r\n", "FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\r\n", "@A01125:63:HLYCLDRXX:1:2101:5746:1016 1:N:0:GTCAGG\r\n", "ACCATCACCTGGACAACTTCTGGAGGACCATCATCTGGACAACAACTACTGGTGGACCATCATTTTGACAACAACTACTGGAGGACCATAATCTAGACAA\r\n" ] } ], "source": [ "# Sample 302 index is GTCAGG. \n", "! head -n 10 {workingdir}/raw-data/Batch1_69plex_lane1_done/302_S15_L001_R1_001.fastq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Looks like all index sequences are included in the Sequence Identifier line for each read (line #1), but not in the actual sequences. Good - now I need to figure out which Illumina adapter sequences I need to trim. \n", "\n", "### Poly-a tails, etc.\n", "\n", "I inspected some fastq files to see what was happening at the 3' end of my reads. Lots of poly-a tails with up to ~18 bp, but I also found many poly-G tails. \n", "\n", "![poly tails](https://github.com/fish546-2018/laura-quantseq/blob/master/notebooks/screen-shots/2020-05-07_untrimmed-reads-poly-tails.png?raw=true)\n", "\n", "The Cutadapt poly-N trimming is quite flexible. From their manual: \n", "\n", "_If you want to trim a poly-A tail from the 3’ end of your reads, use the 3’ adapter type (-a) with an adapter sequence of many repeated A nucleotides. Starting with version 1.8 of Cutadapt, you can use the following notation to specify a sequence that consists of 100 A:_\n", "\n", " cutadapt -a \"A{100}\" -o output.fastq input.fastq\n", "\n", "_This also works when there are sequencing errors in the poly-A tail. So this read_\n", "\n", " TACGTACGTACGTACGAAATAAAAAAAAAAA\n", "\n", "_will be trimmed to:_\n", "\n", " TACGTACGTACGTACG\n", "\n", "_If for some reason you would like to use a shorter sequence of A, you can do so: The matching algorithm always picks the leftmost match that it can find, so Cutadapt will do the right thing even when the tail has more A than you used in the adapter sequence. However, sequencing errors may result in shorter matches than desired. For example, using -a \"A{10}\", the read above (where the AAAT is followed by eleven A) would be trimmed to:_\n", "\n", " TACGTACGTACGTACGAAAT" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Adaptor trimming, deduplicating, and quality filtering\n", "\n", "Run `cutadapt` to trim reads for 1) poly-A tails, 2) poly-G tails, and 3) Illumina universal adapter sequences. I also filter for quality 15 and greater, and for read lenths 20 and greater. \n", "\n", "Note: I am not hard-trimming the first 12bp. That is one of the QuantSeq manual's recommeded options, but only if I don't use a soft-clipping option (which I do, with Bowtie2 using the --local setting). Also, in my [2020-QuantSeq-Testing-Pipelines jupyter notebook](https://nbviewer.jupyter.org/github/laurahspencer/O.lurida_QuantSeq-2020/blob/master/notebooks/2020-QuantSeq-Testing-Pipelines.ipynb) I tested out a pipeline which compared alignment rates w/ and w/o hard-trimming. The highest alignment rate was achieved by NOT hard-trimming (and using local-alignment). " ] }, { "cell_type": "code", "execution_count": 44, "metadata": {}, "outputs": [], "source": [ "# start by trimming batch1\n", "! cd {workingdir}/raw-data/Batch1_69plex_lane1_done/" ] }, { "cell_type": "code", "execution_count": 47, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "137_S63_L001_R1_001.fastq\r\n", "139_S54_L001_R1_001.fastq\r\n", "140_S64_L001_R1_001.fastq\r\n", "141_S61_L001_R1_001.fastq\r\n", "156_S66_L001_R1_001.fastq\r\n", "159_S68_L001_R1_001.fastq\r\n", "161_S57_L001_R1_001.fastq\r\n", "162_S62_L001_R1_001.fastq\r\n", "168_S67_L001_R1_001.fastq\r\n", "169_S65_L001_R1_001.fastq\r\n" ] } ], "source": [ "! ls | head " ] }, { "cell_type": "code", "execution_count": 48, "metadata": {}, "outputs": [], "source": [ "mkdir {workingdir}qc-processing/cutadapt/" ] }, { "cell_type": "code", "execution_count": 56, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "'/Volumes/Bumblebee/O.lurida_QuantSeq-2020/raw-data/Batch1_69plex_lane1_done'" ] }, "execution_count": 56, "metadata": {}, "output_type": "execute_result" } ], "source": [ "pwd" ] }, { "cell_type": "code", "execution_count": 62, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 137_S63_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/137.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 84.76 s (13 us/read; 4.53 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,404,696\n", "Reads with adapters: 3,488,327 (54.5%)\n", "Reads written (passing filters): 6,248,833 (97.6%)\n", "\n", "Total basepairs processed: 640,469,600 bp\n", "Quality-trimmed: 1,425,774 bp (0.2%)\n", "Total written (filtered): 519,524,792 bp (81.1%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3357519 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.4%\n", " G: 35.2%\n", " T: 35.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t142117\t100073.4\t0\t142117\n", "4\t82436\t25018.3\t0\t82436\n", "5\t60453\t6254.6\t0\t60453\n", "6\t48613\t1563.6\t0\t48613\n", "7\t43135\t390.9\t0\t43135\n", "8\t42457\t97.7\t0\t42457\n", "9\t41784\t97.7\t0\t41784\n", "10\t39227\t97.7\t0\t39227\n", "11\t39744\t97.7\t0\t39744\n", "12\t40273\t97.7\t0\t40273\n", "13\t45196\t97.7\t0\t45196\n", "14\t46589\t97.7\t0\t46589\n", "15\t43308\t97.7\t0\t43308\n", "16\t44935\t97.7\t0\t44935\n", "17\t49708\t97.7\t0\t49708\n", "18\t60599\t97.7\t0\t60599\n", "19\t54728\t97.7\t0\t54728\n", "20\t45288\t97.7\t0\t45288\n", "21\t45525\t97.7\t0\t45525\n", "22\t41361\t97.7\t0\t41361\n", "23\t45650\t97.7\t0\t45650\n", "24\t54467\t97.7\t0\t54467\n", "25\t54521\t97.7\t0\t54521\n", "26\t62612\t97.7\t0\t62612\n", "27\t68868\t97.7\t0\t68868\n", "28\t62466\t97.7\t0\t62466\n", "29\t58716\t97.7\t0\t58716\n", "30\t60051\t97.7\t0\t60051\n", "31\t65298\t97.7\t0\t65298\n", "32\t62416\t97.7\t0\t62416\n", "33\t55677\t97.7\t0\t55677\n", "34\t55053\t97.7\t0\t55053\n", "35\t63799\t97.7\t0\t63799\n", "36\t76751\t97.7\t0\t76751\n", "37\t86155\t97.7\t0\t86155\n", "38\t66744\t97.7\t0\t66744\n", "39\t53136\t97.7\t0\t53136\n", "40\t46818\t97.7\t0\t46818\n", "41\t50800\t97.7\t0\t50800\n", "42\t54913\t97.7\t0\t54913\n", "43\t46846\t97.7\t0\t46846\n", "44\t36007\t97.7\t0\t36007\n", "45\t45295\t97.7\t0\t45295\n", "46\t53637\t97.7\t0\t53637\n", "47\t50011\t97.7\t0\t50011\n", "48\t50874\t97.7\t0\t50874\n", "49\t41390\t97.7\t0\t41390\n", "50\t39000\t97.7\t0\t39000\n", "51\t31808\t97.7\t0\t31808\n", "52\t33573\t97.7\t0\t33573\n", "53\t37243\t97.7\t0\t37243\n", "54\t42776\t97.7\t0\t42776\n", "55\t40840\t97.7\t0\t40840\n", "56\t36751\t97.7\t0\t36751\n", "57\t32744\t97.7\t0\t32744\n", "58\t34026\t97.7\t0\t34026\n", "59\t25700\t97.7\t0\t25700\n", "60\t21624\t97.7\t0\t21624\n", "61\t21005\t97.7\t0\t21005\n", "62\t17379\t97.7\t0\t17379\n", "63\t16890\t97.7\t0\t16890\n", "64\t18640\t97.7\t0\t18640\n", "65\t17523\t97.7\t0\t17523\n", "66\t14911\t97.7\t0\t14911\n", "67\t14244\t97.7\t0\t14244\n", "68\t13516\t97.7\t0\t13516\n", "69\t13496\t97.7\t0\t13496\n", "70\t14173\t97.7\t0\t14173\n", "71\t13684\t97.7\t0\t13684\n", "72\t10267\t97.7\t0\t10267\n", "73\t9431\t97.7\t0\t9431\n", "74\t9596\t97.7\t0\t9596\n", "75\t8609\t97.7\t0\t8609\n", "76\t7333\t97.7\t0\t7333\n", "77\t6462\t97.7\t0\t6462\n", "78\t7516\t97.7\t0\t7516\n", "79\t7498\t97.7\t0\t7498\n", "80\t7487\t97.7\t0\t7487\n", "81\t7190\t97.7\t0\t7190\n", "82\t7169\t97.7\t0\t7169\n", "83\t7827\t97.7\t0\t7827\n", "84\t9423\t97.7\t0\t9423\n", "85\t10992\t97.7\t0\t10992\n", "86\t10922\t97.7\t0\t10922\n", "87\t7991\t97.7\t0\t7991\n", "88\t7477\t97.7\t0\t7477\n", "89\t8177\t97.7\t0\t8177\n", "90\t8668\t97.7\t0\t8668\n", "91\t8719\t97.7\t0\t8719\n", "92\t8828\t97.7\t0\t8828\n", "93\t9409\t97.7\t0\t9409\n", "94\t9254\t97.7\t0\t9254\n", "95\t8153\t97.7\t0\t8153\n", "96\t6142\t97.7\t0\t6142\n", "97\t3820\t97.7\t0\t3820\n", "98\t2340\t97.7\t0\t2340\n", "99\t1600\t97.7\t0\t1600\n", "100\t1226\t97.7\t0\t1226\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27057 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 50.7%\n", " C: 21.2%\n", " G: 0.0%\n", " T: 27.9%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13346\t100073.4\t0\t13346\n", "4\t2858\t25018.3\t0\t2858\n", "5\t769\t6254.6\t0\t769\n", "6\t350\t1563.6\t0\t350\n", "7\t52\t390.9\t0\t52\n", "8\t50\t97.7\t0\t50\n", "9\t37\t97.7\t0\t37\n", "10\t28\t97.7\t0\t28\n", "11\t30\t97.7\t0\t30\n", "12\t32\t97.7\t0\t32\n", "13\t39\t97.7\t0\t39\n", "14\t39\t97.7\t0\t39\n", "15\t28\t97.7\t0\t28\n", "16\t34\t97.7\t0\t34\n", "17\t29\t97.7\t0\t29\n", "18\t45\t97.7\t0\t45\n", "19\t59\t97.7\t0\t59\n", "20\t46\t97.7\t0\t46\n", "21\t55\t97.7\t0\t55\n", "22\t69\t97.7\t0\t69\n", "23\t43\t97.7\t0\t43\n", "24\t46\t97.7\t0\t46\n", "25\t65\t97.7\t0\t65\n", "26\t114\t97.7\t0\t114\n", "27\t122\t97.7\t0\t122\n", "28\t161\t97.7\t0\t161\n", "29\t229\t97.7\t0\t229\n", "30\t446\t97.7\t0\t446\n", "31\t549\t97.7\t0\t549\n", "32\t943\t97.7\t0\t943\n", "33\t833\t97.7\t0\t833\n", "34\t941\t97.7\t0\t941\n", "35\t1109\t97.7\t0\t1109\n", "36\t1124\t97.7\t0\t1124\n", "37\t518\t97.7\t0\t518\n", "38\t59\t97.7\t0\t59\n", "39\t39\t97.7\t0\t39\n", "40\t32\t97.7\t0\t32\n", "41\t30\t97.7\t0\t30\n", "42\t22\t97.7\t0\t22\n", "43\t21\t97.7\t0\t21\n", "44\t23\t97.7\t0\t23\n", "45\t30\t97.7\t0\t30\n", "46\t20\t97.7\t0\t20\n", "47\t24\t97.7\t0\t24\n", "48\t31\t97.7\t0\t31\n", "49\t37\t97.7\t0\t37\n", "50\t22\t97.7\t0\t22\n", "51\t17\t97.7\t0\t17\n", "52\t21\t97.7\t0\t21\n", "53\t12\t97.7\t0\t12\n", "54\t22\t97.7\t0\t22\n", "55\t14\t97.7\t0\t14\n", "56\t21\t97.7\t0\t21\n", "57\t17\t97.7\t0\t17\n", "58\t23\t97.7\t0\t23\n", "59\t13\t97.7\t0\t13\n", "60\t20\t97.7\t0\t20\n", "61\t21\t97.7\t0\t21\n", "62\t18\t97.7\t0\t18\n", "63\t22\t97.7\t0\t22\n", "64\t16\t97.7\t0\t16\n", "65\t18\t97.7\t0\t18\n", "66\t20\t97.7\t0\t20\n", "67\t14\t97.7\t0\t14\n", "68\t18\t97.7\t0\t18\n", "69\t11\t97.7\t0\t11\n", "70\t13\t97.7\t0\t13\n", "71\t11\t97.7\t0\t11\n", "72\t6\t97.7\t0\t6\n", "73\t10\t97.7\t0\t10\n", "74\t9\t97.7\t0\t9\n", "75\t2\t97.7\t0\t2\n", "76\t5\t97.7\t0\t5\n", "77\t7\t97.7\t0\t7\n", "78\t7\t97.7\t0\t7\n", "79\t10\t97.7\t0\t10\n", "80\t9\t97.7\t0\t9\n", "81\t8\t97.7\t0\t8\n", "82\t7\t97.7\t0\t7\n", "83\t5\t97.7\t0\t5\n", "84\t10\t97.7\t0\t10\n", "85\t12\t97.7\t0\t12\n", "86\t6\t97.7\t0\t6\n", "87\t9\t97.7\t0\t9\n", "88\t9\t97.7\t0\t9\n", "89\t13\t97.7\t0\t13\n", "90\t15\t97.7\t0\t15\n", "91\t23\t97.7\t0\t23\n", "92\t31\t97.7\t0\t31\n", "93\t58\t97.7\t0\t58\n", "94\t105\t97.7\t0\t105\n", "95\t142\t97.7\t0\t142\n", "96\t110\t97.7\t0\t110\n", "97\t115\t97.7\t0\t115\n", "98\t87\t97.7\t0\t87\n", "99\t84\t97.7\t0\t84\n", "100\t153\t97.7\t0\t153\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 103751 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.7%\n", " C: 21.6%\n", " G: 14.9%\n", " T: 21.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t79723\t100073.4\t0\t79723\n", "4\t15021\t25018.3\t0\t15021\n", "5\t2610\t6254.6\t0\t2610\n", "6\t238\t1563.6\t0\t238\n", "7\t61\t390.9\t0\t61\n", "8\t55\t390.9\t0\t55\n", "9\t51\t390.9\t0\t51\n", "10\t87\t390.9\t0\t87\n", "11\t92\t390.9\t0\t92\n", "12\t88\t390.9\t0\t88\n", "13\t78\t390.9\t0\t78\n", "14\t58\t390.9\t0\t58\n", "15\t91\t390.9\t0\t91\n", "16\t67\t390.9\t0\t67\n", "17\t88\t390.9\t0\t88\n", "18\t84\t390.9\t0\t84\n", "19\t68\t390.9\t0\t68\n", "20\t76\t390.9\t0\t76\n", "21\t88\t390.9\t0\t88\n", "22\t75\t390.9\t0\t75\n", "23\t53\t390.9\t0\t53\n", "24\t62\t390.9\t0\t62\n", "25\t70\t390.9\t0\t70\n", "26\t65\t390.9\t0\t65\n", "27\t81\t390.9\t0\t81\n", "28\t74\t390.9\t0\t74\n", "29\t65\t390.9\t0\t65\n", "30\t66\t390.9\t0\t66\n", "31\t78\t390.9\t0\t78\n", "32\t87\t390.9\t0\t87\n", "33\t88\t390.9\t0\t88\n", "34\t77\t390.9\t0\t77\n", "35\t83\t390.9\t0\t83\n", "36\t75\t390.9\t0\t75\n", "37\t53\t390.9\t0\t53\n", "38\t54\t390.9\t0\t54\n", "39\t79\t390.9\t0\t79\n", "40\t78\t390.9\t0\t78\n", "41\t57\t390.9\t0\t57\n", "42\t36\t390.9\t0\t36\n", "43\t54\t390.9\t0\t54\n", "44\t53\t390.9\t0\t53\n", "45\t41\t390.9\t0\t41\n", "46\t53\t390.9\t0\t53\n", "47\t56\t390.9\t0\t56\n", "48\t57\t390.9\t0\t57\n", "49\t63\t390.9\t0\t63\n", "50\t58\t390.9\t0\t58\n", "51\t50\t390.9\t0\t50\n", "52\t69\t390.9\t0\t69\n", "53\t69\t390.9\t0\t69\n", "54\t64\t390.9\t0\t64\n", "55\t60\t390.9\t0\t60\n", "56\t51\t390.9\t0\t51\n", "57\t59\t390.9\t0\t59\n", "58\t69\t390.9\t0\t69\n", "59\t56\t390.9\t0\t56\n", "60\t64\t390.9\t0\t64\n", "61\t59\t390.9\t0\t59\n", "62\t60\t390.9\t0\t60\n", "63\t59\t390.9\t0\t59\n", "64\t60\t390.9\t0\t60\n", "65\t46\t390.9\t0\t46\n", "66\t62\t390.9\t0\t62\n", "67\t35\t390.9\t0\t35\n", "68\t47\t390.9\t0\t47\n", "69\t32\t390.9\t0\t32\n", "70\t37\t390.9\t0\t37\n", "71\t34\t390.9\t0\t34\n", "72\t53\t390.9\t0\t53\n", "73\t57\t390.9\t0\t57\n", "74\t68\t390.9\t0\t68\n", "75\t40\t390.9\t0\t40\n", "76\t73\t390.9\t0\t73\n", "77\t65\t390.9\t0\t65\n", "78\t67\t390.9\t0\t67\n", "79\t79\t390.9\t0\t79\n", "80\t89\t390.9\t0\t89\n", "81\t68\t390.9\t0\t68\n", "82\t112\t390.9\t0\t112\n", "83\t107\t390.9\t0\t107\n", "84\t74\t390.9\t0\t74\n", "85\t86\t390.9\t0\t86\n", "86\t46\t390.9\t0\t46\n", "87\t94\t390.9\t0\t94\n", "88\t60\t390.9\t0\t60\n", "89\t62\t390.9\t0\t62\n", "90\t58\t390.9\t0\t58\n", "91\t49\t390.9\t0\t49\n", "92\t43\t390.9\t0\t43\n", "93\t44\t390.9\t0\t44\n", "94\t52\t390.9\t0\t52\n", "95\t72\t390.9\t0\t72\n", "96\t49\t390.9\t0\t49\n", "97\t60\t390.9\t0\t60\n", "98\t73\t390.9\t0\t73\n", "99\t98\t390.9\t0\t98\n", "100\t96\t390.9\t0\t96\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 139_S54_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/139.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 31.11 s (13 us/read; 4.53 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 2,349,211\n", "Reads with adapters: 1,387,262 (59.1%)\n", "Reads written (passing filters): 2,237,155 (95.2%)\n", "\n", "Total basepairs processed: 234,921,100 bp\n", "Quality-trimmed: 718,641 bp (0.3%)\n", "Total written (filtered): 181,649,581 bp (77.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1339889 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.1%\n", " G: 34.8%\n", " T: 35.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t49241\t36706.4\t0\t49241\n", "4\t29141\t9176.6\t0\t29141\n", "5\t21423\t2294.2\t0\t21423\n", "6\t17392\t573.5\t0\t17392\n", "7\t15606\t143.4\t0\t15606\n", "8\t15320\t35.8\t0\t15320\n", "9\t15486\t35.8\t0\t15486\n", "10\t14345\t35.8\t0\t14345\n", "11\t14164\t35.8\t0\t14164\n", "12\t14777\t35.8\t0\t14777\n", "13\t16288\t35.8\t0\t16288\n", "14\t16719\t35.8\t0\t16719\n", "15\t15971\t35.8\t0\t15971\n", "16\t16696\t35.8\t0\t16696\n", "17\t18593\t35.8\t0\t18593\n", "18\t22735\t35.8\t0\t22735\n", "19\t20009\t35.8\t0\t20009\n", "20\t16355\t35.8\t0\t16355\n", "21\t16645\t35.8\t0\t16645\n", "22\t15136\t35.8\t0\t15136\n", "23\t16524\t35.8\t0\t16524\n", "24\t19824\t35.8\t0\t19824\n", "25\t19871\t35.8\t0\t19871\n", "26\t23195\t35.8\t0\t23195\n", "27\t25843\t35.8\t0\t25843\n", "28\t22870\t35.8\t0\t22870\n", "29\t21837\t35.8\t0\t21837\n", "30\t22699\t35.8\t0\t22699\n", "31\t26056\t35.8\t0\t26056\n", "32\t23095\t35.8\t0\t23095\n", "33\t21539\t35.8\t0\t21539\n", "34\t20057\t35.8\t0\t20057\n", "35\t24149\t35.8\t0\t24149\n", "36\t29320\t35.8\t0\t29320\n", "37\t30965\t35.8\t0\t30965\n", "38\t24991\t35.8\t0\t24991\n", "39\t19911\t35.8\t0\t19911\n", "40\t18270\t35.8\t0\t18270\n", "41\t20044\t35.8\t0\t20044\n", "42\t21728\t35.8\t0\t21728\n", "43\t18841\t35.8\t0\t18841\n", "44\t13868\t35.8\t0\t13868\n", "45\t17623\t35.8\t0\t17623\n", "46\t21209\t35.8\t0\t21209\n", "47\t21037\t35.8\t0\t21037\n", "48\t20923\t35.8\t0\t20923\n", "49\t15929\t35.8\t0\t15929\n", "50\t14964\t35.8\t0\t14964\n", "51\t14907\t35.8\t0\t14907\n", "52\t15195\t35.8\t0\t15195\n", "53\t12547\t35.8\t0\t12547\n", "54\t15332\t35.8\t0\t15332\n", "55\t15639\t35.8\t0\t15639\n", "56\t12072\t35.8\t0\t12072\n", "57\t13213\t35.8\t0\t13213\n", "58\t17268\t35.8\t0\t17268\n", "59\t12061\t35.8\t0\t12061\n", "60\t9039\t35.8\t0\t9039\n", "61\t9445\t35.8\t0\t9445\n", "62\t8061\t35.8\t0\t8061\n", "63\t7722\t35.8\t0\t7722\n", "64\t8441\t35.8\t0\t8441\n", "65\t7997\t35.8\t0\t7997\n", "66\t7037\t35.8\t0\t7037\n", "67\t6831\t35.8\t0\t6831\n", "68\t6309\t35.8\t0\t6309\n", "69\t6501\t35.8\t0\t6501\n", "70\t6811\t35.8\t0\t6811\n", "71\t6525\t35.8\t0\t6525\n", "72\t4995\t35.8\t0\t4995\n", "73\t4752\t35.8\t0\t4752\n", "74\t4890\t35.8\t0\t4890\n", "75\t4198\t35.8\t0\t4198\n", "76\t3782\t35.8\t0\t3782\n", "77\t3492\t35.8\t0\t3492\n", "78\t4131\t35.8\t0\t4131\n", "79\t4064\t35.8\t0\t4064\n", "80\t4019\t35.8\t0\t4019\n", "81\t3931\t35.8\t0\t3931\n", "82\t4202\t35.8\t0\t4202\n", "83\t4615\t35.8\t0\t4615\n", "84\t5512\t35.8\t0\t5512\n", "85\t6541\t35.8\t0\t6541\n", "86\t6831\t35.8\t0\t6831\n", "87\t5613\t35.8\t0\t5613\n", "88\t5474\t35.8\t0\t5474\n", "89\t6010\t35.8\t0\t6010\n", "90\t6365\t35.8\t0\t6365\n", "91\t6779\t35.8\t0\t6779\n", "92\t7061\t35.8\t0\t7061\n", "93\t7830\t35.8\t0\t7830\n", "94\t7367\t35.8\t0\t7367\n", "95\t6748\t35.8\t0\t6748\n", "96\t5150\t35.8\t0\t5150\n", "97\t3286\t35.8\t0\t3286\n", "98\t1855\t35.8\t0\t1855\n", "99\t1181\t35.8\t0\t1181\n", "100\t1038\t35.8\t0\t1038\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 12439 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 57.9%\n", " C: 20.4%\n", " G: 0.0%\n", " T: 21.4%\n", " none/other: 0.3%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t4688\t36706.4\t0\t4688\n", "4\t1021\t9176.6\t0\t1021\n", "5\t338\t2294.2\t0\t338\n", "6\t182\t573.5\t0\t182\n", "7\t17\t143.4\t0\t17\n", "8\t14\t35.8\t0\t14\n", "9\t11\t35.8\t0\t11\n", "10\t18\t35.8\t0\t18\n", "11\t18\t35.8\t0\t18\n", "12\t12\t35.8\t0\t12\n", "13\t11\t35.8\t0\t11\n", "14\t16\t35.8\t0\t16\n", "15\t9\t35.8\t0\t9\n", "16\t24\t35.8\t0\t24\n", "17\t21\t35.8\t0\t21\n", "18\t11\t35.8\t0\t11\n", "19\t15\t35.8\t0\t15\n", "20\t37\t35.8\t0\t37\n", "21\t34\t35.8\t0\t34\n", "22\t34\t35.8\t0\t34\n", "23\t25\t35.8\t0\t25\n", "24\t33\t35.8\t0\t33\n", "25\t35\t35.8\t0\t35\n", "26\t82\t35.8\t0\t82\n", "27\t63\t35.8\t0\t63\n", "28\t107\t35.8\t0\t107\n", "29\t158\t35.8\t0\t158\n", "30\t323\t35.8\t0\t323\n", "31\t473\t35.8\t0\t473\n", "32\t673\t35.8\t0\t673\n", "33\t626\t35.8\t0\t626\n", "34\t729\t35.8\t0\t729\n", "35\t830\t35.8\t0\t830\n", "36\t768\t35.8\t0\t768\n", "37\t300\t35.8\t0\t300\n", "38\t34\t35.8\t0\t34\n", "39\t35\t35.8\t0\t35\n", "40\t13\t35.8\t0\t13\n", "41\t11\t35.8\t0\t11\n", "42\t10\t35.8\t0\t10\n", "43\t11\t35.8\t0\t11\n", "44\t10\t35.8\t0\t10\n", "45\t11\t35.8\t0\t11\n", "46\t12\t35.8\t0\t12\n", "47\t5\t35.8\t0\t5\n", "48\t6\t35.8\t0\t6\n", "49\t12\t35.8\t0\t12\n", "50\t12\t35.8\t0\t12\n", "51\t9\t35.8\t0\t9\n", "52\t6\t35.8\t0\t6\n", "53\t6\t35.8\t0\t6\n", "54\t11\t35.8\t0\t11\n", "55\t6\t35.8\t0\t6\n", "56\t4\t35.8\t0\t4\n", "57\t6\t35.8\t0\t6\n", "58\t3\t35.8\t0\t3\n", "59\t6\t35.8\t0\t6\n", "60\t6\t35.8\t0\t6\n", "61\t4\t35.8\t0\t4\n", "62\t8\t35.8\t0\t8\n", "63\t11\t35.8\t0\t11\n", "64\t8\t35.8\t0\t8\n", "65\t6\t35.8\t0\t6\n", "66\t9\t35.8\t0\t9\n", "67\t5\t35.8\t0\t5\n", "68\t11\t35.8\t0\t11\n", "69\t7\t35.8\t0\t7\n", "70\t5\t35.8\t0\t5\n", "71\t3\t35.8\t0\t3\n", "72\t4\t35.8\t0\t4\n", "73\t4\t35.8\t0\t4\n", "74\t3\t35.8\t0\t3\n", "75\t3\t35.8\t0\t3\n", "76\t2\t35.8\t0\t2\n", "77\t2\t35.8\t0\t2\n", "78\t5\t35.8\t0\t5\n", "80\t4\t35.8\t0\t4\n", "82\t7\t35.8\t0\t7\n", "83\t4\t35.8\t0\t4\n", "84\t1\t35.8\t0\t1\n", "85\t2\t35.8\t0\t2\n", "87\t3\t35.8\t0\t3\n", "88\t2\t35.8\t0\t2\n", "89\t1\t35.8\t0\t1\n", "90\t11\t35.8\t0\t11\n", "91\t9\t35.8\t0\t9\n", "92\t8\t35.8\t0\t8\n", "93\t18\t35.8\t0\t18\n", "94\t36\t35.8\t0\t36\n", "95\t38\t35.8\t0\t38\n", "96\t47\t35.8\t0\t47\n", "97\t40\t35.8\t0\t40\n", "98\t29\t35.8\t0\t29\n", "99\t31\t35.8\t0\t31\n", "100\t47\t35.8\t0\t47\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 34934 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.6%\n", " C: 21.0%\n", " G: 15.3%\n", " T: 21.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t26625\t36706.4\t0\t26625\n", "4\t5041\t9176.6\t0\t5041\n", "5\t967\t2294.2\t0\t967\n", "6\t80\t573.5\t0\t80\n", "7\t32\t143.4\t0\t32\n", "8\t28\t143.4\t0\t28\n", "9\t34\t143.4\t0\t34\n", "10\t28\t143.4\t0\t28\n", "11\t36\t143.4\t0\t36\n", "12\t25\t143.4\t0\t25\n", "13\t28\t143.4\t0\t28\n", "14\t34\t143.4\t0\t34\n", "15\t37\t143.4\t0\t37\n", "16\t25\t143.4\t0\t25\n", "17\t26\t143.4\t0\t26\n", "18\t34\t143.4\t0\t34\n", "19\t35\t143.4\t0\t35\n", "20\t30\t143.4\t0\t30\n", "21\t31\t143.4\t0\t31\n", "22\t29\t143.4\t0\t29\n", "23\t31\t143.4\t0\t31\n", "24\t20\t143.4\t0\t20\n", "25\t28\t143.4\t0\t28\n", "26\t25\t143.4\t0\t25\n", "27\t36\t143.4\t0\t36\n", "28\t25\t143.4\t0\t25\n", "29\t33\t143.4\t0\t33\n", "30\t31\t143.4\t0\t31\n", "31\t33\t143.4\t0\t33\n", "32\t25\t143.4\t0\t25\n", "33\t26\t143.4\t0\t26\n", "34\t23\t143.4\t0\t23\n", "35\t24\t143.4\t0\t24\n", "36\t28\t143.4\t0\t28\n", "37\t25\t143.4\t0\t25\n", "38\t30\t143.4\t0\t30\n", "39\t33\t143.4\t0\t33\n", "40\t29\t143.4\t0\t29\n", "41\t23\t143.4\t0\t23\n", "42\t17\t143.4\t0\t17\n", "43\t23\t143.4\t0\t23\n", "44\t20\t143.4\t0\t20\n", "45\t15\t143.4\t0\t15\n", "46\t24\t143.4\t0\t24\n", "47\t20\t143.4\t0\t20\n", "48\t25\t143.4\t0\t25\n", "49\t19\t143.4\t0\t19\n", "50\t28\t143.4\t0\t28\n", "51\t23\t143.4\t0\t23\n", "52\t17\t143.4\t0\t17\n", "53\t25\t143.4\t0\t25\n", "54\t16\t143.4\t0\t16\n", "55\t14\t143.4\t0\t14\n", "56\t21\t143.4\t0\t21\n", "57\t19\t143.4\t0\t19\n", "58\t18\t143.4\t0\t18\n", "59\t17\t143.4\t0\t17\n", "60\t30\t143.4\t0\t30\n", "61\t15\t143.4\t0\t15\n", "62\t28\t143.4\t0\t28\n", "63\t18\t143.4\t0\t18\n", "64\t17\t143.4\t0\t17\n", "65\t14\t143.4\t0\t14\n", "66\t20\t143.4\t0\t20\n", "67\t9\t143.4\t0\t9\n", "68\t19\t143.4\t0\t19\n", "69\t24\t143.4\t0\t24\n", "70\t22\t143.4\t0\t22\n", "71\t20\t143.4\t0\t20\n", "72\t15\t143.4\t0\t15\n", "73\t14\t143.4\t0\t14\n", "74\t27\t143.4\t0\t27\n", "75\t18\t143.4\t0\t18\n", "76\t19\t143.4\t0\t19\n", "77\t28\t143.4\t0\t28\n", "78\t21\t143.4\t0\t21\n", "79\t15\t143.4\t0\t15\n", "80\t26\t143.4\t0\t26\n", "81\t21\t143.4\t0\t21\n", "82\t24\t143.4\t0\t24\n", "83\t18\t143.4\t0\t18\n", "84\t34\t143.4\t0\t34\n", "85\t32\t143.4\t0\t32\n", "86\t25\t143.4\t0\t25\n", "87\t30\t143.4\t0\t30\n", "88\t21\t143.4\t0\t21\n", "89\t14\t143.4\t0\t14\n", "90\t18\t143.4\t0\t18\n", "91\t24\t143.4\t0\t24\n", "92\t8\t143.4\t0\t8\n", "93\t15\t143.4\t0\t15\n", "94\t15\t143.4\t0\t15\n", "95\t15\t143.4\t0\t15\n", "96\t27\t143.4\t0\t27\n", "97\t21\t143.4\t0\t21\n", "98\t18\t143.4\t0\t18\n", "99\t26\t143.4\t0\t26\n", "100\t15\t143.4\t0\t15\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 140_S64_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/140.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 77.67 s (13 us/read; 4.55 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,892,333\n", "Reads with adapters: 3,249,986 (55.2%)\n", "Reads written (passing filters): 5,697,993 (96.7%)\n", "\n", "Total basepairs processed: 589,233,300 bp\n", "Quality-trimmed: 1,611,579 bp (0.3%)\n", "Total written (filtered): 469,271,636 bp (79.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3134408 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.8%\n", " G: 34.1%\n", " T: 37.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t129033\t92067.7\t0\t129033\n", "4\t76400\t23016.9\t0\t76400\n", "5\t55761\t5754.2\t0\t55761\n", "6\t43595\t1438.6\t0\t43595\n", "7\t37082\t359.6\t0\t37082\n", "8\t35707\t89.9\t0\t35707\n", "9\t34637\t89.9\t0\t34637\n", "10\t32824\t89.9\t0\t32824\n", "11\t32155\t89.9\t0\t32155\n", "12\t32683\t89.9\t0\t32683\n", "13\t35777\t89.9\t0\t35777\n", "14\t36738\t89.9\t0\t36738\n", "15\t35133\t89.9\t0\t35133\n", "16\t36338\t89.9\t0\t36338\n", "17\t40662\t89.9\t0\t40662\n", "18\t48123\t89.9\t0\t48123\n", "19\t45637\t89.9\t0\t45637\n", "20\t37918\t89.9\t0\t37918\n", "21\t38116\t89.9\t0\t38116\n", "22\t34613\t89.9\t0\t34613\n", "23\t38679\t89.9\t0\t38679\n", "24\t46898\t89.9\t0\t46898\n", "25\t48196\t89.9\t0\t48196\n", "26\t55586\t89.9\t0\t55586\n", "27\t61788\t89.9\t0\t61788\n", "28\t57168\t89.9\t0\t57168\n", "29\t54666\t89.9\t0\t54666\n", "30\t56068\t89.9\t0\t56068\n", "31\t61296\t89.9\t0\t61296\n", "32\t59003\t89.9\t0\t59003\n", "33\t51066\t89.9\t0\t51066\n", "34\t49224\t89.9\t0\t49224\n", "35\t57276\t89.9\t0\t57276\n", "36\t71113\t89.9\t0\t71113\n", "37\t82893\t89.9\t0\t82893\n", "38\t62523\t89.9\t0\t62523\n", "39\t47380\t89.9\t0\t47380\n", "40\t42593\t89.9\t0\t42593\n", "41\t44267\t89.9\t0\t44267\n", "42\t47119\t89.9\t0\t47119\n", "43\t41210\t89.9\t0\t41210\n", "44\t32340\t89.9\t0\t32340\n", "45\t41419\t89.9\t0\t41419\n", "46\t50996\t89.9\t0\t50996\n", "47\t48496\t89.9\t0\t48496\n", "48\t52459\t89.9\t0\t52459\n", "49\t41532\t89.9\t0\t41532\n", "50\t38834\t89.9\t0\t38834\n", "51\t34579\t89.9\t0\t34579\n", "52\t35877\t89.9\t0\t35877\n", "53\t32783\t89.9\t0\t32783\n", "54\t41812\t89.9\t0\t41812\n", "55\t40747\t89.9\t0\t40747\n", "56\t37064\t89.9\t0\t37064\n", "57\t33034\t89.9\t0\t33034\n", "58\t38767\t89.9\t0\t38767\n", "59\t25968\t89.9\t0\t25968\n", "60\t22145\t89.9\t0\t22145\n", "61\t22391\t89.9\t0\t22391\n", "62\t18497\t89.9\t0\t18497\n", "63\t18072\t89.9\t0\t18072\n", "64\t19886\t89.9\t0\t19886\n", "65\t18754\t89.9\t0\t18754\n", "66\t16522\t89.9\t0\t16522\n", "67\t15882\t89.9\t0\t15882\n", "68\t14764\t89.9\t0\t14764\n", "69\t14411\t89.9\t0\t14411\n", "70\t14879\t89.9\t0\t14879\n", "71\t14690\t89.9\t0\t14690\n", "72\t11751\t89.9\t0\t11751\n", "73\t10964\t89.9\t0\t10964\n", "74\t10873\t89.9\t0\t10873\n", "75\t9446\t89.9\t0\t9446\n", "76\t8399\t89.9\t0\t8399\n", "77\t7631\t89.9\t0\t7631\n", "78\t8436\t89.9\t0\t8436\n", "79\t8327\t89.9\t0\t8327\n", "80\t8601\t89.9\t0\t8601\n", "81\t8303\t89.9\t0\t8303\n", "82\t8614\t89.9\t0\t8614\n", "83\t9589\t89.9\t0\t9589\n", "84\t11198\t89.9\t0\t11198\n", "85\t12961\t89.9\t0\t12961\n", "86\t12664\t89.9\t0\t12664\n", "87\t10218\t89.9\t0\t10218\n", "88\t9688\t89.9\t0\t9688\n", "89\t10383\t89.9\t0\t10383\n", "90\t10624\t89.9\t0\t10624\n", "91\t10860\t89.9\t0\t10860\n", "92\t10717\t89.9\t0\t10717\n", "93\t11090\t89.9\t0\t11090\n", "94\t11091\t89.9\t0\t11091\n", "95\t10010\t89.9\t0\t10010\n", "96\t7823\t89.9\t0\t7823\n", "97\t5003\t89.9\t0\t5003\n", "98\t2942\t89.9\t0\t2942\n", "99\t2111\t89.9\t0\t2111\n", "100\t1547\t89.9\t0\t1547\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 23756 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 56.9%\n", " C: 18.0%\n", " G: 0.0%\n", " T: 24.4%\n", " none/other: 0.7%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10218\t92067.7\t0\t10218\n", "4\t2274\t23016.9\t0\t2274\n", "5\t528\t5754.2\t0\t528\n", "6\t162\t1438.6\t0\t162\n", "7\t33\t359.6\t0\t33\n", "8\t26\t89.9\t0\t26\n", "9\t37\t89.9\t0\t37\n", "10\t28\t89.9\t0\t28\n", "11\t23\t89.9\t0\t23\n", "12\t16\t89.9\t0\t16\n", "13\t32\t89.9\t0\t32\n", "14\t44\t89.9\t0\t44\n", "15\t22\t89.9\t0\t22\n", "16\t42\t89.9\t0\t42\n", "17\t30\t89.9\t0\t30\n", "18\t36\t89.9\t0\t36\n", "19\t54\t89.9\t0\t54\n", "20\t60\t89.9\t0\t60\n", "21\t51\t89.9\t0\t51\n", "22\t50\t89.9\t0\t50\n", "23\t51\t89.9\t0\t51\n", "24\t44\t89.9\t0\t44\n", "25\t65\t89.9\t0\t65\n", "26\t100\t89.9\t0\t100\n", "27\t122\t89.9\t0\t122\n", "28\t168\t89.9\t0\t168\n", "29\t244\t89.9\t0\t244\n", "30\t505\t89.9\t0\t505\n", "31\t575\t89.9\t0\t575\n", "32\t1072\t89.9\t0\t1072\n", "33\t943\t89.9\t0\t943\n", "34\t1049\t89.9\t0\t1049\n", "35\t1342\t89.9\t0\t1342\n", "36\t1195\t89.9\t0\t1195\n", "37\t666\t89.9\t0\t666\n", "38\t78\t89.9\t0\t78\n", "39\t62\t89.9\t0\t62\n", "40\t21\t89.9\t0\t21\n", "41\t22\t89.9\t0\t22\n", "42\t26\t89.9\t0\t26\n", "43\t29\t89.9\t0\t29\n", "44\t13\t89.9\t0\t13\n", "45\t21\t89.9\t0\t21\n", "46\t29\t89.9\t0\t29\n", "47\t18\t89.9\t0\t18\n", "48\t21\t89.9\t0\t21\n", "49\t21\t89.9\t0\t21\n", "50\t20\t89.9\t0\t20\n", "51\t21\t89.9\t0\t21\n", "52\t9\t89.9\t0\t9\n", "53\t26\t89.9\t0\t26\n", "54\t13\t89.9\t0\t13\n", "55\t19\t89.9\t0\t19\n", "56\t23\t89.9\t0\t23\n", "57\t13\t89.9\t0\t13\n", "58\t21\t89.9\t0\t21\n", "59\t21\t89.9\t0\t21\n", "60\t11\t89.9\t0\t11\n", "61\t17\t89.9\t0\t17\n", "62\t8\t89.9\t0\t8\n", "63\t12\t89.9\t0\t12\n", "64\t32\t89.9\t0\t32\n", "65\t11\t89.9\t0\t11\n", "66\t14\t89.9\t0\t14\n", "67\t16\t89.9\t0\t16\n", "68\t18\t89.9\t0\t18\n", "69\t12\t89.9\t0\t12\n", "70\t7\t89.9\t0\t7\n", "71\t11\t89.9\t0\t11\n", "72\t5\t89.9\t0\t5\n", "73\t5\t89.9\t0\t5\n", "74\t7\t89.9\t0\t7\n", "75\t8\t89.9\t0\t8\n", "76\t5\t89.9\t0\t5\n", "77\t4\t89.9\t0\t4\n", "78\t3\t89.9\t0\t3\n", "79\t4\t89.9\t0\t4\n", "80\t8\t89.9\t0\t8\n", "81\t3\t89.9\t0\t3\n", "82\t6\t89.9\t0\t6\n", "83\t5\t89.9\t0\t5\n", "84\t8\t89.9\t0\t8\n", "85\t10\t89.9\t0\t10\n", "86\t1\t89.9\t0\t1\n", "87\t7\t89.9\t0\t7\n", "88\t7\t89.9\t0\t7\n", "89\t15\t89.9\t0\t15\n", "90\t19\t89.9\t0\t19\n", "91\t20\t89.9\t0\t20\n", "92\t32\t89.9\t0\t32\n", "93\t84\t89.9\t0\t84\n", "94\t115\t89.9\t0\t115\n", "95\t124\t89.9\t0\t124\n", "96\t138\t89.9\t0\t138\n", "97\t133\t89.9\t0\t133\n", "98\t89\t89.9\t0\t89\n", "99\t101\t89.9\t0\t101\n", "100\t167\t89.9\t0\t167\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 91822 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.2%\n", " C: 22.4%\n", " G: 13.8%\n", " T: 23.6%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t70760\t92067.7\t0\t70760\n", "4\t13974\t23016.9\t0\t13974\n", "5\t2413\t5754.2\t0\t2413\n", "6\t180\t1438.6\t0\t180\n", "7\t39\t359.6\t0\t39\n", "8\t48\t359.6\t0\t48\n", "9\t50\t359.6\t0\t50\n", "10\t51\t359.6\t0\t51\n", "11\t59\t359.6\t0\t59\n", "12\t64\t359.6\t0\t64\n", "13\t64\t359.6\t0\t64\n", "14\t46\t359.6\t0\t46\n", "15\t57\t359.6\t0\t57\n", "16\t39\t359.6\t0\t39\n", "17\t54\t359.6\t0\t54\n", "18\t44\t359.6\t0\t44\n", "19\t44\t359.6\t0\t44\n", "20\t36\t359.6\t0\t36\n", "21\t42\t359.6\t0\t42\n", "22\t56\t359.6\t0\t56\n", "23\t30\t359.6\t0\t30\n", "24\t38\t359.6\t0\t38\n", "25\t37\t359.6\t0\t37\n", "26\t48\t359.6\t0\t48\n", "27\t60\t359.6\t0\t60\n", "28\t54\t359.6\t0\t54\n", "29\t38\t359.6\t0\t38\n", "30\t59\t359.6\t0\t59\n", "31\t50\t359.6\t0\t50\n", "32\t54\t359.6\t0\t54\n", "33\t74\t359.6\t0\t74\n", "34\t57\t359.6\t0\t57\n", "35\t63\t359.6\t0\t63\n", "36\t46\t359.6\t0\t46\n", "37\t47\t359.6\t0\t47\n", "38\t45\t359.6\t0\t45\n", "39\t43\t359.6\t0\t43\n", "40\t50\t359.6\t0\t50\n", "41\t42\t359.6\t0\t42\n", "42\t38\t359.6\t0\t38\n", "43\t54\t359.6\t0\t54\n", "44\t35\t359.6\t0\t35\n", "45\t43\t359.6\t0\t43\n", "46\t37\t359.6\t0\t37\n", "47\t49\t359.6\t0\t49\n", "48\t49\t359.6\t0\t49\n", "49\t44\t359.6\t0\t44\n", "50\t45\t359.6\t0\t45\n", "51\t30\t359.6\t0\t30\n", "52\t45\t359.6\t0\t45\n", "53\t36\t359.6\t0\t36\n", "54\t35\t359.6\t0\t35\n", "55\t16\t359.6\t0\t16\n", "56\t33\t359.6\t0\t33\n", "57\t34\t359.6\t0\t34\n", "58\t40\t359.6\t0\t40\n", "59\t38\t359.6\t0\t38\n", "60\t46\t359.6\t0\t46\n", "61\t36\t359.6\t0\t36\n", "62\t36\t359.6\t0\t36\n", "63\t36\t359.6\t0\t36\n", "64\t43\t359.6\t0\t43\n", "65\t34\t359.6\t0\t34\n", "66\t36\t359.6\t0\t36\n", "67\t22\t359.6\t0\t22\n", "68\t29\t359.6\t0\t29\n", "69\t37\t359.6\t0\t37\n", "70\t35\t359.6\t0\t35\n", "71\t51\t359.6\t0\t51\n", "72\t30\t359.6\t0\t30\n", "73\t45\t359.6\t0\t45\n", "74\t45\t359.6\t0\t45\n", "75\t26\t359.6\t0\t26\n", "76\t57\t359.6\t0\t57\n", "77\t59\t359.6\t0\t59\n", "78\t66\t359.6\t0\t66\n", "79\t41\t359.6\t0\t41\n", "80\t60\t359.6\t0\t60\n", "81\t77\t359.6\t0\t77\n", "82\t83\t359.6\t0\t83\n", "83\t78\t359.6\t0\t78\n", "84\t56\t359.6\t0\t56\n", "85\t55\t359.6\t0\t55\n", "86\t60\t359.6\t0\t60\n", "87\t57\t359.6\t0\t57\n", "88\t55\t359.6\t0\t55\n", "89\t41\t359.6\t0\t41\n", "90\t44\t359.6\t0\t44\n", "91\t33\t359.6\t0\t33\n", "92\t35\t359.6\t0\t35\n", "93\t33\t359.6\t0\t33\n", "94\t41\t359.6\t0\t41\n", "95\t51\t359.6\t0\t51\n", "96\t39\t359.6\t0\t39\n", "97\t90\t359.6\t0\t90\n", "98\t76\t359.6\t0\t76\n", "99\t87\t359.6\t0\t87\n", "100\t105\t359.6\t0\t105\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 141_S61_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/141.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 27.73 s (14 us/read; 4.41 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 2,037,213\n", "Reads with adapters: 1,148,925 (56.4%)\n", "Reads written (passing filters): 1,974,587 (96.9%)\n", "\n", "Total basepairs processed: 203,721,300 bp\n", "Quality-trimmed: 543,906 bp (0.3%)\n", "Total written (filtered): 163,561,756 bp (80.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1108115 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.0%\n", " G: 33.9%\n", " T: 36.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t46961\t31831.5\t0\t46961\n", "4\t29136\t7957.9\t0\t29136\n", "5\t21939\t1989.5\t0\t21939\n", "6\t17619\t497.4\t0\t17619\n", "7\t15536\t124.3\t0\t15536\n", "8\t14584\t31.1\t0\t14584\n", "9\t14353\t31.1\t0\t14353\n", "10\t13461\t31.1\t0\t13461\n", "11\t13301\t31.1\t0\t13301\n", "12\t13457\t31.1\t0\t13457\n", "13\t14592\t31.1\t0\t14592\n", "14\t15050\t31.1\t0\t15050\n", "15\t14448\t31.1\t0\t14448\n", "16\t14971\t31.1\t0\t14971\n", "17\t16976\t31.1\t0\t16976\n", "18\t20398\t31.1\t0\t20398\n", "19\t18090\t31.1\t0\t18090\n", "20\t15311\t31.1\t0\t15311\n", "21\t15198\t31.1\t0\t15198\n", "22\t13845\t31.1\t0\t13845\n", "23\t15352\t31.1\t0\t15352\n", "24\t18394\t31.1\t0\t18394\n", "25\t18517\t31.1\t0\t18517\n", "26\t21055\t31.1\t0\t21055\n", "27\t22790\t31.1\t0\t22790\n", "28\t20059\t31.1\t0\t20059\n", "29\t19263\t31.1\t0\t19263\n", "30\t19688\t31.1\t0\t19688\n", "31\t22168\t31.1\t0\t22168\n", "32\t20339\t31.1\t0\t20339\n", "33\t18057\t31.1\t0\t18057\n", "34\t17764\t31.1\t0\t17764\n", "35\t20861\t31.1\t0\t20861\n", "36\t23771\t31.1\t0\t23771\n", "37\t26595\t31.1\t0\t26595\n", "38\t20595\t31.1\t0\t20595\n", "39\t16895\t31.1\t0\t16895\n", "40\t14731\t31.1\t0\t14731\n", "41\t15753\t31.1\t0\t15753\n", "42\t17483\t31.1\t0\t17483\n", "43\t14822\t31.1\t0\t14822\n", "44\t11264\t31.1\t0\t11264\n", "45\t14178\t31.1\t0\t14178\n", "46\t16858\t31.1\t0\t16858\n", "47\t15896\t31.1\t0\t15896\n", "48\t16135\t31.1\t0\t16135\n", "49\t13200\t31.1\t0\t13200\n", "50\t12327\t31.1\t0\t12327\n", "51\t10827\t31.1\t0\t10827\n", "52\t10984\t31.1\t0\t10984\n", "53\t10379\t31.1\t0\t10379\n", "54\t9693\t31.1\t0\t9693\n", "55\t10759\t31.1\t0\t10759\n", "56\t10752\t31.1\t0\t10752\n", "57\t10775\t31.1\t0\t10775\n", "58\t12297\t31.1\t0\t12297\n", "59\t9056\t31.1\t0\t9056\n", "60\t7216\t31.1\t0\t7216\n", "61\t6847\t31.1\t0\t6847\n", "62\t5868\t31.1\t0\t5868\n", "63\t6272\t31.1\t0\t6272\n", "64\t7254\t31.1\t0\t7254\n", "65\t5374\t31.1\t0\t5374\n", "66\t4812\t31.1\t0\t4812\n", "67\t5178\t31.1\t0\t5178\n", "68\t4672\t31.1\t0\t4672\n", "69\t4596\t31.1\t0\t4596\n", "70\t5375\t31.1\t0\t5375\n", "71\t4572\t31.1\t0\t4572\n", "72\t3624\t31.1\t0\t3624\n", "73\t2618\t31.1\t0\t2618\n", "74\t2413\t31.1\t0\t2413\n", "75\t2291\t31.1\t0\t2291\n", "76\t2038\t31.1\t0\t2038\n", "77\t2479\t31.1\t0\t2479\n", "78\t3074\t31.1\t0\t3074\n", "79\t2564\t31.1\t0\t2564\n", "80\t2230\t31.1\t0\t2230\n", "81\t2472\t31.1\t0\t2472\n", "82\t2387\t31.1\t0\t2387\n", "83\t2425\t31.1\t0\t2425\n", "84\t3093\t31.1\t0\t3093\n", "85\t4030\t31.1\t0\t4030\n", "86\t4385\t31.1\t0\t4385\n", "87\t3167\t31.1\t0\t3167\n", "88\t2911\t31.1\t0\t2911\n", "89\t2948\t31.1\t0\t2948\n", "90\t3318\t31.1\t0\t3318\n", "91\t3741\t31.1\t0\t3741\n", "92\t3738\t31.1\t0\t3738\n", "93\t3922\t31.1\t0\t3922\n", "94\t4052\t31.1\t0\t4052\n", "95\t3543\t31.1\t0\t3543\n", "96\t2730\t31.1\t0\t2730\n", "97\t1728\t31.1\t0\t1728\n", "98\t1118\t31.1\t0\t1118\n", "99\t766\t31.1\t0\t766\n", "100\t716\t31.1\t0\t716\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 9475 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 60.2%\n", " C: 16.0%\n", " G: 0.0%\n", " T: 23.5%\n", " none/other: 0.3%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t3724\t31831.5\t0\t3724\n", "4\t766\t7957.9\t0\t766\n", "5\t221\t1989.5\t0\t221\n", "6\t58\t497.4\t0\t58\n", "7\t13\t124.3\t0\t13\n", "8\t15\t31.1\t0\t15\n", "9\t12\t31.1\t0\t12\n", "10\t8\t31.1\t0\t8\n", "11\t7\t31.1\t0\t7\n", "12\t8\t31.1\t0\t8\n", "13\t12\t31.1\t0\t12\n", "14\t7\t31.1\t0\t7\n", "15\t15\t31.1\t0\t15\n", "16\t11\t31.1\t0\t11\n", "17\t8\t31.1\t0\t8\n", "18\t13\t31.1\t0\t13\n", "19\t24\t31.1\t0\t24\n", "20\t22\t31.1\t0\t22\n", "21\t24\t31.1\t0\t24\n", "22\t22\t31.1\t0\t22\n", "23\t17\t31.1\t0\t17\n", "24\t28\t31.1\t0\t28\n", "25\t27\t31.1\t0\t27\n", "26\t48\t31.1\t0\t48\n", "27\t58\t31.1\t0\t58\n", "28\t91\t31.1\t0\t91\n", "29\t141\t31.1\t0\t141\n", "30\t264\t31.1\t0\t264\n", "31\t371\t31.1\t0\t371\n", "32\t500\t31.1\t0\t500\n", "33\t439\t31.1\t0\t439\n", "34\t535\t31.1\t0\t535\n", "35\t629\t31.1\t0\t629\n", "36\t466\t31.1\t0\t466\n", "37\t214\t31.1\t0\t214\n", "38\t26\t31.1\t0\t26\n", "39\t12\t31.1\t0\t12\n", "40\t6\t31.1\t0\t6\n", "41\t5\t31.1\t0\t5\n", "42\t11\t31.1\t0\t11\n", "43\t11\t31.1\t0\t11\n", "44\t16\t31.1\t0\t16\n", "45\t7\t31.1\t0\t7\n", "46\t18\t31.1\t0\t18\n", "47\t20\t31.1\t0\t20\n", "48\t14\t31.1\t0\t14\n", "49\t13\t31.1\t0\t13\n", "50\t18\t31.1\t0\t18\n", "51\t9\t31.1\t0\t9\n", "52\t12\t31.1\t0\t12\n", "53\t3\t31.1\t0\t3\n", "54\t3\t31.1\t0\t3\n", "55\t9\t31.1\t0\t9\n", "56\t3\t31.1\t0\t3\n", "57\t10\t31.1\t0\t10\n", "58\t7\t31.1\t0\t7\n", "59\t5\t31.1\t0\t5\n", "60\t4\t31.1\t0\t4\n", "61\t5\t31.1\t0\t5\n", "62\t7\t31.1\t0\t7\n", "63\t7\t31.1\t0\t7\n", "64\t6\t31.1\t0\t6\n", "65\t3\t31.1\t0\t3\n", "66\t4\t31.1\t0\t4\n", "67\t3\t31.1\t0\t3\n", "68\t4\t31.1\t0\t4\n", "69\t4\t31.1\t0\t4\n", "70\t5\t31.1\t0\t5\n", "71\t1\t31.1\t0\t1\n", "72\t3\t31.1\t0\t3\n", "74\t5\t31.1\t0\t5\n", "75\t4\t31.1\t0\t4\n", "77\t1\t31.1\t0\t1\n", "78\t2\t31.1\t0\t2\n", "79\t1\t31.1\t0\t1\n", "80\t2\t31.1\t0\t2\n", "81\t3\t31.1\t0\t3\n", "82\t1\t31.1\t0\t1\n", "83\t3\t31.1\t0\t3\n", "84\t5\t31.1\t0\t5\n", "85\t4\t31.1\t0\t4\n", "86\t1\t31.1\t0\t1\n", "87\t2\t31.1\t0\t2\n", "88\t1\t31.1\t0\t1\n", "89\t3\t31.1\t0\t3\n", "90\t6\t31.1\t0\t6\n", "91\t5\t31.1\t0\t5\n", "92\t7\t31.1\t0\t7\n", "93\t23\t31.1\t0\t23\n", "94\t35\t31.1\t0\t35\n", "95\t48\t31.1\t0\t48\n", "96\t39\t31.1\t0\t39\n", "97\t37\t31.1\t0\t37\n", "98\t39\t31.1\t0\t39\n", "99\t24\t31.1\t0\t24\n", "100\t62\t31.1\t0\t62\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 31335 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.1%\n", " C: 21.5%\n", " G: 15.3%\n", " T: 21.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t23974\t31831.5\t0\t23974\n", "4\t4491\t7957.9\t0\t4491\n", "5\t821\t1989.5\t0\t821\n", "6\t55\t497.4\t0\t55\n", "7\t21\t124.3\t0\t21\n", "8\t11\t124.3\t0\t11\n", "9\t16\t124.3\t0\t16\n", "10\t13\t124.3\t0\t13\n", "11\t35\t124.3\t0\t35\n", "12\t35\t124.3\t0\t35\n", "13\t26\t124.3\t0\t26\n", "14\t17\t124.3\t0\t17\n", "15\t26\t124.3\t0\t26\n", "16\t20\t124.3\t0\t20\n", "17\t24\t124.3\t0\t24\n", "18\t27\t124.3\t0\t27\n", "19\t36\t124.3\t0\t36\n", "20\t26\t124.3\t0\t26\n", "21\t18\t124.3\t0\t18\n", "22\t25\t124.3\t0\t25\n", "23\t15\t124.3\t0\t15\n", "24\t19\t124.3\t0\t19\n", "25\t16\t124.3\t0\t16\n", "26\t30\t124.3\t0\t30\n", "27\t27\t124.3\t0\t27\n", "28\t24\t124.3\t0\t24\n", "29\t22\t124.3\t0\t22\n", "30\t29\t124.3\t0\t29\n", "31\t14\t124.3\t0\t14\n", "32\t24\t124.3\t0\t24\n", "33\t33\t124.3\t0\t33\n", "34\t23\t124.3\t0\t23\n", "35\t23\t124.3\t0\t23\n", "36\t22\t124.3\t0\t22\n", "37\t25\t124.3\t0\t25\n", "38\t17\t124.3\t0\t17\n", "39\t19\t124.3\t0\t19\n", "40\t16\t124.3\t0\t16\n", "41\t15\t124.3\t0\t15\n", "42\t16\t124.3\t0\t16\n", "43\t16\t124.3\t0\t16\n", "44\t9\t124.3\t0\t9\n", "45\t17\t124.3\t0\t17\n", "46\t27\t124.3\t0\t27\n", "47\t16\t124.3\t0\t16\n", "48\t20\t124.3\t0\t20\n", "49\t30\t124.3\t0\t30\n", "50\t13\t124.3\t0\t13\n", "51\t24\t124.3\t0\t24\n", "52\t20\t124.3\t0\t20\n", "53\t18\t124.3\t0\t18\n", "54\t23\t124.3\t0\t23\n", "55\t22\t124.3\t0\t22\n", "56\t11\t124.3\t0\t11\n", "57\t24\t124.3\t0\t24\n", "58\t21\t124.3\t0\t21\n", "59\t25\t124.3\t0\t25\n", "60\t28\t124.3\t0\t28\n", "61\t22\t124.3\t0\t22\n", "62\t20\t124.3\t0\t20\n", "63\t22\t124.3\t0\t22\n", "64\t15\t124.3\t0\t15\n", "65\t18\t124.3\t0\t18\n", "66\t8\t124.3\t0\t8\n", "67\t15\t124.3\t0\t15\n", "68\t10\t124.3\t0\t10\n", "69\t10\t124.3\t0\t10\n", "70\t12\t124.3\t0\t12\n", "71\t16\t124.3\t0\t16\n", "72\t20\t124.3\t0\t20\n", "73\t14\t124.3\t0\t14\n", "74\t13\t124.3\t0\t13\n", "75\t19\t124.3\t0\t19\n", "76\t20\t124.3\t0\t20\n", "77\t29\t124.3\t0\t29\n", "78\t26\t124.3\t0\t26\n", "79\t30\t124.3\t0\t30\n", "80\t21\t124.3\t0\t21\n", "81\t23\t124.3\t0\t23\n", "82\t45\t124.3\t0\t45\n", "83\t37\t124.3\t0\t37\n", "84\t20\t124.3\t0\t20\n", "85\t29\t124.3\t0\t29\n", "86\t17\t124.3\t0\t17\n", "87\t24\t124.3\t0\t24\n", "88\t17\t124.3\t0\t17\n", "89\t13\t124.3\t0\t13\n", "90\t16\t124.3\t0\t16\n", "91\t9\t124.3\t0\t9\n", "92\t18\t124.3\t0\t18\n", "93\t14\t124.3\t0\t14\n", "94\t18\t124.3\t0\t18\n", "95\t16\t124.3\t0\t16\n", "96\t18\t124.3\t0\t18\n", "97\t33\t124.3\t0\t33\n", "98\t25\t124.3\t0\t25\n", "99\t32\t124.3\t0\t32\n", "100\t41\t124.3\t0\t41\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 156_S66_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/156.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 74.51 s (14 us/read; 4.17 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,179,056\n", "Reads with adapters: 2,777,222 (53.6%)\n", "Reads written (passing filters): 5,120,968 (98.9%)\n", "\n", "Total basepairs processed: 517,905,600 bp\n", "Quality-trimmed: 1,026,382 bp (0.2%)\n", "Total written (filtered): 431,180,203 bp (83.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2687559 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.5%\n", " G: 33.2%\n", " T: 39.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t133774\t80922.8\t0\t133774\n", "4\t79028\t20230.7\t0\t79028\n", "5\t60229\t5057.7\t0\t60229\n", "6\t46114\t1264.4\t0\t46114\n", "7\t39438\t316.1\t0\t39438\n", "8\t38479\t79.0\t0\t38479\n", "9\t37252\t79.0\t0\t37252\n", "10\t33344\t79.0\t0\t33344\n", "11\t34714\t79.0\t0\t34714\n", "12\t34478\t79.0\t0\t34478\n", "13\t36476\t79.0\t0\t36476\n", "14\t36695\t79.0\t0\t36695\n", "15\t36519\t79.0\t0\t36519\n", "16\t37255\t79.0\t0\t37255\n", "17\t42662\t79.0\t0\t42662\n", "18\t51784\t79.0\t0\t51784\n", "19\t45536\t79.0\t0\t45536\n", "20\t38677\t79.0\t0\t38677\n", "21\t39709\t79.0\t0\t39709\n", "22\t34816\t79.0\t0\t34816\n", "23\t39546\t79.0\t0\t39546\n", "24\t47439\t79.0\t0\t47439\n", "25\t46902\t79.0\t0\t46902\n", "26\t55064\t79.0\t0\t55064\n", "27\t62048\t79.0\t0\t62048\n", "28\t56441\t79.0\t0\t56441\n", "29\t54136\t79.0\t0\t54136\n", "30\t56089\t79.0\t0\t56089\n", "31\t59539\t79.0\t0\t59539\n", "32\t57476\t79.0\t0\t57476\n", "33\t48619\t79.0\t0\t48619\n", "34\t46040\t79.0\t0\t46040\n", "35\t52574\t79.0\t0\t52574\n", "36\t66289\t79.0\t0\t66289\n", "37\t77032\t79.0\t0\t77032\n", "38\t58158\t79.0\t0\t58158\n", "39\t42874\t79.0\t0\t42874\n", "40\t36255\t79.0\t0\t36255\n", "41\t36180\t79.0\t0\t36180\n", "42\t37762\t79.0\t0\t37762\n", "43\t33059\t79.0\t0\t33059\n", "44\t25092\t79.0\t0\t25092\n", "45\t33870\t79.0\t0\t33870\n", "46\t41996\t79.0\t0\t41996\n", "47\t39404\t79.0\t0\t39404\n", "48\t45220\t79.0\t0\t45220\n", "49\t38812\t79.0\t0\t38812\n", "50\t32948\t79.0\t0\t32948\n", "51\t24745\t79.0\t0\t24745\n", "52\t25652\t79.0\t0\t25652\n", "53\t27292\t79.0\t0\t27292\n", "54\t28530\t79.0\t0\t28530\n", "55\t29158\t79.0\t0\t29158\n", "56\t26811\t79.0\t0\t26811\n", "57\t20631\t79.0\t0\t20631\n", "58\t24436\t79.0\t0\t24436\n", "59\t15541\t79.0\t0\t15541\n", "60\t13398\t79.0\t0\t13398\n", "61\t13576\t79.0\t0\t13576\n", "62\t10447\t79.0\t0\t10447\n", "63\t10226\t79.0\t0\t10226\n", "64\t10992\t79.0\t0\t10992\n", "65\t10279\t79.0\t0\t10279\n", "66\t8339\t79.0\t0\t8339\n", "67\t7926\t79.0\t0\t7926\n", "68\t7193\t79.0\t0\t7193\n", "69\t6717\t79.0\t0\t6717\n", "70\t6568\t79.0\t0\t6568\n", "71\t6494\t79.0\t0\t6494\n", "72\t4980\t79.0\t0\t4980\n", "73\t4731\t79.0\t0\t4731\n", "74\t4751\t79.0\t0\t4751\n", "75\t4164\t79.0\t0\t4164\n", "76\t3574\t79.0\t0\t3574\n", "77\t2987\t79.0\t0\t2987\n", "78\t3399\t79.0\t0\t3399\n", "79\t3174\t79.0\t0\t3174\n", "80\t3248\t79.0\t0\t3248\n", "81\t3116\t79.0\t0\t3116\n", "82\t3107\t79.0\t0\t3107\n", "83\t3454\t79.0\t0\t3454\n", "84\t4097\t79.0\t0\t4097\n", "85\t4646\t79.0\t0\t4646\n", "86\t4303\t79.0\t0\t4303\n", "87\t3055\t79.0\t0\t3055\n", "88\t2586\t79.0\t0\t2586\n", "89\t2977\t79.0\t0\t2977\n", "90\t3018\t79.0\t0\t3018\n", "91\t2914\t79.0\t0\t2914\n", "92\t2841\t79.0\t0\t2841\n", "93\t3009\t79.0\t0\t3009\n", "94\t2864\t79.0\t0\t2864\n", "95\t2530\t79.0\t0\t2530\n", "96\t1836\t79.0\t0\t1836\n", "97\t1246\t79.0\t0\t1246\n", "98\t788\t79.0\t0\t788\n", "99\t906\t79.0\t0\t906\n", "100\t464\t79.0\t0\t464\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 15940 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 62.5%\n", " C: 13.6%\n", " G: 0.0%\n", " T: 23.4%\n", " none/other: 0.6%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t6307\t80922.8\t0\t6307\n", "4\t1072\t20230.7\t0\t1072\n", "5\t216\t5057.7\t0\t216\n", "6\t68\t1264.4\t0\t68\n", "7\t15\t316.1\t0\t15\n", "8\t18\t79.0\t0\t18\n", "9\t16\t79.0\t0\t16\n", "10\t11\t79.0\t0\t11\n", "11\t17\t79.0\t0\t17\n", "12\t16\t79.0\t0\t16\n", "13\t8\t79.0\t0\t8\n", "14\t14\t79.0\t0\t14\n", "15\t15\t79.0\t0\t15\n", "16\t15\t79.0\t0\t15\n", "17\t15\t79.0\t0\t15\n", "18\t19\t79.0\t0\t19\n", "19\t22\t79.0\t0\t22\n", "20\t40\t79.0\t0\t40\n", "21\t37\t79.0\t0\t37\n", "22\t34\t79.0\t0\t34\n", "23\t25\t79.0\t0\t25\n", "24\t33\t79.0\t0\t33\n", "25\t38\t79.0\t0\t38\n", "26\t81\t79.0\t0\t81\n", "27\t91\t79.0\t0\t91\n", "28\t128\t79.0\t0\t128\n", "29\t219\t79.0\t0\t219\n", "30\t448\t79.0\t0\t448\n", "31\t535\t79.0\t0\t535\n", "32\t893\t79.0\t0\t893\n", "33\t835\t79.0\t0\t835\n", "34\t1001\t79.0\t0\t1001\n", "35\t1148\t79.0\t0\t1148\n", "36\t1171\t79.0\t0\t1171\n", "37\t544\t79.0\t0\t544\n", "38\t38\t79.0\t0\t38\n", "39\t20\t79.0\t0\t20\n", "40\t5\t79.0\t0\t5\n", "41\t6\t79.0\t0\t6\n", "42\t6\t79.0\t0\t6\n", "43\t7\t79.0\t0\t7\n", "44\t16\t79.0\t0\t16\n", "45\t13\t79.0\t0\t13\n", "46\t8\t79.0\t0\t8\n", "47\t11\t79.0\t0\t11\n", "48\t8\t79.0\t0\t8\n", "49\t6\t79.0\t0\t6\n", "50\t7\t79.0\t0\t7\n", "51\t5\t79.0\t0\t5\n", "52\t9\t79.0\t0\t9\n", "53\t6\t79.0\t0\t6\n", "54\t1\t79.0\t0\t1\n", "55\t3\t79.0\t0\t3\n", "56\t4\t79.0\t0\t4\n", "57\t6\t79.0\t0\t6\n", "58\t6\t79.0\t0\t6\n", "59\t4\t79.0\t0\t4\n", "60\t6\t79.0\t0\t6\n", "61\t4\t79.0\t0\t4\n", "62\t3\t79.0\t0\t3\n", "63\t4\t79.0\t0\t4\n", "64\t4\t79.0\t0\t4\n", "65\t5\t79.0\t0\t5\n", "66\t3\t79.0\t0\t3\n", "67\t5\t79.0\t0\t5\n", "68\t3\t79.0\t0\t3\n", "69\t5\t79.0\t0\t5\n", "70\t2\t79.0\t0\t2\n", "71\t3\t79.0\t0\t3\n", "72\t2\t79.0\t0\t2\n", "73\t1\t79.0\t0\t1\n", "74\t5\t79.0\t0\t5\n", "75\t1\t79.0\t0\t1\n", "76\t2\t79.0\t0\t2\n", "78\t1\t79.0\t0\t1\n", "79\t3\t79.0\t0\t3\n", "80\t2\t79.0\t0\t2\n", "81\t1\t79.0\t0\t1\n", "82\t2\t79.0\t0\t2\n", "83\t3\t79.0\t0\t3\n", "84\t1\t79.0\t0\t1\n", "85\t3\t79.0\t0\t3\n", "86\t4\t79.0\t0\t4\n", "87\t3\t79.0\t0\t3\n", "88\t3\t79.0\t0\t3\n", "89\t7\t79.0\t0\t7\n", "90\t2\t79.0\t0\t2\n", "91\t4\t79.0\t0\t4\n", "92\t14\t79.0\t0\t14\n", "93\t40\t79.0\t0\t40\n", "94\t62\t79.0\t0\t62\n", "95\t75\t79.0\t0\t75\n", "96\t51\t79.0\t0\t51\n", "97\t50\t79.0\t0\t50\n", "98\t43\t79.0\t0\t43\n", "99\t60\t79.0\t0\t60\n", "100\t88\t79.0\t0\t88\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 73723 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.4%\n", " C: 18.5%\n", " G: 11.5%\n", " T: 24.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t55551\t80922.8\t0\t55551\n", "4\t12073\t20230.7\t0\t12073\n", "5\t2057\t5057.7\t0\t2057\n", "6\t178\t1264.4\t0\t178\n", "7\t23\t316.1\t0\t23\n", "8\t30\t316.1\t0\t30\n", "9\t36\t316.1\t0\t36\n", "10\t39\t316.1\t0\t39\n", "11\t54\t316.1\t0\t54\n", "12\t39\t316.1\t0\t39\n", "13\t48\t316.1\t0\t48\n", "14\t29\t316.1\t0\t29\n", "15\t45\t316.1\t0\t45\n", "16\t24\t316.1\t0\t24\n", "17\t37\t316.1\t0\t37\n", "18\t40\t316.1\t0\t40\n", "19\t27\t316.1\t0\t27\n", "20\t18\t316.1\t0\t18\n", "21\t23\t316.1\t0\t23\n", "22\t28\t316.1\t0\t28\n", "23\t24\t316.1\t0\t24\n", "24\t17\t316.1\t0\t17\n", "25\t22\t316.1\t0\t22\n", "26\t36\t316.1\t0\t36\n", "27\t20\t316.1\t0\t20\n", "28\t27\t316.1\t0\t27\n", "29\t37\t316.1\t0\t37\n", "30\t39\t316.1\t0\t39\n", "31\t35\t316.1\t0\t35\n", "32\t56\t316.1\t0\t56\n", "33\t35\t316.1\t0\t35\n", "34\t42\t316.1\t0\t42\n", "35\t33\t316.1\t0\t33\n", "36\t27\t316.1\t0\t27\n", "37\t21\t316.1\t0\t21\n", "38\t27\t316.1\t0\t27\n", "39\t51\t316.1\t0\t51\n", "40\t37\t316.1\t0\t37\n", "41\t40\t316.1\t0\t40\n", "42\t35\t316.1\t0\t35\n", "43\t38\t316.1\t0\t38\n", "44\t40\t316.1\t0\t40\n", "45\t46\t316.1\t0\t46\n", "46\t35\t316.1\t0\t35\n", "47\t35\t316.1\t0\t35\n", "48\t53\t316.1\t0\t53\n", "49\t45\t316.1\t0\t45\n", "50\t37\t316.1\t0\t37\n", "51\t26\t316.1\t0\t26\n", "52\t46\t316.1\t0\t46\n", "53\t55\t316.1\t0\t55\n", "54\t30\t316.1\t0\t30\n", "55\t30\t316.1\t0\t30\n", "56\t24\t316.1\t0\t24\n", "57\t35\t316.1\t0\t35\n", "58\t39\t316.1\t0\t39\n", "59\t34\t316.1\t0\t34\n", "60\t38\t316.1\t0\t38\n", "61\t41\t316.1\t0\t41\n", "62\t51\t316.1\t0\t51\n", "63\t60\t316.1\t0\t60\n", "64\t53\t316.1\t0\t53\n", "65\t34\t316.1\t0\t34\n", "66\t30\t316.1\t0\t30\n", "67\t28\t316.1\t0\t28\n", "68\t24\t316.1\t0\t24\n", "69\t24\t316.1\t0\t24\n", "70\t12\t316.1\t0\t12\n", "71\t30\t316.1\t0\t30\n", "72\t45\t316.1\t0\t45\n", "73\t45\t316.1\t0\t45\n", "74\t91\t316.1\t0\t91\n", "75\t52\t316.1\t0\t52\n", "76\t71\t316.1\t0\t71\n", "77\t59\t316.1\t0\t59\n", "78\t62\t316.1\t0\t62\n", "79\t76\t316.1\t0\t76\n", "80\t83\t316.1\t0\t83\n", "81\t71\t316.1\t0\t71\n", "82\t75\t316.1\t0\t75\n", "83\t98\t316.1\t0\t98\n", "84\t48\t316.1\t0\t48\n", "85\t41\t316.1\t0\t41\n", "86\t36\t316.1\t0\t36\n", "87\t43\t316.1\t0\t43\n", "88\t42\t316.1\t0\t42\n", "89\t33\t316.1\t0\t33\n", "90\t35\t316.1\t0\t35\n", "91\t40\t316.1\t0\t40\n", "92\t9\t316.1\t0\t9\n", "93\t33\t316.1\t0\t33\n", "94\t46\t316.1\t0\t46\n", "95\t39\t316.1\t0\t39\n", "96\t49\t316.1\t0\t49\n", "97\t55\t316.1\t0\t55\n", "98\t75\t316.1\t0\t75\n", "99\t49\t316.1\t0\t49\n", "100\t89\t316.1\t0\t89\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 159_S68_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/159.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 135.45 s (15 us/read; 4.06 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 9,159,117\n", "Reads with adapters: 5,841,890 (63.8%)\n", "Reads written (passing filters): 9,025,275 (98.5%)\n", "\n", "Total basepairs processed: 915,911,700 bp\n", "Quality-trimmed: 2,203,479 bp (0.2%)\n", "Total written (filtered): 716,310,046 bp (78.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5712365 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.6%\n", " G: 32.2%\n", " T: 37.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t201007\t143111.2\t0\t201007\n", "4\t121573\t35777.8\t0\t121573\n", "5\t94377\t8944.5\t0\t94377\n", "6\t78823\t2236.1\t0\t78823\n", "7\t70953\t559.0\t0\t70953\n", "8\t66532\t139.8\t0\t66532\n", "9\t65377\t139.8\t0\t65377\n", "10\t63309\t139.8\t0\t63309\n", "11\t65512\t139.8\t0\t65512\n", "12\t66812\t139.8\t0\t66812\n", "13\t70345\t139.8\t0\t70345\n", "14\t73887\t139.8\t0\t73887\n", "15\t72605\t139.8\t0\t72605\n", "16\t75949\t139.8\t0\t75949\n", "17\t88411\t139.8\t0\t88411\n", "18\t106526\t139.8\t0\t106526\n", "19\t93845\t139.8\t0\t93845\n", "20\t79425\t139.8\t0\t79425\n", "21\t79880\t139.8\t0\t79880\n", "22\t73902\t139.8\t0\t73902\n", "23\t83633\t139.8\t0\t83633\n", "24\t98911\t139.8\t0\t98911\n", "25\t97868\t139.8\t0\t97868\n", "26\t113991\t139.8\t0\t113991\n", "27\t127983\t139.8\t0\t127983\n", "28\t116228\t139.8\t0\t116228\n", "29\t104941\t139.8\t0\t104941\n", "30\t111000\t139.8\t0\t111000\n", "31\t123169\t139.8\t0\t123169\n", "32\t105857\t139.8\t0\t105857\n", "33\t99291\t139.8\t0\t99291\n", "34\t92886\t139.8\t0\t92886\n", "35\t111746\t139.8\t0\t111746\n", "36\t137920\t139.8\t0\t137920\n", "37\t148427\t139.8\t0\t148427\n", "38\t120942\t139.8\t0\t120942\n", "39\t92823\t139.8\t0\t92823\n", "40\t83932\t139.8\t0\t83932\n", "41\t88879\t139.8\t0\t88879\n", "42\t95455\t139.8\t0\t95455\n", "43\t84383\t139.8\t0\t84383\n", "44\t66604\t139.8\t0\t66604\n", "45\t87912\t139.8\t0\t87912\n", "46\t107316\t139.8\t0\t107316\n", "47\t98349\t139.8\t0\t98349\n", "48\t106674\t139.8\t0\t106674\n", "49\t91074\t139.8\t0\t91074\n", "50\t79130\t139.8\t0\t79130\n", "51\t66323\t139.8\t0\t66323\n", "52\t62596\t139.8\t0\t62596\n", "53\t61283\t139.8\t0\t61283\n", "54\t76447\t139.8\t0\t76447\n", "55\t80929\t139.8\t0\t80929\n", "56\t76583\t139.8\t0\t76583\n", "57\t66686\t139.8\t0\t66686\n", "58\t72072\t139.8\t0\t72072\n", "59\t46896\t139.8\t0\t46896\n", "60\t37483\t139.8\t0\t37483\n", "61\t36199\t139.8\t0\t36199\n", "62\t28564\t139.8\t0\t28564\n", "63\t27544\t139.8\t0\t27544\n", "64\t29343\t139.8\t0\t29343\n", "65\t27891\t139.8\t0\t27891\n", "66\t23695\t139.8\t0\t23695\n", "67\t22354\t139.8\t0\t22354\n", "68\t19612\t139.8\t0\t19612\n", "69\t18172\t139.8\t0\t18172\n", "70\t17926\t139.8\t0\t17926\n", "71\t16092\t139.8\t0\t16092\n", "72\t12285\t139.8\t0\t12285\n", "73\t11693\t139.8\t0\t11693\n", "74\t11720\t139.8\t0\t11720\n", "75\t9732\t139.8\t0\t9732\n", "76\t8543\t139.8\t0\t8543\n", "77\t7239\t139.8\t0\t7239\n", "78\t7865\t139.8\t0\t7865\n", "79\t7849\t139.8\t0\t7849\n", "80\t8283\t139.8\t0\t8283\n", "81\t7756\t139.8\t0\t7756\n", "82\t7848\t139.8\t0\t7848\n", "83\t8715\t139.8\t0\t8715\n", "84\t10646\t139.8\t0\t10646\n", "85\t12002\t139.8\t0\t12002\n", "86\t11356\t139.8\t0\t11356\n", "87\t7378\t139.8\t0\t7378\n", "88\t6380\t139.8\t0\t6380\n", "89\t6947\t139.8\t0\t6947\n", "90\t7068\t139.8\t0\t7068\n", "91\t6656\t139.8\t0\t6656\n", "92\t5901\t139.8\t0\t5901\n", "93\t6168\t139.8\t0\t6168\n", "94\t6019\t139.8\t0\t6019\n", "95\t5142\t139.8\t0\t5142\n", "96\t3723\t139.8\t0\t3723\n", "97\t2397\t139.8\t0\t2397\n", "98\t1427\t139.8\t0\t1427\n", "99\t1747\t139.8\t0\t1747\n", "100\t816\t139.8\t0\t816\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 30425 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 64.8%\n", " C: 12.8%\n", " G: 0.0%\n", " T: 22.3%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t11307\t143111.2\t0\t11307\n", "4\t1707\t35777.8\t0\t1707\n", "5\t382\t8944.5\t0\t382\n", "6\t129\t2236.1\t0\t129\n", "7\t35\t559.0\t0\t35\n", "8\t38\t139.8\t0\t38\n", "9\t18\t139.8\t0\t18\n", "10\t21\t139.8\t0\t21\n", "11\t30\t139.8\t0\t30\n", "12\t31\t139.8\t0\t31\n", "13\t25\t139.8\t0\t25\n", "14\t22\t139.8\t0\t22\n", "15\t23\t139.8\t0\t23\n", "16\t29\t139.8\t0\t29\n", "17\t24\t139.8\t0\t24\n", "18\t45\t139.8\t0\t45\n", "19\t42\t139.8\t0\t42\n", "20\t99\t139.8\t0\t99\n", "21\t69\t139.8\t0\t69\n", "22\t61\t139.8\t0\t61\n", "23\t52\t139.8\t0\t52\n", "24\t54\t139.8\t0\t54\n", "25\t60\t139.8\t0\t60\n", "26\t152\t139.8\t0\t152\n", "27\t185\t139.8\t0\t185\n", "28\t237\t139.8\t0\t237\n", "29\t325\t139.8\t0\t325\n", "30\t717\t139.8\t0\t717\n", "31\t976\t139.8\t0\t976\n", "32\t1755\t139.8\t0\t1755\n", "33\t1715\t139.8\t0\t1715\n", "34\t2079\t139.8\t0\t2079\n", "35\t2706\t139.8\t0\t2706\n", "36\t2722\t139.8\t0\t2722\n", "37\t1543\t139.8\t0\t1543\n", "38\t105\t139.8\t0\t105\n", "39\t56\t139.8\t0\t56\n", "40\t12\t139.8\t0\t12\n", "41\t8\t139.8\t0\t8\n", "42\t13\t139.8\t0\t13\n", "43\t5\t139.8\t0\t5\n", "44\t5\t139.8\t0\t5\n", "45\t6\t139.8\t0\t6\n", "46\t10\t139.8\t0\t10\n", "47\t5\t139.8\t0\t5\n", "48\t13\t139.8\t0\t13\n", "49\t6\t139.8\t0\t6\n", "50\t4\t139.8\t0\t4\n", "51\t14\t139.8\t0\t14\n", "52\t12\t139.8\t0\t12\n", "53\t6\t139.8\t0\t6\n", "54\t8\t139.8\t0\t8\n", "55\t8\t139.8\t0\t8\n", "56\t10\t139.8\t0\t10\n", "57\t8\t139.8\t0\t8\n", "59\t6\t139.8\t0\t6\n", "60\t4\t139.8\t0\t4\n", "61\t1\t139.8\t0\t1\n", "62\t4\t139.8\t0\t4\n", "63\t5\t139.8\t0\t5\n", "64\t8\t139.8\t0\t8\n", "65\t10\t139.8\t0\t10\n", "66\t4\t139.8\t0\t4\n", "67\t6\t139.8\t0\t6\n", "68\t3\t139.8\t0\t3\n", "69\t2\t139.8\t0\t2\n", "70\t3\t139.8\t0\t3\n", "71\t1\t139.8\t0\t1\n", "72\t3\t139.8\t0\t3\n", "73\t2\t139.8\t0\t2\n", "74\t1\t139.8\t0\t1\n", "75\t3\t139.8\t0\t3\n", "77\t3\t139.8\t0\t3\n", "78\t5\t139.8\t0\t5\n", "79\t2\t139.8\t0\t2\n", "80\t4\t139.8\t0\t4\n", "81\t2\t139.8\t0\t2\n", "82\t1\t139.8\t0\t1\n", "83\t2\t139.8\t0\t2\n", "84\t1\t139.8\t0\t1\n", "85\t1\t139.8\t0\t1\n", "86\t3\t139.8\t0\t3\n", "87\t3\t139.8\t0\t3\n", "88\t2\t139.8\t0\t2\n", "89\t2\t139.8\t0\t2\n", "90\t2\t139.8\t0\t2\n", "91\t5\t139.8\t0\t5\n", "92\t14\t139.8\t0\t14\n", "93\t45\t139.8\t0\t45\n", "94\t73\t139.8\t0\t73\n", "95\t85\t139.8\t0\t85\n", "96\t59\t139.8\t0\t59\n", "97\t79\t139.8\t0\t79\n", "98\t43\t139.8\t0\t43\n", "99\t69\t139.8\t0\t69\n", "100\t125\t139.8\t0\t125\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 99100 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 46.5%\n", " C: 16.9%\n", " G: 12.9%\n", " T: 23.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t73659\t143111.2\t0\t73659\n", "4\t16846\t35777.8\t0\t16846\n", "5\t2275\t8944.5\t0\t2275\n", "6\t340\t2236.1\t0\t340\n", "7\t43\t559.0\t0\t43\n", "8\t44\t559.0\t0\t44\n", "9\t50\t559.0\t0\t50\n", "10\t65\t559.0\t0\t65\n", "11\t58\t559.0\t0\t58\n", "12\t52\t559.0\t0\t52\n", "13\t60\t559.0\t0\t60\n", "14\t66\t559.0\t0\t66\n", "15\t45\t559.0\t0\t45\n", "16\t44\t559.0\t0\t44\n", "17\t28\t559.0\t0\t28\n", "18\t59\t559.0\t0\t59\n", "19\t42\t559.0\t0\t42\n", "20\t49\t559.0\t0\t49\n", "21\t39\t559.0\t0\t39\n", "22\t33\t559.0\t0\t33\n", "23\t24\t559.0\t0\t24\n", "24\t43\t559.0\t0\t43\n", "25\t57\t559.0\t0\t57\n", "26\t72\t559.0\t0\t72\n", "27\t52\t559.0\t0\t52\n", "28\t41\t559.0\t0\t41\n", "29\t40\t559.0\t0\t40\n", "30\t57\t559.0\t0\t57\n", "31\t49\t559.0\t0\t49\n", "32\t64\t559.0\t0\t64\n", "33\t70\t559.0\t0\t70\n", "34\t60\t559.0\t0\t60\n", "35\t73\t559.0\t0\t73\n", "36\t35\t559.0\t0\t35\n", "37\t33\t559.0\t0\t33\n", "38\t38\t559.0\t0\t38\n", "39\t76\t559.0\t0\t76\n", "40\t72\t559.0\t0\t72\n", "41\t51\t559.0\t0\t51\n", "42\t63\t559.0\t0\t63\n", "43\t42\t559.0\t0\t42\n", "44\t47\t559.0\t0\t47\n", "45\t63\t559.0\t0\t63\n", "46\t53\t559.0\t0\t53\n", "47\t43\t559.0\t0\t43\n", "48\t48\t559.0\t0\t48\n", "49\t55\t559.0\t0\t55\n", "50\t41\t559.0\t0\t41\n", "51\t68\t559.0\t0\t68\n", "52\t44\t559.0\t0\t44\n", "53\t44\t559.0\t0\t44\n", "54\t62\t559.0\t0\t62\n", "55\t35\t559.0\t0\t35\n", "56\t27\t559.0\t0\t27\n", "57\t40\t559.0\t0\t40\n", "58\t47\t559.0\t0\t47\n", "59\t44\t559.0\t0\t44\n", "60\t51\t559.0\t0\t51\n", "61\t65\t559.0\t0\t65\n", "62\t52\t559.0\t0\t52\n", "63\t44\t559.0\t0\t44\n", "64\t48\t559.0\t0\t48\n", "65\t46\t559.0\t0\t46\n", "66\t45\t559.0\t0\t45\n", "67\t46\t559.0\t0\t46\n", "68\t28\t559.0\t0\t28\n", "69\t20\t559.0\t0\t20\n", "70\t36\t559.0\t0\t36\n", "71\t42\t559.0\t0\t42\n", "72\t96\t559.0\t0\t96\n", "73\t147\t559.0\t0\t147\n", "74\t146\t559.0\t0\t146\n", "75\t75\t559.0\t0\t75\n", "76\t97\t559.0\t0\t97\n", "77\t169\t559.0\t0\t169\n", "78\t101\t559.0\t0\t101\n", "79\t136\t559.0\t0\t136\n", "80\t118\t559.0\t0\t118\n", "81\t135\t559.0\t0\t135\n", "82\t202\t559.0\t0\t202\n", "83\t159\t559.0\t0\t159\n", "84\t88\t559.0\t0\t88\n", "85\t89\t559.0\t0\t89\n", "86\t62\t559.0\t0\t62\n", "87\t117\t559.0\t0\t117\n", "88\t42\t559.0\t0\t42\n", "89\t44\t559.0\t0\t44\n", "90\t44\t559.0\t0\t44\n", "91\t56\t559.0\t0\t56\n", "92\t48\t559.0\t0\t48\n", "93\t42\t559.0\t0\t42\n", "94\t54\t559.0\t0\t54\n", "95\t55\t559.0\t0\t55\n", "96\t65\t559.0\t0\t65\n", "97\t95\t559.0\t0\t95\n", "98\t100\t559.0\t0\t100\n", "99\t99\t559.0\t0\t99\n", "100\t126\t559.0\t0\t126\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 161_S57_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/161.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 93.80 s (14 us/read; 4.41 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,891,720\n", "Reads with adapters: 3,856,478 (56.0%)\n", "Reads written (passing filters): 6,763,567 (98.1%)\n", "\n", "Total basepairs processed: 689,172,000 bp\n", "Quality-trimmed: 1,541,037 bp (0.2%)\n", "Total written (filtered): 556,285,105 bp (80.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3724869 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.1%\n", " G: 32.9%\n", " T: 37.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t154533\t107683.1\t0\t154533\n", "4\t92561\t26920.8\t0\t92561\n", "5\t67888\t6730.2\t0\t67888\n", "6\t57579\t1682.5\t0\t57579\n", "7\t50004\t420.6\t0\t50004\n", "8\t44661\t105.2\t0\t44661\n", "9\t43064\t105.2\t0\t43064\n", "10\t42748\t105.2\t0\t42748\n", "11\t43948\t105.2\t0\t43948\n", "12\t44009\t105.2\t0\t44009\n", "13\t48181\t105.2\t0\t48181\n", "14\t48639\t105.2\t0\t48639\n", "15\t48055\t105.2\t0\t48055\n", "16\t50676\t105.2\t0\t50676\n", "17\t54560\t105.2\t0\t54560\n", "18\t65303\t105.2\t0\t65303\n", "19\t57108\t105.2\t0\t57108\n", "20\t48847\t105.2\t0\t48847\n", "21\t50803\t105.2\t0\t50803\n", "22\t45654\t105.2\t0\t45654\n", "23\t51575\t105.2\t0\t51575\n", "24\t64079\t105.2\t0\t64079\n", "25\t64604\t105.2\t0\t64604\n", "26\t74652\t105.2\t0\t74652\n", "27\t76770\t105.2\t0\t76770\n", "28\t69239\t105.2\t0\t69239\n", "29\t64770\t105.2\t0\t64770\n", "30\t62615\t105.2\t0\t62615\n", "31\t68415\t105.2\t0\t68415\n", "32\t67841\t105.2\t0\t67841\n", "33\t59662\t105.2\t0\t59662\n", "34\t59022\t105.2\t0\t59022\n", "35\t70046\t105.2\t0\t70046\n", "36\t83442\t105.2\t0\t83442\n", "37\t87966\t105.2\t0\t87966\n", "38\t70979\t105.2\t0\t70979\n", "39\t55128\t105.2\t0\t55128\n", "40\t51263\t105.2\t0\t51263\n", "41\t57154\t105.2\t0\t57154\n", "42\t63609\t105.2\t0\t63609\n", "43\t55778\t105.2\t0\t55778\n", "44\t40765\t105.2\t0\t40765\n", "45\t52088\t105.2\t0\t52088\n", "46\t64000\t105.2\t0\t64000\n", "47\t56298\t105.2\t0\t56298\n", "48\t56599\t105.2\t0\t56599\n", "49\t48772\t105.2\t0\t48772\n", "50\t49787\t105.2\t0\t49787\n", "51\t41351\t105.2\t0\t41351\n", "52\t44616\t105.2\t0\t44616\n", "53\t49109\t105.2\t0\t49109\n", "54\t46584\t105.2\t0\t46584\n", "55\t42226\t105.2\t0\t42226\n", "56\t40849\t105.2\t0\t40849\n", "57\t43216\t105.2\t0\t43216\n", "58\t48664\t105.2\t0\t48664\n", "59\t32591\t105.2\t0\t32591\n", "60\t25774\t105.2\t0\t25774\n", "61\t24780\t105.2\t0\t24780\n", "62\t20424\t105.2\t0\t20424\n", "63\t19058\t105.2\t0\t19058\n", "64\t22449\t105.2\t0\t22449\n", "65\t20547\t105.2\t0\t20547\n", "66\t15758\t105.2\t0\t15758\n", "67\t16315\t105.2\t0\t16315\n", "68\t15547\t105.2\t0\t15547\n", "69\t15703\t105.2\t0\t15703\n", "70\t16759\t105.2\t0\t16759\n", "71\t15777\t105.2\t0\t15777\n", "72\t11943\t105.2\t0\t11943\n", "73\t10680\t105.2\t0\t10680\n", "74\t10895\t105.2\t0\t10895\n", "75\t9708\t105.2\t0\t9708\n", "76\t7824\t105.2\t0\t7824\n", "77\t7532\t105.2\t0\t7532\n", "78\t9076\t105.2\t0\t9076\n", "79\t8231\t105.2\t0\t8231\n", "80\t7951\t105.2\t0\t7951\n", "81\t7591\t105.2\t0\t7591\n", "82\t7402\t105.2\t0\t7402\n", "83\t7445\t105.2\t0\t7445\n", "84\t8644\t105.2\t0\t8644\n", "85\t9790\t105.2\t0\t9790\n", "86\t9462\t105.2\t0\t9462\n", "87\t6607\t105.2\t0\t6607\n", "88\t6102\t105.2\t0\t6102\n", "89\t6272\t105.2\t0\t6272\n", "90\t6479\t105.2\t0\t6479\n", "91\t6315\t105.2\t0\t6315\n", "92\t6326\t105.2\t0\t6326\n", "93\t6444\t105.2\t0\t6444\n", "94\t6154\t105.2\t0\t6154\n", "95\t5464\t105.2\t0\t5464\n", "96\t4149\t105.2\t0\t4149\n", "97\t2765\t105.2\t0\t2765\n", "98\t1637\t105.2\t0\t1637\n", "99\t1120\t105.2\t0\t1120\n", "100\t1025\t105.2\t0\t1025\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29908 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 53.9%\n", " C: 17.4%\n", " G: 0.0%\n", " T: 28.5%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13402\t107683.1\t0\t13402\n", "4\t2577\t26920.8\t0\t2577\n", "5\t762\t6730.2\t0\t762\n", "6\t327\t1682.5\t0\t327\n", "7\t54\t420.6\t0\t54\n", "8\t37\t105.2\t0\t37\n", "9\t39\t105.2\t0\t39\n", "10\t38\t105.2\t0\t38\n", "11\t46\t105.2\t0\t46\n", "12\t52\t105.2\t0\t52\n", "13\t47\t105.2\t0\t47\n", "14\t46\t105.2\t0\t46\n", "15\t57\t105.2\t0\t57\n", "16\t48\t105.2\t0\t48\n", "17\t47\t105.2\t0\t47\n", "18\t74\t105.2\t0\t74\n", "19\t81\t105.2\t0\t81\n", "20\t98\t105.2\t0\t98\n", "21\t96\t105.2\t0\t96\n", "22\t61\t105.2\t0\t61\n", "23\t75\t105.2\t0\t75\n", "24\t61\t105.2\t0\t61\n", "25\t73\t105.2\t0\t73\n", "26\t118\t105.2\t0\t118\n", "27\t148\t105.2\t0\t148\n", "28\t171\t105.2\t0\t171\n", "29\t280\t105.2\t0\t280\n", "30\t496\t105.2\t0\t496\n", "31\t620\t105.2\t0\t620\n", "32\t1012\t105.2\t0\t1012\n", "33\t1109\t105.2\t0\t1109\n", "34\t1339\t105.2\t0\t1339\n", "35\t1742\t105.2\t0\t1742\n", "36\t1646\t105.2\t0\t1646\n", "37\t806\t105.2\t0\t806\n", "38\t88\t105.2\t0\t88\n", "39\t68\t105.2\t0\t68\n", "40\t31\t105.2\t0\t31\n", "41\t39\t105.2\t0\t39\n", "42\t34\t105.2\t0\t34\n", "43\t36\t105.2\t0\t36\n", "44\t39\t105.2\t0\t39\n", "45\t34\t105.2\t0\t34\n", "46\t35\t105.2\t0\t35\n", "47\t36\t105.2\t0\t36\n", "48\t36\t105.2\t0\t36\n", "49\t32\t105.2\t0\t32\n", "50\t34\t105.2\t0\t34\n", "51\t31\t105.2\t0\t31\n", "52\t25\t105.2\t0\t25\n", "53\t35\t105.2\t0\t35\n", "54\t23\t105.2\t0\t23\n", "55\t30\t105.2\t0\t30\n", "56\t33\t105.2\t0\t33\n", "57\t25\t105.2\t0\t25\n", "58\t22\t105.2\t0\t22\n", "59\t27\t105.2\t0\t27\n", "60\t23\t105.2\t0\t23\n", "61\t23\t105.2\t0\t23\n", "62\t31\t105.2\t0\t31\n", "63\t26\t105.2\t0\t26\n", "64\t19\t105.2\t0\t19\n", "65\t31\t105.2\t0\t31\n", "66\t24\t105.2\t0\t24\n", "67\t20\t105.2\t0\t20\n", "68\t14\t105.2\t0\t14\n", "69\t14\t105.2\t0\t14\n", "70\t21\t105.2\t0\t21\n", "71\t20\t105.2\t0\t20\n", "72\t16\t105.2\t0\t16\n", "73\t16\t105.2\t0\t16\n", "74\t15\t105.2\t0\t15\n", "75\t16\t105.2\t0\t16\n", "76\t19\t105.2\t0\t19\n", "77\t18\t105.2\t0\t18\n", "78\t8\t105.2\t0\t8\n", "79\t20\t105.2\t0\t20\n", "80\t13\t105.2\t0\t13\n", "81\t20\t105.2\t0\t20\n", "82\t15\t105.2\t0\t15\n", "83\t17\t105.2\t0\t17\n", "84\t19\t105.2\t0\t19\n", "85\t20\t105.2\t0\t20\n", "86\t15\t105.2\t0\t15\n", "87\t14\t105.2\t0\t14\n", "88\t15\t105.2\t0\t15\n", "89\t21\t105.2\t0\t21\n", "90\t18\t105.2\t0\t18\n", "91\t37\t105.2\t0\t37\n", "92\t49\t105.2\t0\t49\n", "93\t65\t105.2\t0\t65\n", "94\t111\t105.2\t0\t111\n", "95\t102\t105.2\t0\t102\n", "96\t134\t105.2\t0\t134\n", "97\t94\t105.2\t0\t94\n", "98\t89\t105.2\t0\t89\n", "99\t55\t105.2\t0\t55\n", "100\t113\t105.2\t0\t113\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 101701 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.2%\n", " C: 21.8%\n", " G: 15.6%\n", " T: 22.4%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t77193\t107683.1\t0\t77193\n", "4\t16322\t26920.8\t0\t16322\n", "5\t1912\t6730.2\t0\t1912\n", "6\t238\t1682.5\t0\t238\n", "7\t47\t420.6\t0\t47\n", "8\t56\t420.6\t0\t56\n", "9\t54\t420.6\t0\t54\n", "10\t66\t420.6\t0\t66\n", "11\t74\t420.6\t0\t74\n", "12\t63\t420.6\t0\t63\n", "13\t52\t420.6\t0\t52\n", "14\t66\t420.6\t0\t66\n", "15\t55\t420.6\t0\t55\n", "16\t68\t420.6\t0\t68\n", "17\t60\t420.6\t0\t60\n", "18\t58\t420.6\t0\t58\n", "19\t66\t420.6\t0\t66\n", "20\t60\t420.6\t0\t60\n", "21\t61\t420.6\t0\t61\n", "22\t47\t420.6\t0\t47\n", "23\t49\t420.6\t0\t49\n", "24\t49\t420.6\t0\t49\n", "25\t67\t420.6\t0\t67\n", "26\t59\t420.6\t0\t59\n", "27\t81\t420.6\t0\t81\n", "28\t60\t420.6\t0\t60\n", "29\t69\t420.6\t0\t69\n", "30\t84\t420.6\t0\t84\n", "31\t74\t420.6\t0\t74\n", "32\t97\t420.6\t0\t97\n", "33\t98\t420.6\t0\t98\n", "34\t74\t420.6\t0\t74\n", "35\t57\t420.6\t0\t57\n", "36\t45\t420.6\t0\t45\n", "37\t56\t420.6\t0\t56\n", "38\t67\t420.6\t0\t67\n", "39\t66\t420.6\t0\t66\n", "40\t81\t420.6\t0\t81\n", "41\t64\t420.6\t0\t64\n", "42\t45\t420.6\t0\t45\n", "43\t58\t420.6\t0\t58\n", "44\t43\t420.6\t0\t43\n", "45\t51\t420.6\t0\t51\n", "46\t58\t420.6\t0\t58\n", "47\t67\t420.6\t0\t67\n", "48\t52\t420.6\t0\t52\n", "49\t52\t420.6\t0\t52\n", "50\t51\t420.6\t0\t51\n", "51\t36\t420.6\t0\t36\n", "52\t50\t420.6\t0\t50\n", "53\t48\t420.6\t0\t48\n", "54\t39\t420.6\t0\t39\n", "55\t45\t420.6\t0\t45\n", "56\t40\t420.6\t0\t40\n", "57\t44\t420.6\t0\t44\n", "58\t47\t420.6\t0\t47\n", "59\t48\t420.6\t0\t48\n", "60\t48\t420.6\t0\t48\n", "61\t47\t420.6\t0\t47\n", "62\t44\t420.6\t0\t44\n", "63\t52\t420.6\t0\t52\n", "64\t43\t420.6\t0\t43\n", "65\t49\t420.6\t0\t49\n", "66\t56\t420.6\t0\t56\n", "67\t53\t420.6\t0\t53\n", "68\t60\t420.6\t0\t60\n", "69\t50\t420.6\t0\t50\n", "70\t38\t420.6\t0\t38\n", "71\t48\t420.6\t0\t48\n", "72\t54\t420.6\t0\t54\n", "73\t56\t420.6\t0\t56\n", "74\t50\t420.6\t0\t50\n", "75\t53\t420.6\t0\t53\n", "76\t68\t420.6\t0\t68\n", "77\t102\t420.6\t0\t102\n", "78\t69\t420.6\t0\t69\n", "79\t80\t420.6\t0\t80\n", "80\t116\t420.6\t0\t116\n", "81\t115\t420.6\t0\t115\n", "82\t111\t420.6\t0\t111\n", "83\t92\t420.6\t0\t92\n", "84\t93\t420.6\t0\t93\n", "85\t82\t420.6\t0\t82\n", "86\t69\t420.6\t0\t69\n", "87\t108\t420.6\t0\t108\n", "88\t100\t420.6\t0\t100\n", "89\t56\t420.6\t0\t56\n", "90\t65\t420.6\t0\t65\n", "91\t53\t420.6\t0\t53\n", "92\t45\t420.6\t0\t45\n", "93\t42\t420.6\t0\t42\n", "94\t70\t420.6\t0\t70\n", "95\t55\t420.6\t0\t55\n", "96\t68\t420.6\t0\t68\n", "97\t68\t420.6\t0\t68\n", "98\t105\t420.6\t0\t105\n", "99\t123\t420.6\t0\t123\n", "100\t156\t420.6\t0\t156\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 162_S62_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/162.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 85.33 s (14 us/read; 4.42 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,282,792\n", "Reads with adapters: 3,760,832 (59.9%)\n", "Reads written (passing filters): 6,049,165 (96.3%)\n", "\n", "Total basepairs processed: 628,279,200 bp\n", "Quality-trimmed: 1,734,445 bp (0.3%)\n", "Total written (filtered): 482,197,868 bp (76.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3649866 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 26.7%\n", " G: 34.8%\n", " T: 38.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t128190\t98168.6\t0\t128190\n", "4\t75004\t24542.2\t0\t75004\n", "5\t54762\t6135.5\t0\t54762\n", "6\t44846\t1533.9\t0\t44846\n", "7\t37758\t383.5\t0\t37758\n", "8\t35172\t95.9\t0\t35172\n", "9\t34969\t95.9\t0\t34969\n", "10\t33588\t95.9\t0\t33588\n", "11\t34467\t95.9\t0\t34467\n", "12\t35611\t95.9\t0\t35611\n", "13\t39817\t95.9\t0\t39817\n", "14\t40342\t95.9\t0\t40342\n", "15\t38964\t95.9\t0\t38964\n", "16\t40288\t95.9\t0\t40288\n", "17\t44875\t95.9\t0\t44875\n", "18\t53422\t95.9\t0\t53422\n", "19\t46978\t95.9\t0\t46978\n", "20\t39677\t95.9\t0\t39677\n", "21\t42136\t95.9\t0\t42136\n", "22\t37961\t95.9\t0\t37961\n", "23\t43227\t95.9\t0\t43227\n", "24\t52939\t95.9\t0\t52939\n", "25\t52824\t95.9\t0\t52824\n", "26\t62616\t95.9\t0\t62616\n", "27\t69163\t95.9\t0\t69163\n", "28\t63239\t95.9\t0\t63239\n", "29\t61044\t95.9\t0\t61044\n", "30\t62252\t95.9\t0\t62252\n", "31\t68995\t95.9\t0\t68995\n", "32\t68721\t95.9\t0\t68721\n", "33\t59456\t95.9\t0\t59456\n", "34\t57083\t95.9\t0\t57083\n", "35\t66192\t95.9\t0\t66192\n", "36\t83268\t95.9\t0\t83268\n", "37\t97398\t95.9\t0\t97398\n", "38\t74454\t95.9\t0\t74454\n", "39\t56656\t95.9\t0\t56656\n", "40\t50021\t95.9\t0\t50021\n", "41\t52374\t95.9\t0\t52374\n", "42\t56810\t95.9\t0\t56810\n", "43\t49596\t95.9\t0\t49596\n", "44\t38415\t95.9\t0\t38415\n", "45\t50522\t95.9\t0\t50522\n", "46\t62702\t95.9\t0\t62702\n", "47\t59177\t95.9\t0\t59177\n", "48\t65972\t95.9\t0\t65972\n", "49\t52807\t95.9\t0\t52807\n", "50\t48809\t95.9\t0\t48809\n", "51\t39110\t95.9\t0\t39110\n", "52\t38779\t95.9\t0\t38779\n", "53\t43595\t95.9\t0\t43595\n", "54\t50433\t95.9\t0\t50433\n", "55\t56620\t95.9\t0\t56620\n", "56\t53708\t95.9\t0\t53708\n", "57\t48369\t95.9\t0\t48369\n", "58\t46876\t95.9\t0\t46876\n", "59\t34198\t95.9\t0\t34198\n", "60\t29478\t95.9\t0\t29478\n", "61\t30476\t95.9\t0\t30476\n", "62\t23471\t95.9\t0\t23471\n", "63\t23036\t95.9\t0\t23036\n", "64\t27058\t95.9\t0\t27058\n", "65\t25841\t95.9\t0\t25841\n", "66\t21383\t95.9\t0\t21383\n", "67\t20731\t95.9\t0\t20731\n", "68\t19176\t95.9\t0\t19176\n", "69\t19247\t95.9\t0\t19247\n", "70\t20030\t95.9\t0\t20030\n", "71\t19627\t95.9\t0\t19627\n", "72\t15395\t95.9\t0\t15395\n", "73\t14353\t95.9\t0\t14353\n", "74\t14919\t95.9\t0\t14919\n", "75\t12891\t95.9\t0\t12891\n", "76\t11077\t95.9\t0\t11077\n", "77\t10135\t95.9\t0\t10135\n", "78\t11438\t95.9\t0\t11438\n", "79\t11136\t95.9\t0\t11136\n", "80\t11702\t95.9\t0\t11702\n", "81\t11164\t95.9\t0\t11164\n", "82\t10715\t95.9\t0\t10715\n", "83\t11720\t95.9\t0\t11720\n", "84\t13780\t95.9\t0\t13780\n", "85\t16106\t95.9\t0\t16106\n", "86\t15843\t95.9\t0\t15843\n", "87\t11116\t95.9\t0\t11116\n", "88\t10581\t95.9\t0\t10581\n", "89\t11920\t95.9\t0\t11920\n", "90\t12735\t95.9\t0\t12735\n", "91\t13156\t95.9\t0\t13156\n", "92\t13258\t95.9\t0\t13258\n", "93\t14132\t95.9\t0\t14132\n", "94\t13684\t95.9\t0\t13684\n", "95\t12475\t95.9\t0\t12475\n", "96\t9834\t95.9\t0\t9834\n", "97\t6700\t95.9\t0\t6700\n", "98\t4186\t95.9\t0\t4186\n", "99\t3878\t95.9\t0\t3878\n", "100\t3036\t95.9\t0\t3036\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 25706 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 63.0%\n", " C: 14.9%\n", " G: 0.0%\n", " T: 21.9%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t8718\t98168.6\t0\t8718\n", "4\t1843\t24542.2\t0\t1843\n", "5\t391\t6135.5\t0\t391\n", "6\t137\t1533.9\t0\t137\n", "7\t52\t383.5\t0\t52\n", "8\t39\t95.9\t0\t39\n", "9\t31\t95.9\t0\t31\n", "10\t32\t95.9\t0\t32\n", "11\t34\t95.9\t0\t34\n", "12\t41\t95.9\t0\t41\n", "13\t35\t95.9\t0\t35\n", "14\t31\t95.9\t0\t31\n", "15\t37\t95.9\t0\t37\n", "16\t43\t95.9\t0\t43\n", "17\t43\t95.9\t0\t43\n", "18\t57\t95.9\t0\t57\n", "19\t64\t95.9\t0\t64\n", "20\t83\t95.9\t0\t83\n", "21\t78\t95.9\t0\t78\n", "22\t72\t95.9\t0\t72\n", "23\t66\t95.9\t0\t66\n", "24\t81\t95.9\t0\t81\n", "25\t92\t95.9\t0\t92\n", "26\t158\t95.9\t0\t158\n", "27\t167\t95.9\t0\t167\n", "28\t243\t95.9\t0\t243\n", "29\t403\t95.9\t0\t403\n", "30\t769\t95.9\t0\t769\n", "31\t944\t95.9\t0\t944\n", "32\t1547\t95.9\t0\t1547\n", "33\t1436\t95.9\t0\t1436\n", "34\t1571\t95.9\t0\t1571\n", "35\t1996\t95.9\t0\t1996\n", "36\t1899\t95.9\t0\t1899\n", "37\t845\t95.9\t0\t845\n", "38\t77\t95.9\t0\t77\n", "39\t49\t95.9\t0\t49\n", "40\t24\t95.9\t0\t24\n", "41\t20\t95.9\t0\t20\n", "42\t26\t95.9\t0\t26\n", "43\t22\t95.9\t0\t22\n", "44\t24\t95.9\t0\t24\n", "45\t22\t95.9\t0\t22\n", "46\t26\t95.9\t0\t26\n", "47\t27\t95.9\t0\t27\n", "48\t24\t95.9\t0\t24\n", "49\t36\t95.9\t0\t36\n", "50\t30\t95.9\t0\t30\n", "51\t29\t95.9\t0\t29\n", "52\t27\t95.9\t0\t27\n", "53\t26\t95.9\t0\t26\n", "54\t14\t95.9\t0\t14\n", "55\t25\t95.9\t0\t25\n", "56\t24\t95.9\t0\t24\n", "57\t16\t95.9\t0\t16\n", "58\t20\t95.9\t0\t20\n", "59\t19\t95.9\t0\t19\n", "60\t16\t95.9\t0\t16\n", "61\t28\t95.9\t0\t28\n", "62\t19\t95.9\t0\t19\n", "63\t18\t95.9\t0\t18\n", "64\t22\t95.9\t0\t22\n", "65\t18\t95.9\t0\t18\n", "66\t14\t95.9\t0\t14\n", "67\t19\t95.9\t0\t19\n", "68\t15\t95.9\t0\t15\n", "69\t7\t95.9\t0\t7\n", "70\t10\t95.9\t0\t10\n", "71\t6\t95.9\t0\t6\n", "72\t5\t95.9\t0\t5\n", "73\t4\t95.9\t0\t4\n", "74\t11\t95.9\t0\t11\n", "75\t2\t95.9\t0\t2\n", "76\t10\t95.9\t0\t10\n", "77\t11\t95.9\t0\t11\n", "78\t8\t95.9\t0\t8\n", "79\t5\t95.9\t0\t5\n", "80\t12\t95.9\t0\t12\n", "81\t4\t95.9\t0\t4\n", "82\t7\t95.9\t0\t7\n", "83\t8\t95.9\t0\t8\n", "84\t6\t95.9\t0\t6\n", "85\t4\t95.9\t0\t4\n", "86\t10\t95.9\t0\t10\n", "87\t6\t95.9\t0\t6\n", "88\t15\t95.9\t0\t15\n", "89\t6\t95.9\t0\t6\n", "90\t12\t95.9\t0\t12\n", "91\t16\t95.9\t0\t16\n", "92\t17\t95.9\t0\t17\n", "93\t45\t95.9\t0\t45\n", "94\t91\t95.9\t0\t91\n", "95\t91\t95.9\t0\t91\n", "96\t76\t95.9\t0\t76\n", "97\t81\t95.9\t0\t81\n", "98\t85\t95.9\t0\t85\n", "99\t61\t95.9\t0\t61\n", "100\t120\t95.9\t0\t120\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 85260 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.6%\n", " C: 22.4%\n", " G: 13.0%\n", " T: 24.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t65524\t98168.6\t0\t65524\n", "4\t13224\t24542.2\t0\t13224\n", "5\t1691\t6135.5\t0\t1691\n", "6\t167\t1533.9\t0\t167\n", "7\t36\t383.5\t0\t36\n", "8\t51\t383.5\t0\t51\n", "9\t52\t383.5\t0\t52\n", "10\t49\t383.5\t0\t49\n", "11\t45\t383.5\t0\t45\n", "12\t45\t383.5\t0\t45\n", "13\t51\t383.5\t0\t51\n", "14\t54\t383.5\t0\t54\n", "15\t51\t383.5\t0\t51\n", "16\t43\t383.5\t0\t43\n", "17\t52\t383.5\t0\t52\n", "18\t56\t383.5\t0\t56\n", "19\t43\t383.5\t0\t43\n", "20\t40\t383.5\t0\t40\n", "21\t52\t383.5\t0\t52\n", "22\t43\t383.5\t0\t43\n", "23\t49\t383.5\t0\t49\n", "24\t52\t383.5\t0\t52\n", "25\t42\t383.5\t0\t42\n", "26\t44\t383.5\t0\t44\n", "27\t58\t383.5\t0\t58\n", "28\t54\t383.5\t0\t54\n", "29\t45\t383.5\t0\t45\n", "30\t52\t383.5\t0\t52\n", "31\t52\t383.5\t0\t52\n", "32\t61\t383.5\t0\t61\n", "33\t55\t383.5\t0\t55\n", "34\t53\t383.5\t0\t53\n", "35\t53\t383.5\t0\t53\n", "36\t38\t383.5\t0\t38\n", "37\t48\t383.5\t0\t48\n", "38\t41\t383.5\t0\t41\n", "39\t52\t383.5\t0\t52\n", "40\t52\t383.5\t0\t52\n", "41\t40\t383.5\t0\t40\n", "42\t34\t383.5\t0\t34\n", "43\t57\t383.5\t0\t57\n", "44\t49\t383.5\t0\t49\n", "45\t37\t383.5\t0\t37\n", "46\t50\t383.5\t0\t50\n", "47\t47\t383.5\t0\t47\n", "48\t39\t383.5\t0\t39\n", "49\t58\t383.5\t0\t58\n", "50\t27\t383.5\t0\t27\n", "51\t40\t383.5\t0\t40\n", "52\t50\t383.5\t0\t50\n", "53\t54\t383.5\t0\t54\n", "54\t46\t383.5\t0\t46\n", "55\t45\t383.5\t0\t45\n", "56\t62\t383.5\t0\t62\n", "57\t35\t383.5\t0\t35\n", "58\t37\t383.5\t0\t37\n", "59\t43\t383.5\t0\t43\n", "60\t37\t383.5\t0\t37\n", "61\t43\t383.5\t0\t43\n", "62\t29\t383.5\t0\t29\n", "63\t45\t383.5\t0\t45\n", "64\t33\t383.5\t0\t33\n", "65\t45\t383.5\t0\t45\n", "66\t44\t383.5\t0\t44\n", "67\t41\t383.5\t0\t41\n", "68\t43\t383.5\t0\t43\n", "69\t24\t383.5\t0\t24\n", "70\t31\t383.5\t0\t31\n", "71\t50\t383.5\t0\t50\n", "72\t43\t383.5\t0\t43\n", "73\t53\t383.5\t0\t53\n", "74\t55\t383.5\t0\t55\n", "75\t51\t383.5\t0\t51\n", "76\t52\t383.5\t0\t52\n", "77\t67\t383.5\t0\t67\n", "78\t56\t383.5\t0\t56\n", "79\t48\t383.5\t0\t48\n", "80\t74\t383.5\t0\t74\n", "81\t75\t383.5\t0\t75\n", "82\t95\t383.5\t0\t95\n", "83\t79\t383.5\t0\t79\n", "84\t74\t383.5\t0\t74\n", "85\t72\t383.5\t0\t72\n", "86\t44\t383.5\t0\t44\n", "87\t65\t383.5\t0\t65\n", "88\t57\t383.5\t0\t57\n", "89\t43\t383.5\t0\t43\n", "90\t46\t383.5\t0\t46\n", "91\t41\t383.5\t0\t41\n", "92\t34\t383.5\t0\t34\n", "93\t36\t383.5\t0\t36\n", "94\t40\t383.5\t0\t40\n", "95\t27\t383.5\t0\t27\n", "96\t40\t383.5\t0\t40\n", "97\t62\t383.5\t0\t62\n", "98\t68\t383.5\t0\t68\n", "99\t86\t383.5\t0\t86\n", "100\t92\t383.5\t0\t92\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 168_S67_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/168.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 41.13 s (13 us/read; 4.46 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 3,059,208\n", "Reads with adapters: 1,638,290 (53.6%)\n", "Reads written (passing filters): 2,986,013 (97.6%)\n", "\n", "Total basepairs processed: 305,920,800 bp\n", "Quality-trimmed: 703,689 bp (0.2%)\n", "Total written (filtered): 250,083,458 bp (81.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1580137 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.0%\n", " G: 31.3%\n", " T: 40.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t72673\t47800.1\t0\t72673\n", "4\t44261\t11950.0\t0\t44261\n", "5\t32137\t2987.5\t0\t32137\n", "6\t25157\t746.9\t0\t25157\n", "7\t21853\t186.7\t0\t21853\n", "8\t20596\t46.7\t0\t20596\n", "9\t20229\t46.7\t0\t20229\n", "10\t18570\t46.7\t0\t18570\n", "11\t18694\t46.7\t0\t18694\n", "12\t19093\t46.7\t0\t19093\n", "13\t20086\t46.7\t0\t20086\n", "14\t20027\t46.7\t0\t20027\n", "15\t19759\t46.7\t0\t19759\n", "16\t20399\t46.7\t0\t20399\n", "17\t23506\t46.7\t0\t23506\n", "18\t28285\t46.7\t0\t28285\n", "19\t24840\t46.7\t0\t24840\n", "20\t20894\t46.7\t0\t20894\n", "21\t21311\t46.7\t0\t21311\n", "22\t19296\t46.7\t0\t19296\n", "23\t21345\t46.7\t0\t21345\n", "24\t25557\t46.7\t0\t25557\n", "25\t25530\t46.7\t0\t25530\n", "26\t29978\t46.7\t0\t29978\n", "27\t33616\t46.7\t0\t33616\n", "28\t30076\t46.7\t0\t30076\n", "29\t28803\t46.7\t0\t28803\n", "30\t30288\t46.7\t0\t30288\n", "31\t33287\t46.7\t0\t33287\n", "32\t29896\t46.7\t0\t29896\n", "33\t27232\t46.7\t0\t27232\n", "34\t25547\t46.7\t0\t25547\n", "35\t29747\t46.7\t0\t29747\n", "36\t36349\t46.7\t0\t36349\n", "37\t41258\t46.7\t0\t41258\n", "38\t32200\t46.7\t0\t32200\n", "39\t24700\t46.7\t0\t24700\n", "40\t21927\t46.7\t0\t21927\n", "41\t22691\t46.7\t0\t22691\n", "42\t23480\t46.7\t0\t23480\n", "43\t20787\t46.7\t0\t20787\n", "44\t16071\t46.7\t0\t16071\n", "45\t20602\t46.7\t0\t20602\n", "46\t24973\t46.7\t0\t24973\n", "47\t23626\t46.7\t0\t23626\n", "48\t24393\t46.7\t0\t24393\n", "49\t19816\t46.7\t0\t19816\n", "50\t18208\t46.7\t0\t18208\n", "51\t15632\t46.7\t0\t15632\n", "52\t14913\t46.7\t0\t14913\n", "53\t15111\t46.7\t0\t15111\n", "54\t14669\t46.7\t0\t14669\n", "55\t18451\t46.7\t0\t18451\n", "56\t18211\t46.7\t0\t18211\n", "57\t13786\t46.7\t0\t13786\n", "58\t15711\t46.7\t0\t15711\n", "59\t11982\t46.7\t0\t11982\n", "60\t9948\t46.7\t0\t9948\n", "61\t10043\t46.7\t0\t10043\n", "62\t7957\t46.7\t0\t7957\n", "63\t7888\t46.7\t0\t7888\n", "64\t8345\t46.7\t0\t8345\n", "65\t7899\t46.7\t0\t7899\n", "66\t6858\t46.7\t0\t6858\n", "67\t6552\t46.7\t0\t6552\n", "68\t6055\t46.7\t0\t6055\n", "69\t5852\t46.7\t0\t5852\n", "70\t5813\t46.7\t0\t5813\n", "71\t5399\t46.7\t0\t5399\n", "72\t4290\t46.7\t0\t4290\n", "73\t4080\t46.7\t0\t4080\n", "74\t4092\t46.7\t0\t4092\n", "75\t3636\t46.7\t0\t3636\n", "76\t3163\t46.7\t0\t3163\n", "77\t2909\t46.7\t0\t2909\n", "78\t3111\t46.7\t0\t3111\n", "79\t3270\t46.7\t0\t3270\n", "80\t3128\t46.7\t0\t3128\n", "81\t3127\t46.7\t0\t3127\n", "82\t3198\t46.7\t0\t3198\n", "83\t3484\t46.7\t0\t3484\n", "84\t4126\t46.7\t0\t4126\n", "85\t4816\t46.7\t0\t4816\n", "86\t5000\t46.7\t0\t5000\n", "87\t3875\t46.7\t0\t3875\n", "88\t3625\t46.7\t0\t3625\n", "89\t3772\t46.7\t0\t3772\n", "90\t4170\t46.7\t0\t4170\n", "91\t4128\t46.7\t0\t4128\n", "92\t4189\t46.7\t0\t4189\n", "93\t4238\t46.7\t0\t4238\n", "94\t4153\t46.7\t0\t4153\n", "95\t3953\t46.7\t0\t3953\n", "96\t3051\t46.7\t0\t3051\n", "97\t1865\t46.7\t0\t1865\n", "98\t1254\t46.7\t0\t1254\n", "99\t963\t46.7\t0\t963\n", "100\t747\t46.7\t0\t747\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 11413 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 52.5%\n", " C: 17.8%\n", " G: 0.0%\n", " T: 29.4%\n", " none/other: 0.4%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t5792\t47800.1\t0\t5792\n", "4\t1106\t11950.0\t0\t1106\n", "5\t277\t2987.5\t0\t277\n", "6\t71\t746.9\t0\t71\n", "7\t12\t186.7\t0\t12\n", "8\t13\t46.7\t0\t13\n", "9\t9\t46.7\t0\t9\n", "10\t17\t46.7\t0\t17\n", "11\t8\t46.7\t0\t8\n", "12\t14\t46.7\t0\t14\n", "13\t9\t46.7\t0\t9\n", "14\t12\t46.7\t0\t12\n", "15\t12\t46.7\t0\t12\n", "16\t9\t46.7\t0\t9\n", "17\t9\t46.7\t0\t9\n", "18\t23\t46.7\t0\t23\n", "19\t12\t46.7\t0\t12\n", "20\t31\t46.7\t0\t31\n", "21\t26\t46.7\t0\t26\n", "22\t25\t46.7\t0\t25\n", "23\t23\t46.7\t0\t23\n", "24\t18\t46.7\t0\t18\n", "25\t29\t46.7\t0\t29\n", "26\t35\t46.7\t0\t35\n", "27\t60\t46.7\t0\t60\n", "28\t70\t46.7\t0\t70\n", "29\t88\t46.7\t0\t88\n", "30\t220\t46.7\t0\t220\n", "31\t249\t46.7\t0\t249\n", "32\t422\t46.7\t0\t422\n", "33\t381\t46.7\t0\t381\n", "34\t418\t46.7\t0\t418\n", "35\t480\t46.7\t0\t480\n", "36\t474\t46.7\t0\t474\n", "37\t230\t46.7\t0\t230\n", "38\t16\t46.7\t0\t16\n", "39\t17\t46.7\t0\t17\n", "40\t7\t46.7\t0\t7\n", "41\t11\t46.7\t0\t11\n", "42\t10\t46.7\t0\t10\n", "43\t7\t46.7\t0\t7\n", "44\t3\t46.7\t0\t3\n", "45\t11\t46.7\t0\t11\n", "46\t11\t46.7\t0\t11\n", "47\t8\t46.7\t0\t8\n", "48\t4\t46.7\t0\t4\n", "49\t5\t46.7\t0\t5\n", "50\t7\t46.7\t0\t7\n", "51\t9\t46.7\t0\t9\n", "52\t10\t46.7\t0\t10\n", "53\t6\t46.7\t0\t6\n", "54\t7\t46.7\t0\t7\n", "55\t3\t46.7\t0\t3\n", "56\t7\t46.7\t0\t7\n", "57\t2\t46.7\t0\t2\n", "58\t3\t46.7\t0\t3\n", "59\t3\t46.7\t0\t3\n", "60\t6\t46.7\t0\t6\n", "61\t5\t46.7\t0\t5\n", "62\t5\t46.7\t0\t5\n", "63\t3\t46.7\t0\t3\n", "64\t2\t46.7\t0\t2\n", "65\t2\t46.7\t0\t2\n", "66\t3\t46.7\t0\t3\n", "67\t5\t46.7\t0\t5\n", "68\t2\t46.7\t0\t2\n", "69\t6\t46.7\t0\t6\n", "70\t3\t46.7\t0\t3\n", "71\t3\t46.7\t0\t3\n", "72\t4\t46.7\t0\t4\n", "74\t1\t46.7\t0\t1\n", "75\t3\t46.7\t0\t3\n", "76\t2\t46.7\t0\t2\n", "77\t1\t46.7\t0\t1\n", "78\t2\t46.7\t0\t2\n", "79\t2\t46.7\t0\t2\n", "80\t6\t46.7\t0\t6\n", "81\t5\t46.7\t0\t5\n", "82\t2\t46.7\t0\t2\n", "83\t2\t46.7\t0\t2\n", "84\t1\t46.7\t0\t1\n", "85\t6\t46.7\t0\t6\n", "86\t2\t46.7\t0\t2\n", "87\t1\t46.7\t0\t1\n", "88\t6\t46.7\t0\t6\n", "89\t5\t46.7\t0\t5\n", "90\t3\t46.7\t0\t3\n", "91\t7\t46.7\t0\t7\n", "92\t11\t46.7\t0\t11\n", "93\t19\t46.7\t0\t19\n", "94\t51\t46.7\t0\t51\n", "95\t63\t46.7\t0\t63\n", "96\t63\t46.7\t0\t63\n", "97\t59\t46.7\t0\t59\n", "98\t53\t46.7\t0\t53\n", "99\t51\t46.7\t0\t51\n", "100\t86\t46.7\t0\t86\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 46740 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.1%\n", " C: 20.9%\n", " G: 12.9%\n", " T: 23.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t36173\t47800.1\t0\t36173\n", "4\t6873\t11950.0\t0\t6873\n", "5\t1114\t2987.5\t0\t1114\n", "6\t93\t746.9\t0\t93\n", "7\t18\t186.7\t0\t18\n", "8\t23\t186.7\t0\t23\n", "9\t22\t186.7\t0\t22\n", "10\t39\t186.7\t0\t39\n", "11\t28\t186.7\t0\t28\n", "12\t21\t186.7\t0\t21\n", "13\t29\t186.7\t0\t29\n", "14\t16\t186.7\t0\t16\n", "15\t26\t186.7\t0\t26\n", "16\t20\t186.7\t0\t20\n", "17\t25\t186.7\t0\t25\n", "18\t19\t186.7\t0\t19\n", "19\t18\t186.7\t0\t18\n", "20\t27\t186.7\t0\t27\n", "21\t12\t186.7\t0\t12\n", "22\t21\t186.7\t0\t21\n", "23\t18\t186.7\t0\t18\n", "24\t16\t186.7\t0\t16\n", "25\t28\t186.7\t0\t28\n", "26\t33\t186.7\t0\t33\n", "27\t38\t186.7\t0\t38\n", "28\t18\t186.7\t0\t18\n", "29\t36\t186.7\t0\t36\n", "30\t24\t186.7\t0\t24\n", "31\t30\t186.7\t0\t30\n", "32\t25\t186.7\t0\t25\n", "33\t35\t186.7\t0\t35\n", "34\t23\t186.7\t0\t23\n", "35\t31\t186.7\t0\t31\n", "36\t22\t186.7\t0\t22\n", "37\t29\t186.7\t0\t29\n", "38\t23\t186.7\t0\t23\n", "39\t35\t186.7\t0\t35\n", "40\t34\t186.7\t0\t34\n", "41\t30\t186.7\t0\t30\n", "42\t14\t186.7\t0\t14\n", "43\t28\t186.7\t0\t28\n", "44\t23\t186.7\t0\t23\n", "45\t20\t186.7\t0\t20\n", "46\t24\t186.7\t0\t24\n", "47\t29\t186.7\t0\t29\n", "48\t30\t186.7\t0\t30\n", "49\t23\t186.7\t0\t23\n", "50\t13\t186.7\t0\t13\n", "51\t25\t186.7\t0\t25\n", "52\t28\t186.7\t0\t28\n", "53\t20\t186.7\t0\t20\n", "54\t21\t186.7\t0\t21\n", "55\t17\t186.7\t0\t17\n", "56\t22\t186.7\t0\t22\n", "57\t18\t186.7\t0\t18\n", "58\t13\t186.7\t0\t13\n", "59\t23\t186.7\t0\t23\n", "60\t27\t186.7\t0\t27\n", "61\t24\t186.7\t0\t24\n", "62\t37\t186.7\t0\t37\n", "63\t21\t186.7\t0\t21\n", "64\t29\t186.7\t0\t29\n", "65\t23\t186.7\t0\t23\n", "66\t20\t186.7\t0\t20\n", "67\t20\t186.7\t0\t20\n", "68\t13\t186.7\t0\t13\n", "69\t24\t186.7\t0\t24\n", "70\t22\t186.7\t0\t22\n", "71\t18\t186.7\t0\t18\n", "72\t20\t186.7\t0\t20\n", "73\t34\t186.7\t0\t34\n", "74\t35\t186.7\t0\t35\n", "75\t21\t186.7\t0\t21\n", "76\t42\t186.7\t0\t42\n", "77\t28\t186.7\t0\t28\n", "78\t35\t186.7\t0\t35\n", "79\t32\t186.7\t0\t32\n", "80\t27\t186.7\t0\t27\n", "81\t40\t186.7\t0\t40\n", "82\t60\t186.7\t0\t60\n", "83\t47\t186.7\t0\t47\n", "84\t30\t186.7\t0\t30\n", "85\t42\t186.7\t0\t42\n", "86\t23\t186.7\t0\t23\n", "87\t30\t186.7\t0\t30\n", "88\t21\t186.7\t0\t21\n", "89\t27\t186.7\t0\t27\n", "90\t39\t186.7\t0\t39\n", "91\t19\t186.7\t0\t19\n", "92\t13\t186.7\t0\t13\n", "93\t27\t186.7\t0\t27\n", "94\t12\t186.7\t0\t12\n", "95\t31\t186.7\t0\t31\n", "96\t24\t186.7\t0\t24\n", "97\t37\t186.7\t0\t37\n", "98\t42\t186.7\t0\t42\n", "99\t41\t186.7\t0\t41\n", "100\t47\t186.7\t0\t47\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 169_S65_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/169.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 142.08 s (13 us/read; 4.68 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 11,072,381\n", "Reads with adapters: 6,415,245 (57.9%)\n", "Reads written (passing filters): 10,573,113 (95.5%)\n", "\n", "Total basepairs processed: 1,107,238,100 bp\n", "Quality-trimmed: 4,037,254 bp (0.4%)\n", "Total written (filtered): 866,872,658 bp (78.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 6209210 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.4%\n", " G: 32.1%\n", " T: 37.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t239632\t173006.0\t0\t239632\n", "4\t142076\t43251.5\t0\t142076\n", "5\t104896\t10812.9\t0\t104896\n", "6\t85492\t2703.2\t0\t85492\n", "7\t76595\t675.8\t0\t76595\n", "8\t73281\t169.0\t0\t73281\n", "9\t72357\t169.0\t0\t72357\n", "10\t68349\t169.0\t0\t68349\n", "11\t68874\t169.0\t0\t68874\n", "12\t71011\t169.0\t0\t71011\n", "13\t78331\t169.0\t0\t78331\n", "14\t79608\t169.0\t0\t79608\n", "15\t75683\t169.0\t0\t75683\n", "16\t78844\t169.0\t0\t78844\n", "17\t88138\t169.0\t0\t88138\n", "18\t106456\t169.0\t0\t106456\n", "19\t93475\t169.0\t0\t93475\n", "20\t79458\t169.0\t0\t79458\n", "21\t80809\t169.0\t0\t80809\n", "22\t73206\t169.0\t0\t73206\n", "23\t80539\t169.0\t0\t80539\n", "24\t94519\t169.0\t0\t94519\n", "25\t96882\t169.0\t0\t96882\n", "26\t111844\t169.0\t0\t111844\n", "27\t121498\t169.0\t0\t121498\n", "28\t110551\t169.0\t0\t110551\n", "29\t105078\t169.0\t0\t105078\n", "30\t106665\t169.0\t0\t106665\n", "31\t116254\t169.0\t0\t116254\n", "32\t111662\t169.0\t0\t111662\n", "33\t101099\t169.0\t0\t101099\n", "34\t98077\t169.0\t0\t98077\n", "35\t111276\t169.0\t0\t111276\n", "36\t132273\t169.0\t0\t132273\n", "37\t146651\t169.0\t0\t146651\n", "38\t116207\t169.0\t0\t116207\n", "39\t96847\t169.0\t0\t96847\n", "40\t86044\t169.0\t0\t86044\n", "41\t92064\t169.0\t0\t92064\n", "42\t99978\t169.0\t0\t99978\n", "43\t86441\t169.0\t0\t86441\n", "44\t66956\t169.0\t0\t66956\n", "45\t82138\t169.0\t0\t82138\n", "46\t95365\t169.0\t0\t95365\n", "47\t92397\t169.0\t0\t92397\n", "48\t97048\t169.0\t0\t97048\n", "49\t78345\t169.0\t0\t78345\n", "50\t73535\t169.0\t0\t73535\n", "51\t66133\t169.0\t0\t66133\n", "52\t66587\t169.0\t0\t66587\n", "53\t61001\t169.0\t0\t61001\n", "54\t68796\t169.0\t0\t68796\n", "55\t69690\t169.0\t0\t69690\n", "56\t70967\t169.0\t0\t70967\n", "57\t68842\t169.0\t0\t68842\n", "58\t66739\t169.0\t0\t66739\n", "59\t50686\t169.0\t0\t50686\n", "60\t42541\t169.0\t0\t42541\n", "61\t40960\t169.0\t0\t40960\n", "62\t34664\t169.0\t0\t34664\n", "63\t33256\t169.0\t0\t33256\n", "64\t35388\t169.0\t0\t35388\n", "65\t33734\t169.0\t0\t33734\n", "66\t29547\t169.0\t0\t29547\n", "67\t28807\t169.0\t0\t28807\n", "68\t27218\t169.0\t0\t27218\n", "69\t26206\t169.0\t0\t26206\n", "70\t26592\t169.0\t0\t26592\n", "71\t25277\t169.0\t0\t25277\n", "72\t20624\t169.0\t0\t20624\n", "73\t18554\t169.0\t0\t18554\n", "74\t18687\t169.0\t0\t18687\n", "75\t17465\t169.0\t0\t17465\n", "76\t15909\t169.0\t0\t15909\n", "77\t15291\t169.0\t0\t15291\n", "78\t16730\t169.0\t0\t16730\n", "79\t16979\t169.0\t0\t16979\n", "80\t17736\t169.0\t0\t17736\n", "81\t18396\t169.0\t0\t18396\n", "82\t19483\t169.0\t0\t19483\n", "83\t22207\t169.0\t0\t22207\n", "84\t25774\t169.0\t0\t25774\n", "85\t29624\t169.0\t0\t29624\n", "86\t31909\t169.0\t0\t31909\n", "87\t30290\t169.0\t0\t30290\n", "88\t30529\t169.0\t0\t30529\n", "89\t29165\t169.0\t0\t29165\n", "90\t28666\t169.0\t0\t28666\n", "91\t27719\t169.0\t0\t27719\n", "92\t27043\t169.0\t0\t27043\n", "93\t26939\t169.0\t0\t26939\n", "94\t24865\t169.0\t0\t24865\n", "95\t21445\t169.0\t0\t21445\n", "96\t16071\t169.0\t0\t16071\n", "97\t10177\t169.0\t0\t10177\n", "98\t5803\t169.0\t0\t5803\n", "99\t3980\t169.0\t0\t3980\n", "100\t2715\t169.0\t0\t2715\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 48070 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 46.6%\n", " C: 26.3%\n", " G: 0.0%\n", " T: 27.0%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t24491\t173006.0\t0\t24491\n", "4\t5208\t43251.5\t0\t5208\n", "5\t1900\t10812.9\t0\t1900\n", "6\t1083\t2703.2\t0\t1083\n", "7\t61\t675.8\t0\t61\n", "8\t47\t169.0\t0\t47\n", "9\t43\t169.0\t0\t43\n", "10\t45\t169.0\t0\t45\n", "11\t42\t169.0\t0\t42\n", "12\t39\t169.0\t0\t39\n", "13\t36\t169.0\t0\t36\n", "14\t38\t169.0\t0\t38\n", "15\t38\t169.0\t0\t38\n", "16\t47\t169.0\t0\t47\n", "17\t38\t169.0\t0\t38\n", "18\t63\t169.0\t0\t63\n", "19\t83\t169.0\t0\t83\n", "20\t85\t169.0\t0\t85\n", "21\t61\t169.0\t0\t61\n", "22\t80\t169.0\t0\t80\n", "23\t69\t169.0\t0\t69\n", "24\t63\t169.0\t0\t63\n", "25\t72\t169.0\t0\t72\n", "26\t118\t169.0\t0\t118\n", "27\t153\t169.0\t0\t153\n", "28\t228\t169.0\t0\t228\n", "29\t336\t169.0\t0\t336\n", "30\t704\t169.0\t0\t704\n", "31\t888\t169.0\t0\t888\n", "32\t1567\t169.0\t0\t1567\n", "33\t1435\t169.0\t0\t1435\n", "34\t1534\t169.0\t0\t1534\n", "35\t1824\t169.0\t0\t1824\n", "36\t1755\t169.0\t0\t1755\n", "37\t965\t169.0\t0\t965\n", "38\t133\t169.0\t0\t133\n", "39\t114\t169.0\t0\t114\n", "40\t27\t169.0\t0\t27\n", "41\t35\t169.0\t0\t35\n", "42\t32\t169.0\t0\t32\n", "43\t40\t169.0\t0\t40\n", "44\t27\t169.0\t0\t27\n", "45\t36\t169.0\t0\t36\n", "46\t29\t169.0\t0\t29\n", "47\t24\t169.0\t0\t24\n", "48\t18\t169.0\t0\t18\n", "49\t40\t169.0\t0\t40\n", "50\t35\t169.0\t0\t35\n", "51\t28\t169.0\t0\t28\n", "52\t35\t169.0\t0\t35\n", "53\t23\t169.0\t0\t23\n", "54\t23\t169.0\t0\t23\n", "55\t22\t169.0\t0\t22\n", "56\t31\t169.0\t0\t31\n", "57\t43\t169.0\t0\t43\n", "58\t31\t169.0\t0\t31\n", "59\t26\t169.0\t0\t26\n", "60\t21\t169.0\t0\t21\n", "61\t22\t169.0\t0\t22\n", "62\t27\t169.0\t0\t27\n", "63\t21\t169.0\t0\t21\n", "64\t25\t169.0\t0\t25\n", "65\t20\t169.0\t0\t20\n", "66\t30\t169.0\t0\t30\n", "67\t11\t169.0\t0\t11\n", "68\t10\t169.0\t0\t10\n", "69\t15\t169.0\t0\t15\n", "70\t6\t169.0\t0\t6\n", "71\t9\t169.0\t0\t9\n", "72\t16\t169.0\t0\t16\n", "73\t8\t169.0\t0\t8\n", "74\t14\t169.0\t0\t14\n", "75\t7\t169.0\t0\t7\n", "76\t7\t169.0\t0\t7\n", "77\t16\t169.0\t0\t16\n", "78\t14\t169.0\t0\t14\n", "79\t12\t169.0\t0\t12\n", "80\t11\t169.0\t0\t11\n", "81\t8\t169.0\t0\t8\n", "82\t6\t169.0\t0\t6\n", "83\t15\t169.0\t0\t15\n", "84\t9\t169.0\t0\t9\n", "85\t16\t169.0\t0\t16\n", "86\t16\t169.0\t0\t16\n", "87\t13\t169.0\t0\t13\n", "88\t11\t169.0\t0\t11\n", "89\t15\t169.0\t0\t15\n", "90\t10\t169.0\t0\t10\n", "91\t35\t169.0\t0\t35\n", "92\t50\t169.0\t0\t50\n", "93\t107\t169.0\t0\t107\n", "94\t171\t169.0\t0\t171\n", "95\t208\t169.0\t0\t208\n", "96\t196\t169.0\t0\t196\n", "97\t213\t169.0\t0\t213\n", "98\t158\t169.0\t0\t158\n", "99\t146\t169.0\t0\t146\n", "100\t254\t169.0\t0\t254\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 157965 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.8%\n", " C: 21.1%\n", " G: 14.7%\n", " T: 21.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t121928\t173006.0\t0\t121928\n", "4\t22726\t43251.5\t0\t22726\n", "5\t3851\t10812.9\t0\t3851\n", "6\t356\t2703.2\t0\t356\n", "7\t92\t675.8\t0\t92\n", "8\t94\t675.8\t0\t94\n", "9\t105\t675.8\t0\t105\n", "10\t131\t675.8\t0\t131\n", "11\t110\t675.8\t0\t110\n", "12\t121\t675.8\t0\t121\n", "13\t119\t675.8\t0\t119\n", "14\t103\t675.8\t0\t103\n", "15\t109\t675.8\t0\t109\n", "16\t111\t675.8\t0\t111\n", "17\t118\t675.8\t0\t118\n", "18\t103\t675.8\t0\t103\n", "19\t119\t675.8\t0\t119\n", "20\t109\t675.8\t0\t109\n", "21\t85\t675.8\t0\t85\n", "22\t82\t675.8\t0\t82\n", "23\t81\t675.8\t0\t81\n", "24\t96\t675.8\t0\t96\n", "25\t86\t675.8\t0\t86\n", "26\t83\t675.8\t0\t83\n", "27\t104\t675.8\t0\t104\n", "28\t109\t675.8\t0\t109\n", "29\t109\t675.8\t0\t109\n", "30\t126\t675.8\t0\t126\n", "31\t130\t675.8\t0\t130\n", "32\t138\t675.8\t0\t138\n", "33\t115\t675.8\t0\t115\n", "34\t101\t675.8\t0\t101\n", "35\t118\t675.8\t0\t118\n", "36\t96\t675.8\t0\t96\n", "37\t88\t675.8\t0\t88\n", "38\t85\t675.8\t0\t85\n", "39\t122\t675.8\t0\t122\n", "40\t100\t675.8\t0\t100\n", "41\t70\t675.8\t0\t70\n", "42\t61\t675.8\t0\t61\n", "43\t67\t675.8\t0\t67\n", "44\t56\t675.8\t0\t56\n", "45\t79\t675.8\t0\t79\n", "46\t102\t675.8\t0\t102\n", "47\t95\t675.8\t0\t95\n", "48\t106\t675.8\t0\t106\n", "49\t88\t675.8\t0\t88\n", "50\t75\t675.8\t0\t75\n", "51\t96\t675.8\t0\t96\n", "52\t53\t675.8\t0\t53\n", "53\t89\t675.8\t0\t89\n", "54\t93\t675.8\t0\t93\n", "55\t79\t675.8\t0\t79\n", "56\t53\t675.8\t0\t53\n", "57\t54\t675.8\t0\t54\n", "58\t67\t675.8\t0\t67\n", "59\t76\t675.8\t0\t76\n", "60\t86\t675.8\t0\t86\n", "61\t89\t675.8\t0\t89\n", "62\t71\t675.8\t0\t71\n", "63\t99\t675.8\t0\t99\n", "64\t90\t675.8\t0\t90\n", "65\t81\t675.8\t0\t81\n", "66\t97\t675.8\t0\t97\n", "67\t54\t675.8\t0\t54\n", "68\t73\t675.8\t0\t73\n", "69\t73\t675.8\t0\t73\n", "70\t72\t675.8\t0\t72\n", "71\t64\t675.8\t0\t64\n", "72\t92\t675.8\t0\t92\n", "73\t92\t675.8\t0\t92\n", "74\t120\t675.8\t0\t120\n", "75\t88\t675.8\t0\t88\n", "76\t110\t675.8\t0\t110\n", "77\t124\t675.8\t0\t124\n", "78\t117\t675.8\t0\t117\n", "79\t122\t675.8\t0\t122\n", "80\t131\t675.8\t0\t131\n", "81\t108\t675.8\t0\t108\n", "82\t169\t675.8\t0\t169\n", "83\t155\t675.8\t0\t155\n", "84\t125\t675.8\t0\t125\n", "85\t116\t675.8\t0\t116\n", "86\t90\t675.8\t0\t90\n", "87\t114\t675.8\t0\t114\n", "88\t96\t675.8\t0\t96\n", "89\t110\t675.8\t0\t110\n", "90\t90\t675.8\t0\t90\n", "91\t73\t675.8\t0\t73\n", "92\t76\t675.8\t0\t76\n", "93\t65\t675.8\t0\t65\n", "94\t88\t675.8\t0\t88\n", "95\t67\t675.8\t0\t67\n", "96\t77\t675.8\t0\t77\n", "97\t96\t675.8\t0\t96\n", "98\t102\t675.8\t0\t102\n", "99\t145\t675.8\t0\t145\n", "100\t140\t675.8\t0\t140\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 171_S58_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/171.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 106.43 s (13 us/read; 4.67 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,290,001\n", "Reads with adapters: 4,820,882 (58.2%)\n", "Reads written (passing filters): 8,008,438 (96.6%)\n", "\n", "Total basepairs processed: 829,000,100 bp\n", "Quality-trimmed: 2,297,538 bp (0.3%)\n", "Total written (filtered): 652,197,421 bp (78.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4672201 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.4%\n", " G: 31.4%\n", " T: 39.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t184047\t129531.3\t0\t184047\n", "4\t110642\t32382.8\t0\t110642\n", "5\t81475\t8095.7\t0\t81475\n", "6\t64532\t2023.9\t0\t64532\n", "7\t57407\t506.0\t0\t57407\n", "8\t54267\t126.5\t0\t54267\n", "9\t53804\t126.5\t0\t53804\n", "10\t49492\t126.5\t0\t49492\n", "11\t50326\t126.5\t0\t50326\n", "12\t50974\t126.5\t0\t50974\n", "13\t53035\t126.5\t0\t53035\n", "14\t54167\t126.5\t0\t54167\n", "15\t54019\t126.5\t0\t54019\n", "16\t57055\t126.5\t0\t57055\n", "17\t64886\t126.5\t0\t64886\n", "18\t77881\t126.5\t0\t77881\n", "19\t67701\t126.5\t0\t67701\n", "20\t57931\t126.5\t0\t57931\n", "21\t59393\t126.5\t0\t59393\n", "22\t54431\t126.5\t0\t54431\n", "23\t61597\t126.5\t0\t61597\n", "24\t72350\t126.5\t0\t72350\n", "25\t72775\t126.5\t0\t72775\n", "26\t84823\t126.5\t0\t84823\n", "27\t95100\t126.5\t0\t95100\n", "28\t85301\t126.5\t0\t85301\n", "29\t81114\t126.5\t0\t81114\n", "30\t84089\t126.5\t0\t84089\n", "31\t94336\t126.5\t0\t94336\n", "32\t85887\t126.5\t0\t85887\n", "33\t79179\t126.5\t0\t79179\n", "34\t74237\t126.5\t0\t74237\n", "35\t86462\t126.5\t0\t86462\n", "36\t103522\t126.5\t0\t103522\n", "37\t112878\t126.5\t0\t112878\n", "38\t91476\t126.5\t0\t91476\n", "39\t74784\t126.5\t0\t74784\n", "40\t66661\t126.5\t0\t66661\n", "41\t69533\t126.5\t0\t69533\n", "42\t74116\t126.5\t0\t74116\n", "43\t63675\t126.5\t0\t63675\n", "44\t50174\t126.5\t0\t50174\n", "45\t65484\t126.5\t0\t65484\n", "46\t79676\t126.5\t0\t79676\n", "47\t68733\t126.5\t0\t68733\n", "48\t75423\t126.5\t0\t75423\n", "49\t60419\t126.5\t0\t60419\n", "50\t58233\t126.5\t0\t58233\n", "51\t49535\t126.5\t0\t49535\n", "52\t55485\t126.5\t0\t55485\n", "53\t59562\t126.5\t0\t59562\n", "54\t49545\t126.5\t0\t49545\n", "55\t54219\t126.5\t0\t54219\n", "56\t52381\t126.5\t0\t52381\n", "57\t44609\t126.5\t0\t44609\n", "58\t57229\t126.5\t0\t57229\n", "59\t46569\t126.5\t0\t46569\n", "60\t36095\t126.5\t0\t36095\n", "61\t33911\t126.5\t0\t33911\n", "62\t26553\t126.5\t0\t26553\n", "63\t26601\t126.5\t0\t26601\n", "64\t29845\t126.5\t0\t29845\n", "65\t27296\t126.5\t0\t27296\n", "66\t22144\t126.5\t0\t22144\n", "67\t21877\t126.5\t0\t21877\n", "68\t20888\t126.5\t0\t20888\n", "69\t20691\t126.5\t0\t20691\n", "70\t21577\t126.5\t0\t21577\n", "71\t20209\t126.5\t0\t20209\n", "72\t15143\t126.5\t0\t15143\n", "73\t13320\t126.5\t0\t13320\n", "74\t13435\t126.5\t0\t13435\n", "75\t12299\t126.5\t0\t12299\n", "76\t10071\t126.5\t0\t10071\n", "77\t10059\t126.5\t0\t10059\n", "78\t11913\t126.5\t0\t11913\n", "79\t10946\t126.5\t0\t10946\n", "80\t10612\t126.5\t0\t10612\n", "81\t10973\t126.5\t0\t10973\n", "82\t11283\t126.5\t0\t11283\n", "83\t12110\t126.5\t0\t12110\n", "84\t14602\t126.5\t0\t14602\n", "85\t17545\t126.5\t0\t17545\n", "86\t18062\t126.5\t0\t18062\n", "87\t14018\t126.5\t0\t14018\n", "88\t13636\t126.5\t0\t13636\n", "89\t14684\t126.5\t0\t14684\n", "90\t15615\t126.5\t0\t15615\n", "91\t16929\t126.5\t0\t16929\n", "92\t17138\t126.5\t0\t17138\n", "93\t17748\t126.5\t0\t17748\n", "94\t17104\t126.5\t0\t17104\n", "95\t15603\t126.5\t0\t15603\n", "96\t11969\t126.5\t0\t11969\n", "97\t7923\t126.5\t0\t7923\n", "98\t4860\t126.5\t0\t4860\n", "99\t3556\t126.5\t0\t3556\n", "100\t2722\t126.5\t0\t2722\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 33702 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 59.1%\n", " C: 15.4%\n", " G: 0.0%\n", " T: 25.3%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13974\t129531.3\t0\t13974\n", "4\t2874\t32382.8\t0\t2874\n", "5\t613\t8095.7\t0\t613\n", "6\t223\t2023.9\t0\t223\n", "7\t52\t506.0\t0\t52\n", "8\t38\t126.5\t0\t38\n", "9\t30\t126.5\t0\t30\n", "10\t19\t126.5\t0\t19\n", "11\t25\t126.5\t0\t25\n", "12\t33\t126.5\t0\t33\n", "13\t28\t126.5\t0\t28\n", "14\t28\t126.5\t0\t28\n", "15\t37\t126.5\t0\t37\n", "16\t33\t126.5\t0\t33\n", "17\t39\t126.5\t0\t39\n", "18\t50\t126.5\t0\t50\n", "19\t55\t126.5\t0\t55\n", "20\t97\t126.5\t0\t97\n", "21\t90\t126.5\t0\t90\n", "22\t76\t126.5\t0\t76\n", "23\t81\t126.5\t0\t81\n", "24\t75\t126.5\t0\t75\n", "25\t70\t126.5\t0\t70\n", "26\t148\t126.5\t0\t148\n", "27\t157\t126.5\t0\t157\n", "28\t283\t126.5\t0\t283\n", "29\t474\t126.5\t0\t474\n", "30\t892\t126.5\t0\t892\n", "31\t1113\t126.5\t0\t1113\n", "32\t1770\t126.5\t0\t1770\n", "33\t1619\t126.5\t0\t1619\n", "34\t1832\t126.5\t0\t1832\n", "35\t2043\t126.5\t0\t2043\n", "36\t1951\t126.5\t0\t1951\n", "37\t915\t126.5\t0\t915\n", "38\t98\t126.5\t0\t98\n", "39\t54\t126.5\t0\t54\n", "40\t24\t126.5\t0\t24\n", "41\t26\t126.5\t0\t26\n", "42\t24\t126.5\t0\t24\n", "43\t17\t126.5\t0\t17\n", "44\t21\t126.5\t0\t21\n", "45\t21\t126.5\t0\t21\n", "46\t15\t126.5\t0\t15\n", "47\t22\t126.5\t0\t22\n", "48\t11\t126.5\t0\t11\n", "49\t18\t126.5\t0\t18\n", "50\t23\t126.5\t0\t23\n", "51\t13\t126.5\t0\t13\n", "52\t16\t126.5\t0\t16\n", "53\t20\t126.5\t0\t20\n", "54\t13\t126.5\t0\t13\n", "55\t25\t126.5\t0\t25\n", "56\t11\t126.5\t0\t11\n", "57\t14\t126.5\t0\t14\n", "58\t15\t126.5\t0\t15\n", "59\t9\t126.5\t0\t9\n", "60\t10\t126.5\t0\t10\n", "61\t14\t126.5\t0\t14\n", "62\t22\t126.5\t0\t22\n", "63\t23\t126.5\t0\t23\n", "64\t8\t126.5\t0\t8\n", "65\t15\t126.5\t0\t15\n", "66\t6\t126.5\t0\t6\n", "67\t14\t126.5\t0\t14\n", "68\t14\t126.5\t0\t14\n", "69\t7\t126.5\t0\t7\n", "70\t8\t126.5\t0\t8\n", "71\t7\t126.5\t0\t7\n", "72\t7\t126.5\t0\t7\n", "73\t10\t126.5\t0\t10\n", "74\t8\t126.5\t0\t8\n", "75\t11\t126.5\t0\t11\n", "76\t10\t126.5\t0\t10\n", "77\t6\t126.5\t0\t6\n", "78\t9\t126.5\t0\t9\n", "79\t5\t126.5\t0\t5\n", "80\t6\t126.5\t0\t6\n", "81\t6\t126.5\t0\t6\n", "82\t5\t126.5\t0\t5\n", "83\t6\t126.5\t0\t6\n", "84\t3\t126.5\t0\t3\n", "85\t9\t126.5\t0\t9\n", "86\t10\t126.5\t0\t10\n", "87\t8\t126.5\t0\t8\n", "88\t11\t126.5\t0\t11\n", "89\t13\t126.5\t0\t13\n", "90\t16\t126.5\t0\t16\n", "91\t18\t126.5\t0\t18\n", "92\t33\t126.5\t0\t33\n", "93\t73\t126.5\t0\t73\n", "94\t110\t126.5\t0\t110\n", "95\t148\t126.5\t0\t148\n", "96\t130\t126.5\t0\t130\n", "97\t144\t126.5\t0\t144\n", "98\t114\t126.5\t0\t114\n", "99\t110\t126.5\t0\t110\n", "100\t168\t126.5\t0\t168\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 114979 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.8%\n", " C: 20.3%\n", " G: 13.2%\n", " T: 23.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t87667\t129531.3\t0\t87667\n", "4\t17970\t32382.8\t0\t17970\n", "5\t2600\t8095.7\t0\t2600\n", "6\t275\t2023.9\t0\t275\n", "7\t40\t506.0\t0\t40\n", "8\t62\t506.0\t0\t62\n", "9\t55\t506.0\t0\t55\n", "10\t58\t506.0\t0\t58\n", "11\t51\t506.0\t0\t51\n", "12\t68\t506.0\t0\t68\n", "13\t70\t506.0\t0\t70\n", "14\t61\t506.0\t0\t61\n", "15\t57\t506.0\t0\t57\n", "16\t69\t506.0\t0\t69\n", "17\t64\t506.0\t0\t64\n", "18\t79\t506.0\t0\t79\n", "19\t62\t506.0\t0\t62\n", "20\t42\t506.0\t0\t42\n", "21\t46\t506.0\t0\t46\n", "22\t44\t506.0\t0\t44\n", "23\t52\t506.0\t0\t52\n", "24\t54\t506.0\t0\t54\n", "25\t59\t506.0\t0\t59\n", "26\t50\t506.0\t0\t50\n", "27\t69\t506.0\t0\t69\n", "28\t71\t506.0\t0\t71\n", "29\t62\t506.0\t0\t62\n", "30\t91\t506.0\t0\t91\n", "31\t80\t506.0\t0\t80\n", "32\t79\t506.0\t0\t79\n", "33\t97\t506.0\t0\t97\n", "34\t77\t506.0\t0\t77\n", "35\t80\t506.0\t0\t80\n", "36\t75\t506.0\t0\t75\n", "37\t73\t506.0\t0\t73\n", "38\t67\t506.0\t0\t67\n", "39\t104\t506.0\t0\t104\n", "40\t104\t506.0\t0\t104\n", "41\t89\t506.0\t0\t89\n", "42\t63\t506.0\t0\t63\n", "43\t48\t506.0\t0\t48\n", "44\t57\t506.0\t0\t57\n", "45\t52\t506.0\t0\t52\n", "46\t69\t506.0\t0\t69\n", "47\t69\t506.0\t0\t69\n", "48\t70\t506.0\t0\t70\n", "49\t63\t506.0\t0\t63\n", "50\t56\t506.0\t0\t56\n", "51\t60\t506.0\t0\t60\n", "52\t52\t506.0\t0\t52\n", "53\t70\t506.0\t0\t70\n", "54\t61\t506.0\t0\t61\n", "55\t56\t506.0\t0\t56\n", "56\t43\t506.0\t0\t43\n", "57\t61\t506.0\t0\t61\n", "58\t60\t506.0\t0\t60\n", "59\t56\t506.0\t0\t56\n", "60\t79\t506.0\t0\t79\n", "61\t72\t506.0\t0\t72\n", "62\t82\t506.0\t0\t82\n", "63\t75\t506.0\t0\t75\n", "64\t40\t506.0\t0\t40\n", "65\t52\t506.0\t0\t52\n", "66\t56\t506.0\t0\t56\n", "67\t52\t506.0\t0\t52\n", "68\t53\t506.0\t0\t53\n", "69\t39\t506.0\t0\t39\n", "70\t64\t506.0\t0\t64\n", "71\t53\t506.0\t0\t53\n", "72\t54\t506.0\t0\t54\n", "73\t70\t506.0\t0\t70\n", "74\t77\t506.0\t0\t77\n", "75\t66\t506.0\t0\t66\n", "76\t90\t506.0\t0\t90\n", "77\t112\t506.0\t0\t112\n", "78\t79\t506.0\t0\t79\n", "79\t100\t506.0\t0\t100\n", "80\t97\t506.0\t0\t97\n", "81\t123\t506.0\t0\t123\n", "82\t153\t506.0\t0\t153\n", "83\t111\t506.0\t0\t111\n", "84\t94\t506.0\t0\t94\n", "85\t80\t506.0\t0\t80\n", "86\t51\t506.0\t0\t51\n", "87\t62\t506.0\t0\t62\n", "88\t59\t506.0\t0\t59\n", "89\t60\t506.0\t0\t60\n", "90\t57\t506.0\t0\t57\n", "91\t57\t506.0\t0\t57\n", "92\t57\t506.0\t0\t57\n", "93\t44\t506.0\t0\t44\n", "94\t64\t506.0\t0\t64\n", "95\t56\t506.0\t0\t56\n", "96\t69\t506.0\t0\t69\n", "97\t72\t506.0\t0\t72\n", "98\t86\t506.0\t0\t86\n", "99\t108\t506.0\t0\t108\n", "100\t115\t506.0\t0\t115\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 172_S59_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/172.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 63.24 s (13 us/read; 4.75 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,002,990\n", "Reads with adapters: 2,900,000 (58.0%)\n", "Reads written (passing filters): 4,809,404 (96.1%)\n", "\n", "Total basepairs processed: 500,299,000 bp\n", "Quality-trimmed: 1,191,877 bp (0.2%)\n", "Total written (filtered): 394,286,841 bp (78.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2801210 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.0%\n", " G: 33.2%\n", " T: 36.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t109603\t78171.7\t0\t109603\n", "4\t66022\t19542.9\t0\t66022\n", "5\t49648\t4885.7\t0\t49648\n", "6\t40104\t1221.4\t0\t40104\n", "7\t35680\t305.4\t0\t35680\n", "8\t34763\t76.3\t0\t34763\n", "9\t34061\t76.3\t0\t34061\n", "10\t32155\t76.3\t0\t32155\n", "11\t32134\t76.3\t0\t32134\n", "12\t32807\t76.3\t0\t32807\n", "13\t35022\t76.3\t0\t35022\n", "14\t36494\t76.3\t0\t36494\n", "15\t34750\t76.3\t0\t34750\n", "16\t36197\t76.3\t0\t36197\n", "17\t40758\t76.3\t0\t40758\n", "18\t49837\t76.3\t0\t49837\n", "19\t44545\t76.3\t0\t44545\n", "20\t36268\t76.3\t0\t36268\n", "21\t36317\t76.3\t0\t36317\n", "22\t33217\t76.3\t0\t33217\n", "23\t37379\t76.3\t0\t37379\n", "24\t44565\t76.3\t0\t44565\n", "25\t44437\t76.3\t0\t44437\n", "26\t51170\t76.3\t0\t51170\n", "27\t55971\t76.3\t0\t55971\n", "28\t50358\t76.3\t0\t50358\n", "29\t47875\t76.3\t0\t47875\n", "30\t48902\t76.3\t0\t48902\n", "31\t54388\t76.3\t0\t54388\n", "32\t50859\t76.3\t0\t50859\n", "33\t46356\t76.3\t0\t46356\n", "34\t44588\t76.3\t0\t44588\n", "35\t51933\t76.3\t0\t51933\n", "36\t61887\t76.3\t0\t61887\n", "37\t67226\t76.3\t0\t67226\n", "38\t52758\t76.3\t0\t52758\n", "39\t44020\t76.3\t0\t44020\n", "40\t39256\t76.3\t0\t39256\n", "41\t42235\t76.3\t0\t42235\n", "42\t45776\t76.3\t0\t45776\n", "43\t38751\t76.3\t0\t38751\n", "44\t29300\t76.3\t0\t29300\n", "45\t36244\t76.3\t0\t36244\n", "46\t43034\t76.3\t0\t43034\n", "47\t40709\t76.3\t0\t40709\n", "48\t41695\t76.3\t0\t41695\n", "49\t33011\t76.3\t0\t33011\n", "50\t30931\t76.3\t0\t30931\n", "51\t25278\t76.3\t0\t25278\n", "52\t26328\t76.3\t0\t26328\n", "53\t29132\t76.3\t0\t29132\n", "54\t34541\t76.3\t0\t34541\n", "55\t29698\t76.3\t0\t29698\n", "56\t24663\t76.3\t0\t24663\n", "57\t26927\t76.3\t0\t26927\n", "58\t33809\t76.3\t0\t33809\n", "59\t23577\t76.3\t0\t23577\n", "60\t17920\t76.3\t0\t17920\n", "61\t18075\t76.3\t0\t18075\n", "62\t14751\t76.3\t0\t14751\n", "63\t14508\t76.3\t0\t14508\n", "64\t15704\t76.3\t0\t15704\n", "65\t14877\t76.3\t0\t14877\n", "66\t12943\t76.3\t0\t12943\n", "67\t12657\t76.3\t0\t12657\n", "68\t11797\t76.3\t0\t11797\n", "69\t11933\t76.3\t0\t11933\n", "70\t12584\t76.3\t0\t12584\n", "71\t12284\t76.3\t0\t12284\n", "72\t9187\t76.3\t0\t9187\n", "73\t8269\t76.3\t0\t8269\n", "74\t8648\t76.3\t0\t8648\n", "75\t7598\t76.3\t0\t7598\n", "76\t6447\t76.3\t0\t6447\n", "77\t6003\t76.3\t0\t6003\n", "78\t6957\t76.3\t0\t6957\n", "79\t6692\t76.3\t0\t6692\n", "80\t7006\t76.3\t0\t7006\n", "81\t6928\t76.3\t0\t6928\n", "82\t7005\t76.3\t0\t7005\n", "83\t8119\t76.3\t0\t8119\n", "84\t9729\t76.3\t0\t9729\n", "85\t12005\t76.3\t0\t12005\n", "86\t12038\t76.3\t0\t12038\n", "87\t9269\t76.3\t0\t9269\n", "88\t8982\t76.3\t0\t8982\n", "89\t9627\t76.3\t0\t9627\n", "90\t11004\t76.3\t0\t11004\n", "91\t12089\t76.3\t0\t12089\n", "92\t12878\t76.3\t0\t12878\n", "93\t14030\t76.3\t0\t14030\n", "94\t13926\t76.3\t0\t13926\n", "95\t12723\t76.3\t0\t12723\n", "96\t9711\t76.3\t0\t9711\n", "97\t6161\t76.3\t0\t6161\n", "98\t3788\t76.3\t0\t3788\n", "99\t2337\t76.3\t0\t2337\n", "100\t2072\t76.3\t0\t2072\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 25200 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 60.2%\n", " C: 16.4%\n", " G: 0.0%\n", " T: 23.1%\n", " none/other: 0.3%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9717\t78171.7\t0\t9717\n", "4\t1918\t19542.9\t0\t1918\n", "5\t615\t4885.7\t0\t615\n", "6\t328\t1221.4\t0\t328\n", "7\t42\t305.4\t0\t42\n", "8\t25\t76.3\t0\t25\n", "9\t25\t76.3\t0\t25\n", "10\t21\t76.3\t0\t21\n", "11\t17\t76.3\t0\t17\n", "12\t15\t76.3\t0\t15\n", "13\t26\t76.3\t0\t26\n", "14\t21\t76.3\t0\t21\n", "15\t21\t76.3\t0\t21\n", "16\t31\t76.3\t0\t31\n", "17\t32\t76.3\t0\t32\n", "18\t32\t76.3\t0\t32\n", "19\t57\t76.3\t0\t57\n", "20\t73\t76.3\t0\t73\n", "21\t58\t76.3\t0\t58\n", "22\t53\t76.3\t0\t53\n", "23\t53\t76.3\t0\t53\n", "24\t45\t76.3\t0\t45\n", "25\t69\t76.3\t0\t69\n", "26\t151\t76.3\t0\t151\n", "27\t172\t76.3\t0\t172\n", "28\t212\t76.3\t0\t212\n", "29\t338\t76.3\t0\t338\n", "30\t700\t76.3\t0\t700\n", "31\t835\t76.3\t0\t835\n", "32\t1515\t76.3\t0\t1515\n", "33\t1310\t76.3\t0\t1310\n", "34\t1417\t76.3\t0\t1417\n", "35\t1645\t76.3\t0\t1645\n", "36\t1650\t76.3\t0\t1650\n", "37\t727\t76.3\t0\t727\n", "38\t62\t76.3\t0\t62\n", "39\t36\t76.3\t0\t36\n", "40\t22\t76.3\t0\t22\n", "41\t5\t76.3\t0\t5\n", "42\t17\t76.3\t0\t17\n", "43\t12\t76.3\t0\t12\n", "44\t17\t76.3\t0\t17\n", "45\t10\t76.3\t0\t10\n", "46\t17\t76.3\t0\t17\n", "47\t11\t76.3\t0\t11\n", "48\t15\t76.3\t0\t15\n", "49\t18\t76.3\t0\t18\n", "50\t20\t76.3\t0\t20\n", "51\t20\t76.3\t0\t20\n", "52\t15\t76.3\t0\t15\n", "53\t20\t76.3\t0\t20\n", "54\t15\t76.3\t0\t15\n", "55\t11\t76.3\t0\t11\n", "56\t14\t76.3\t0\t14\n", "57\t8\t76.3\t0\t8\n", "58\t14\t76.3\t0\t14\n", "59\t10\t76.3\t0\t10\n", "60\t12\t76.3\t0\t12\n", "61\t12\t76.3\t0\t12\n", "62\t9\t76.3\t0\t9\n", "63\t8\t76.3\t0\t8\n", "64\t9\t76.3\t0\t9\n", "65\t15\t76.3\t0\t15\n", "66\t9\t76.3\t0\t9\n", "67\t5\t76.3\t0\t5\n", "68\t3\t76.3\t0\t3\n", "69\t5\t76.3\t0\t5\n", "70\t7\t76.3\t0\t7\n", "71\t7\t76.3\t0\t7\n", "72\t3\t76.3\t0\t3\n", "73\t6\t76.3\t0\t6\n", "74\t4\t76.3\t0\t4\n", "75\t1\t76.3\t0\t1\n", "76\t10\t76.3\t0\t10\n", "77\t3\t76.3\t0\t3\n", "78\t7\t76.3\t0\t7\n", "79\t4\t76.3\t0\t4\n", "80\t8\t76.3\t0\t8\n", "81\t7\t76.3\t0\t7\n", "82\t9\t76.3\t0\t9\n", "83\t8\t76.3\t0\t8\n", "84\t4\t76.3\t0\t4\n", "85\t8\t76.3\t0\t8\n", "86\t8\t76.3\t0\t8\n", "87\t3\t76.3\t0\t3\n", "88\t5\t76.3\t0\t5\n", "89\t7\t76.3\t0\t7\n", "90\t16\t76.3\t0\t16\n", "91\t15\t76.3\t0\t15\n", "92\t26\t76.3\t0\t26\n", "93\t39\t76.3\t0\t39\n", "94\t61\t76.3\t0\t61\n", "95\t79\t76.3\t0\t79\n", "96\t95\t76.3\t0\t95\n", "97\t88\t76.3\t0\t88\n", "98\t66\t76.3\t0\t66\n", "99\t59\t76.3\t0\t59\n", "100\t95\t76.3\t0\t95\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 73590 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.9%\n", " C: 21.5%\n", " G: 14.4%\n", " T: 21.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t56312\t78171.7\t0\t56312\n", "4\t10429\t19542.9\t0\t10429\n", "5\t1771\t4885.7\t0\t1771\n", "6\t167\t1221.4\t0\t167\n", "7\t46\t305.4\t0\t46\n", "8\t54\t305.4\t0\t54\n", "9\t52\t305.4\t0\t52\n", "10\t60\t305.4\t0\t60\n", "11\t68\t305.4\t0\t68\n", "12\t72\t305.4\t0\t72\n", "13\t67\t305.4\t0\t67\n", "14\t33\t305.4\t0\t33\n", "15\t71\t305.4\t0\t71\n", "16\t82\t305.4\t0\t82\n", "17\t53\t305.4\t0\t53\n", "18\t67\t305.4\t0\t67\n", "19\t55\t305.4\t0\t55\n", "20\t48\t305.4\t0\t48\n", "21\t68\t305.4\t0\t68\n", "22\t72\t305.4\t0\t72\n", "23\t60\t305.4\t0\t60\n", "24\t54\t305.4\t0\t54\n", "25\t59\t305.4\t0\t59\n", "26\t46\t305.4\t0\t46\n", "27\t60\t305.4\t0\t60\n", "28\t50\t305.4\t0\t50\n", "29\t47\t305.4\t0\t47\n", "30\t61\t305.4\t0\t61\n", "31\t68\t305.4\t0\t68\n", "32\t87\t305.4\t0\t87\n", "33\t80\t305.4\t0\t80\n", "34\t61\t305.4\t0\t61\n", "35\t68\t305.4\t0\t68\n", "36\t46\t305.4\t0\t46\n", "37\t46\t305.4\t0\t46\n", "38\t43\t305.4\t0\t43\n", "39\t51\t305.4\t0\t51\n", "40\t59\t305.4\t0\t59\n", "41\t62\t305.4\t0\t62\n", "42\t44\t305.4\t0\t44\n", "43\t51\t305.4\t0\t51\n", "44\t35\t305.4\t0\t35\n", "45\t53\t305.4\t0\t53\n", "46\t30\t305.4\t0\t30\n", "47\t55\t305.4\t0\t55\n", "48\t43\t305.4\t0\t43\n", "49\t40\t305.4\t0\t40\n", "50\t42\t305.4\t0\t42\n", "51\t48\t305.4\t0\t48\n", "52\t53\t305.4\t0\t53\n", "53\t50\t305.4\t0\t50\n", "54\t63\t305.4\t0\t63\n", "55\t34\t305.4\t0\t34\n", "56\t55\t305.4\t0\t55\n", "57\t44\t305.4\t0\t44\n", "58\t38\t305.4\t0\t38\n", "59\t36\t305.4\t0\t36\n", "60\t47\t305.4\t0\t47\n", "61\t50\t305.4\t0\t50\n", "62\t51\t305.4\t0\t51\n", "63\t54\t305.4\t0\t54\n", "64\t28\t305.4\t0\t28\n", "65\t35\t305.4\t0\t35\n", "66\t34\t305.4\t0\t34\n", "67\t32\t305.4\t0\t32\n", "68\t27\t305.4\t0\t27\n", "69\t31\t305.4\t0\t31\n", "70\t30\t305.4\t0\t30\n", "71\t44\t305.4\t0\t44\n", "72\t45\t305.4\t0\t45\n", "73\t45\t305.4\t0\t45\n", "74\t62\t305.4\t0\t62\n", "75\t47\t305.4\t0\t47\n", "76\t44\t305.4\t0\t44\n", "77\t65\t305.4\t0\t65\n", "78\t47\t305.4\t0\t47\n", "79\t41\t305.4\t0\t41\n", "80\t66\t305.4\t0\t66\n", "81\t55\t305.4\t0\t55\n", "82\t97\t305.4\t0\t97\n", "83\t68\t305.4\t0\t68\n", "84\t74\t305.4\t0\t74\n", "85\t78\t305.4\t0\t78\n", "86\t61\t305.4\t0\t61\n", "87\t54\t305.4\t0\t54\n", "88\t45\t305.4\t0\t45\n", "89\t42\t305.4\t0\t42\n", "90\t53\t305.4\t0\t53\n", "91\t52\t305.4\t0\t52\n", "92\t38\t305.4\t0\t38\n", "93\t30\t305.4\t0\t30\n", "94\t44\t305.4\t0\t44\n", "95\t39\t305.4\t0\t39\n", "96\t41\t305.4\t0\t41\n", "97\t54\t305.4\t0\t54\n", "98\t47\t305.4\t0\t47\n", "99\t60\t305.4\t0\t60\n", "100\t64\t305.4\t0\t64\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 181_S69_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/181.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 36.46 s (13 us/read; 4.49 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 2,730,129\n", "Reads with adapters: 1,654,355 (60.6%)\n", "Reads written (passing filters): 2,688,049 (98.5%)\n", "\n", "Total basepairs processed: 273,012,900 bp\n", "Quality-trimmed: 656,153 bp (0.2%)\n", "Total written (filtered): 216,035,701 bp (79.1%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1614608 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.7%\n", " G: 33.0%\n", " T: 35.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t61643\t42658.3\t0\t61643\n", "4\t37221\t10664.6\t0\t37221\n", "5\t27788\t2666.1\t0\t27788\n", "6\t22279\t666.5\t0\t22279\n", "7\t20311\t166.6\t0\t20311\n", "8\t19554\t41.7\t0\t19554\n", "9\t18938\t41.7\t0\t18938\n", "10\t17643\t41.7\t0\t17643\n", "11\t18331\t41.7\t0\t18331\n", "12\t18366\t41.7\t0\t18366\n", "13\t18589\t41.7\t0\t18589\n", "14\t19423\t41.7\t0\t19423\n", "15\t19941\t41.7\t0\t19941\n", "16\t20182\t41.7\t0\t20182\n", "17\t23295\t41.7\t0\t23295\n", "18\t27969\t41.7\t0\t27969\n", "19\t26280\t41.7\t0\t26280\n", "20\t22289\t41.7\t0\t22289\n", "21\t21774\t41.7\t0\t21774\n", "22\t20495\t41.7\t0\t20495\n", "23\t22354\t41.7\t0\t22354\n", "24\t26738\t41.7\t0\t26738\n", "25\t27572\t41.7\t0\t27572\n", "26\t30745\t41.7\t0\t30745\n", "27\t32750\t41.7\t0\t32750\n", "28\t30973\t41.7\t0\t30973\n", "29\t29167\t41.7\t0\t29167\n", "30\t30312\t41.7\t0\t30312\n", "31\t32959\t41.7\t0\t32959\n", "32\t29564\t41.7\t0\t29564\n", "33\t27029\t41.7\t0\t27029\n", "34\t26332\t41.7\t0\t26332\n", "35\t30356\t41.7\t0\t30356\n", "36\t34764\t41.7\t0\t34764\n", "37\t36732\t41.7\t0\t36732\n", "38\t30574\t41.7\t0\t30574\n", "39\t26832\t41.7\t0\t26832\n", "40\t24481\t41.7\t0\t24481\n", "41\t26421\t41.7\t0\t26421\n", "42\t28517\t41.7\t0\t28517\n", "43\t25266\t41.7\t0\t25266\n", "44\t20241\t41.7\t0\t20241\n", "45\t25364\t41.7\t0\t25364\n", "46\t31193\t41.7\t0\t31193\n", "47\t30397\t41.7\t0\t30397\n", "48\t34029\t41.7\t0\t34029\n", "49\t30493\t41.7\t0\t30493\n", "50\t24876\t41.7\t0\t24876\n", "51\t21155\t41.7\t0\t21155\n", "52\t18530\t41.7\t0\t18530\n", "53\t17904\t41.7\t0\t17904\n", "54\t20625\t41.7\t0\t20625\n", "55\t22322\t41.7\t0\t22322\n", "56\t20961\t41.7\t0\t20961\n", "57\t16606\t41.7\t0\t16606\n", "58\t20377\t41.7\t0\t20377\n", "59\t14024\t41.7\t0\t14024\n", "60\t11029\t41.7\t0\t11029\n", "61\t10829\t41.7\t0\t10829\n", "62\t8961\t41.7\t0\t8961\n", "63\t8451\t41.7\t0\t8451\n", "64\t8812\t41.7\t0\t8812\n", "65\t8066\t41.7\t0\t8066\n", "66\t6853\t41.7\t0\t6853\n", "67\t6431\t41.7\t0\t6431\n", "68\t5602\t41.7\t0\t5602\n", "69\t5139\t41.7\t0\t5139\n", "70\t4961\t41.7\t0\t4961\n", "71\t4688\t41.7\t0\t4688\n", "72\t3571\t41.7\t0\t3571\n", "73\t3164\t41.7\t0\t3164\n", "74\t3145\t41.7\t0\t3145\n", "75\t2611\t41.7\t0\t2611\n", "76\t2368\t41.7\t0\t2368\n", "77\t2033\t41.7\t0\t2033\n", "78\t2087\t41.7\t0\t2087\n", "79\t2195\t41.7\t0\t2195\n", "80\t2262\t41.7\t0\t2262\n", "81\t2142\t41.7\t0\t2142\n", "82\t2192\t41.7\t0\t2192\n", "83\t2476\t41.7\t0\t2476\n", "84\t2861\t41.7\t0\t2861\n", "85\t3382\t41.7\t0\t3382\n", "86\t3374\t41.7\t0\t3374\n", "87\t2327\t41.7\t0\t2327\n", "88\t2188\t41.7\t0\t2188\n", "89\t2147\t41.7\t0\t2147\n", "90\t2286\t41.7\t0\t2286\n", "91\t2045\t41.7\t0\t2045\n", "92\t1817\t41.7\t0\t1817\n", "93\t1896\t41.7\t0\t1896\n", "94\t1964\t41.7\t0\t1964\n", "95\t1762\t41.7\t0\t1762\n", "96\t1407\t41.7\t0\t1407\n", "97\t937\t41.7\t0\t937\n", "98\t733\t41.7\t0\t733\n", "99\t1046\t41.7\t0\t1046\n", "100\t522\t41.7\t0\t522\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 8827 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 57.4%\n", " C: 16.4%\n", " G: 0.0%\n", " T: 26.0%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t3873\t42658.3\t0\t3873\n", "4\t642\t10664.6\t0\t642\n", "5\t102\t2666.1\t0\t102\n", "6\t39\t666.5\t0\t39\n", "7\t9\t166.6\t0\t9\n", "8\t18\t41.7\t0\t18\n", "9\t6\t41.7\t0\t6\n", "10\t9\t41.7\t0\t9\n", "11\t5\t41.7\t0\t5\n", "12\t5\t41.7\t0\t5\n", "13\t5\t41.7\t0\t5\n", "14\t11\t41.7\t0\t11\n", "15\t4\t41.7\t0\t4\n", "16\t5\t41.7\t0\t5\n", "17\t3\t41.7\t0\t3\n", "18\t7\t41.7\t0\t7\n", "19\t17\t41.7\t0\t17\n", "20\t37\t41.7\t0\t37\n", "21\t27\t41.7\t0\t27\n", "22\t28\t41.7\t0\t28\n", "23\t20\t41.7\t0\t20\n", "24\t16\t41.7\t0\t16\n", "25\t20\t41.7\t0\t20\n", "26\t46\t41.7\t0\t46\n", "27\t43\t41.7\t0\t43\n", "28\t57\t41.7\t0\t57\n", "29\t113\t41.7\t0\t113\n", "30\t256\t41.7\t0\t256\n", "31\t301\t41.7\t0\t301\n", "32\t497\t41.7\t0\t497\n", "33\t408\t41.7\t0\t408\n", "34\t442\t41.7\t0\t442\n", "35\t587\t41.7\t0\t587\n", "36\t605\t41.7\t0\t605\n", "37\t274\t41.7\t0\t274\n", "38\t26\t41.7\t0\t26\n", "39\t19\t41.7\t0\t19\n", "40\t5\t41.7\t0\t5\n", "41\t5\t41.7\t0\t5\n", "42\t2\t41.7\t0\t2\n", "44\t1\t41.7\t0\t1\n", "46\t2\t41.7\t0\t2\n", "47\t1\t41.7\t0\t1\n", "48\t2\t41.7\t0\t2\n", "49\t4\t41.7\t0\t4\n", "50\t2\t41.7\t0\t2\n", "51\t1\t41.7\t0\t1\n", "52\t3\t41.7\t0\t3\n", "53\t1\t41.7\t0\t1\n", "55\t2\t41.7\t0\t2\n", "56\t2\t41.7\t0\t2\n", "57\t1\t41.7\t0\t1\n", "58\t2\t41.7\t0\t2\n", "64\t1\t41.7\t0\t1\n", "65\t3\t41.7\t0\t3\n", "68\t1\t41.7\t0\t1\n", "70\t3\t41.7\t0\t3\n", "71\t1\t41.7\t0\t1\n", "72\t2\t41.7\t0\t2\n", "73\t1\t41.7\t0\t1\n", "75\t3\t41.7\t0\t3\n", "76\t1\t41.7\t0\t1\n", "78\t1\t41.7\t0\t1\n", "85\t1\t41.7\t0\t1\n", "89\t2\t41.7\t0\t2\n", "90\t4\t41.7\t0\t4\n", "91\t3\t41.7\t0\t3\n", "92\t5\t41.7\t0\t5\n", "93\t14\t41.7\t0\t14\n", "94\t19\t41.7\t0\t19\n", "95\t27\t41.7\t0\t27\n", "96\t26\t41.7\t0\t26\n", "97\t25\t41.7\t0\t25\n", "98\t16\t41.7\t0\t16\n", "99\t26\t41.7\t0\t26\n", "100\t24\t41.7\t0\t24\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 30920 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.9%\n", " C: 19.1%\n", " G: 13.4%\n", " T: 21.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t23361\t42658.3\t0\t23361\n", "4\t4797\t10664.6\t0\t4797\n", "5\t825\t2666.1\t0\t825\n", "6\t79\t666.5\t0\t79\n", "7\t15\t166.6\t0\t15\n", "8\t21\t166.6\t0\t21\n", "9\t9\t166.6\t0\t9\n", "10\t25\t166.6\t0\t25\n", "11\t28\t166.6\t0\t28\n", "12\t20\t166.6\t0\t20\n", "13\t22\t166.6\t0\t22\n", "14\t10\t166.6\t0\t10\n", "15\t9\t166.6\t0\t9\n", "16\t1\t166.6\t0\t1\n", "17\t21\t166.6\t0\t21\n", "18\t17\t166.6\t0\t17\n", "19\t9\t166.6\t0\t9\n", "20\t21\t166.6\t0\t21\n", "21\t24\t166.6\t0\t24\n", "22\t23\t166.6\t0\t23\n", "23\t22\t166.6\t0\t22\n", "24\t11\t166.6\t0\t11\n", "25\t19\t166.6\t0\t19\n", "26\t9\t166.6\t0\t9\n", "27\t14\t166.6\t0\t14\n", "28\t10\t166.6\t0\t10\n", "29\t13\t166.6\t0\t13\n", "30\t19\t166.6\t0\t19\n", "31\t15\t166.6\t0\t15\n", "32\t21\t166.6\t0\t21\n", "33\t14\t166.6\t0\t14\n", "34\t12\t166.6\t0\t12\n", "35\t18\t166.6\t0\t18\n", "36\t14\t166.6\t0\t14\n", "37\t23\t166.6\t0\t23\n", "38\t12\t166.6\t0\t12\n", "39\t22\t166.6\t0\t22\n", "40\t32\t166.6\t0\t32\n", "41\t23\t166.6\t0\t23\n", "42\t10\t166.6\t0\t10\n", "43\t19\t166.6\t0\t19\n", "44\t23\t166.6\t0\t23\n", "45\t21\t166.6\t0\t21\n", "46\t23\t166.6\t0\t23\n", "47\t11\t166.6\t0\t11\n", "48\t23\t166.6\t0\t23\n", "49\t16\t166.6\t0\t16\n", "50\t10\t166.6\t0\t10\n", "51\t9\t166.6\t0\t9\n", "52\t16\t166.6\t0\t16\n", "53\t17\t166.6\t0\t17\n", "54\t15\t166.6\t0\t15\n", "55\t11\t166.6\t0\t11\n", "56\t16\t166.6\t0\t16\n", "57\t17\t166.6\t0\t17\n", "58\t20\t166.6\t0\t20\n", "59\t37\t166.6\t0\t37\n", "60\t31\t166.6\t0\t31\n", "61\t26\t166.6\t0\t26\n", "62\t18\t166.6\t0\t18\n", "63\t20\t166.6\t0\t20\n", "64\t19\t166.6\t0\t19\n", "65\t17\t166.6\t0\t17\n", "66\t15\t166.6\t0\t15\n", "67\t14\t166.6\t0\t14\n", "68\t8\t166.6\t0\t8\n", "69\t10\t166.6\t0\t10\n", "70\t9\t166.6\t0\t9\n", "71\t10\t166.6\t0\t10\n", "72\t16\t166.6\t0\t16\n", "73\t48\t166.6\t0\t48\n", "74\t44\t166.6\t0\t44\n", "75\t25\t166.6\t0\t25\n", "76\t25\t166.6\t0\t25\n", "77\t42\t166.6\t0\t42\n", "78\t38\t166.6\t0\t38\n", "79\t28\t166.6\t0\t28\n", "80\t22\t166.6\t0\t22\n", "81\t39\t166.6\t0\t39\n", "82\t40\t166.6\t0\t40\n", "83\t33\t166.6\t0\t33\n", "84\t37\t166.6\t0\t37\n", "85\t14\t166.6\t0\t14\n", "86\t26\t166.6\t0\t26\n", "87\t26\t166.6\t0\t26\n", "88\t20\t166.6\t0\t20\n", "89\t11\t166.6\t0\t11\n", "90\t13\t166.6\t0\t13\n", "91\t13\t166.6\t0\t13\n", "92\t6\t166.6\t0\t6\n", "93\t8\t166.6\t0\t8\n", "94\t24\t166.6\t0\t24\n", "95\t18\t166.6\t0\t18\n", "96\t31\t166.6\t0\t31\n", "97\t21\t166.6\t0\t21\n", "98\t21\t166.6\t0\t21\n", "99\t34\t166.6\t0\t34\n", "100\t26\t166.6\t0\t26\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 183_S56_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/183.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 134.78 s (14 us/read; 4.27 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 9,601,553\n", "Reads with adapters: 5,187,024 (54.0%)\n", "Reads written (passing filters): 9,300,823 (96.9%)\n", "\n", "Total basepairs processed: 960,155,300 bp\n", "Quality-trimmed: 2,618,457 bp (0.3%)\n", "Total written (filtered): 771,490,633 bp (80.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4986053 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.7%\n", " G: 35.4%\n", " T: 34.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t213542\t150024.3\t0\t213542\n", "4\t122752\t37506.1\t0\t122752\n", "5\t88186\t9376.5\t0\t88186\n", "6\t71514\t2344.1\t0\t71514\n", "7\t60731\t586.0\t0\t60731\n", "8\t58300\t146.5\t0\t58300\n", "9\t57189\t146.5\t0\t57189\n", "10\t55443\t146.5\t0\t55443\n", "11\t54779\t146.5\t0\t54779\n", "12\t56405\t146.5\t0\t56405\n", "13\t60868\t146.5\t0\t60868\n", "14\t61938\t146.5\t0\t61938\n", "15\t61014\t146.5\t0\t61014\n", "16\t63897\t146.5\t0\t63897\n", "17\t70005\t146.5\t0\t70005\n", "18\t84283\t146.5\t0\t84283\n", "19\t74608\t146.5\t0\t74608\n", "20\t60970\t146.5\t0\t60970\n", "21\t62410\t146.5\t0\t62410\n", "22\t56233\t146.5\t0\t56233\n", "23\t63877\t146.5\t0\t63877\n", "24\t76815\t146.5\t0\t76815\n", "25\t77839\t146.5\t0\t77839\n", "26\t90347\t146.5\t0\t90347\n", "27\t99573\t146.5\t0\t99573\n", "28\t88638\t146.5\t0\t88638\n", "29\t83718\t146.5\t0\t83718\n", "30\t85524\t146.5\t0\t85524\n", "31\t95903\t146.5\t0\t95903\n", "32\t89170\t146.5\t0\t89170\n", "33\t80157\t146.5\t0\t80157\n", "34\t77227\t146.5\t0\t77227\n", "35\t90217\t146.5\t0\t90217\n", "36\t111100\t146.5\t0\t111100\n", "37\t118777\t146.5\t0\t118777\n", "38\t93320\t146.5\t0\t93320\n", "39\t75702\t146.5\t0\t75702\n", "40\t66447\t146.5\t0\t66447\n", "41\t72247\t146.5\t0\t72247\n", "42\t78979\t146.5\t0\t78979\n", "43\t67907\t146.5\t0\t67907\n", "44\t51462\t146.5\t0\t51462\n", "45\t67042\t146.5\t0\t67042\n", "46\t82117\t146.5\t0\t82117\n", "47\t74844\t146.5\t0\t74844\n", "48\t75798\t146.5\t0\t75798\n", "49\t64893\t146.5\t0\t64893\n", "50\t62961\t146.5\t0\t62961\n", "51\t54011\t146.5\t0\t54011\n", "52\t53671\t146.5\t0\t53671\n", "53\t53538\t146.5\t0\t53538\n", "54\t60465\t146.5\t0\t60465\n", "55\t59905\t146.5\t0\t59905\n", "56\t51911\t146.5\t0\t51911\n", "57\t49760\t146.5\t0\t49760\n", "58\t56707\t146.5\t0\t56707\n", "59\t43331\t146.5\t0\t43331\n", "60\t36498\t146.5\t0\t36498\n", "61\t35201\t146.5\t0\t35201\n", "62\t28096\t146.5\t0\t28096\n", "63\t27303\t146.5\t0\t27303\n", "64\t30550\t146.5\t0\t30550\n", "65\t30072\t146.5\t0\t30072\n", "66\t25634\t146.5\t0\t25634\n", "67\t24843\t146.5\t0\t24843\n", "68\t22821\t146.5\t0\t22821\n", "69\t23340\t146.5\t0\t23340\n", "70\t23990\t146.5\t0\t23990\n", "71\t23377\t146.5\t0\t23377\n", "72\t18369\t146.5\t0\t18369\n", "73\t17412\t146.5\t0\t17412\n", "74\t18655\t146.5\t0\t18655\n", "75\t16190\t146.5\t0\t16190\n", "76\t14628\t146.5\t0\t14628\n", "77\t13006\t146.5\t0\t13006\n", "78\t14519\t146.5\t0\t14519\n", "79\t14217\t146.5\t0\t14217\n", "80\t14819\t146.5\t0\t14819\n", "81\t13963\t146.5\t0\t13963\n", "82\t14059\t146.5\t0\t14059\n", "83\t15529\t146.5\t0\t15529\n", "84\t18269\t146.5\t0\t18269\n", "85\t20972\t146.5\t0\t20972\n", "86\t20384\t146.5\t0\t20384\n", "87\t14369\t146.5\t0\t14369\n", "88\t13421\t146.5\t0\t13421\n", "89\t14677\t146.5\t0\t14677\n", "90\t15917\t146.5\t0\t15917\n", "91\t16135\t146.5\t0\t16135\n", "92\t16276\t146.5\t0\t16276\n", "93\t17092\t146.5\t0\t17092\n", "94\t17001\t146.5\t0\t17001\n", "95\t14909\t146.5\t0\t14909\n", "96\t11495\t146.5\t0\t11495\n", "97\t7320\t146.5\t0\t7320\n", "98\t4344\t146.5\t0\t4344\n", "99\t2944\t146.5\t0\t2944\n", "100\t2470\t146.5\t0\t2470\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 46491 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 56.9%\n", " C: 18.7%\n", " G: 0.0%\n", " T: 24.2%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t18777\t150024.3\t0\t18777\n", "4\t4311\t37506.1\t0\t4311\n", "5\t1073\t9376.5\t0\t1073\n", "6\t403\t2344.1\t0\t403\n", "7\t85\t586.0\t0\t85\n", "8\t73\t146.5\t0\t73\n", "9\t62\t146.5\t0\t62\n", "10\t54\t146.5\t0\t54\n", "11\t68\t146.5\t0\t68\n", "12\t63\t146.5\t0\t63\n", "13\t77\t146.5\t0\t77\n", "14\t77\t146.5\t0\t77\n", "15\t76\t146.5\t0\t76\n", "16\t70\t146.5\t0\t70\n", "17\t74\t146.5\t0\t74\n", "18\t90\t146.5\t0\t90\n", "19\t115\t146.5\t0\t115\n", "20\t117\t146.5\t0\t117\n", "21\t122\t146.5\t0\t122\n", "22\t115\t146.5\t0\t115\n", "23\t109\t146.5\t0\t109\n", "24\t118\t146.5\t0\t118\n", "25\t132\t146.5\t0\t132\n", "26\t225\t146.5\t0\t225\n", "27\t287\t146.5\t0\t287\n", "28\t320\t146.5\t0\t320\n", "29\t555\t146.5\t0\t555\n", "30\t964\t146.5\t0\t964\n", "31\t1234\t146.5\t0\t1234\n", "32\t2200\t146.5\t0\t2200\n", "33\t1950\t146.5\t0\t1950\n", "34\t2194\t146.5\t0\t2194\n", "35\t2651\t146.5\t0\t2651\n", "36\t2572\t146.5\t0\t2572\n", "37\t1318\t146.5\t0\t1318\n", "38\t147\t146.5\t0\t147\n", "39\t136\t146.5\t0\t136\n", "40\t83\t146.5\t0\t83\n", "41\t56\t146.5\t0\t56\n", "42\t56\t146.5\t0\t56\n", "43\t65\t146.5\t0\t65\n", "44\t57\t146.5\t0\t57\n", "45\t53\t146.5\t0\t53\n", "46\t65\t146.5\t0\t65\n", "47\t65\t146.5\t0\t65\n", "48\t73\t146.5\t0\t73\n", "49\t70\t146.5\t0\t70\n", "50\t67\t146.5\t0\t67\n", "51\t63\t146.5\t0\t63\n", "52\t36\t146.5\t0\t36\n", "53\t61\t146.5\t0\t61\n", "54\t53\t146.5\t0\t53\n", "55\t39\t146.5\t0\t39\n", "56\t40\t146.5\t0\t40\n", "57\t45\t146.5\t0\t45\n", "58\t36\t146.5\t0\t36\n", "59\t47\t146.5\t0\t47\n", "60\t37\t146.5\t0\t37\n", "61\t38\t146.5\t0\t38\n", "62\t48\t146.5\t0\t48\n", "63\t33\t146.5\t0\t33\n", "64\t36\t146.5\t0\t36\n", "65\t38\t146.5\t0\t38\n", "66\t38\t146.5\t0\t38\n", "67\t40\t146.5\t0\t40\n", "68\t30\t146.5\t0\t30\n", "69\t25\t146.5\t0\t25\n", "70\t30\t146.5\t0\t30\n", "71\t34\t146.5\t0\t34\n", "72\t27\t146.5\t0\t27\n", "73\t31\t146.5\t0\t31\n", "74\t18\t146.5\t0\t18\n", "75\t17\t146.5\t0\t17\n", "76\t22\t146.5\t0\t22\n", "77\t23\t146.5\t0\t23\n", "78\t18\t146.5\t0\t18\n", "79\t15\t146.5\t0\t15\n", "80\t13\t146.5\t0\t13\n", "81\t11\t146.5\t0\t11\n", "82\t17\t146.5\t0\t17\n", "83\t17\t146.5\t0\t17\n", "84\t31\t146.5\t0\t31\n", "85\t11\t146.5\t0\t11\n", "86\t38\t146.5\t0\t38\n", "87\t23\t146.5\t0\t23\n", "88\t32\t146.5\t0\t32\n", "89\t27\t146.5\t0\t27\n", "90\t32\t146.5\t0\t32\n", "91\t33\t146.5\t0\t33\n", "92\t51\t146.5\t0\t51\n", "93\t115\t146.5\t0\t115\n", "94\t145\t146.5\t0\t145\n", "95\t183\t146.5\t0\t183\n", "96\t215\t146.5\t0\t215\n", "97\t217\t146.5\t0\t217\n", "98\t148\t146.5\t0\t148\n", "99\t134\t146.5\t0\t134\n", "100\t256\t146.5\t0\t256\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 154480 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.0%\n", " C: 22.8%\n", " G: 15.7%\n", " T: 22.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t119132\t150024.3\t0\t119132\n", "4\t22793\t37506.1\t0\t22793\n", "5\t3371\t9376.5\t0\t3371\n", "6\t328\t2344.1\t0\t328\n", "7\t64\t586.0\t0\t64\n", "8\t85\t586.0\t0\t85\n", "9\t85\t586.0\t0\t85\n", "10\t94\t586.0\t0\t94\n", "11\t98\t586.0\t0\t98\n", "12\t90\t586.0\t0\t90\n", "13\t99\t586.0\t0\t99\n", "14\t100\t586.0\t0\t100\n", "15\t103\t586.0\t0\t103\n", "16\t101\t586.0\t0\t101\n", "17\t119\t586.0\t0\t119\n", "18\t105\t586.0\t0\t105\n", "19\t86\t586.0\t0\t86\n", "20\t104\t586.0\t0\t104\n", "21\t95\t586.0\t0\t95\n", "22\t90\t586.0\t0\t90\n", "23\t62\t586.0\t0\t62\n", "24\t79\t586.0\t0\t79\n", "25\t87\t586.0\t0\t87\n", "26\t106\t586.0\t0\t106\n", "27\t118\t586.0\t0\t118\n", "28\t105\t586.0\t0\t105\n", "29\t104\t586.0\t0\t104\n", "30\t109\t586.0\t0\t109\n", "31\t105\t586.0\t0\t105\n", "32\t149\t586.0\t0\t149\n", "33\t144\t586.0\t0\t144\n", "34\t120\t586.0\t0\t120\n", "35\t109\t586.0\t0\t109\n", "36\t99\t586.0\t0\t99\n", "37\t74\t586.0\t0\t74\n", "38\t102\t586.0\t0\t102\n", "39\t77\t586.0\t0\t77\n", "40\t107\t586.0\t0\t107\n", "41\t102\t586.0\t0\t102\n", "42\t88\t586.0\t0\t88\n", "43\t67\t586.0\t0\t67\n", "44\t96\t586.0\t0\t96\n", "45\t79\t586.0\t0\t79\n", "46\t87\t586.0\t0\t87\n", "47\t48\t586.0\t0\t48\n", "48\t85\t586.0\t0\t85\n", "49\t90\t586.0\t0\t90\n", "50\t76\t586.0\t0\t76\n", "51\t54\t586.0\t0\t54\n", "52\t58\t586.0\t0\t58\n", "53\t75\t586.0\t0\t75\n", "54\t71\t586.0\t0\t71\n", "55\t58\t586.0\t0\t58\n", "56\t82\t586.0\t0\t82\n", "57\t55\t586.0\t0\t55\n", "58\t78\t586.0\t0\t78\n", "59\t66\t586.0\t0\t66\n", "60\t62\t586.0\t0\t62\n", "61\t76\t586.0\t0\t76\n", "62\t66\t586.0\t0\t66\n", "63\t81\t586.0\t0\t81\n", "64\t65\t586.0\t0\t65\n", "65\t87\t586.0\t0\t87\n", "66\t78\t586.0\t0\t78\n", "67\t84\t586.0\t0\t84\n", "68\t59\t586.0\t0\t59\n", "69\t56\t586.0\t0\t56\n", "70\t65\t586.0\t0\t65\n", "71\t84\t586.0\t0\t84\n", "72\t69\t586.0\t0\t69\n", "73\t74\t586.0\t0\t74\n", "74\t107\t586.0\t0\t107\n", "75\t93\t586.0\t0\t93\n", "76\t122\t586.0\t0\t122\n", "77\t134\t586.0\t0\t134\n", "78\t143\t586.0\t0\t143\n", "79\t108\t586.0\t0\t108\n", "80\t118\t586.0\t0\t118\n", "81\t141\t586.0\t0\t141\n", "82\t143\t586.0\t0\t143\n", "83\t117\t586.0\t0\t117\n", "84\t129\t586.0\t0\t129\n", "85\t127\t586.0\t0\t127\n", "86\t115\t586.0\t0\t115\n", "87\t138\t586.0\t0\t138\n", "88\t98\t586.0\t0\t98\n", "89\t81\t586.0\t0\t81\n", "90\t95\t586.0\t0\t95\n", "91\t79\t586.0\t0\t79\n", "92\t61\t586.0\t0\t61\n", "93\t65\t586.0\t0\t65\n", "94\t93\t586.0\t0\t93\n", "95\t59\t586.0\t0\t59\n", "96\t110\t586.0\t0\t110\n", "97\t115\t586.0\t0\t115\n", "98\t127\t586.0\t0\t127\n", "99\t174\t586.0\t0\t174\n", "100\t169\t586.0\t0\t169\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 184_S55_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/184.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 47.99 s (14 us/read; 4.29 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 3,429,255\n", "Reads with adapters: 1,932,789 (56.4%)\n", "Reads written (passing filters): 3,260,956 (95.1%)\n", "\n", "Total basepairs processed: 342,925,500 bp\n", "Quality-trimmed: 882,992 bp (0.3%)\n", "Total written (filtered): 269,280,043 bp (78.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1843767 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.1%\n", " G: 34.0%\n", " T: 35.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t73940\t53582.1\t0\t73940\n", "4\t43677\t13395.5\t0\t43677\n", "5\t33029\t3348.9\t0\t33029\n", "6\t26183\t837.2\t0\t26183\n", "7\t22986\t209.3\t0\t22986\n", "8\t22792\t52.3\t0\t22792\n", "9\t21805\t52.3\t0\t21805\n", "10\t20638\t52.3\t0\t20638\n", "11\t20744\t52.3\t0\t20744\n", "12\t21280\t52.3\t0\t21280\n", "13\t22799\t52.3\t0\t22799\n", "14\t23745\t52.3\t0\t23745\n", "15\t22627\t52.3\t0\t22627\n", "16\t23251\t52.3\t0\t23251\n", "17\t26225\t52.3\t0\t26225\n", "18\t32867\t52.3\t0\t32867\n", "19\t28902\t52.3\t0\t28902\n", "20\t23129\t52.3\t0\t23129\n", "21\t23557\t52.3\t0\t23557\n", "22\t20888\t52.3\t0\t20888\n", "23\t23508\t52.3\t0\t23508\n", "24\t28158\t52.3\t0\t28158\n", "25\t28246\t52.3\t0\t28246\n", "26\t32316\t52.3\t0\t32316\n", "27\t34539\t52.3\t0\t34539\n", "28\t31489\t52.3\t0\t31489\n", "29\t28841\t52.3\t0\t28841\n", "30\t29475\t52.3\t0\t29475\n", "31\t33965\t52.3\t0\t33965\n", "32\t29513\t52.3\t0\t29513\n", "33\t28057\t52.3\t0\t28057\n", "34\t27485\t52.3\t0\t27485\n", "35\t32333\t52.3\t0\t32333\n", "36\t38619\t52.3\t0\t38619\n", "37\t41149\t52.3\t0\t41149\n", "38\t32892\t52.3\t0\t32892\n", "39\t27960\t52.3\t0\t27960\n", "40\t23859\t52.3\t0\t23859\n", "41\t26364\t52.3\t0\t26364\n", "42\t28572\t52.3\t0\t28572\n", "43\t24768\t52.3\t0\t24768\n", "44\t17533\t52.3\t0\t17533\n", "45\t22601\t52.3\t0\t22601\n", "46\t27264\t52.3\t0\t27264\n", "47\t25382\t52.3\t0\t25382\n", "48\t26343\t52.3\t0\t26343\n", "49\t21479\t52.3\t0\t21479\n", "50\t21744\t52.3\t0\t21744\n", "51\t18177\t52.3\t0\t18177\n", "52\t19591\t52.3\t0\t19591\n", "53\t18408\t52.3\t0\t18408\n", "54\t21153\t52.3\t0\t21153\n", "55\t16214\t52.3\t0\t16214\n", "56\t15519\t52.3\t0\t15519\n", "57\t16875\t52.3\t0\t16875\n", "58\t20562\t52.3\t0\t20562\n", "59\t15159\t52.3\t0\t15159\n", "60\t12641\t52.3\t0\t12641\n", "61\t12363\t52.3\t0\t12363\n", "62\t9806\t52.3\t0\t9806\n", "63\t9483\t52.3\t0\t9483\n", "64\t10550\t52.3\t0\t10550\n", "65\t10557\t52.3\t0\t10557\n", "66\t8992\t52.3\t0\t8992\n", "67\t9018\t52.3\t0\t9018\n", "68\t8581\t52.3\t0\t8581\n", "69\t8778\t52.3\t0\t8778\n", "70\t9407\t52.3\t0\t9407\n", "71\t9112\t52.3\t0\t9112\n", "72\t6903\t52.3\t0\t6903\n", "73\t6487\t52.3\t0\t6487\n", "74\t6811\t52.3\t0\t6811\n", "75\t6085\t52.3\t0\t6085\n", "76\t5373\t52.3\t0\t5373\n", "77\t4825\t52.3\t0\t4825\n", "78\t5910\t52.3\t0\t5910\n", "79\t5515\t52.3\t0\t5515\n", "80\t5820\t52.3\t0\t5820\n", "81\t5648\t52.3\t0\t5648\n", "82\t5903\t52.3\t0\t5903\n", "83\t6649\t52.3\t0\t6649\n", "84\t8518\t52.3\t0\t8518\n", "85\t10408\t52.3\t0\t10408\n", "86\t10168\t52.3\t0\t10168\n", "87\t6545\t52.3\t0\t6545\n", "88\t6148\t52.3\t0\t6148\n", "89\t7752\t52.3\t0\t7752\n", "90\t8955\t52.3\t0\t8955\n", "91\t10123\t52.3\t0\t10123\n", "92\t11150\t52.3\t0\t11150\n", "93\t12483\t52.3\t0\t12483\n", "94\t13129\t52.3\t0\t13129\n", "95\t11947\t52.3\t0\t11947\n", "96\t9210\t52.3\t0\t9210\n", "97\t6154\t52.3\t0\t6154\n", "98\t3670\t52.3\t0\t3670\n", "99\t2696\t52.3\t0\t2696\n", "100\t2318\t52.3\t0\t2318\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 36114 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 76.5%\n", " C: 9.5%\n", " G: 0.0%\n", " T: 13.9%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t6776\t53582.1\t0\t6776\n", "4\t1424\t13395.5\t0\t1424\n", "5\t431\t3348.9\t0\t431\n", "6\t226\t837.2\t0\t226\n", "7\t24\t209.3\t0\t24\n", "8\t30\t52.3\t0\t30\n", "9\t28\t52.3\t0\t28\n", "10\t28\t52.3\t0\t28\n", "11\t30\t52.3\t0\t30\n", "12\t24\t52.3\t0\t24\n", "13\t10\t52.3\t0\t10\n", "14\t30\t52.3\t0\t30\n", "15\t31\t52.3\t0\t31\n", "16\t25\t52.3\t0\t25\n", "17\t43\t52.3\t0\t43\n", "18\t51\t52.3\t0\t51\n", "19\t60\t52.3\t0\t60\n", "20\t121\t52.3\t0\t121\n", "21\t90\t52.3\t0\t90\n", "22\t91\t52.3\t0\t91\n", "23\t69\t52.3\t0\t69\n", "24\t110\t52.3\t0\t110\n", "25\t139\t52.3\t0\t139\n", "26\t279\t52.3\t0\t279\n", "27\t316\t52.3\t0\t316\n", "28\t544\t52.3\t0\t544\n", "29\t764\t52.3\t0\t764\n", "30\t1560\t52.3\t0\t1560\n", "31\t1884\t52.3\t0\t1884\n", "32\t3256\t52.3\t0\t3256\n", "33\t3037\t52.3\t0\t3037\n", "34\t3369\t52.3\t0\t3369\n", "35\t4093\t52.3\t0\t4093\n", "36\t4035\t52.3\t0\t4035\n", "37\t1993\t52.3\t0\t1993\n", "38\t123\t52.3\t0\t123\n", "39\t63\t52.3\t0\t63\n", "40\t18\t52.3\t0\t18\n", "41\t13\t52.3\t0\t13\n", "42\t14\t52.3\t0\t14\n", "43\t12\t52.3\t0\t12\n", "44\t14\t52.3\t0\t14\n", "45\t13\t52.3\t0\t13\n", "46\t10\t52.3\t0\t10\n", "47\t15\t52.3\t0\t15\n", "48\t9\t52.3\t0\t9\n", "49\t15\t52.3\t0\t15\n", "50\t5\t52.3\t0\t5\n", "51\t3\t52.3\t0\t3\n", "52\t12\t52.3\t0\t12\n", "53\t10\t52.3\t0\t10\n", "54\t5\t52.3\t0\t5\n", "55\t6\t52.3\t0\t6\n", "56\t6\t52.3\t0\t6\n", "57\t9\t52.3\t0\t9\n", "58\t9\t52.3\t0\t9\n", "59\t9\t52.3\t0\t9\n", "60\t11\t52.3\t0\t11\n", "61\t15\t52.3\t0\t15\n", "62\t13\t52.3\t0\t13\n", "63\t11\t52.3\t0\t11\n", "64\t6\t52.3\t0\t6\n", "65\t3\t52.3\t0\t3\n", "66\t6\t52.3\t0\t6\n", "67\t7\t52.3\t0\t7\n", "68\t2\t52.3\t0\t2\n", "69\t2\t52.3\t0\t2\n", "70\t4\t52.3\t0\t4\n", "71\t8\t52.3\t0\t8\n", "72\t2\t52.3\t0\t2\n", "73\t1\t52.3\t0\t1\n", "74\t1\t52.3\t0\t1\n", "75\t4\t52.3\t0\t4\n", "76\t6\t52.3\t0\t6\n", "77\t6\t52.3\t0\t6\n", "78\t2\t52.3\t0\t2\n", "79\t6\t52.3\t0\t6\n", "80\t7\t52.3\t0\t7\n", "81\t5\t52.3\t0\t5\n", "82\t5\t52.3\t0\t5\n", "83\t5\t52.3\t0\t5\n", "84\t4\t52.3\t0\t4\n", "85\t10\t52.3\t0\t10\n", "86\t2\t52.3\t0\t2\n", "87\t5\t52.3\t0\t5\n", "88\t7\t52.3\t0\t7\n", "89\t7\t52.3\t0\t7\n", "90\t8\t52.3\t0\t8\n", "91\t15\t52.3\t0\t15\n", "92\t26\t52.3\t0\t26\n", "93\t39\t52.3\t0\t39\n", "94\t76\t52.3\t0\t76\n", "95\t72\t52.3\t0\t72\n", "96\t71\t52.3\t0\t71\n", "97\t48\t52.3\t0\t48\n", "98\t43\t52.3\t0\t43\n", "99\t50\t52.3\t0\t50\n", "100\t79\t52.3\t0\t79\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 52908 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.4%\n", " C: 21.4%\n", " G: 15.0%\n", " T: 21.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t40278\t53582.1\t0\t40278\n", "4\t7704\t13395.5\t0\t7704\n", "5\t1421\t3348.9\t0\t1421\n", "6\t134\t837.2\t0\t134\n", "7\t39\t209.3\t0\t39\n", "8\t24\t209.3\t0\t24\n", "9\t31\t209.3\t0\t31\n", "10\t39\t209.3\t0\t39\n", "11\t52\t209.3\t0\t52\n", "12\t35\t209.3\t0\t35\n", "13\t28\t209.3\t0\t28\n", "14\t32\t209.3\t0\t32\n", "15\t40\t209.3\t0\t40\n", "16\t47\t209.3\t0\t47\n", "17\t34\t209.3\t0\t34\n", "18\t34\t209.3\t0\t34\n", "19\t36\t209.3\t0\t36\n", "20\t31\t209.3\t0\t31\n", "21\t35\t209.3\t0\t35\n", "22\t25\t209.3\t0\t25\n", "23\t18\t209.3\t0\t18\n", "24\t36\t209.3\t0\t36\n", "25\t33\t209.3\t0\t33\n", "26\t36\t209.3\t0\t36\n", "27\t45\t209.3\t0\t45\n", "28\t41\t209.3\t0\t41\n", "29\t27\t209.3\t0\t27\n", "30\t41\t209.3\t0\t41\n", "31\t32\t209.3\t0\t32\n", "32\t55\t209.3\t0\t55\n", "33\t41\t209.3\t0\t41\n", "34\t35\t209.3\t0\t35\n", "35\t46\t209.3\t0\t46\n", "36\t29\t209.3\t0\t29\n", "37\t37\t209.3\t0\t37\n", "38\t31\t209.3\t0\t31\n", "39\t52\t209.3\t0\t52\n", "40\t65\t209.3\t0\t65\n", "41\t30\t209.3\t0\t30\n", "42\t30\t209.3\t0\t30\n", "43\t33\t209.3\t0\t33\n", "44\t29\t209.3\t0\t29\n", "45\t29\t209.3\t0\t29\n", "46\t45\t209.3\t0\t45\n", "47\t34\t209.3\t0\t34\n", "48\t34\t209.3\t0\t34\n", "49\t34\t209.3\t0\t34\n", "50\t31\t209.3\t0\t31\n", "51\t40\t209.3\t0\t40\n", "52\t27\t209.3\t0\t27\n", "53\t32\t209.3\t0\t32\n", "54\t34\t209.3\t0\t34\n", "55\t28\t209.3\t0\t28\n", "56\t21\t209.3\t0\t21\n", "57\t29\t209.3\t0\t29\n", "58\t47\t209.3\t0\t47\n", "59\t35\t209.3\t0\t35\n", "60\t27\t209.3\t0\t27\n", "61\t36\t209.3\t0\t36\n", "62\t26\t209.3\t0\t26\n", "63\t44\t209.3\t0\t44\n", "64\t34\t209.3\t0\t34\n", "65\t33\t209.3\t0\t33\n", "66\t27\t209.3\t0\t27\n", "67\t36\t209.3\t0\t36\n", "68\t40\t209.3\t0\t40\n", "69\t17\t209.3\t0\t17\n", "70\t35\t209.3\t0\t35\n", "71\t25\t209.3\t0\t25\n", "72\t21\t209.3\t0\t21\n", "73\t34\t209.3\t0\t34\n", "74\t40\t209.3\t0\t40\n", "75\t25\t209.3\t0\t25\n", "76\t39\t209.3\t0\t39\n", "77\t45\t209.3\t0\t45\n", "78\t28\t209.3\t0\t28\n", "79\t55\t209.3\t0\t55\n", "80\t54\t209.3\t0\t54\n", "81\t43\t209.3\t0\t43\n", "82\t69\t209.3\t0\t69\n", "83\t57\t209.3\t0\t57\n", "84\t41\t209.3\t0\t41\n", "85\t42\t209.3\t0\t42\n", "86\t30\t209.3\t0\t30\n", "87\t35\t209.3\t0\t35\n", "88\t37\t209.3\t0\t37\n", "89\t30\t209.3\t0\t30\n", "90\t29\t209.3\t0\t29\n", "91\t29\t209.3\t0\t29\n", "92\t30\t209.3\t0\t30\n", "93\t20\t209.3\t0\t20\n", "94\t35\t209.3\t0\t35\n", "95\t25\t209.3\t0\t25\n", "96\t28\t209.3\t0\t28\n", "97\t35\t209.3\t0\t35\n", "98\t37\t209.3\t0\t37\n", "99\t56\t209.3\t0\t56\n", "100\t58\t209.3\t0\t58\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 185_S60_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/185.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 28.95 s (13 us/read; 4.47 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 2,156,823\n", "Reads with adapters: 1,187,103 (55.0%)\n", "Reads written (passing filters): 2,097,649 (97.3%)\n", "\n", "Total basepairs processed: 215,682,300 bp\n", "Quality-trimmed: 496,084 bp (0.2%)\n", "Total written (filtered): 173,904,814 bp (80.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1144892 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 26.7%\n", " G: 34.1%\n", " T: 39.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t48410\t33700.4\t0\t48410\n", "4\t27440\t8425.1\t0\t27440\n", "5\t20335\t2106.3\t0\t20335\n", "6\t16761\t526.6\t0\t16761\n", "7\t13872\t131.6\t0\t13872\n", "8\t13389\t32.9\t0\t13389\n", "9\t13321\t32.9\t0\t13321\n", "10\t12317\t32.9\t0\t12317\n", "11\t12350\t32.9\t0\t12350\n", "12\t12715\t32.9\t0\t12715\n", "13\t13603\t32.9\t0\t13603\n", "14\t14161\t32.9\t0\t14161\n", "15\t13379\t32.9\t0\t13379\n", "16\t14116\t32.9\t0\t14116\n", "17\t15682\t32.9\t0\t15682\n", "18\t19189\t32.9\t0\t19189\n", "19\t16634\t32.9\t0\t16634\n", "20\t14320\t32.9\t0\t14320\n", "21\t15095\t32.9\t0\t15095\n", "22\t13603\t32.9\t0\t13603\n", "23\t15568\t32.9\t0\t15568\n", "24\t19211\t32.9\t0\t19211\n", "25\t18550\t32.9\t0\t18550\n", "26\t21940\t32.9\t0\t21940\n", "27\t25820\t32.9\t0\t25820\n", "28\t23576\t32.9\t0\t23576\n", "29\t21090\t32.9\t0\t21090\n", "30\t23073\t32.9\t0\t23073\n", "31\t26100\t32.9\t0\t26100\n", "32\t22605\t32.9\t0\t22605\n", "33\t20298\t32.9\t0\t20298\n", "34\t18986\t32.9\t0\t18986\n", "35\t22658\t32.9\t0\t22658\n", "36\t30055\t32.9\t0\t30055\n", "37\t33547\t32.9\t0\t33547\n", "38\t25867\t32.9\t0\t25867\n", "39\t17712\t32.9\t0\t17712\n", "40\t15430\t32.9\t0\t15430\n", "41\t16464\t32.9\t0\t16464\n", "42\t17623\t32.9\t0\t17623\n", "43\t14628\t32.9\t0\t14628\n", "44\t11123\t32.9\t0\t11123\n", "45\t14415\t32.9\t0\t14415\n", "46\t17599\t32.9\t0\t17599\n", "47\t16377\t32.9\t0\t16377\n", "48\t17546\t32.9\t0\t17546\n", "49\t14440\t32.9\t0\t14440\n", "50\t12851\t32.9\t0\t12851\n", "51\t10546\t32.9\t0\t10546\n", "52\t10874\t32.9\t0\t10874\n", "53\t10843\t32.9\t0\t10843\n", "54\t11123\t32.9\t0\t11123\n", "55\t13418\t32.9\t0\t13418\n", "56\t12411\t32.9\t0\t12411\n", "57\t10917\t32.9\t0\t10917\n", "58\t14950\t32.9\t0\t14950\n", "59\t9940\t32.9\t0\t9940\n", "60\t7294\t32.9\t0\t7294\n", "61\t7053\t32.9\t0\t7053\n", "62\t5875\t32.9\t0\t5875\n", "63\t6168\t32.9\t0\t6168\n", "64\t7154\t32.9\t0\t7154\n", "65\t5390\t32.9\t0\t5390\n", "66\t4268\t32.9\t0\t4268\n", "67\t4742\t32.9\t0\t4742\n", "68\t4327\t32.9\t0\t4327\n", "69\t4242\t32.9\t0\t4242\n", "70\t5092\t32.9\t0\t5092\n", "71\t4622\t32.9\t0\t4622\n", "72\t3289\t32.9\t0\t3289\n", "73\t2641\t32.9\t0\t2641\n", "74\t2561\t32.9\t0\t2561\n", "75\t2467\t32.9\t0\t2467\n", "76\t2019\t32.9\t0\t2019\n", "77\t2219\t32.9\t0\t2219\n", "78\t2921\t32.9\t0\t2921\n", "79\t2428\t32.9\t0\t2428\n", "80\t2245\t32.9\t0\t2245\n", "81\t2402\t32.9\t0\t2402\n", "82\t2391\t32.9\t0\t2391\n", "83\t2355\t32.9\t0\t2355\n", "84\t3089\t32.9\t0\t3089\n", "85\t3972\t32.9\t0\t3972\n", "86\t4132\t32.9\t0\t4132\n", "87\t3024\t32.9\t0\t3024\n", "88\t2571\t32.9\t0\t2571\n", "89\t2809\t32.9\t0\t2809\n", "90\t3211\t32.9\t0\t3211\n", "91\t3494\t32.9\t0\t3494\n", "92\t3558\t32.9\t0\t3558\n", "93\t3789\t32.9\t0\t3789\n", "94\t3839\t32.9\t0\t3839\n", "95\t3471\t32.9\t0\t3471\n", "96\t2659\t32.9\t0\t2659\n", "97\t1743\t32.9\t0\t1743\n", "98\t1077\t32.9\t0\t1077\n", "99\t806\t32.9\t0\t806\n", "100\t617\t32.9\t0\t617\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 10179 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 63.2%\n", " C: 16.0%\n", " G: 0.0%\n", " T: 20.6%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t3654\t33700.4\t0\t3654\n", "4\t770\t8425.1\t0\t770\n", "5\t190\t2106.3\t0\t190\n", "6\t74\t526.6\t0\t74\n", "7\t12\t131.6\t0\t12\n", "8\t14\t32.9\t0\t14\n", "9\t8\t32.9\t0\t8\n", "10\t10\t32.9\t0\t10\n", "11\t11\t32.9\t0\t11\n", "12\t14\t32.9\t0\t14\n", "13\t7\t32.9\t0\t7\n", "14\t10\t32.9\t0\t10\n", "15\t14\t32.9\t0\t14\n", "16\t12\t32.9\t0\t12\n", "17\t14\t32.9\t0\t14\n", "18\t21\t32.9\t0\t21\n", "19\t19\t32.9\t0\t19\n", "20\t40\t32.9\t0\t40\n", "21\t24\t32.9\t0\t24\n", "22\t17\t32.9\t0\t17\n", "23\t32\t32.9\t0\t32\n", "24\t21\t32.9\t0\t21\n", "25\t34\t32.9\t0\t34\n", "26\t56\t32.9\t0\t56\n", "27\t73\t32.9\t0\t73\n", "28\t126\t32.9\t0\t126\n", "29\t200\t32.9\t0\t200\n", "30\t300\t32.9\t0\t300\n", "31\t448\t32.9\t0\t448\n", "32\t601\t32.9\t0\t601\n", "33\t619\t32.9\t0\t619\n", "34\t676\t32.9\t0\t676\n", "35\t759\t32.9\t0\t759\n", "36\t593\t32.9\t0\t593\n", "37\t219\t32.9\t0\t219\n", "38\t28\t32.9\t0\t28\n", "39\t17\t32.9\t0\t17\n", "40\t5\t32.9\t0\t5\n", "41\t8\t32.9\t0\t8\n", "42\t10\t32.9\t0\t10\n", "43\t1\t32.9\t0\t1\n", "44\t8\t32.9\t0\t8\n", "45\t5\t32.9\t0\t5\n", "46\t7\t32.9\t0\t7\n", "47\t7\t32.9\t0\t7\n", "48\t8\t32.9\t0\t8\n", "49\t5\t32.9\t0\t5\n", "50\t5\t32.9\t0\t5\n", "51\t3\t32.9\t0\t3\n", "52\t5\t32.9\t0\t5\n", "53\t5\t32.9\t0\t5\n", "54\t2\t32.9\t0\t2\n", "55\t5\t32.9\t0\t5\n", "56\t9\t32.9\t0\t9\n", "57\t5\t32.9\t0\t5\n", "58\t4\t32.9\t0\t4\n", "59\t4\t32.9\t0\t4\n", "60\t4\t32.9\t0\t4\n", "61\t9\t32.9\t0\t9\n", "62\t3\t32.9\t0\t3\n", "63\t2\t32.9\t0\t2\n", "64\t2\t32.9\t0\t2\n", "65\t1\t32.9\t0\t1\n", "67\t4\t32.9\t0\t4\n", "68\t4\t32.9\t0\t4\n", "69\t2\t32.9\t0\t2\n", "70\t1\t32.9\t0\t1\n", "71\t1\t32.9\t0\t1\n", "72\t1\t32.9\t0\t1\n", "73\t2\t32.9\t0\t2\n", "74\t6\t32.9\t0\t6\n", "75\t1\t32.9\t0\t1\n", "78\t1\t32.9\t0\t1\n", "79\t1\t32.9\t0\t1\n", "80\t2\t32.9\t0\t2\n", "81\t2\t32.9\t0\t2\n", "82\t2\t32.9\t0\t2\n", "83\t1\t32.9\t0\t1\n", "84\t1\t32.9\t0\t1\n", "85\t1\t32.9\t0\t1\n", "86\t2\t32.9\t0\t2\n", "87\t2\t32.9\t0\t2\n", "88\t2\t32.9\t0\t2\n", "89\t1\t32.9\t0\t1\n", "90\t4\t32.9\t0\t4\n", "91\t5\t32.9\t0\t5\n", "92\t4\t32.9\t0\t4\n", "93\t21\t32.9\t0\t21\n", "94\t27\t32.9\t0\t27\n", "95\t48\t32.9\t0\t48\n", "96\t31\t32.9\t0\t31\n", "97\t30\t32.9\t0\t30\n", "98\t21\t32.9\t0\t21\n", "99\t20\t32.9\t0\t20\n", "100\t59\t32.9\t0\t59\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 32032 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.1%\n", " C: 21.6%\n", " G: 12.3%\n", " T: 25.0%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t24734\t33700.4\t0\t24734\n", "4\t4842\t8425.1\t0\t4842\n", "5\t637\t2106.3\t0\t637\n", "6\t89\t526.6\t0\t89\n", "7\t16\t131.6\t0\t16\n", "8\t16\t131.6\t0\t16\n", "9\t16\t131.6\t0\t16\n", "10\t24\t131.6\t0\t24\n", "11\t23\t131.6\t0\t23\n", "12\t20\t131.6\t0\t20\n", "13\t23\t131.6\t0\t23\n", "14\t15\t131.6\t0\t15\n", "15\t21\t131.6\t0\t21\n", "16\t32\t131.6\t0\t32\n", "17\t19\t131.6\t0\t19\n", "18\t22\t131.6\t0\t22\n", "19\t27\t131.6\t0\t27\n", "20\t20\t131.6\t0\t20\n", "21\t19\t131.6\t0\t19\n", "22\t12\t131.6\t0\t12\n", "23\t26\t131.6\t0\t26\n", "24\t24\t131.6\t0\t24\n", "25\t17\t131.6\t0\t17\n", "26\t13\t131.6\t0\t13\n", "27\t23\t131.6\t0\t23\n", "28\t20\t131.6\t0\t20\n", "29\t12\t131.6\t0\t12\n", "30\t18\t131.6\t0\t18\n", "31\t20\t131.6\t0\t20\n", "32\t24\t131.6\t0\t24\n", "33\t22\t131.6\t0\t22\n", "34\t17\t131.6\t0\t17\n", "35\t17\t131.6\t0\t17\n", "36\t19\t131.6\t0\t19\n", "37\t16\t131.6\t0\t16\n", "38\t25\t131.6\t0\t25\n", "39\t24\t131.6\t0\t24\n", "40\t29\t131.6\t0\t29\n", "41\t16\t131.6\t0\t16\n", "42\t12\t131.6\t0\t12\n", "43\t16\t131.6\t0\t16\n", "44\t21\t131.6\t0\t21\n", "45\t12\t131.6\t0\t12\n", "46\t19\t131.6\t0\t19\n", "47\t19\t131.6\t0\t19\n", "48\t14\t131.6\t0\t14\n", "49\t21\t131.6\t0\t21\n", "50\t18\t131.6\t0\t18\n", "51\t11\t131.6\t0\t11\n", "52\t13\t131.6\t0\t13\n", "53\t15\t131.6\t0\t15\n", "54\t17\t131.6\t0\t17\n", "55\t14\t131.6\t0\t14\n", "56\t16\t131.6\t0\t16\n", "57\t13\t131.6\t0\t13\n", "58\t22\t131.6\t0\t22\n", "59\t19\t131.6\t0\t19\n", "60\t19\t131.6\t0\t19\n", "61\t26\t131.6\t0\t26\n", "62\t13\t131.6\t0\t13\n", "63\t20\t131.6\t0\t20\n", "64\t16\t131.6\t0\t16\n", "65\t17\t131.6\t0\t17\n", "66\t11\t131.6\t0\t11\n", "67\t6\t131.6\t0\t6\n", "68\t14\t131.6\t0\t14\n", "69\t13\t131.6\t0\t13\n", "70\t6\t131.6\t0\t6\n", "71\t10\t131.6\t0\t10\n", "72\t7\t131.6\t0\t7\n", "73\t16\t131.6\t0\t16\n", "74\t14\t131.6\t0\t14\n", "75\t13\t131.6\t0\t13\n", "76\t23\t131.6\t0\t23\n", "77\t19\t131.6\t0\t19\n", "78\t15\t131.6\t0\t15\n", "79\t25\t131.6\t0\t25\n", "80\t28\t131.6\t0\t28\n", "81\t25\t131.6\t0\t25\n", "82\t31\t131.6\t0\t31\n", "83\t26\t131.6\t0\t26\n", "84\t14\t131.6\t0\t14\n", "85\t23\t131.6\t0\t23\n", "86\t18\t131.6\t0\t18\n", "87\t15\t131.6\t0\t15\n", "88\t9\t131.6\t0\t9\n", "89\t16\t131.6\t0\t16\n", "90\t6\t131.6\t0\t6\n", "91\t13\t131.6\t0\t13\n", "92\t10\t131.6\t0\t10\n", "93\t11\t131.6\t0\t11\n", "94\t18\t131.6\t0\t18\n", "95\t18\t131.6\t0\t18\n", "96\t17\t131.6\t0\t17\n", "97\t26\t131.6\t0\t26\n", "98\t30\t131.6\t0\t30\n", "99\t36\t131.6\t0\t36\n", "100\t38\t131.6\t0\t38\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 291_S42_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/291.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 98.17 s (14 us/read; 4.44 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,256,905\n", "Reads with adapters: 4,161,785 (57.3%)\n", "Reads written (passing filters): 6,950,103 (95.8%)\n", "\n", "Total basepairs processed: 725,690,500 bp\n", "Quality-trimmed: 2,383,051 bp (0.3%)\n", "Total written (filtered): 563,061,738 bp (77.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4004630 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.4%\n", " G: 38.6%\n", " T: 30.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t149481\t113389.1\t0\t149481\n", "4\t85452\t28347.3\t0\t85452\n", "5\t62219\t7086.8\t0\t62219\n", "6\t51557\t1771.7\t0\t51557\n", "7\t47360\t442.9\t0\t47360\n", "8\t46027\t110.7\t0\t46027\n", "9\t47036\t110.7\t0\t47036\n", "10\t45634\t110.7\t0\t45634\n", "11\t47144\t110.7\t0\t47144\n", "12\t47464\t110.7\t0\t47464\n", "13\t52820\t110.7\t0\t52820\n", "14\t54184\t110.7\t0\t54184\n", "15\t51597\t110.7\t0\t51597\n", "16\t54656\t110.7\t0\t54656\n", "17\t57637\t110.7\t0\t57637\n", "18\t63578\t110.7\t0\t63578\n", "19\t56447\t110.7\t0\t56447\n", "20\t47213\t110.7\t0\t47213\n", "21\t45649\t110.7\t0\t45649\n", "22\t43105\t110.7\t0\t43105\n", "23\t46762\t110.7\t0\t46762\n", "24\t53344\t110.7\t0\t53344\n", "25\t54800\t110.7\t0\t54800\n", "26\t61413\t110.7\t0\t61413\n", "27\t65986\t110.7\t0\t65986\n", "28\t60062\t110.7\t0\t60062\n", "29\t54602\t110.7\t0\t54602\n", "30\t53856\t110.7\t0\t53856\n", "31\t58146\t110.7\t0\t58146\n", "32\t59490\t110.7\t0\t59490\n", "33\t56596\t110.7\t0\t56596\n", "34\t55377\t110.7\t0\t55377\n", "35\t61531\t110.7\t0\t61531\n", "36\t67717\t110.7\t0\t67717\n", "37\t68386\t110.7\t0\t68386\n", "38\t58797\t110.7\t0\t58797\n", "39\t53863\t110.7\t0\t53863\n", "40\t53421\t110.7\t0\t53421\n", "41\t64177\t110.7\t0\t64177\n", "42\t73055\t110.7\t0\t73055\n", "43\t66359\t110.7\t0\t66359\n", "44\t53248\t110.7\t0\t53248\n", "45\t61425\t110.7\t0\t61425\n", "46\t73885\t110.7\t0\t73885\n", "47\t68822\t110.7\t0\t68822\n", "48\t64407\t110.7\t0\t64407\n", "49\t56587\t110.7\t0\t56587\n", "50\t52811\t110.7\t0\t52811\n", "51\t46163\t110.7\t0\t46163\n", "52\t45801\t110.7\t0\t45801\n", "53\t42209\t110.7\t0\t42209\n", "54\t44972\t110.7\t0\t44972\n", "55\t46031\t110.7\t0\t46031\n", "56\t41173\t110.7\t0\t41173\n", "57\t42002\t110.7\t0\t42002\n", "58\t46109\t110.7\t0\t46109\n", "59\t40024\t110.7\t0\t40024\n", "60\t33638\t110.7\t0\t33638\n", "61\t31818\t110.7\t0\t31818\n", "62\t28352\t110.7\t0\t28352\n", "63\t27991\t110.7\t0\t27991\n", "64\t30215\t110.7\t0\t30215\n", "65\t28509\t110.7\t0\t28509\n", "66\t25171\t110.7\t0\t25171\n", "67\t26374\t110.7\t0\t26374\n", "68\t26803\t110.7\t0\t26803\n", "69\t27941\t110.7\t0\t27941\n", "70\t30430\t110.7\t0\t30430\n", "71\t29070\t110.7\t0\t29070\n", "72\t22106\t110.7\t0\t22106\n", "73\t19224\t110.7\t0\t19224\n", "74\t18485\t110.7\t0\t18485\n", "75\t17027\t110.7\t0\t17027\n", "76\t14869\t110.7\t0\t14869\n", "77\t15316\t110.7\t0\t15316\n", "78\t17630\t110.7\t0\t17630\n", "79\t16192\t110.7\t0\t16192\n", "80\t15800\t110.7\t0\t15800\n", "81\t16084\t110.7\t0\t16084\n", "82\t15630\t110.7\t0\t15630\n", "83\t15925\t110.7\t0\t15925\n", "84\t17886\t110.7\t0\t17886\n", "85\t20425\t110.7\t0\t20425\n", "86\t21358\t110.7\t0\t21358\n", "87\t18098\t110.7\t0\t18098\n", "88\t17441\t110.7\t0\t17441\n", "89\t16325\t110.7\t0\t16325\n", "90\t16142\t110.7\t0\t16142\n", "91\t15854\t110.7\t0\t15854\n", "92\t15826\t110.7\t0\t15826\n", "93\t15889\t110.7\t0\t15889\n", "94\t14620\t110.7\t0\t14620\n", "95\t12057\t110.7\t0\t12057\n", "96\t8702\t110.7\t0\t8702\n", "97\t5871\t110.7\t0\t5871\n", "98\t3353\t110.7\t0\t3353\n", "99\t2478\t110.7\t0\t2478\n", "100\t2036\t110.7\t0\t2036\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 43085 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 48.5%\n", " C: 26.8%\n", " G: 0.0%\n", " T: 24.3%\n", " none/other: 0.4%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t17138\t113389.1\t0\t17138\n", "4\t4511\t28347.3\t0\t4511\n", "5\t2147\t7086.8\t0\t2147\n", "6\t699\t1771.7\t0\t699\n", "7\t83\t442.9\t0\t83\n", "8\t73\t110.7\t0\t73\n", "9\t67\t110.7\t0\t67\n", "10\t81\t110.7\t0\t81\n", "11\t77\t110.7\t0\t77\n", "12\t76\t110.7\t0\t76\n", "13\t73\t110.7\t0\t73\n", "14\t94\t110.7\t0\t94\n", "15\t86\t110.7\t0\t86\n", "16\t86\t110.7\t0\t86\n", "17\t112\t110.7\t0\t112\n", "18\t159\t110.7\t0\t159\n", "19\t170\t110.7\t0\t170\n", "20\t269\t110.7\t0\t269\n", "21\t188\t110.7\t0\t188\n", "22\t109\t110.7\t0\t109\n", "23\t127\t110.7\t0\t127\n", "24\t110\t110.7\t0\t110\n", "25\t163\t110.7\t0\t163\n", "26\t206\t110.7\t0\t206\n", "27\t224\t110.7\t0\t224\n", "28\t280\t110.7\t0\t280\n", "29\t446\t110.7\t0\t446\n", "30\t729\t110.7\t0\t729\n", "31\t869\t110.7\t0\t869\n", "32\t1219\t110.7\t0\t1219\n", "33\t1344\t110.7\t0\t1344\n", "34\t1545\t110.7\t0\t1545\n", "35\t1741\t110.7\t0\t1741\n", "36\t1710\t110.7\t0\t1710\n", "37\t690\t110.7\t0\t690\n", "38\t89\t110.7\t0\t89\n", "39\t79\t110.7\t0\t79\n", "40\t56\t110.7\t0\t56\n", "41\t68\t110.7\t0\t68\n", "42\t67\t110.7\t0\t67\n", "43\t66\t110.7\t0\t66\n", "44\t60\t110.7\t0\t60\n", "45\t64\t110.7\t0\t64\n", "46\t58\t110.7\t0\t58\n", "47\t65\t110.7\t0\t65\n", "48\t55\t110.7\t0\t55\n", "49\t60\t110.7\t0\t60\n", "50\t72\t110.7\t0\t72\n", "51\t44\t110.7\t0\t44\n", "52\t63\t110.7\t0\t63\n", "53\t46\t110.7\t0\t46\n", "54\t51\t110.7\t0\t51\n", "55\t51\t110.7\t0\t51\n", "56\t61\t110.7\t0\t61\n", "57\t48\t110.7\t0\t48\n", "58\t46\t110.7\t0\t46\n", "59\t44\t110.7\t0\t44\n", "60\t43\t110.7\t0\t43\n", "61\t32\t110.7\t0\t32\n", "62\t41\t110.7\t0\t41\n", "63\t50\t110.7\t0\t50\n", "64\t53\t110.7\t0\t53\n", "65\t49\t110.7\t0\t49\n", "66\t46\t110.7\t0\t46\n", "67\t40\t110.7\t0\t40\n", "68\t38\t110.7\t0\t38\n", "69\t47\t110.7\t0\t47\n", "70\t34\t110.7\t0\t34\n", "71\t26\t110.7\t0\t26\n", "72\t22\t110.7\t0\t22\n", "73\t28\t110.7\t0\t28\n", "74\t35\t110.7\t0\t35\n", "75\t35\t110.7\t0\t35\n", "76\t23\t110.7\t0\t23\n", "77\t23\t110.7\t0\t23\n", "78\t48\t110.7\t0\t48\n", "79\t41\t110.7\t0\t41\n", "80\t35\t110.7\t0\t35\n", "81\t34\t110.7\t0\t34\n", "82\t38\t110.7\t0\t38\n", "83\t54\t110.7\t0\t54\n", "84\t57\t110.7\t0\t57\n", "85\t67\t110.7\t0\t67\n", "86\t64\t110.7\t0\t64\n", "87\t68\t110.7\t0\t68\n", "88\t57\t110.7\t0\t57\n", "89\t73\t110.7\t0\t73\n", "90\t75\t110.7\t0\t75\n", "91\t83\t110.7\t0\t83\n", "92\t170\t110.7\t0\t170\n", "93\t212\t110.7\t0\t212\n", "94\t299\t110.7\t0\t299\n", "95\t350\t110.7\t0\t350\n", "96\t397\t110.7\t0\t397\n", "97\t426\t110.7\t0\t426\n", "98\t278\t110.7\t0\t278\n", "99\t151\t110.7\t0\t151\n", "100\t329\t110.7\t0\t329\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 114070 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.3%\n", " C: 19.7%\n", " G: 18.1%\n", " T: 22.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t85203\t113389.1\t0\t85203\n", "4\t18501\t28347.3\t0\t18501\n", "5\t2817\t7086.8\t0\t2817\n", "6\t323\t1771.7\t0\t323\n", "7\t94\t442.9\t0\t94\n", "8\t94\t442.9\t0\t94\n", "9\t77\t442.9\t0\t77\n", "10\t83\t442.9\t0\t83\n", "11\t95\t442.9\t0\t95\n", "12\t91\t442.9\t0\t91\n", "13\t115\t442.9\t0\t115\n", "14\t103\t442.9\t0\t103\n", "15\t99\t442.9\t0\t99\n", "16\t113\t442.9\t0\t113\n", "17\t120\t442.9\t0\t120\n", "18\t121\t442.9\t0\t121\n", "19\t124\t442.9\t0\t124\n", "20\t118\t442.9\t0\t118\n", "21\t93\t442.9\t0\t93\n", "22\t95\t442.9\t0\t95\n", "23\t83\t442.9\t0\t83\n", "24\t99\t442.9\t0\t99\n", "25\t101\t442.9\t0\t101\n", "26\t105\t442.9\t0\t105\n", "27\t92\t442.9\t0\t92\n", "28\t118\t442.9\t0\t118\n", "29\t119\t442.9\t0\t119\n", "30\t109\t442.9\t0\t109\n", "31\t103\t442.9\t0\t103\n", "32\t94\t442.9\t0\t94\n", "33\t105\t442.9\t0\t105\n", "34\t83\t442.9\t0\t83\n", "35\t89\t442.9\t0\t89\n", "36\t86\t442.9\t0\t86\n", "37\t61\t442.9\t0\t61\n", "38\t69\t442.9\t0\t69\n", "39\t78\t442.9\t0\t78\n", "40\t81\t442.9\t0\t81\n", "41\t88\t442.9\t0\t88\n", "42\t66\t442.9\t0\t66\n", "43\t64\t442.9\t0\t64\n", "44\t58\t442.9\t0\t58\n", "45\t76\t442.9\t0\t76\n", "46\t90\t442.9\t0\t90\n", "47\t63\t442.9\t0\t63\n", "48\t54\t442.9\t0\t54\n", "49\t71\t442.9\t0\t71\n", "50\t53\t442.9\t0\t53\n", "51\t71\t442.9\t0\t71\n", "52\t54\t442.9\t0\t54\n", "53\t75\t442.9\t0\t75\n", "54\t89\t442.9\t0\t89\n", "55\t78\t442.9\t0\t78\n", "56\t70\t442.9\t0\t70\n", "57\t71\t442.9\t0\t71\n", "58\t67\t442.9\t0\t67\n", "59\t52\t442.9\t0\t52\n", "60\t73\t442.9\t0\t73\n", "61\t64\t442.9\t0\t64\n", "62\t64\t442.9\t0\t64\n", "63\t57\t442.9\t0\t57\n", "64\t64\t442.9\t0\t64\n", "65\t59\t442.9\t0\t59\n", "66\t45\t442.9\t0\t45\n", "67\t42\t442.9\t0\t42\n", "68\t67\t442.9\t0\t67\n", "69\t44\t442.9\t0\t44\n", "70\t37\t442.9\t0\t37\n", "71\t40\t442.9\t0\t40\n", "72\t44\t442.9\t0\t44\n", "73\t59\t442.9\t0\t59\n", "74\t72\t442.9\t0\t72\n", "75\t36\t442.9\t0\t36\n", "76\t69\t442.9\t0\t69\n", "77\t61\t442.9\t0\t61\n", "78\t69\t442.9\t0\t69\n", "79\t75\t442.9\t0\t75\n", "80\t63\t442.9\t0\t63\n", "81\t72\t442.9\t0\t72\n", "82\t63\t442.9\t0\t63\n", "83\t88\t442.9\t0\t88\n", "84\t82\t442.9\t0\t82\n", "85\t77\t442.9\t0\t77\n", "86\t82\t442.9\t0\t82\n", "87\t73\t442.9\t0\t73\n", "88\t86\t442.9\t0\t86\n", "89\t68\t442.9\t0\t68\n", "90\t59\t442.9\t0\t59\n", "91\t52\t442.9\t0\t52\n", "92\t36\t442.9\t0\t36\n", "93\t31\t442.9\t0\t31\n", "94\t53\t442.9\t0\t53\n", "95\t42\t442.9\t0\t42\n", "96\t43\t442.9\t0\t43\n", "97\t71\t442.9\t0\t71\n", "98\t81\t442.9\t0\t81\n", "99\t112\t442.9\t0\t112\n", "100\t131\t442.9\t0\t131\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 292_S32_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/292.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 73.92 s (14 us/read; 4.28 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,276,160\n", "Reads with adapters: 4,092,045 (77.6%)\n", "Reads written (passing filters): 4,745,334 (89.9%)\n", "\n", "Total basepairs processed: 527,616,000 bp\n", "Quality-trimmed: 2,113,551 bp (0.4%)\n", "Total written (filtered): 337,843,592 bp (64.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3929347 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 36.5%\n", " G: 39.4%\n", " T: 24.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t65912\t82440.0\t0\t65912\n", "4\t45997\t20610.0\t0\t45997\n", "5\t37881\t5152.5\t0\t37881\n", "6\t33527\t1288.1\t0\t33527\n", "7\t33646\t322.0\t0\t33646\n", "8\t33617\t80.5\t0\t33617\n", "9\t34808\t80.5\t0\t34808\n", "10\t34526\t80.5\t0\t34526\n", "11\t35621\t80.5\t0\t35621\n", "12\t36903\t80.5\t0\t36903\n", "13\t39293\t80.5\t0\t39293\n", "14\t40305\t80.5\t0\t40305\n", "15\t39663\t80.5\t0\t39663\n", "16\t41657\t80.5\t0\t41657\n", "17\t46923\t80.5\t0\t46923\n", "18\t53250\t80.5\t0\t53250\n", "19\t47457\t80.5\t0\t47457\n", "20\t40532\t80.5\t0\t40532\n", "21\t39215\t80.5\t0\t39215\n", "22\t37028\t80.5\t0\t37028\n", "23\t41002\t80.5\t0\t41002\n", "24\t46897\t80.5\t0\t46897\n", "25\t49761\t80.5\t0\t49761\n", "26\t56734\t80.5\t0\t56734\n", "27\t60960\t80.5\t0\t60960\n", "28\t54144\t80.5\t0\t54144\n", "29\t50786\t80.5\t0\t50786\n", "30\t50422\t80.5\t0\t50422\n", "31\t55912\t80.5\t0\t55912\n", "32\t57391\t80.5\t0\t57391\n", "33\t54737\t80.5\t0\t54737\n", "34\t54138\t80.5\t0\t54138\n", "35\t61200\t80.5\t0\t61200\n", "36\t68346\t80.5\t0\t68346\n", "37\t69544\t80.5\t0\t69544\n", "38\t58923\t80.5\t0\t58923\n", "39\t53218\t80.5\t0\t53218\n", "40\t50519\t80.5\t0\t50519\n", "41\t57129\t80.5\t0\t57129\n", "42\t62004\t80.5\t0\t62004\n", "43\t54065\t80.5\t0\t54065\n", "44\t43552\t80.5\t0\t43552\n", "45\t54835\t80.5\t0\t54835\n", "46\t65411\t80.5\t0\t65411\n", "47\t59423\t80.5\t0\t59423\n", "48\t58842\t80.5\t0\t58842\n", "49\t50311\t80.5\t0\t50311\n", "50\t49629\t80.5\t0\t49629\n", "51\t42920\t80.5\t0\t42920\n", "52\t43033\t80.5\t0\t43033\n", "53\t43169\t80.5\t0\t43169\n", "54\t48666\t80.5\t0\t48666\n", "55\t51396\t80.5\t0\t51396\n", "56\t51078\t80.5\t0\t51078\n", "57\t48422\t80.5\t0\t48422\n", "58\t54433\t80.5\t0\t54433\n", "59\t48713\t80.5\t0\t48713\n", "60\t39446\t80.5\t0\t39446\n", "61\t37879\t80.5\t0\t37879\n", "62\t32667\t80.5\t0\t32667\n", "63\t34806\t80.5\t0\t34806\n", "64\t42149\t80.5\t0\t42149\n", "65\t34266\t80.5\t0\t34266\n", "66\t28829\t80.5\t0\t28829\n", "67\t33332\t80.5\t0\t33332\n", "68\t33020\t80.5\t0\t33020\n", "69\t36275\t80.5\t0\t36275\n", "70\t44224\t80.5\t0\t44224\n", "71\t39959\t80.5\t0\t39959\n", "72\t28687\t80.5\t0\t28687\n", "73\t22137\t80.5\t0\t22137\n", "74\t20493\t80.5\t0\t20493\n", "75\t19966\t80.5\t0\t19966\n", "76\t16112\t80.5\t0\t16112\n", "77\t20400\t80.5\t0\t20400\n", "78\t27484\t80.5\t0\t27484\n", "79\t20932\t80.5\t0\t20932\n", "80\t18943\t80.5\t0\t18943\n", "81\t20434\t80.5\t0\t20434\n", "82\t19842\t80.5\t0\t19842\n", "83\t19277\t80.5\t0\t19277\n", "84\t27174\t80.5\t0\t27174\n", "85\t37225\t80.5\t0\t37225\n", "86\t39763\t80.5\t0\t39763\n", "87\t26924\t80.5\t0\t26924\n", "88\t20575\t80.5\t0\t20575\n", "89\t23317\t80.5\t0\t23317\n", "90\t28394\t80.5\t0\t28394\n", "91\t32998\t80.5\t0\t32998\n", "92\t36255\t80.5\t0\t36255\n", "93\t40598\t80.5\t0\t40598\n", "94\t39967\t80.5\t0\t39967\n", "95\t32361\t80.5\t0\t32361\n", "96\t22290\t80.5\t0\t22290\n", "97\t13410\t80.5\t0\t13410\n", "98\t6491\t80.5\t0\t6491\n", "99\t7830\t80.5\t0\t7830\n", "100\t2790\t80.5\t0\t2790\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 87889 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 79.7%\n", " C: 10.1%\n", " G: 0.0%\n", " T: 10.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9512\t82440.0\t0\t9512\n", "4\t3115\t20610.0\t0\t3115\n", "5\t1946\t5152.5\t0\t1946\n", "6\t1502\t1288.1\t0\t1502\n", "7\t1081\t322.0\t0\t1081\n", "8\t917\t80.5\t0\t917\n", "9\t938\t80.5\t0\t938\n", "10\t1045\t80.5\t0\t1045\n", "11\t823\t80.5\t0\t823\n", "12\t772\t80.5\t0\t772\n", "13\t822\t80.5\t0\t822\n", "14\t648\t80.5\t0\t648\n", "15\t743\t80.5\t0\t743\n", "16\t825\t80.5\t0\t825\n", "17\t973\t80.5\t0\t973\n", "18\t1216\t80.5\t0\t1216\n", "19\t1347\t80.5\t0\t1347\n", "20\t1439\t80.5\t0\t1439\n", "21\t1098\t80.5\t0\t1098\n", "22\t976\t80.5\t0\t976\n", "23\t887\t80.5\t0\t887\n", "24\t1248\t80.5\t0\t1248\n", "25\t1839\t80.5\t0\t1839\n", "26\t2625\t80.5\t0\t2625\n", "27\t2524\t80.5\t0\t2524\n", "28\t2875\t80.5\t0\t2875\n", "29\t3751\t80.5\t0\t3751\n", "30\t5306\t80.5\t0\t5306\n", "31\t6013\t80.5\t0\t6013\n", "32\t6362\t80.5\t0\t6362\n", "33\t5781\t80.5\t0\t5781\n", "34\t5298\t80.5\t0\t5298\n", "35\t5054\t80.5\t0\t5054\n", "36\t4068\t80.5\t0\t4068\n", "37\t1126\t80.5\t0\t1126\n", "38\t62\t80.5\t0\t62\n", "39\t30\t80.5\t0\t30\n", "40\t28\t80.5\t0\t28\n", "41\t43\t80.5\t0\t43\n", "42\t29\t80.5\t0\t29\n", "43\t39\t80.5\t0\t39\n", "44\t32\t80.5\t0\t32\n", "45\t31\t80.5\t0\t31\n", "46\t36\t80.5\t0\t36\n", "47\t33\t80.5\t0\t33\n", "48\t30\t80.5\t0\t30\n", "49\t32\t80.5\t0\t32\n", "50\t27\t80.5\t0\t27\n", "51\t24\t80.5\t0\t24\n", "52\t16\t80.5\t0\t16\n", "53\t26\t80.5\t0\t26\n", "54\t24\t80.5\t0\t24\n", "55\t12\t80.5\t0\t12\n", "56\t18\t80.5\t0\t18\n", "57\t19\t80.5\t0\t19\n", "58\t14\t80.5\t0\t14\n", "59\t14\t80.5\t0\t14\n", "60\t13\t80.5\t0\t13\n", "61\t14\t80.5\t0\t14\n", "62\t12\t80.5\t0\t12\n", "63\t8\t80.5\t0\t8\n", "64\t19\t80.5\t0\t19\n", "65\t17\t80.5\t0\t17\n", "66\t8\t80.5\t0\t8\n", "67\t12\t80.5\t0\t12\n", "68\t21\t80.5\t0\t21\n", "69\t12\t80.5\t0\t12\n", "70\t14\t80.5\t0\t14\n", "71\t8\t80.5\t0\t8\n", "72\t13\t80.5\t0\t13\n", "73\t8\t80.5\t0\t8\n", "74\t6\t80.5\t0\t6\n", "75\t2\t80.5\t0\t2\n", "76\t1\t80.5\t0\t1\n", "77\t6\t80.5\t0\t6\n", "78\t1\t80.5\t0\t1\n", "79\t4\t80.5\t0\t4\n", "80\t3\t80.5\t0\t3\n", "81\t4\t80.5\t0\t4\n", "82\t5\t80.5\t0\t5\n", "83\t4\t80.5\t0\t4\n", "84\t10\t80.5\t0\t10\n", "85\t10\t80.5\t0\t10\n", "86\t8\t80.5\t0\t8\n", "87\t4\t80.5\t0\t4\n", "88\t4\t80.5\t0\t4\n", "89\t7\t80.5\t0\t7\n", "90\t12\t80.5\t0\t12\n", "91\t13\t80.5\t0\t13\n", "92\t15\t80.5\t0\t15\n", "93\t35\t80.5\t0\t35\n", "94\t49\t80.5\t0\t49\n", "95\t68\t80.5\t0\t68\n", "96\t88\t80.5\t0\t88\n", "97\t62\t80.5\t0\t62\n", "98\t61\t80.5\t0\t61\n", "99\t41\t80.5\t0\t41\n", "100\t73\t80.5\t0\t73\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 74809 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.6%\n", " C: 20.9%\n", " G: 21.7%\n", " T: 13.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t38195\t82440.0\t0\t38195\n", "4\t6453\t20610.0\t0\t6453\n", "5\t1699\t5152.5\t0\t1699\n", "6\t761\t1288.1\t0\t761\n", "7\t638\t322.0\t0\t638\n", "8\t643\t322.0\t0\t643\n", "9\t690\t322.0\t0\t690\n", "10\t690\t322.0\t0\t690\n", "11\t611\t322.0\t0\t611\n", "12\t595\t322.0\t0\t595\n", "13\t714\t322.0\t0\t714\n", "14\t717\t322.0\t0\t717\n", "15\t741\t322.0\t0\t741\n", "16\t742\t322.0\t0\t742\n", "17\t676\t322.0\t0\t676\n", "18\t711\t322.0\t0\t711\n", "19\t584\t322.0\t0\t584\n", "20\t576\t322.0\t0\t576\n", "21\t558\t322.0\t0\t558\n", "22\t558\t322.0\t0\t558\n", "23\t496\t322.0\t0\t496\n", "24\t524\t322.0\t0\t524\n", "25\t530\t322.0\t0\t530\n", "26\t496\t322.0\t0\t496\n", "27\t588\t322.0\t0\t588\n", "28\t513\t322.0\t0\t513\n", "29\t532\t322.0\t0\t532\n", "30\t520\t322.0\t0\t520\n", "31\t425\t322.0\t0\t425\n", "32\t525\t322.0\t0\t525\n", "33\t444\t322.0\t0\t444\n", "34\t479\t322.0\t0\t479\n", "35\t397\t322.0\t0\t397\n", "36\t370\t322.0\t0\t370\n", "37\t373\t322.0\t0\t373\n", "38\t339\t322.0\t0\t339\n", "39\t406\t322.0\t0\t406\n", "40\t411\t322.0\t0\t411\n", "41\t288\t322.0\t0\t288\n", "42\t309\t322.0\t0\t309\n", "43\t464\t322.0\t0\t464\n", "44\t89\t322.0\t0\t89\n", "45\t294\t322.0\t0\t294\n", "46\t439\t322.0\t0\t439\n", "47\t268\t322.0\t0\t268\n", "48\t140\t322.0\t0\t140\n", "49\t324\t322.0\t0\t324\n", "50\t253\t322.0\t0\t253\n", "51\t215\t322.0\t0\t215\n", "52\t284\t322.0\t0\t284\n", "53\t272\t322.0\t0\t272\n", "54\t160\t322.0\t0\t160\n", "55\t302\t322.0\t0\t302\n", "56\t194\t322.0\t0\t194\n", "57\t269\t322.0\t0\t269\n", "58\t213\t322.0\t0\t213\n", "59\t101\t322.0\t0\t101\n", "60\t240\t322.0\t0\t240\n", "61\t226\t322.0\t0\t226\n", "62\t114\t322.0\t0\t114\n", "63\t163\t322.0\t0\t163\n", "64\t250\t322.0\t0\t250\n", "65\t83\t322.0\t0\t83\n", "66\t153\t322.0\t0\t153\n", "67\t172\t322.0\t0\t172\n", "68\t282\t322.0\t0\t282\n", "69\t49\t322.0\t0\t49\n", "70\t41\t322.0\t0\t41\n", "71\t105\t322.0\t0\t105\n", "72\t143\t322.0\t0\t143\n", "73\t127\t322.0\t0\t127\n", "74\t163\t322.0\t0\t163\n", "75\t138\t322.0\t0\t138\n", "76\t104\t322.0\t0\t104\n", "77\t86\t322.0\t0\t86\n", "78\t67\t322.0\t0\t67\n", "79\t77\t322.0\t0\t77\n", "80\t87\t322.0\t0\t87\n", "81\t67\t322.0\t0\t67\n", "82\t100\t322.0\t0\t100\n", "83\t70\t322.0\t0\t70\n", "84\t94\t322.0\t0\t94\n", "85\t66\t322.0\t0\t66\n", "86\t84\t322.0\t0\t84\n", "87\t73\t322.0\t0\t73\n", "88\t65\t322.0\t0\t65\n", "89\t51\t322.0\t0\t51\n", "90\t72\t322.0\t0\t72\n", "91\t44\t322.0\t0\t44\n", "92\t34\t322.0\t0\t34\n", "93\t41\t322.0\t0\t41\n", "94\t46\t322.0\t0\t46\n", "95\t20\t322.0\t0\t20\n", "96\t34\t322.0\t0\t34\n", "97\t37\t322.0\t0\t37\n", "98\t42\t322.0\t0\t42\n", "99\t50\t322.0\t0\t50\n", "100\t51\t322.0\t0\t51\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 293_S11_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/293.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 75.18 s (15 us/read; 4.09 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,118,828\n", "Reads with adapters: 3,769,653 (73.6%)\n", "Reads written (passing filters): 4,921,084 (96.1%)\n", "\n", "Total basepairs processed: 511,882,800 bp\n", "Quality-trimmed: 1,685,479 bp (0.3%)\n", "Total written (filtered): 363,633,127 bp (71.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3670390 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 34.5%\n", " G: 43.6%\n", " T: 21.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t83911\t79981.7\t0\t83911\n", "4\t51528\t19995.4\t0\t51528\n", "5\t43046\t4998.9\t0\t43046\n", "6\t38874\t1249.7\t0\t38874\n", "7\t39172\t312.4\t0\t39172\n", "8\t39780\t78.1\t0\t39780\n", "9\t40316\t78.1\t0\t40316\n", "10\t41651\t78.1\t0\t41651\n", "11\t42845\t78.1\t0\t42845\n", "12\t45674\t78.1\t0\t45674\n", "13\t55218\t78.1\t0\t55218\n", "14\t55154\t78.1\t0\t55154\n", "15\t48734\t78.1\t0\t48734\n", "16\t49296\t78.1\t0\t49296\n", "17\t52221\t78.1\t0\t52221\n", "18\t59276\t78.1\t0\t59276\n", "19\t55410\t78.1\t0\t55410\n", "20\t47371\t78.1\t0\t47371\n", "21\t45886\t78.1\t0\t45886\n", "22\t41614\t78.1\t0\t41614\n", "23\t44917\t78.1\t0\t44917\n", "24\t50705\t78.1\t0\t50705\n", "25\t53270\t78.1\t0\t53270\n", "26\t59672\t78.1\t0\t59672\n", "27\t65058\t78.1\t0\t65058\n", "28\t59393\t78.1\t0\t59393\n", "29\t53044\t78.1\t0\t53044\n", "30\t54499\t78.1\t0\t54499\n", "31\t61733\t78.1\t0\t61733\n", "32\t56827\t78.1\t0\t56827\n", "33\t58450\t78.1\t0\t58450\n", "34\t56199\t78.1\t0\t56199\n", "35\t62852\t78.1\t0\t62852\n", "36\t69985\t78.1\t0\t69985\n", "37\t66635\t78.1\t0\t66635\n", "38\t59847\t78.1\t0\t59847\n", "39\t54437\t78.1\t0\t54437\n", "40\t54763\t78.1\t0\t54763\n", "41\t62827\t78.1\t0\t62827\n", "42\t69703\t78.1\t0\t69703\n", "43\t60462\t78.1\t0\t60462\n", "44\t46764\t78.1\t0\t46764\n", "45\t57162\t78.1\t0\t57162\n", "46\t63505\t78.1\t0\t63505\n", "47\t60175\t78.1\t0\t60175\n", "48\t57205\t78.1\t0\t57205\n", "49\t47868\t78.1\t0\t47868\n", "50\t46835\t78.1\t0\t46835\n", "51\t41926\t78.1\t0\t41926\n", "52\t41152\t78.1\t0\t41152\n", "53\t46299\t78.1\t0\t46299\n", "54\t50157\t78.1\t0\t50157\n", "55\t42504\t78.1\t0\t42504\n", "56\t45843\t78.1\t0\t45843\n", "57\t51469\t78.1\t0\t51469\n", "58\t50856\t78.1\t0\t50856\n", "59\t40808\t78.1\t0\t40808\n", "60\t34342\t78.1\t0\t34342\n", "61\t32594\t78.1\t0\t32594\n", "62\t28946\t78.1\t0\t28946\n", "63\t28731\t78.1\t0\t28731\n", "64\t33158\t78.1\t0\t33158\n", "65\t28235\t78.1\t0\t28235\n", "66\t23184\t78.1\t0\t23184\n", "67\t26261\t78.1\t0\t26261\n", "68\t26793\t78.1\t0\t26793\n", "69\t28810\t78.1\t0\t28810\n", "70\t32430\t78.1\t0\t32430\n", "71\t30054\t78.1\t0\t30054\n", "72\t21265\t78.1\t0\t21265\n", "73\t16643\t78.1\t0\t16643\n", "74\t14988\t78.1\t0\t14988\n", "75\t13915\t78.1\t0\t13915\n", "76\t11525\t78.1\t0\t11525\n", "77\t13417\t78.1\t0\t13417\n", "78\t16661\t78.1\t0\t16661\n", "79\t13157\t78.1\t0\t13157\n", "80\t11351\t78.1\t0\t11351\n", "81\t11296\t78.1\t0\t11296\n", "82\t10055\t78.1\t0\t10055\n", "83\t9662\t78.1\t0\t9662\n", "84\t12084\t78.1\t0\t12084\n", "85\t14616\t78.1\t0\t14616\n", "86\t14306\t78.1\t0\t14306\n", "87\t9858\t78.1\t0\t9858\n", "88\t8195\t78.1\t0\t8195\n", "89\t8154\t78.1\t0\t8154\n", "90\t9185\t78.1\t0\t9185\n", "91\t9525\t78.1\t0\t9525\n", "92\t10210\t78.1\t0\t10210\n", "93\t11250\t78.1\t0\t11250\n", "94\t11121\t78.1\t0\t11121\n", "95\t9644\t78.1\t0\t9644\n", "96\t7257\t78.1\t0\t7257\n", "97\t4678\t78.1\t0\t4678\n", "98\t2993\t78.1\t0\t2993\n", "99\t4892\t78.1\t0\t4892\n", "100\t2166\t78.1\t0\t2166\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 37539 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 60.0%\n", " C: 24.9%\n", " G: 0.0%\n", " T: 14.9%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t12080\t79981.7\t0\t12080\n", "4\t3114\t19995.4\t0\t3114\n", "5\t1675\t4998.9\t0\t1675\n", "6\t1463\t1249.7\t0\t1463\n", "7\t288\t312.4\t0\t288\n", "8\t259\t78.1\t0\t259\n", "9\t246\t78.1\t0\t246\n", "10\t281\t78.1\t0\t281\n", "11\t227\t78.1\t0\t227\n", "12\t211\t78.1\t0\t211\n", "13\t216\t78.1\t0\t216\n", "14\t194\t78.1\t0\t194\n", "15\t214\t78.1\t0\t214\n", "16\t215\t78.1\t0\t215\n", "17\t248\t78.1\t0\t248\n", "18\t394\t78.1\t0\t394\n", "19\t423\t78.1\t0\t423\n", "20\t501\t78.1\t0\t501\n", "21\t359\t78.1\t0\t359\n", "22\t264\t78.1\t0\t264\n", "23\t223\t78.1\t0\t223\n", "24\t267\t78.1\t0\t267\n", "25\t330\t78.1\t0\t330\n", "26\t499\t78.1\t0\t499\n", "27\t461\t78.1\t0\t461\n", "28\t533\t78.1\t0\t533\n", "29\t688\t78.1\t0\t688\n", "30\t1072\t78.1\t0\t1072\n", "31\t1333\t78.1\t0\t1333\n", "32\t1599\t78.1\t0\t1599\n", "33\t1462\t78.1\t0\t1462\n", "34\t1560\t78.1\t0\t1560\n", "35\t1620\t78.1\t0\t1620\n", "36\t1240\t78.1\t0\t1240\n", "37\t328\t78.1\t0\t328\n", "38\t36\t78.1\t0\t36\n", "39\t36\t78.1\t0\t36\n", "40\t32\t78.1\t0\t32\n", "41\t23\t78.1\t0\t23\n", "42\t20\t78.1\t0\t20\n", "43\t36\t78.1\t0\t36\n", "44\t30\t78.1\t0\t30\n", "45\t35\t78.1\t0\t35\n", "46\t31\t78.1\t0\t31\n", "47\t28\t78.1\t0\t28\n", "48\t22\t78.1\t0\t22\n", "49\t26\t78.1\t0\t26\n", "50\t32\t78.1\t0\t32\n", "51\t31\t78.1\t0\t31\n", "52\t22\t78.1\t0\t22\n", "53\t32\t78.1\t0\t32\n", "54\t18\t78.1\t0\t18\n", "55\t13\t78.1\t0\t13\n", "56\t25\t78.1\t0\t25\n", "57\t27\t78.1\t0\t27\n", "58\t23\t78.1\t0\t23\n", "59\t21\t78.1\t0\t21\n", "60\t26\t78.1\t0\t26\n", "61\t20\t78.1\t0\t20\n", "62\t22\t78.1\t0\t22\n", "63\t20\t78.1\t0\t20\n", "64\t21\t78.1\t0\t21\n", "65\t17\t78.1\t0\t17\n", "66\t13\t78.1\t0\t13\n", "67\t15\t78.1\t0\t15\n", "68\t5\t78.1\t0\t5\n", "69\t17\t78.1\t0\t17\n", "70\t4\t78.1\t0\t4\n", "71\t11\t78.1\t0\t11\n", "72\t8\t78.1\t0\t8\n", "73\t6\t78.1\t0\t6\n", "74\t5\t78.1\t0\t5\n", "75\t5\t78.1\t0\t5\n", "76\t4\t78.1\t0\t4\n", "77\t1\t78.1\t0\t1\n", "78\t5\t78.1\t0\t5\n", "79\t10\t78.1\t0\t10\n", "80\t2\t78.1\t0\t2\n", "81\t11\t78.1\t0\t11\n", "82\t9\t78.1\t0\t9\n", "83\t9\t78.1\t0\t9\n", "84\t10\t78.1\t0\t10\n", "85\t13\t78.1\t0\t13\n", "86\t9\t78.1\t0\t9\n", "87\t6\t78.1\t0\t6\n", "88\t11\t78.1\t0\t11\n", "89\t6\t78.1\t0\t6\n", "90\t7\t78.1\t0\t7\n", "91\t19\t78.1\t0\t19\n", "92\t27\t78.1\t0\t27\n", "93\t45\t78.1\t0\t45\n", "94\t52\t78.1\t0\t52\n", "95\t67\t78.1\t0\t67\n", "96\t79\t78.1\t0\t79\n", "97\t83\t78.1\t0\t83\n", "98\t51\t78.1\t0\t51\n", "99\t38\t78.1\t0\t38\n", "100\t64\t78.1\t0\t64\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 61724 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.6%\n", " C: 18.3%\n", " G: 22.6%\n", " T: 16.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t38300\t79981.7\t0\t38300\n", "4\t7624\t19995.4\t0\t7624\n", "5\t1767\t4998.9\t0\t1767\n", "6\t372\t1249.7\t0\t372\n", "7\t253\t312.4\t0\t253\n", "8\t294\t312.4\t0\t294\n", "9\t266\t312.4\t0\t266\n", "10\t273\t312.4\t0\t273\n", "11\t283\t312.4\t0\t283\n", "12\t268\t312.4\t0\t268\n", "13\t288\t312.4\t0\t288\n", "14\t294\t312.4\t0\t294\n", "15\t310\t312.4\t0\t310\n", "16\t315\t312.4\t0\t315\n", "17\t312\t312.4\t0\t312\n", "18\t314\t312.4\t0\t314\n", "19\t291\t312.4\t0\t291\n", "20\t287\t312.4\t0\t287\n", "21\t264\t312.4\t0\t264\n", "22\t280\t312.4\t0\t280\n", "23\t258\t312.4\t0\t258\n", "24\t232\t312.4\t0\t232\n", "25\t217\t312.4\t0\t217\n", "26\t251\t312.4\t0\t251\n", "27\t239\t312.4\t0\t239\n", "28\t247\t312.4\t0\t247\n", "29\t234\t312.4\t0\t234\n", "30\t249\t312.4\t0\t249\n", "31\t219\t312.4\t0\t219\n", "32\t242\t312.4\t0\t242\n", "33\t242\t312.4\t0\t242\n", "34\t211\t312.4\t0\t211\n", "35\t221\t312.4\t0\t221\n", "36\t214\t312.4\t0\t214\n", "37\t176\t312.4\t0\t176\n", "38\t200\t312.4\t0\t200\n", "39\t218\t312.4\t0\t218\n", "40\t179\t312.4\t0\t179\n", "41\t185\t312.4\t0\t185\n", "42\t127\t312.4\t0\t127\n", "43\t236\t312.4\t0\t236\n", "44\t69\t312.4\t0\t69\n", "45\t117\t312.4\t0\t117\n", "46\t172\t312.4\t0\t172\n", "47\t141\t312.4\t0\t141\n", "48\t92\t312.4\t0\t92\n", "49\t122\t312.4\t0\t122\n", "50\t125\t312.4\t0\t125\n", "51\t108\t312.4\t0\t108\n", "52\t109\t312.4\t0\t109\n", "53\t143\t312.4\t0\t143\n", "54\t77\t312.4\t0\t77\n", "55\t127\t312.4\t0\t127\n", "56\t100\t312.4\t0\t100\n", "57\t87\t312.4\t0\t87\n", "58\t104\t312.4\t0\t104\n", "59\t55\t312.4\t0\t55\n", "60\t127\t312.4\t0\t127\n", "61\t121\t312.4\t0\t121\n", "62\t62\t312.4\t0\t62\n", "63\t71\t312.4\t0\t71\n", "64\t117\t312.4\t0\t117\n", "65\t49\t312.4\t0\t49\n", "66\t70\t312.4\t0\t70\n", "67\t107\t312.4\t0\t107\n", "68\t103\t312.4\t0\t103\n", "69\t34\t312.4\t0\t34\n", "70\t46\t312.4\t0\t46\n", "71\t51\t312.4\t0\t51\n", "72\t65\t312.4\t0\t65\n", "73\t74\t312.4\t0\t74\n", "74\t81\t312.4\t0\t81\n", "75\t71\t312.4\t0\t71\n", "76\t71\t312.4\t0\t71\n", "77\t68\t312.4\t0\t68\n", "78\t60\t312.4\t0\t60\n", "79\t59\t312.4\t0\t59\n", "80\t69\t312.4\t0\t69\n", "81\t72\t312.4\t0\t72\n", "82\t74\t312.4\t0\t74\n", "83\t78\t312.4\t0\t78\n", "84\t76\t312.4\t0\t76\n", "85\t76\t312.4\t0\t76\n", "86\t58\t312.4\t0\t58\n", "87\t62\t312.4\t0\t62\n", "88\t79\t312.4\t0\t79\n", "89\t64\t312.4\t0\t64\n", "90\t50\t312.4\t0\t50\n", "91\t30\t312.4\t0\t30\n", "92\t29\t312.4\t0\t29\n", "93\t45\t312.4\t0\t45\n", "94\t36\t312.4\t0\t36\n", "95\t36\t312.4\t0\t36\n", "96\t37\t312.4\t0\t37\n", "97\t42\t312.4\t0\t42\n", "98\t46\t312.4\t0\t46\n", "99\t76\t312.4\t0\t76\n", "100\t82\t312.4\t0\t82\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 294_S7_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/294.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 105.46 s (14 us/read; 4.20 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,382,060\n", "Reads with adapters: 5,402,617 (73.2%)\n", "Reads written (passing filters): 7,135,974 (96.7%)\n", "\n", "Total basepairs processed: 738,206,000 bp\n", "Quality-trimmed: 2,628,727 bp (0.4%)\n", "Total written (filtered): 527,986,667 bp (71.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5279031 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.9%\n", " G: 40.0%\n", " T: 26.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t130332\t115344.7\t0\t130332\n", "4\t82157\t28836.2\t0\t82157\n", "5\t68339\t7209.0\t0\t68339\n", "6\t59348\t1802.3\t0\t59348\n", "7\t58490\t450.6\t0\t58490\n", "8\t60126\t112.6\t0\t60126\n", "9\t60472\t112.6\t0\t60472\n", "10\t59321\t112.6\t0\t59321\n", "11\t61407\t112.6\t0\t61407\n", "12\t63408\t112.6\t0\t63408\n", "13\t69471\t112.6\t0\t69471\n", "14\t70984\t112.6\t0\t70984\n", "15\t67472\t112.6\t0\t67472\n", "16\t72038\t112.6\t0\t72038\n", "17\t78407\t112.6\t0\t78407\n", "18\t87849\t112.6\t0\t87849\n", "19\t81832\t112.6\t0\t81832\n", "20\t67281\t112.6\t0\t67281\n", "21\t63595\t112.6\t0\t63595\n", "22\t59960\t112.6\t0\t59960\n", "23\t64915\t112.6\t0\t64915\n", "24\t74529\t112.6\t0\t74529\n", "25\t78992\t112.6\t0\t78992\n", "26\t85943\t112.6\t0\t85943\n", "27\t90694\t112.6\t0\t90694\n", "28\t82920\t112.6\t0\t82920\n", "29\t81234\t112.6\t0\t81234\n", "30\t82806\t112.6\t0\t82806\n", "31\t89020\t112.6\t0\t89020\n", "32\t88112\t112.6\t0\t88112\n", "33\t84004\t112.6\t0\t84004\n", "34\t80405\t112.6\t0\t80405\n", "35\t88529\t112.6\t0\t88529\n", "36\t96156\t112.6\t0\t96156\n", "37\t97485\t112.6\t0\t97485\n", "38\t86440\t112.6\t0\t86440\n", "39\t77529\t112.6\t0\t77529\n", "40\t74938\t112.6\t0\t74938\n", "41\t81556\t112.6\t0\t81556\n", "42\t89918\t112.6\t0\t89918\n", "43\t80416\t112.6\t0\t80416\n", "44\t68455\t112.6\t0\t68455\n", "45\t83108\t112.6\t0\t83108\n", "46\t96681\t112.6\t0\t96681\n", "47\t86914\t112.6\t0\t86914\n", "48\t85418\t112.6\t0\t85418\n", "49\t73916\t112.6\t0\t73916\n", "50\t73043\t112.6\t0\t73043\n", "51\t65960\t112.6\t0\t65960\n", "52\t65342\t112.6\t0\t65342\n", "53\t63496\t112.6\t0\t63496\n", "54\t63049\t112.6\t0\t63049\n", "55\t67623\t112.6\t0\t67623\n", "56\t65475\t112.6\t0\t65475\n", "57\t65405\t112.6\t0\t65405\n", "58\t68320\t112.6\t0\t68320\n", "59\t64579\t112.6\t0\t64579\n", "60\t55146\t112.6\t0\t55146\n", "61\t50856\t112.6\t0\t50856\n", "62\t44298\t112.6\t0\t44298\n", "63\t45557\t112.6\t0\t45557\n", "64\t51257\t112.6\t0\t51257\n", "65\t43416\t112.6\t0\t43416\n", "66\t38070\t112.6\t0\t38070\n", "67\t41898\t112.6\t0\t41898\n", "68\t40492\t112.6\t0\t40492\n", "69\t42046\t112.6\t0\t42046\n", "70\t46961\t112.6\t0\t46961\n", "71\t41095\t112.6\t0\t41095\n", "72\t30394\t112.6\t0\t30394\n", "73\t22574\t112.6\t0\t22574\n", "74\t19803\t112.6\t0\t19803\n", "75\t18845\t112.6\t0\t18845\n", "76\t16358\t112.6\t0\t16358\n", "77\t19487\t112.6\t0\t19487\n", "78\t23107\t112.6\t0\t23107\n", "79\t17825\t112.6\t0\t17825\n", "80\t15604\t112.6\t0\t15604\n", "81\t15541\t112.6\t0\t15541\n", "82\t14532\t112.6\t0\t14532\n", "83\t13081\t112.6\t0\t13081\n", "84\t16020\t112.6\t0\t16020\n", "85\t18986\t112.6\t0\t18986\n", "86\t18307\t112.6\t0\t18307\n", "87\t12690\t112.6\t0\t12690\n", "88\t9802\t112.6\t0\t9802\n", "89\t9802\t112.6\t0\t9802\n", "90\t10915\t112.6\t0\t10915\n", "91\t11477\t112.6\t0\t11477\n", "92\t11870\t112.6\t0\t11870\n", "93\t11896\t112.6\t0\t11896\n", "94\t11186\t112.6\t0\t11186\n", "95\t9287\t112.6\t0\t9287\n", "96\t7283\t112.6\t0\t7283\n", "97\t4830\t112.6\t0\t4830\n", "98\t3123\t112.6\t0\t3123\n", "99\t4428\t112.6\t0\t4428\n", "100\t3272\t112.6\t0\t3272\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 31810 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 65.8%\n", " C: 14.8%\n", " G: 0.0%\n", " T: 19.4%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9467\t115344.7\t0\t9467\n", "4\t2202\t28836.2\t0\t2202\n", "5\t794\t7209.0\t0\t794\n", "6\t513\t1802.3\t0\t513\n", "7\t146\t450.6\t0\t146\n", "8\t156\t112.6\t0\t156\n", "9\t109\t112.6\t0\t109\n", "10\t122\t112.6\t0\t122\n", "11\t114\t112.6\t0\t114\n", "12\t118\t112.6\t0\t118\n", "13\t118\t112.6\t0\t118\n", "14\t122\t112.6\t0\t122\n", "15\t131\t112.6\t0\t131\n", "16\t159\t112.6\t0\t159\n", "17\t226\t112.6\t0\t226\n", "18\t420\t112.6\t0\t420\n", "19\t703\t112.6\t0\t703\n", "20\t925\t112.6\t0\t925\n", "21\t521\t112.6\t0\t521\n", "22\t331\t112.6\t0\t331\n", "23\t251\t112.6\t0\t251\n", "24\t197\t112.6\t0\t197\n", "25\t229\t112.6\t0\t229\n", "26\t291\t112.6\t0\t291\n", "27\t350\t112.6\t0\t350\n", "28\t416\t112.6\t0\t416\n", "29\t630\t112.6\t0\t630\n", "30\t1009\t112.6\t0\t1009\n", "31\t1180\t112.6\t0\t1180\n", "32\t1408\t112.6\t0\t1408\n", "33\t1512\t112.6\t0\t1512\n", "34\t1607\t112.6\t0\t1607\n", "35\t1828\t112.6\t0\t1828\n", "36\t1421\t112.6\t0\t1421\n", "37\t411\t112.6\t0\t411\n", "38\t46\t112.6\t0\t46\n", "39\t33\t112.6\t0\t33\n", "40\t27\t112.6\t0\t27\n", "41\t25\t112.6\t0\t25\n", "42\t36\t112.6\t0\t36\n", "43\t33\t112.6\t0\t33\n", "44\t29\t112.6\t0\t29\n", "45\t46\t112.6\t0\t46\n", "46\t38\t112.6\t0\t38\n", "47\t33\t112.6\t0\t33\n", "48\t32\t112.6\t0\t32\n", "49\t48\t112.6\t0\t48\n", "50\t36\t112.6\t0\t36\n", "51\t37\t112.6\t0\t37\n", "52\t24\t112.6\t0\t24\n", "53\t29\t112.6\t0\t29\n", "54\t23\t112.6\t0\t23\n", "55\t38\t112.6\t0\t38\n", "56\t39\t112.6\t0\t39\n", "57\t24\t112.6\t0\t24\n", "58\t26\t112.6\t0\t26\n", "59\t23\t112.6\t0\t23\n", "60\t24\t112.6\t0\t24\n", "61\t29\t112.6\t0\t29\n", "62\t27\t112.6\t0\t27\n", "63\t29\t112.6\t0\t29\n", "64\t26\t112.6\t0\t26\n", "65\t19\t112.6\t0\t19\n", "66\t24\t112.6\t0\t24\n", "67\t13\t112.6\t0\t13\n", "68\t11\t112.6\t0\t11\n", "69\t16\t112.6\t0\t16\n", "70\t12\t112.6\t0\t12\n", "71\t11\t112.6\t0\t11\n", "72\t10\t112.6\t0\t10\n", "73\t19\t112.6\t0\t19\n", "74\t9\t112.6\t0\t9\n", "75\t8\t112.6\t0\t8\n", "76\t10\t112.6\t0\t10\n", "77\t5\t112.6\t0\t5\n", "78\t8\t112.6\t0\t8\n", "79\t9\t112.6\t0\t9\n", "80\t10\t112.6\t0\t10\n", "81\t9\t112.6\t0\t9\n", "82\t15\t112.6\t0\t15\n", "83\t22\t112.6\t0\t22\n", "84\t8\t112.6\t0\t8\n", "85\t20\t112.6\t0\t20\n", "86\t25\t112.6\t0\t25\n", "87\t11\t112.6\t0\t11\n", "88\t11\t112.6\t0\t11\n", "89\t17\t112.6\t0\t17\n", "90\t16\t112.6\t0\t16\n", "91\t12\t112.6\t0\t12\n", "92\t26\t112.6\t0\t26\n", "93\t41\t112.6\t0\t41\n", "94\t48\t112.6\t0\t48\n", "95\t62\t112.6\t0\t62\n", "96\t84\t112.6\t0\t84\n", "97\t67\t112.6\t0\t67\n", "98\t33\t112.6\t0\t33\n", "99\t41\t112.6\t0\t41\n", "100\t51\t112.6\t0\t51\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 91776 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.8%\n", " C: 17.3%\n", " G: 17.7%\n", " T: 22.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t61180\t115344.7\t0\t61180\n", "4\t15844\t28836.2\t0\t15844\n", "5\t2573\t7209.0\t0\t2573\n", "6\t314\t1802.3\t0\t314\n", "7\t131\t450.6\t0\t131\n", "8\t158\t450.6\t0\t158\n", "9\t127\t450.6\t0\t127\n", "10\t141\t450.6\t0\t141\n", "11\t133\t450.6\t0\t133\n", "12\t169\t450.6\t0\t169\n", "13\t163\t450.6\t0\t163\n", "14\t151\t450.6\t0\t151\n", "15\t179\t450.6\t0\t179\n", "16\t178\t450.6\t0\t178\n", "17\t165\t450.6\t0\t165\n", "18\t213\t450.6\t0\t213\n", "19\t154\t450.6\t0\t154\n", "20\t142\t450.6\t0\t142\n", "21\t175\t450.6\t0\t175\n", "22\t137\t450.6\t0\t137\n", "23\t142\t450.6\t0\t142\n", "24\t159\t450.6\t0\t159\n", "25\t128\t450.6\t0\t128\n", "26\t152\t450.6\t0\t152\n", "27\t156\t450.6\t0\t156\n", "28\t179\t450.6\t0\t179\n", "29\t156\t450.6\t0\t156\n", "30\t177\t450.6\t0\t177\n", "31\t151\t450.6\t0\t151\n", "32\t172\t450.6\t0\t172\n", "33\t171\t450.6\t0\t171\n", "34\t157\t450.6\t0\t157\n", "35\t171\t450.6\t0\t171\n", "36\t137\t450.6\t0\t137\n", "37\t135\t450.6\t0\t135\n", "38\t163\t450.6\t0\t163\n", "39\t187\t450.6\t0\t187\n", "40\t143\t450.6\t0\t143\n", "41\t122\t450.6\t0\t122\n", "42\t128\t450.6\t0\t128\n", "43\t213\t450.6\t0\t213\n", "44\t76\t450.6\t0\t76\n", "45\t118\t450.6\t0\t118\n", "46\t220\t450.6\t0\t220\n", "47\t116\t450.6\t0\t116\n", "48\t77\t450.6\t0\t77\n", "49\t141\t450.6\t0\t141\n", "50\t110\t450.6\t0\t110\n", "51\t96\t450.6\t0\t96\n", "52\t165\t450.6\t0\t165\n", "53\t167\t450.6\t0\t167\n", "54\t91\t450.6\t0\t91\n", "55\t117\t450.6\t0\t117\n", "56\t95\t450.6\t0\t95\n", "57\t181\t450.6\t0\t181\n", "58\t103\t450.6\t0\t103\n", "59\t104\t450.6\t0\t104\n", "60\t267\t450.6\t0\t267\n", "61\t119\t450.6\t0\t119\n", "62\t114\t450.6\t0\t114\n", "63\t129\t450.6\t0\t129\n", "64\t205\t450.6\t0\t205\n", "65\t56\t450.6\t0\t56\n", "66\t75\t450.6\t0\t75\n", "67\t95\t450.6\t0\t95\n", "68\t115\t450.6\t0\t115\n", "69\t59\t450.6\t0\t59\n", "70\t51\t450.6\t0\t51\n", "71\t76\t450.6\t0\t76\n", "72\t104\t450.6\t0\t104\n", "73\t94\t450.6\t0\t94\n", "74\t91\t450.6\t0\t91\n", "75\t76\t450.6\t0\t76\n", "76\t96\t450.6\t0\t96\n", "77\t112\t450.6\t0\t112\n", "78\t103\t450.6\t0\t103\n", "79\t112\t450.6\t0\t112\n", "80\t104\t450.6\t0\t104\n", "81\t91\t450.6\t0\t91\n", "82\t132\t450.6\t0\t132\n", "83\t136\t450.6\t0\t136\n", "84\t124\t450.6\t0\t124\n", "85\t110\t450.6\t0\t110\n", "86\t93\t450.6\t0\t93\n", "87\t119\t450.6\t0\t119\n", "88\t171\t450.6\t0\t171\n", "89\t101\t450.6\t0\t101\n", "90\t72\t450.6\t0\t72\n", "91\t55\t450.6\t0\t55\n", "92\t64\t450.6\t0\t64\n", "93\t52\t450.6\t0\t52\n", "94\t52\t450.6\t0\t52\n", "95\t39\t450.6\t0\t39\n", "96\t44\t450.6\t0\t44\n", "97\t78\t450.6\t0\t78\n", "98\t80\t450.6\t0\t80\n", "99\t116\t450.6\t0\t116\n", "100\t91\t450.6\t0\t91\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 295_S41_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/295.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 126.68 s (13 us/read; 4.67 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 9,865,164\n", "Reads with adapters: 5,841,358 (59.2%)\n", "Reads written (passing filters): 9,324,833 (94.5%)\n", "\n", "Total basepairs processed: 986,516,400 bp\n", "Quality-trimmed: 3,926,357 bp (0.4%)\n", "Total written (filtered): 749,607,946 bp (76.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5624304 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.4%\n", " G: 40.0%\n", " T: 28.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t204830\t154143.2\t0\t204830\n", "4\t112940\t38535.8\t0\t112940\n", "5\t83819\t9633.9\t0\t83819\n", "6\t70372\t2408.5\t0\t70372\n", "7\t65720\t602.1\t0\t65720\n", "8\t64890\t150.5\t0\t64890\n", "9\t66080\t150.5\t0\t66080\n", "10\t65737\t150.5\t0\t65737\n", "11\t66718\t150.5\t0\t66718\n", "12\t67633\t150.5\t0\t67633\n", "13\t74272\t150.5\t0\t74272\n", "14\t74883\t150.5\t0\t74883\n", "15\t72075\t150.5\t0\t72075\n", "16\t76147\t150.5\t0\t76147\n", "17\t82396\t150.5\t0\t82396\n", "18\t90468\t150.5\t0\t90468\n", "19\t81369\t150.5\t0\t81369\n", "20\t68666\t150.5\t0\t68666\n", "21\t65208\t150.5\t0\t65208\n", "22\t61070\t150.5\t0\t61070\n", "23\t65966\t150.5\t0\t65966\n", "24\t74208\t150.5\t0\t74208\n", "25\t77456\t150.5\t0\t77456\n", "26\t85264\t150.5\t0\t85264\n", "27\t88980\t150.5\t0\t88980\n", "28\t80742\t150.5\t0\t80742\n", "29\t75051\t150.5\t0\t75051\n", "30\t74837\t150.5\t0\t74837\n", "31\t82247\t150.5\t0\t82247\n", "32\t78754\t150.5\t0\t78754\n", "33\t78721\t150.5\t0\t78721\n", "34\t77744\t150.5\t0\t77744\n", "35\t84655\t150.5\t0\t84655\n", "36\t88411\t150.5\t0\t88411\n", "37\t84896\t150.5\t0\t84896\n", "38\t75410\t150.5\t0\t75410\n", "39\t73823\t150.5\t0\t73823\n", "40\t71082\t150.5\t0\t71082\n", "41\t80015\t150.5\t0\t80015\n", "42\t87055\t150.5\t0\t87055\n", "43\t78897\t150.5\t0\t78897\n", "44\t64375\t150.5\t0\t64375\n", "45\t76105\t150.5\t0\t76105\n", "46\t82554\t150.5\t0\t82554\n", "47\t78820\t150.5\t0\t78820\n", "48\t74245\t150.5\t0\t74245\n", "49\t68511\t150.5\t0\t68511\n", "50\t69451\t150.5\t0\t69451\n", "51\t66807\t150.5\t0\t66807\n", "52\t66919\t150.5\t0\t66919\n", "53\t58917\t150.5\t0\t58917\n", "54\t64296\t150.5\t0\t64296\n", "55\t63889\t150.5\t0\t63889\n", "56\t54797\t150.5\t0\t54797\n", "57\t61946\t150.5\t0\t61946\n", "58\t72034\t150.5\t0\t72034\n", "59\t62979\t150.5\t0\t62979\n", "60\t55198\t150.5\t0\t55198\n", "61\t50801\t150.5\t0\t50801\n", "62\t45668\t150.5\t0\t45668\n", "63\t40739\t150.5\t0\t40739\n", "64\t44197\t150.5\t0\t44197\n", "65\t43919\t150.5\t0\t43919\n", "66\t39871\t150.5\t0\t39871\n", "67\t40751\t150.5\t0\t40751\n", "68\t40177\t150.5\t0\t40177\n", "69\t41318\t150.5\t0\t41318\n", "70\t43573\t150.5\t0\t43573\n", "71\t42893\t150.5\t0\t42893\n", "72\t34284\t150.5\t0\t34284\n", "73\t30958\t150.5\t0\t30958\n", "74\t31018\t150.5\t0\t31018\n", "75\t28979\t150.5\t0\t28979\n", "76\t25919\t150.5\t0\t25919\n", "77\t25101\t150.5\t0\t25101\n", "78\t27597\t150.5\t0\t27597\n", "79\t26924\t150.5\t0\t26924\n", "80\t26687\t150.5\t0\t26687\n", "81\t26681\t150.5\t0\t26681\n", "82\t26453\t150.5\t0\t26453\n", "83\t27791\t150.5\t0\t27791\n", "84\t30921\t150.5\t0\t30921\n", "85\t34563\t150.5\t0\t34563\n", "86\t35199\t150.5\t0\t35199\n", "87\t30824\t150.5\t0\t30824\n", "88\t30053\t150.5\t0\t30053\n", "89\t29335\t150.5\t0\t29335\n", "90\t29328\t150.5\t0\t29328\n", "91\t28953\t150.5\t0\t28953\n", "92\t28456\t150.5\t0\t28456\n", "93\t27974\t150.5\t0\t27974\n", "94\t25425\t150.5\t0\t25425\n", "95\t20999\t150.5\t0\t20999\n", "96\t15059\t150.5\t0\t15059\n", "97\t9557\t150.5\t0\t9557\n", "98\t5833\t150.5\t0\t5833\n", "99\t4556\t150.5\t0\t4556\n", "100\t3620\t150.5\t0\t3620\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 59709 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 48.6%\n", " C: 25.1%\n", " G: 0.0%\n", " T: 26.1%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t27484\t154143.2\t0\t27484\n", "4\t6796\t38535.8\t0\t6796\n", "5\t2704\t9633.9\t0\t2704\n", "6\t755\t2408.5\t0\t755\n", "7\t181\t602.1\t0\t181\n", "8\t161\t150.5\t0\t161\n", "9\t170\t150.5\t0\t170\n", "10\t192\t150.5\t0\t192\n", "11\t158\t150.5\t0\t158\n", "12\t154\t150.5\t0\t154\n", "13\t179\t150.5\t0\t179\n", "14\t179\t150.5\t0\t179\n", "15\t163\t150.5\t0\t163\n", "16\t194\t150.5\t0\t194\n", "17\t201\t150.5\t0\t201\n", "18\t229\t150.5\t0\t229\n", "19\t218\t150.5\t0\t218\n", "20\t308\t150.5\t0\t308\n", "21\t301\t150.5\t0\t301\n", "22\t189\t150.5\t0\t189\n", "23\t200\t150.5\t0\t200\n", "24\t218\t150.5\t0\t218\n", "25\t240\t150.5\t0\t240\n", "26\t299\t150.5\t0\t299\n", "27\t270\t150.5\t0\t270\n", "28\t304\t150.5\t0\t304\n", "29\t418\t150.5\t0\t418\n", "30\t682\t150.5\t0\t682\n", "31\t831\t150.5\t0\t831\n", "32\t1270\t150.5\t0\t1270\n", "33\t1368\t150.5\t0\t1368\n", "34\t1466\t150.5\t0\t1466\n", "35\t1694\t150.5\t0\t1694\n", "36\t1653\t150.5\t0\t1653\n", "37\t843\t150.5\t0\t843\n", "38\t164\t150.5\t0\t164\n", "39\t146\t150.5\t0\t146\n", "40\t129\t150.5\t0\t129\n", "41\t123\t150.5\t0\t123\n", "42\t108\t150.5\t0\t108\n", "43\t90\t150.5\t0\t90\n", "44\t119\t150.5\t0\t119\n", "45\t132\t150.5\t0\t132\n", "46\t113\t150.5\t0\t113\n", "47\t120\t150.5\t0\t120\n", "48\t141\t150.5\t0\t141\n", "49\t138\t150.5\t0\t138\n", "50\t125\t150.5\t0\t125\n", "51\t111\t150.5\t0\t111\n", "52\t117\t150.5\t0\t117\n", "53\t94\t150.5\t0\t94\n", "54\t81\t150.5\t0\t81\n", "55\t68\t150.5\t0\t68\n", "56\t107\t150.5\t0\t107\n", "57\t99\t150.5\t0\t99\n", "58\t93\t150.5\t0\t93\n", "59\t92\t150.5\t0\t92\n", "60\t94\t150.5\t0\t94\n", "61\t85\t150.5\t0\t85\n", "62\t76\t150.5\t0\t76\n", "63\t86\t150.5\t0\t86\n", "64\t83\t150.5\t0\t83\n", "65\t72\t150.5\t0\t72\n", "66\t61\t150.5\t0\t61\n", "67\t66\t150.5\t0\t66\n", "68\t57\t150.5\t0\t57\n", "69\t51\t150.5\t0\t51\n", "70\t58\t150.5\t0\t58\n", "71\t40\t150.5\t0\t40\n", "72\t37\t150.5\t0\t37\n", "73\t47\t150.5\t0\t47\n", "74\t37\t150.5\t0\t37\n", "75\t42\t150.5\t0\t42\n", "76\t48\t150.5\t0\t48\n", "77\t55\t150.5\t0\t55\n", "78\t48\t150.5\t0\t48\n", "79\t25\t150.5\t0\t25\n", "80\t50\t150.5\t0\t50\n", "81\t44\t150.5\t0\t44\n", "82\t43\t150.5\t0\t43\n", "83\t55\t150.5\t0\t55\n", "84\t55\t150.5\t0\t55\n", "85\t66\t150.5\t0\t66\n", "86\t64\t150.5\t0\t64\n", "87\t39\t150.5\t0\t39\n", "88\t47\t150.5\t0\t47\n", "89\t76\t150.5\t0\t76\n", "90\t77\t150.5\t0\t77\n", "91\t103\t150.5\t0\t103\n", "92\t152\t150.5\t0\t152\n", "93\t242\t150.5\t0\t242\n", "94\t326\t150.5\t0\t326\n", "95\t352\t150.5\t0\t352\n", "96\t399\t150.5\t0\t399\n", "97\t407\t150.5\t0\t407\n", "98\t276\t150.5\t0\t276\n", "99\t158\t150.5\t0\t158\n", "100\t328\t150.5\t0\t328\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 157345 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.0%\n", " C: 18.4%\n", " G: 23.3%\n", " T: 18.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t118680\t154143.2\t0\t118680\n", "4\t22881\t38535.8\t0\t22881\n", "5\t3689\t9633.9\t0\t3689\n", "6\t424\t2408.5\t0\t424\n", "7\t136\t602.1\t0\t136\n", "8\t123\t602.1\t0\t123\n", "9\t107\t602.1\t0\t107\n", "10\t147\t602.1\t0\t147\n", "11\t151\t602.1\t0\t151\n", "12\t152\t602.1\t0\t152\n", "13\t167\t602.1\t0\t167\n", "14\t172\t602.1\t0\t172\n", "15\t196\t602.1\t0\t196\n", "16\t188\t602.1\t0\t188\n", "17\t205\t602.1\t0\t205\n", "18\t164\t602.1\t0\t164\n", "19\t167\t602.1\t0\t167\n", "20\t171\t602.1\t0\t171\n", "21\t145\t602.1\t0\t145\n", "22\t152\t602.1\t0\t152\n", "23\t112\t602.1\t0\t112\n", "24\t104\t602.1\t0\t104\n", "25\t137\t602.1\t0\t137\n", "26\t116\t602.1\t0\t116\n", "27\t154\t602.1\t0\t154\n", "28\t159\t602.1\t0\t159\n", "29\t118\t602.1\t0\t118\n", "30\t145\t602.1\t0\t145\n", "31\t141\t602.1\t0\t141\n", "32\t166\t602.1\t0\t166\n", "33\t160\t602.1\t0\t160\n", "34\t147\t602.1\t0\t147\n", "35\t138\t602.1\t0\t138\n", "36\t126\t602.1\t0\t126\n", "37\t106\t602.1\t0\t106\n", "38\t119\t602.1\t0\t119\n", "39\t141\t602.1\t0\t141\n", "40\t144\t602.1\t0\t144\n", "41\t146\t602.1\t0\t146\n", "42\t107\t602.1\t0\t107\n", "43\t135\t602.1\t0\t135\n", "44\t109\t602.1\t0\t109\n", "45\t106\t602.1\t0\t106\n", "46\t117\t602.1\t0\t117\n", "47\t146\t602.1\t0\t146\n", "48\t146\t602.1\t0\t146\n", "49\t131\t602.1\t0\t131\n", "50\t107\t602.1\t0\t107\n", "51\t110\t602.1\t0\t110\n", "52\t93\t602.1\t0\t93\n", "53\t105\t602.1\t0\t105\n", "54\t112\t602.1\t0\t112\n", "55\t110\t602.1\t0\t110\n", "56\t109\t602.1\t0\t109\n", "57\t101\t602.1\t0\t101\n", "58\t108\t602.1\t0\t108\n", "59\t98\t602.1\t0\t98\n", "60\t103\t602.1\t0\t103\n", "61\t120\t602.1\t0\t120\n", "62\t83\t602.1\t0\t83\n", "63\t136\t602.1\t0\t136\n", "64\t111\t602.1\t0\t111\n", "65\t95\t602.1\t0\t95\n", "66\t131\t602.1\t0\t131\n", "67\t117\t602.1\t0\t117\n", "68\t108\t602.1\t0\t108\n", "69\t86\t602.1\t0\t86\n", "70\t105\t602.1\t0\t105\n", "71\t78\t602.1\t0\t78\n", "72\t111\t602.1\t0\t111\n", "73\t97\t602.1\t0\t97\n", "74\t109\t602.1\t0\t109\n", "75\t101\t602.1\t0\t101\n", "76\t126\t602.1\t0\t126\n", "77\t118\t602.1\t0\t118\n", "78\t140\t602.1\t0\t140\n", "79\t109\t602.1\t0\t109\n", "80\t102\t602.1\t0\t102\n", "81\t95\t602.1\t0\t95\n", "82\t126\t602.1\t0\t126\n", "83\t110\t602.1\t0\t110\n", "84\t124\t602.1\t0\t124\n", "85\t146\t602.1\t0\t146\n", "86\t112\t602.1\t0\t112\n", "87\t142\t602.1\t0\t142\n", "88\t137\t602.1\t0\t137\n", "89\t127\t602.1\t0\t127\n", "90\t114\t602.1\t0\t114\n", "91\t97\t602.1\t0\t97\n", "92\t76\t602.1\t0\t76\n", "93\t70\t602.1\t0\t70\n", "94\t73\t602.1\t0\t73\n", "95\t76\t602.1\t0\t76\n", "96\t75\t602.1\t0\t75\n", "97\t107\t602.1\t0\t107\n", "98\t97\t602.1\t0\t97\n", "99\t158\t602.1\t0\t158\n", "100\t151\t602.1\t0\t151\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 296_S40_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/296.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 160.06 s (13 us/read; 4.54 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 12,099,476\n", "Reads with adapters: 9,289,030 (76.8%)\n", "Reads written (passing filters): 11,560,606 (95.5%)\n", "\n", "Total basepairs processed: 1,209,947,600 bp\n", "Quality-trimmed: 3,812,461 bp (0.3%)\n", "Total written (filtered): 816,882,513 bp (67.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 9123388 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 34.6%\n", " G: 37.9%\n", " T: 27.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t181792\t189054.3\t0\t181792\n", "4\t119277\t47263.6\t0\t119277\n", "5\t96368\t11815.9\t0\t96368\n", "6\t85149\t2954.0\t0\t85149\n", "7\t83020\t738.5\t0\t83020\n", "8\t84673\t184.6\t0\t84673\n", "9\t86056\t184.6\t0\t86056\n", "10\t84516\t184.6\t0\t84516\n", "11\t86127\t184.6\t0\t86127\n", "12\t88195\t184.6\t0\t88195\n", "13\t91467\t184.6\t0\t91467\n", "14\t95090\t184.6\t0\t95090\n", "15\t94514\t184.6\t0\t94514\n", "16\t101364\t184.6\t0\t101364\n", "17\t113226\t184.6\t0\t113226\n", "18\t128766\t184.6\t0\t128766\n", "19\t118647\t184.6\t0\t118647\n", "20\t100411\t184.6\t0\t100411\n", "21\t95423\t184.6\t0\t95423\n", "22\t89932\t184.6\t0\t89932\n", "23\t100248\t184.6\t0\t100248\n", "24\t115522\t184.6\t0\t115522\n", "25\t120425\t184.6\t0\t120425\n", "26\t137800\t184.6\t0\t137800\n", "27\t150840\t184.6\t0\t150840\n", "28\t137125\t184.6\t0\t137125\n", "29\t129516\t184.6\t0\t129516\n", "30\t132361\t184.6\t0\t132361\n", "31\t146531\t184.6\t0\t146531\n", "32\t141339\t184.6\t0\t141339\n", "33\t138014\t184.6\t0\t138014\n", "34\t132090\t184.6\t0\t132090\n", "35\t150598\t184.6\t0\t150598\n", "36\t168137\t184.6\t0\t168137\n", "37\t164057\t184.6\t0\t164057\n", "38\t145960\t184.6\t0\t145960\n", "39\t132722\t184.6\t0\t132722\n", "40\t129289\t184.6\t0\t129289\n", "41\t143291\t184.6\t0\t143291\n", "42\t158464\t184.6\t0\t158464\n", "43\t142155\t184.6\t0\t142155\n", "44\t118487\t184.6\t0\t118487\n", "45\t146089\t184.6\t0\t146089\n", "46\t172240\t184.6\t0\t172240\n", "47\t158280\t184.6\t0\t158280\n", "48\t152982\t184.6\t0\t152982\n", "49\t132341\t184.6\t0\t132341\n", "50\t130130\t184.6\t0\t130130\n", "51\t119892\t184.6\t0\t119892\n", "52\t133145\t184.6\t0\t133145\n", "53\t138931\t184.6\t0\t138931\n", "54\t117806\t184.6\t0\t117806\n", "55\t134775\t184.6\t0\t134775\n", "56\t148892\t184.6\t0\t148892\n", "57\t141064\t184.6\t0\t141064\n", "58\t132574\t184.6\t0\t132574\n", "59\t119585\t184.6\t0\t119585\n", "60\t104777\t184.6\t0\t104777\n", "61\t99693\t184.6\t0\t99693\n", "62\t82534\t184.6\t0\t82534\n", "63\t78298\t184.6\t0\t78298\n", "64\t89255\t184.6\t0\t89255\n", "65\t91290\t184.6\t0\t91290\n", "66\t80283\t184.6\t0\t80283\n", "67\t79472\t184.6\t0\t79472\n", "68\t77255\t184.6\t0\t77255\n", "69\t79951\t184.6\t0\t79951\n", "70\t82091\t184.6\t0\t82091\n", "71\t79558\t184.6\t0\t79558\n", "72\t64469\t184.6\t0\t64469\n", "73\t59763\t184.6\t0\t59763\n", "74\t59981\t184.6\t0\t59981\n", "75\t52414\t184.6\t0\t52414\n", "76\t44477\t184.6\t0\t44477\n", "77\t39871\t184.6\t0\t39871\n", "78\t44011\t184.6\t0\t44011\n", "79\t42037\t184.6\t0\t42037\n", "80\t40559\t184.6\t0\t40559\n", "81\t36858\t184.6\t0\t36858\n", "82\t35568\t184.6\t0\t35568\n", "83\t36986\t184.6\t0\t36986\n", "84\t41919\t184.6\t0\t41919\n", "85\t45523\t184.6\t0\t45523\n", "86\t41897\t184.6\t0\t41897\n", "87\t27636\t184.6\t0\t27636\n", "88\t24023\t184.6\t0\t24023\n", "89\t25096\t184.6\t0\t25096\n", "90\t25602\t184.6\t0\t25602\n", "91\t24896\t184.6\t0\t24896\n", "92\t24374\t184.6\t0\t24374\n", "93\t25963\t184.6\t0\t25963\n", "94\t25567\t184.6\t0\t25567\n", "95\t22016\t184.6\t0\t22016\n", "96\t16923\t184.6\t0\t16923\n", "97\t11043\t184.6\t0\t11043\n", "98\t6281\t184.6\t0\t6281\n", "99\t11953\t184.6\t0\t11953\n", "100\t3515\t184.6\t0\t3515\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 44908 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 64.9%\n", " C: 16.2%\n", " G: 0.0%\n", " T: 18.8%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t12956\t189054.3\t0\t12956\n", "4\t2885\t47263.6\t0\t2885\n", "5\t941\t11815.9\t0\t941\n", "6\t600\t2954.0\t0\t600\n", "7\t135\t738.5\t0\t135\n", "8\t115\t184.6\t0\t115\n", "9\t106\t184.6\t0\t106\n", "10\t107\t184.6\t0\t107\n", "11\t104\t184.6\t0\t104\n", "12\t114\t184.6\t0\t114\n", "13\t115\t184.6\t0\t115\n", "14\t112\t184.6\t0\t112\n", "15\t140\t184.6\t0\t140\n", "16\t139\t184.6\t0\t139\n", "17\t168\t184.6\t0\t168\n", "18\t238\t184.6\t0\t238\n", "19\t310\t184.6\t0\t310\n", "20\t544\t184.6\t0\t544\n", "21\t369\t184.6\t0\t369\n", "22\t262\t184.6\t0\t262\n", "23\t217\t184.6\t0\t217\n", "24\t247\t184.6\t0\t247\n", "25\t259\t184.6\t0\t259\n", "26\t438\t184.6\t0\t438\n", "27\t486\t184.6\t0\t486\n", "28\t560\t184.6\t0\t560\n", "29\t817\t184.6\t0\t817\n", "30\t1534\t184.6\t0\t1534\n", "31\t1775\t184.6\t0\t1775\n", "32\t2473\t184.6\t0\t2473\n", "33\t2528\t184.6\t0\t2528\n", "34\t2567\t184.6\t0\t2567\n", "35\t3029\t184.6\t0\t3029\n", "36\t2990\t184.6\t0\t2990\n", "37\t1133\t184.6\t0\t1133\n", "38\t94\t184.6\t0\t94\n", "39\t98\t184.6\t0\t98\n", "40\t72\t184.6\t0\t72\n", "41\t68\t184.6\t0\t68\n", "42\t66\t184.6\t0\t66\n", "43\t80\t184.6\t0\t80\n", "44\t95\t184.6\t0\t95\n", "45\t95\t184.6\t0\t95\n", "46\t75\t184.6\t0\t75\n", "47\t80\t184.6\t0\t80\n", "48\t75\t184.6\t0\t75\n", "49\t78\t184.6\t0\t78\n", "50\t101\t184.6\t0\t101\n", "51\t95\t184.6\t0\t95\n", "52\t69\t184.6\t0\t69\n", "53\t71\t184.6\t0\t71\n", "54\t86\t184.6\t0\t86\n", "55\t81\t184.6\t0\t81\n", "56\t72\t184.6\t0\t72\n", "57\t61\t184.6\t0\t61\n", "58\t64\t184.6\t0\t64\n", "59\t65\t184.6\t0\t65\n", "60\t52\t184.6\t0\t52\n", "61\t70\t184.6\t0\t70\n", "62\t42\t184.6\t0\t42\n", "63\t56\t184.6\t0\t56\n", "64\t44\t184.6\t0\t44\n", "65\t52\t184.6\t0\t52\n", "66\t39\t184.6\t0\t39\n", "67\t42\t184.6\t0\t42\n", "68\t30\t184.6\t0\t30\n", "69\t30\t184.6\t0\t30\n", "70\t22\t184.6\t0\t22\n", "71\t17\t184.6\t0\t17\n", "72\t14\t184.6\t0\t14\n", "73\t10\t184.6\t0\t10\n", "74\t11\t184.6\t0\t11\n", "75\t13\t184.6\t0\t13\n", "76\t21\t184.6\t0\t21\n", "77\t11\t184.6\t0\t11\n", "78\t16\t184.6\t0\t16\n", "79\t12\t184.6\t0\t12\n", "80\t15\t184.6\t0\t15\n", "81\t18\t184.6\t0\t18\n", "82\t20\t184.6\t0\t20\n", "83\t21\t184.6\t0\t21\n", "84\t18\t184.6\t0\t18\n", "85\t25\t184.6\t0\t25\n", "86\t27\t184.6\t0\t27\n", "87\t17\t184.6\t0\t17\n", "88\t28\t184.6\t0\t28\n", "89\t22\t184.6\t0\t22\n", "90\t20\t184.6\t0\t20\n", "91\t25\t184.6\t0\t25\n", "92\t44\t184.6\t0\t44\n", "93\t81\t184.6\t0\t81\n", "94\t78\t184.6\t0\t78\n", "95\t115\t184.6\t0\t115\n", "96\t118\t184.6\t0\t118\n", "97\t124\t184.6\t0\t124\n", "98\t98\t184.6\t0\t98\n", "99\t52\t184.6\t0\t52\n", "100\t84\t184.6\t0\t84\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 120734 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.2%\n", " C: 17.8%\n", " G: 17.7%\n", " T: 22.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t84834\t189054.3\t0\t84834\n", "4\t20331\t47263.6\t0\t20331\n", "5\t3363\t11815.9\t0\t3363\n", "6\t379\t2954.0\t0\t379\n", "7\t124\t738.5\t0\t124\n", "8\t161\t738.5\t0\t161\n", "9\t165\t738.5\t0\t165\n", "10\t147\t738.5\t0\t147\n", "11\t131\t738.5\t0\t131\n", "12\t156\t738.5\t0\t156\n", "13\t145\t738.5\t0\t145\n", "14\t140\t738.5\t0\t140\n", "15\t182\t738.5\t0\t182\n", "16\t152\t738.5\t0\t152\n", "17\t174\t738.5\t0\t174\n", "18\t164\t738.5\t0\t164\n", "19\t164\t738.5\t0\t164\n", "20\t168\t738.5\t0\t168\n", "21\t167\t738.5\t0\t167\n", "22\t175\t738.5\t0\t175\n", "23\t154\t738.5\t0\t154\n", "24\t140\t738.5\t0\t140\n", "25\t178\t738.5\t0\t178\n", "26\t148\t738.5\t0\t148\n", "27\t168\t738.5\t0\t168\n", "28\t172\t738.5\t0\t172\n", "29\t198\t738.5\t0\t198\n", "30\t172\t738.5\t0\t172\n", "31\t170\t738.5\t0\t170\n", "32\t211\t738.5\t0\t211\n", "33\t205\t738.5\t0\t205\n", "34\t167\t738.5\t0\t167\n", "35\t161\t738.5\t0\t161\n", "36\t171\t738.5\t0\t171\n", "37\t151\t738.5\t0\t151\n", "38\t167\t738.5\t0\t167\n", "39\t186\t738.5\t0\t186\n", "40\t183\t738.5\t0\t183\n", "41\t163\t738.5\t0\t163\n", "42\t141\t738.5\t0\t141\n", "43\t144\t738.5\t0\t144\n", "44\t67\t738.5\t0\t67\n", "45\t147\t738.5\t0\t147\n", "46\t120\t738.5\t0\t120\n", "47\t126\t738.5\t0\t126\n", "48\t127\t738.5\t0\t127\n", "49\t113\t738.5\t0\t113\n", "50\t109\t738.5\t0\t109\n", "51\t99\t738.5\t0\t99\n", "52\t120\t738.5\t0\t120\n", "53\t120\t738.5\t0\t120\n", "54\t112\t738.5\t0\t112\n", "55\t117\t738.5\t0\t117\n", "56\t129\t738.5\t0\t129\n", "57\t89\t738.5\t0\t89\n", "58\t93\t738.5\t0\t93\n", "59\t109\t738.5\t0\t109\n", "60\t90\t738.5\t0\t90\n", "61\t102\t738.5\t0\t102\n", "62\t136\t738.5\t0\t136\n", "63\t157\t738.5\t0\t157\n", "64\t85\t738.5\t0\t85\n", "65\t70\t738.5\t0\t70\n", "66\t71\t738.5\t0\t71\n", "67\t84\t738.5\t0\t84\n", "68\t90\t738.5\t0\t90\n", "69\t88\t738.5\t0\t88\n", "70\t77\t738.5\t0\t77\n", "71\t79\t738.5\t0\t79\n", "72\t64\t738.5\t0\t64\n", "73\t103\t738.5\t0\t103\n", "74\t101\t738.5\t0\t101\n", "75\t73\t738.5\t0\t73\n", "76\t99\t738.5\t0\t99\n", "77\t111\t738.5\t0\t111\n", "78\t98\t738.5\t0\t98\n", "79\t93\t738.5\t0\t93\n", "80\t120\t738.5\t0\t120\n", "81\t134\t738.5\t0\t134\n", "82\t162\t738.5\t0\t162\n", "83\t113\t738.5\t0\t113\n", "84\t130\t738.5\t0\t130\n", "85\t118\t738.5\t0\t118\n", "86\t80\t738.5\t0\t80\n", "87\t129\t738.5\t0\t129\n", "88\t130\t738.5\t0\t130\n", "89\t93\t738.5\t0\t93\n", "90\t86\t738.5\t0\t86\n", "91\t64\t738.5\t0\t64\n", "92\t61\t738.5\t0\t61\n", "93\t56\t738.5\t0\t56\n", "94\t67\t738.5\t0\t67\n", "95\t58\t738.5\t0\t58\n", "96\t40\t738.5\t0\t40\n", "97\t76\t738.5\t0\t76\n", "98\t108\t738.5\t0\t108\n", "99\t120\t738.5\t0\t120\n", "100\t149\t738.5\t0\t149\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 298_S25_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/298.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 96.36 s (15 us/read; 4.13 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,634,152\n", "Reads with adapters: 4,795,888 (72.3%)\n", "Reads written (passing filters): 6,324,004 (95.3%)\n", "\n", "Total basepairs processed: 663,415,200 bp\n", "Quality-trimmed: 2,823,141 bp (0.4%)\n", "Total written (filtered): 465,556,409 bp (70.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4684477 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 32.9%\n", " G: 39.7%\n", " T: 27.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t113905\t103658.6\t0\t113905\n", "4\t71306\t25914.7\t0\t71306\n", "5\t57941\t6478.7\t0\t57941\n", "6\t50367\t1619.7\t0\t50367\n", "7\t48984\t404.9\t0\t48984\n", "8\t49925\t101.2\t0\t49925\n", "9\t49250\t101.2\t0\t49250\n", "10\t49059\t101.2\t0\t49059\n", "11\t50371\t101.2\t0\t50371\n", "12\t51993\t101.2\t0\t51993\n", "13\t57846\t101.2\t0\t57846\n", "14\t58467\t101.2\t0\t58467\n", "15\t54746\t101.2\t0\t54746\n", "16\t56948\t101.2\t0\t56948\n", "17\t62671\t101.2\t0\t62671\n", "18\t71323\t101.2\t0\t71323\n", "19\t65555\t101.2\t0\t65555\n", "20\t54898\t101.2\t0\t54898\n", "21\t53313\t101.2\t0\t53313\n", "22\t48999\t101.2\t0\t48999\n", "23\t53363\t101.2\t0\t53363\n", "24\t60871\t101.2\t0\t60871\n", "25\t64312\t101.2\t0\t64312\n", "26\t71868\t101.2\t0\t71868\n", "27\t77072\t101.2\t0\t77072\n", "28\t70151\t101.2\t0\t70151\n", "29\t65013\t101.2\t0\t65013\n", "30\t65810\t101.2\t0\t65810\n", "31\t71829\t101.2\t0\t71829\n", "32\t69409\t101.2\t0\t69409\n", "33\t68055\t101.2\t0\t68055\n", "34\t66366\t101.2\t0\t66366\n", "35\t74669\t101.2\t0\t74669\n", "36\t82090\t101.2\t0\t82090\n", "37\t84657\t101.2\t0\t84657\n", "38\t71659\t101.2\t0\t71659\n", "39\t66374\t101.2\t0\t66374\n", "40\t65537\t101.2\t0\t65537\n", "41\t73298\t101.2\t0\t73298\n", "42\t77685\t101.2\t0\t77685\n", "43\t70382\t101.2\t0\t70382\n", "44\t55732\t101.2\t0\t55732\n", "45\t68295\t101.2\t0\t68295\n", "46\t81091\t101.2\t0\t81091\n", "47\t78032\t101.2\t0\t78032\n", "48\t73834\t101.2\t0\t73834\n", "49\t60572\t101.2\t0\t60572\n", "50\t59182\t101.2\t0\t59182\n", "51\t60200\t101.2\t0\t60200\n", "52\t64739\t101.2\t0\t64739\n", "53\t59331\t101.2\t0\t59331\n", "54\t61911\t101.2\t0\t61911\n", "55\t55613\t101.2\t0\t55613\n", "56\t56683\t101.2\t0\t56683\n", "57\t58309\t101.2\t0\t58309\n", "58\t66672\t101.2\t0\t66672\n", "59\t62436\t101.2\t0\t62436\n", "60\t53246\t101.2\t0\t53246\n", "61\t49433\t101.2\t0\t49433\n", "62\t43993\t101.2\t0\t43993\n", "63\t46297\t101.2\t0\t46297\n", "64\t54403\t101.2\t0\t54403\n", "65\t44939\t101.2\t0\t44939\n", "66\t42399\t101.2\t0\t42399\n", "67\t46943\t101.2\t0\t46943\n", "68\t42929\t101.2\t0\t42929\n", "69\t41146\t101.2\t0\t41146\n", "70\t46155\t101.2\t0\t46155\n", "71\t40332\t101.2\t0\t40332\n", "72\t31807\t101.2\t0\t31807\n", "73\t22243\t101.2\t0\t22243\n", "74\t18682\t101.2\t0\t18682\n", "75\t17611\t101.2\t0\t17611\n", "76\t16024\t101.2\t0\t16024\n", "77\t19796\t101.2\t0\t19796\n", "78\t25169\t101.2\t0\t25169\n", "79\t20424\t101.2\t0\t20424\n", "80\t18036\t101.2\t0\t18036\n", "81\t17884\t101.2\t0\t17884\n", "82\t16871\t101.2\t0\t16871\n", "83\t14633\t101.2\t0\t14633\n", "84\t17889\t101.2\t0\t17889\n", "85\t22852\t101.2\t0\t22852\n", "86\t23873\t101.2\t0\t23873\n", "87\t17709\t101.2\t0\t17709\n", "88\t13318\t101.2\t0\t13318\n", "89\t12665\t101.2\t0\t12665\n", "90\t14059\t101.2\t0\t14059\n", "91\t14821\t101.2\t0\t14821\n", "92\t14964\t101.2\t0\t14964\n", "93\t16378\t101.2\t0\t16378\n", "94\t15748\t101.2\t0\t15748\n", "95\t13189\t101.2\t0\t13189\n", "96\t9453\t101.2\t0\t9453\n", "97\t5759\t101.2\t0\t5759\n", "98\t3385\t101.2\t0\t3385\n", "99\t3907\t101.2\t0\t3907\n", "100\t2144\t101.2\t0\t2144\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 33473 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 62.4%\n", " C: 18.5%\n", " G: 0.0%\n", " T: 19.1%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9757\t103658.6\t0\t9757\n", "4\t2479\t25914.7\t0\t2479\n", "5\t1233\t6478.7\t0\t1233\n", "6\t853\t1619.7\t0\t853\n", "7\t303\t404.9\t0\t303\n", "8\t256\t101.2\t0\t256\n", "9\t216\t101.2\t0\t216\n", "10\t246\t101.2\t0\t246\n", "11\t219\t101.2\t0\t219\n", "12\t205\t101.2\t0\t205\n", "13\t185\t101.2\t0\t185\n", "14\t187\t101.2\t0\t187\n", "15\t170\t101.2\t0\t170\n", "16\t170\t101.2\t0\t170\n", "17\t187\t101.2\t0\t187\n", "18\t307\t101.2\t0\t307\n", "19\t357\t101.2\t0\t357\n", "20\t310\t101.2\t0\t310\n", "21\t252\t101.2\t0\t252\n", "22\t216\t101.2\t0\t216\n", "23\t213\t101.2\t0\t213\n", "24\t270\t101.2\t0\t270\n", "25\t313\t101.2\t0\t313\n", "26\t408\t101.2\t0\t408\n", "27\t428\t101.2\t0\t428\n", "28\t499\t101.2\t0\t499\n", "29\t742\t101.2\t0\t742\n", "30\t1052\t101.2\t0\t1052\n", "31\t1331\t101.2\t0\t1331\n", "32\t1506\t101.2\t0\t1506\n", "33\t1540\t101.2\t0\t1540\n", "34\t1799\t101.2\t0\t1799\n", "35\t1738\t101.2\t0\t1738\n", "36\t1067\t101.2\t0\t1067\n", "37\t283\t101.2\t0\t283\n", "38\t63\t101.2\t0\t63\n", "39\t53\t101.2\t0\t53\n", "40\t45\t101.2\t0\t45\n", "41\t53\t101.2\t0\t53\n", "42\t66\t101.2\t0\t66\n", "43\t76\t101.2\t0\t76\n", "44\t57\t101.2\t0\t57\n", "45\t57\t101.2\t0\t57\n", "46\t101\t101.2\t0\t101\n", "47\t91\t101.2\t0\t91\n", "48\t61\t101.2\t0\t61\n", "49\t50\t101.2\t0\t50\n", "50\t53\t101.2\t0\t53\n", "51\t50\t101.2\t0\t50\n", "52\t52\t101.2\t0\t52\n", "53\t35\t101.2\t0\t35\n", "54\t16\t101.2\t0\t16\n", "55\t22\t101.2\t0\t22\n", "56\t26\t101.2\t0\t26\n", "57\t30\t101.2\t0\t30\n", "58\t27\t101.2\t0\t27\n", "59\t22\t101.2\t0\t22\n", "60\t30\t101.2\t0\t30\n", "61\t29\t101.2\t0\t29\n", "62\t22\t101.2\t0\t22\n", "63\t22\t101.2\t0\t22\n", "64\t16\t101.2\t0\t16\n", "65\t22\t101.2\t0\t22\n", "66\t25\t101.2\t0\t25\n", "67\t14\t101.2\t0\t14\n", "68\t15\t101.2\t0\t15\n", "69\t15\t101.2\t0\t15\n", "70\t14\t101.2\t0\t14\n", "71\t8\t101.2\t0\t8\n", "72\t15\t101.2\t0\t15\n", "73\t9\t101.2\t0\t9\n", "74\t7\t101.2\t0\t7\n", "75\t8\t101.2\t0\t8\n", "76\t13\t101.2\t0\t13\n", "77\t8\t101.2\t0\t8\n", "78\t4\t101.2\t0\t4\n", "79\t17\t101.2\t0\t17\n", "80\t5\t101.2\t0\t5\n", "81\t13\t101.2\t0\t13\n", "82\t19\t101.2\t0\t19\n", "83\t12\t101.2\t0\t12\n", "84\t17\t101.2\t0\t17\n", "85\t12\t101.2\t0\t12\n", "86\t7\t101.2\t0\t7\n", "87\t13\t101.2\t0\t13\n", "88\t15\t101.2\t0\t15\n", "89\t16\t101.2\t0\t16\n", "90\t18\t101.2\t0\t18\n", "91\t25\t101.2\t0\t25\n", "92\t35\t101.2\t0\t35\n", "93\t44\t101.2\t0\t44\n", "94\t93\t101.2\t0\t93\n", "95\t94\t101.2\t0\t94\n", "96\t81\t101.2\t0\t81\n", "97\t74\t101.2\t0\t74\n", "98\t59\t101.2\t0\t59\n", "99\t38\t101.2\t0\t38\n", "100\t67\t101.2\t0\t67\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 77938 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.6%\n", " C: 19.0%\n", " G: 18.1%\n", " T: 19.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t52699\t103658.6\t0\t52699\n", "4\t11450\t25914.7\t0\t11450\n", "5\t1978\t6478.7\t0\t1978\n", "6\t325\t1619.7\t0\t325\n", "7\t169\t404.9\t0\t169\n", "8\t198\t404.9\t0\t198\n", "9\t165\t404.9\t0\t165\n", "10\t211\t404.9\t0\t211\n", "11\t185\t404.9\t0\t185\n", "12\t197\t404.9\t0\t197\n", "13\t208\t404.9\t0\t208\n", "14\t203\t404.9\t0\t203\n", "15\t221\t404.9\t0\t221\n", "16\t209\t404.9\t0\t209\n", "17\t205\t404.9\t0\t205\n", "18\t225\t404.9\t0\t225\n", "19\t208\t404.9\t0\t208\n", "20\t195\t404.9\t0\t195\n", "21\t180\t404.9\t0\t180\n", "22\t161\t404.9\t0\t161\n", "23\t181\t404.9\t0\t181\n", "24\t190\t404.9\t0\t190\n", "25\t183\t404.9\t0\t183\n", "26\t203\t404.9\t0\t203\n", "27\t219\t404.9\t0\t219\n", "28\t165\t404.9\t0\t165\n", "29\t188\t404.9\t0\t188\n", "30\t192\t404.9\t0\t192\n", "31\t195\t404.9\t0\t195\n", "32\t200\t404.9\t0\t200\n", "33\t192\t404.9\t0\t192\n", "34\t186\t404.9\t0\t186\n", "35\t164\t404.9\t0\t164\n", "36\t175\t404.9\t0\t175\n", "37\t178\t404.9\t0\t178\n", "38\t178\t404.9\t0\t178\n", "39\t179\t404.9\t0\t179\n", "40\t139\t404.9\t0\t139\n", "41\t156\t404.9\t0\t156\n", "42\t136\t404.9\t0\t136\n", "43\t205\t404.9\t0\t205\n", "44\t71\t404.9\t0\t71\n", "45\t130\t404.9\t0\t130\n", "46\t247\t404.9\t0\t247\n", "47\t97\t404.9\t0\t97\n", "48\t63\t404.9\t0\t63\n", "49\t179\t404.9\t0\t179\n", "50\t86\t404.9\t0\t86\n", "51\t68\t404.9\t0\t68\n", "52\t191\t404.9\t0\t191\n", "53\t102\t404.9\t0\t102\n", "54\t61\t404.9\t0\t61\n", "55\t110\t404.9\t0\t110\n", "56\t74\t404.9\t0\t74\n", "57\t123\t404.9\t0\t123\n", "58\t60\t404.9\t0\t60\n", "59\t49\t404.9\t0\t49\n", "60\t121\t404.9\t0\t121\n", "61\t55\t404.9\t0\t55\n", "62\t65\t404.9\t0\t65\n", "63\t78\t404.9\t0\t78\n", "64\t96\t404.9\t0\t96\n", "65\t33\t404.9\t0\t33\n", "66\t64\t404.9\t0\t64\n", "67\t73\t404.9\t0\t73\n", "68\t69\t404.9\t0\t69\n", "69\t48\t404.9\t0\t48\n", "70\t27\t404.9\t0\t27\n", "71\t58\t404.9\t0\t58\n", "72\t71\t404.9\t0\t71\n", "73\t55\t404.9\t0\t55\n", "74\t84\t404.9\t0\t84\n", "75\t59\t404.9\t0\t59\n", "76\t64\t404.9\t0\t64\n", "77\t67\t404.9\t0\t67\n", "78\t67\t404.9\t0\t67\n", "79\t60\t404.9\t0\t60\n", "80\t94\t404.9\t0\t94\n", "81\t80\t404.9\t0\t80\n", "82\t89\t404.9\t0\t89\n", "83\t104\t404.9\t0\t104\n", "84\t90\t404.9\t0\t90\n", "85\t69\t404.9\t0\t69\n", "86\t56\t404.9\t0\t56\n", "87\t86\t404.9\t0\t86\n", "88\t81\t404.9\t0\t81\n", "89\t64\t404.9\t0\t64\n", "90\t64\t404.9\t0\t64\n", "91\t55\t404.9\t0\t55\n", "92\t57\t404.9\t0\t57\n", "93\t46\t404.9\t0\t46\n", "94\t79\t404.9\t0\t79\n", "95\t55\t404.9\t0\t55\n", "96\t49\t404.9\t0\t49\n", "97\t81\t404.9\t0\t81\n", "98\t69\t404.9\t0\t69\n", "99\t75\t404.9\t0\t75\n", "100\t74\t404.9\t0\t74\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 299_S21_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/299.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 137.41 s (14 us/read; 4.28 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 9,795,350\n", "Reads with adapters: 8,119,763 (82.9%)\n", "Reads written (passing filters): 9,113,464 (93.0%)\n", "\n", "Total basepairs processed: 979,535,000 bp\n", "Quality-trimmed: 3,655,502 bp (0.4%)\n", "Total written (filtered): 602,749,275 bp (61.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 7911939 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 35.4%\n", " G: 41.6%\n", " T: 22.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t98236\t153052.3\t0\t98236\n", "4\t67945\t38263.1\t0\t67945\n", "5\t54647\t9565.8\t0\t54647\n", "6\t51864\t2391.4\t0\t51864\n", "7\t52782\t597.9\t0\t52782\n", "8\t54361\t149.5\t0\t54361\n", "9\t56296\t149.5\t0\t56296\n", "10\t57495\t149.5\t0\t57495\n", "11\t59633\t149.5\t0\t59633\n", "12\t62498\t149.5\t0\t62498\n", "13\t68778\t149.5\t0\t68778\n", "14\t71296\t149.5\t0\t71296\n", "15\t68581\t149.5\t0\t68581\n", "16\t73606\t149.5\t0\t73606\n", "17\t82414\t149.5\t0\t82414\n", "18\t94924\t149.5\t0\t94924\n", "19\t89840\t149.5\t0\t89840\n", "20\t75398\t149.5\t0\t75398\n", "21\t73578\t149.5\t0\t73578\n", "22\t69690\t149.5\t0\t69690\n", "23\t76891\t149.5\t0\t76891\n", "24\t89819\t149.5\t0\t89819\n", "25\t96075\t149.5\t0\t96075\n", "26\t108597\t149.5\t0\t108597\n", "27\t115269\t149.5\t0\t115269\n", "28\t106558\t149.5\t0\t106558\n", "29\t97696\t149.5\t0\t97696\n", "30\t101445\t149.5\t0\t101445\n", "31\t116115\t149.5\t0\t116115\n", "32\t113165\t149.5\t0\t113165\n", "33\t111037\t149.5\t0\t111037\n", "34\t108544\t149.5\t0\t108544\n", "35\t124571\t149.5\t0\t124571\n", "36\t136887\t149.5\t0\t136887\n", "37\t132417\t149.5\t0\t132417\n", "38\t119871\t149.5\t0\t119871\n", "39\t114845\t149.5\t0\t114845\n", "40\t112654\t149.5\t0\t112654\n", "41\t129512\t149.5\t0\t129512\n", "42\t146139\t149.5\t0\t146139\n", "43\t130119\t149.5\t0\t130119\n", "44\t105044\t149.5\t0\t105044\n", "45\t130561\t149.5\t0\t130561\n", "46\t152192\t149.5\t0\t152192\n", "47\t140603\t149.5\t0\t140603\n", "48\t137870\t149.5\t0\t137870\n", "49\t116565\t149.5\t0\t116565\n", "50\t115771\t149.5\t0\t115771\n", "51\t96299\t149.5\t0\t96299\n", "52\t108200\t149.5\t0\t108200\n", "53\t122158\t149.5\t0\t122158\n", "54\t134325\t149.5\t0\t134325\n", "55\t112683\t149.5\t0\t112683\n", "56\t113649\t149.5\t0\t113649\n", "57\t118568\t149.5\t0\t118568\n", "58\t135778\t149.5\t0\t135778\n", "59\t131173\t149.5\t0\t131173\n", "60\t108598\t149.5\t0\t108598\n", "61\t98771\t149.5\t0\t98771\n", "62\t82541\t149.5\t0\t82541\n", "63\t80012\t149.5\t0\t80012\n", "64\t95061\t149.5\t0\t95061\n", "65\t88099\t149.5\t0\t88099\n", "66\t73553\t149.5\t0\t73553\n", "67\t77728\t149.5\t0\t77728\n", "68\t79989\t149.5\t0\t79989\n", "69\t86317\t149.5\t0\t86317\n", "70\t93736\t149.5\t0\t93736\n", "71\t90289\t149.5\t0\t90289\n", "72\t68259\t149.5\t0\t68259\n", "73\t59880\t149.5\t0\t59880\n", "74\t58543\t149.5\t0\t58543\n", "75\t52567\t149.5\t0\t52567\n", "76\t41813\t149.5\t0\t41813\n", "77\t44189\t149.5\t0\t44189\n", "78\t55047\t149.5\t0\t55047\n", "79\t47943\t149.5\t0\t47943\n", "80\t44307\t149.5\t0\t44307\n", "81\t43425\t149.5\t0\t43425\n", "82\t39742\t149.5\t0\t39742\n", "83\t39505\t149.5\t0\t39505\n", "84\t46830\t149.5\t0\t46830\n", "85\t54137\t149.5\t0\t54137\n", "86\t51382\t149.5\t0\t51382\n", "87\t33449\t149.5\t0\t33449\n", "88\t28072\t149.5\t0\t28072\n", "89\t29326\t149.5\t0\t29326\n", "90\t32419\t149.5\t0\t32419\n", "91\t33342\t149.5\t0\t33342\n", "92\t35144\t149.5\t0\t35144\n", "93\t39461\t149.5\t0\t39461\n", "94\t36830\t149.5\t0\t36830\n", "95\t30731\t149.5\t0\t30731\n", "96\t22726\t149.5\t0\t22726\n", "97\t14661\t149.5\t0\t14661\n", "98\t8681\t149.5\t0\t8681\n", "99\t14370\t149.5\t0\t14370\n", "100\t6937\t149.5\t0\t6937\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 92554 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 79.4%\n", " C: 10.2%\n", " G: 0.0%\n", " T: 10.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10687\t153052.3\t0\t10687\n", "4\t4094\t38263.1\t0\t4094\n", "5\t2982\t9565.8\t0\t2982\n", "6\t2519\t2391.4\t0\t2519\n", "7\t1852\t597.9\t0\t1852\n", "8\t1477\t149.5\t0\t1477\n", "9\t1439\t149.5\t0\t1439\n", "10\t1502\t149.5\t0\t1502\n", "11\t1173\t149.5\t0\t1173\n", "12\t1101\t149.5\t0\t1101\n", "13\t1046\t149.5\t0\t1046\n", "14\t1072\t149.5\t0\t1072\n", "15\t1031\t149.5\t0\t1031\n", "16\t968\t149.5\t0\t968\n", "17\t1049\t149.5\t0\t1049\n", "18\t1263\t149.5\t0\t1263\n", "19\t1450\t149.5\t0\t1450\n", "20\t1816\t149.5\t0\t1816\n", "21\t1278\t149.5\t0\t1278\n", "22\t1041\t149.5\t0\t1041\n", "23\t904\t149.5\t0\t904\n", "24\t926\t149.5\t0\t926\n", "25\t1202\t149.5\t0\t1202\n", "26\t1989\t149.5\t0\t1989\n", "27\t1861\t149.5\t0\t1861\n", "28\t2018\t149.5\t0\t2018\n", "29\t2410\t149.5\t0\t2410\n", "30\t3993\t149.5\t0\t3993\n", "31\t4427\t149.5\t0\t4427\n", "32\t5236\t149.5\t0\t5236\n", "33\t5261\t149.5\t0\t5261\n", "34\t5419\t149.5\t0\t5419\n", "35\t6222\t149.5\t0\t6222\n", "36\t6475\t149.5\t0\t6475\n", "37\t1775\t149.5\t0\t1775\n", "38\t73\t149.5\t0\t73\n", "39\t44\t149.5\t0\t44\n", "40\t38\t149.5\t0\t38\n", "41\t42\t149.5\t0\t42\n", "42\t34\t149.5\t0\t34\n", "43\t31\t149.5\t0\t31\n", "44\t35\t149.5\t0\t35\n", "45\t41\t149.5\t0\t41\n", "46\t50\t149.5\t0\t50\n", "47\t40\t149.5\t0\t40\n", "48\t41\t149.5\t0\t41\n", "49\t34\t149.5\t0\t34\n", "50\t44\t149.5\t0\t44\n", "51\t37\t149.5\t0\t37\n", "52\t43\t149.5\t0\t43\n", "53\t37\t149.5\t0\t37\n", "54\t38\t149.5\t0\t38\n", "55\t32\t149.5\t0\t32\n", "56\t35\t149.5\t0\t35\n", "57\t39\t149.5\t0\t39\n", "58\t24\t149.5\t0\t24\n", "59\t22\t149.5\t0\t22\n", "60\t24\t149.5\t0\t24\n", "61\t22\t149.5\t0\t22\n", "62\t22\t149.5\t0\t22\n", "63\t35\t149.5\t0\t35\n", "64\t17\t149.5\t0\t17\n", "65\t18\t149.5\t0\t18\n", "66\t18\t149.5\t0\t18\n", "67\t13\t149.5\t0\t13\n", "68\t19\t149.5\t0\t19\n", "69\t12\t149.5\t0\t12\n", "70\t14\t149.5\t0\t14\n", "71\t8\t149.5\t0\t8\n", "72\t7\t149.5\t0\t7\n", "73\t7\t149.5\t0\t7\n", "74\t6\t149.5\t0\t6\n", "75\t3\t149.5\t0\t3\n", "76\t4\t149.5\t0\t4\n", "77\t5\t149.5\t0\t5\n", "78\t4\t149.5\t0\t4\n", "79\t7\t149.5\t0\t7\n", "80\t3\t149.5\t0\t3\n", "81\t5\t149.5\t0\t5\n", "82\t6\t149.5\t0\t6\n", "83\t11\t149.5\t0\t11\n", "84\t5\t149.5\t0\t5\n", "85\t5\t149.5\t0\t5\n", "86\t10\t149.5\t0\t10\n", "87\t8\t149.5\t0\t8\n", "88\t6\t149.5\t0\t6\n", "89\t8\t149.5\t0\t8\n", "90\t8\t149.5\t0\t8\n", "91\t17\t149.5\t0\t17\n", "92\t15\t149.5\t0\t15\n", "93\t29\t149.5\t0\t29\n", "94\t37\t149.5\t0\t37\n", "95\t54\t149.5\t0\t54\n", "96\t51\t149.5\t0\t51\n", "97\t46\t149.5\t0\t46\n", "98\t58\t149.5\t0\t58\n", "99\t34\t149.5\t0\t34\n", "100\t61\t149.5\t0\t61\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 115270 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.8%\n", " C: 19.9%\n", " G: 20.5%\n", " T: 14.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t49472\t153052.3\t0\t49472\n", "4\t9608\t38263.1\t0\t9608\n", "5\t2450\t9565.8\t0\t2450\n", "6\t1177\t2391.4\t0\t1177\n", "7\t1064\t597.9\t0\t1064\n", "8\t1207\t597.9\t0\t1207\n", "9\t979\t597.9\t0\t979\n", "10\t1032\t597.9\t0\t1032\n", "11\t1144\t597.9\t0\t1144\n", "12\t1141\t597.9\t0\t1141\n", "13\t1231\t597.9\t0\t1231\n", "14\t1070\t597.9\t0\t1070\n", "15\t1298\t597.9\t0\t1298\n", "16\t1209\t597.9\t0\t1209\n", "17\t1223\t597.9\t0\t1223\n", "18\t1234\t597.9\t0\t1234\n", "19\t1074\t597.9\t0\t1074\n", "20\t1255\t597.9\t0\t1255\n", "21\t1146\t597.9\t0\t1146\n", "22\t1091\t597.9\t0\t1091\n", "23\t1065\t597.9\t0\t1065\n", "24\t952\t597.9\t0\t952\n", "25\t999\t597.9\t0\t999\n", "26\t985\t597.9\t0\t985\n", "27\t1095\t597.9\t0\t1095\n", "28\t1039\t597.9\t0\t1039\n", "29\t1000\t597.9\t0\t1000\n", "30\t1007\t597.9\t0\t1007\n", "31\t925\t597.9\t0\t925\n", "32\t1023\t597.9\t0\t1023\n", "33\t950\t597.9\t0\t950\n", "34\t1049\t597.9\t0\t1049\n", "35\t966\t597.9\t0\t966\n", "36\t934\t597.9\t0\t934\n", "37\t873\t597.9\t0\t873\n", "38\t866\t597.9\t0\t866\n", "39\t945\t597.9\t0\t945\n", "40\t791\t597.9\t0\t791\n", "41\t760\t597.9\t0\t760\n", "42\t747\t597.9\t0\t747\n", "43\t1127\t597.9\t0\t1127\n", "44\t195\t597.9\t0\t195\n", "45\t649\t597.9\t0\t649\n", "46\t696\t597.9\t0\t696\n", "47\t657\t597.9\t0\t657\n", "48\t461\t597.9\t0\t461\n", "49\t621\t597.9\t0\t621\n", "50\t529\t597.9\t0\t529\n", "51\t534\t597.9\t0\t534\n", "52\t511\t597.9\t0\t511\n", "53\t569\t597.9\t0\t569\n", "54\t438\t597.9\t0\t438\n", "55\t540\t597.9\t0\t540\n", "56\t431\t597.9\t0\t431\n", "57\t361\t597.9\t0\t361\n", "58\t494\t597.9\t0\t494\n", "59\t247\t597.9\t0\t247\n", "60\t396\t597.9\t0\t396\n", "61\t419\t597.9\t0\t419\n", "62\t370\t597.9\t0\t370\n", "63\t318\t597.9\t0\t318\n", "64\t339\t597.9\t0\t339\n", "65\t223\t597.9\t0\t223\n", "66\t319\t597.9\t0\t319\n", "67\t301\t597.9\t0\t301\n", "68\t401\t597.9\t0\t401\n", "69\t104\t597.9\t0\t104\n", "70\t97\t597.9\t0\t97\n", "71\t199\t597.9\t0\t199\n", "72\t219\t597.9\t0\t219\n", "73\t177\t597.9\t0\t177\n", "74\t191\t597.9\t0\t191\n", "75\t141\t597.9\t0\t141\n", "76\t136\t597.9\t0\t136\n", "77\t99\t597.9\t0\t99\n", "78\t93\t597.9\t0\t93\n", "79\t79\t597.9\t0\t79\n", "80\t77\t597.9\t0\t77\n", "81\t87\t597.9\t0\t87\n", "82\t101\t597.9\t0\t101\n", "83\t64\t597.9\t0\t64\n", "84\t122\t597.9\t0\t122\n", "85\t80\t597.9\t0\t80\n", "86\t59\t597.9\t0\t59\n", "87\t96\t597.9\t0\t96\n", "88\t119\t597.9\t0\t119\n", "89\t88\t597.9\t0\t88\n", "90\t81\t597.9\t0\t81\n", "91\t58\t597.9\t0\t58\n", "92\t36\t597.9\t0\t36\n", "93\t61\t597.9\t0\t61\n", "94\t54\t597.9\t0\t54\n", "95\t50\t597.9\t0\t50\n", "96\t37\t597.9\t0\t37\n", "97\t48\t597.9\t0\t48\n", "98\t66\t597.9\t0\t66\n", "99\t63\t597.9\t0\t63\n", "100\t66\t597.9\t0\t66\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 301_S22_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/301.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 102.74 s (14 us/read; 4.32 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,403,289\n", "Reads with adapters: 5,678,554 (76.7%)\n", "Reads written (passing filters): 7,081,848 (95.7%)\n", "\n", "Total basepairs processed: 740,328,900 bp\n", "Quality-trimmed: 2,473,774 bp (0.3%)\n", "Total written (filtered): 501,038,625 bp (67.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5558749 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 34.2%\n", " G: 39.6%\n", " T: 26.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t101929\t115676.4\t0\t101929\n", "4\t67841\t28919.1\t0\t67841\n", "5\t53865\t7229.8\t0\t53865\n", "6\t48745\t1807.4\t0\t48745\n", "7\t48364\t451.9\t0\t48364\n", "8\t48858\t113.0\t0\t48858\n", "9\t49290\t113.0\t0\t49290\n", "10\t49852\t113.0\t0\t49852\n", "11\t50991\t113.0\t0\t50991\n", "12\t52715\t113.0\t0\t52715\n", "13\t57060\t113.0\t0\t57060\n", "14\t58884\t113.0\t0\t58884\n", "15\t57727\t113.0\t0\t57727\n", "16\t61455\t113.0\t0\t61455\n", "17\t68939\t113.0\t0\t68939\n", "18\t77596\t113.0\t0\t77596\n", "19\t70092\t113.0\t0\t70092\n", "20\t60998\t113.0\t0\t60998\n", "21\t58500\t113.0\t0\t58500\n", "22\t55128\t113.0\t0\t55128\n", "23\t61140\t113.0\t0\t61140\n", "24\t71250\t113.0\t0\t71250\n", "25\t75830\t113.0\t0\t75830\n", "26\t85632\t113.0\t0\t85632\n", "27\t90643\t113.0\t0\t90643\n", "28\t81854\t113.0\t0\t81854\n", "29\t77193\t113.0\t0\t77193\n", "30\t76900\t113.0\t0\t76900\n", "31\t85149\t113.0\t0\t85149\n", "32\t88206\t113.0\t0\t88206\n", "33\t85288\t113.0\t0\t85288\n", "34\t84345\t113.0\t0\t84345\n", "35\t94421\t113.0\t0\t94421\n", "36\t103408\t113.0\t0\t103408\n", "37\t101494\t113.0\t0\t101494\n", "38\t91540\t113.0\t0\t91540\n", "39\t87040\t113.0\t0\t87040\n", "40\t85035\t113.0\t0\t85035\n", "41\t97419\t113.0\t0\t97419\n", "42\t110305\t113.0\t0\t110305\n", "43\t98394\t113.0\t0\t98394\n", "44\t79485\t113.0\t0\t79485\n", "45\t96523\t113.0\t0\t96523\n", "46\t118006\t113.0\t0\t118006\n", "47\t108332\t113.0\t0\t108332\n", "48\t106167\t113.0\t0\t106167\n", "49\t91754\t113.0\t0\t91754\n", "50\t87222\t113.0\t0\t87222\n", "51\t74138\t113.0\t0\t74138\n", "52\t71477\t113.0\t0\t71477\n", "53\t73206\t113.0\t0\t73206\n", "54\t82637\t113.0\t0\t82637\n", "55\t89835\t113.0\t0\t89835\n", "56\t80435\t113.0\t0\t80435\n", "57\t79237\t113.0\t0\t79237\n", "58\t79882\t113.0\t0\t79882\n", "59\t65178\t113.0\t0\t65178\n", "60\t59552\t113.0\t0\t59552\n", "61\t56419\t113.0\t0\t56419\n", "62\t47100\t113.0\t0\t47100\n", "63\t44479\t113.0\t0\t44479\n", "64\t52584\t113.0\t0\t52584\n", "65\t52291\t113.0\t0\t52291\n", "66\t44261\t113.0\t0\t44261\n", "67\t45334\t113.0\t0\t45334\n", "68\t46122\t113.0\t0\t46122\n", "69\t48029\t113.0\t0\t48029\n", "70\t49019\t113.0\t0\t49019\n", "71\t46820\t113.0\t0\t46820\n", "72\t36658\t113.0\t0\t36658\n", "73\t32178\t113.0\t0\t32178\n", "74\t32018\t113.0\t0\t32018\n", "75\t28713\t113.0\t0\t28713\n", "76\t23308\t113.0\t0\t23308\n", "77\t22020\t113.0\t0\t22020\n", "78\t26124\t113.0\t0\t26124\n", "79\t24398\t113.0\t0\t24398\n", "80\t23142\t113.0\t0\t23142\n", "81\t22181\t113.0\t0\t22181\n", "82\t20315\t113.0\t0\t20315\n", "83\t20420\t113.0\t0\t20420\n", "84\t23363\t113.0\t0\t23363\n", "85\t25901\t113.0\t0\t25901\n", "86\t23896\t113.0\t0\t23896\n", "87\t16137\t113.0\t0\t16137\n", "88\t14149\t113.0\t0\t14149\n", "89\t14959\t113.0\t0\t14959\n", "90\t15545\t113.0\t0\t15545\n", "91\t15701\t113.0\t0\t15701\n", "92\t16251\t113.0\t0\t16251\n", "93\t18098\t113.0\t0\t18098\n", "94\t16151\t113.0\t0\t16151\n", "95\t13428\t113.0\t0\t13428\n", "96\t9843\t113.0\t0\t9843\n", "97\t6221\t113.0\t0\t6221\n", "98\t3726\t113.0\t0\t3726\n", "99\t4881\t113.0\t0\t4881\n", "100\t2185\t113.0\t0\t2185\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 32907 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 65.7%\n", " C: 17.3%\n", " G: 0.0%\n", " T: 16.9%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t8672\t115676.4\t0\t8672\n", "4\t2485\t28919.1\t0\t2485\n", "5\t1405\t7229.8\t0\t1405\n", "6\t1182\t1807.4\t0\t1182\n", "7\t606\t451.9\t0\t606\n", "8\t456\t113.0\t0\t456\n", "9\t427\t113.0\t0\t427\n", "10\t419\t113.0\t0\t419\n", "11\t403\t113.0\t0\t403\n", "12\t346\t113.0\t0\t346\n", "13\t356\t113.0\t0\t356\n", "14\t304\t113.0\t0\t304\n", "15\t299\t113.0\t0\t299\n", "16\t317\t113.0\t0\t317\n", "17\t351\t113.0\t0\t351\n", "18\t444\t113.0\t0\t444\n", "19\t479\t113.0\t0\t479\n", "20\t726\t113.0\t0\t726\n", "21\t540\t113.0\t0\t540\n", "22\t389\t113.0\t0\t389\n", "23\t285\t113.0\t0\t285\n", "24\t306\t113.0\t0\t306\n", "25\t319\t113.0\t0\t319\n", "26\t576\t113.0\t0\t576\n", "27\t475\t113.0\t0\t475\n", "28\t454\t113.0\t0\t454\n", "29\t473\t113.0\t0\t473\n", "30\t779\t113.0\t0\t779\n", "31\t850\t113.0\t0\t850\n", "32\t1196\t113.0\t0\t1196\n", "33\t1051\t113.0\t0\t1051\n", "34\t1110\t113.0\t0\t1110\n", "35\t1311\t113.0\t0\t1311\n", "36\t1268\t113.0\t0\t1268\n", "37\t461\t113.0\t0\t461\n", "38\t44\t113.0\t0\t44\n", "39\t36\t113.0\t0\t36\n", "40\t33\t113.0\t0\t33\n", "41\t27\t113.0\t0\t27\n", "42\t29\t113.0\t0\t29\n", "43\t25\t113.0\t0\t25\n", "44\t31\t113.0\t0\t31\n", "45\t42\t113.0\t0\t42\n", "46\t25\t113.0\t0\t25\n", "47\t47\t113.0\t0\t47\n", "48\t36\t113.0\t0\t36\n", "49\t30\t113.0\t0\t30\n", "50\t32\t113.0\t0\t32\n", "51\t28\t113.0\t0\t28\n", "52\t29\t113.0\t0\t29\n", "53\t34\t113.0\t0\t34\n", "54\t29\t113.0\t0\t29\n", "55\t24\t113.0\t0\t24\n", "56\t28\t113.0\t0\t28\n", "57\t28\t113.0\t0\t28\n", "58\t21\t113.0\t0\t21\n", "59\t22\t113.0\t0\t22\n", "60\t24\t113.0\t0\t24\n", "61\t20\t113.0\t0\t20\n", "62\t21\t113.0\t0\t21\n", "63\t21\t113.0\t0\t21\n", "64\t19\t113.0\t0\t19\n", "65\t20\t113.0\t0\t20\n", "66\t20\t113.0\t0\t20\n", "67\t13\t113.0\t0\t13\n", "68\t14\t113.0\t0\t14\n", "69\t19\t113.0\t0\t19\n", "70\t7\t113.0\t0\t7\n", "71\t13\t113.0\t0\t13\n", "72\t9\t113.0\t0\t9\n", "73\t8\t113.0\t0\t8\n", "74\t3\t113.0\t0\t3\n", "75\t6\t113.0\t0\t6\n", "76\t6\t113.0\t0\t6\n", "77\t6\t113.0\t0\t6\n", "78\t6\t113.0\t0\t6\n", "79\t6\t113.0\t0\t6\n", "80\t6\t113.0\t0\t6\n", "81\t7\t113.0\t0\t7\n", "82\t6\t113.0\t0\t6\n", "83\t6\t113.0\t0\t6\n", "84\t5\t113.0\t0\t5\n", "85\t9\t113.0\t0\t9\n", "86\t9\t113.0\t0\t9\n", "87\t15\t113.0\t0\t15\n", "88\t5\t113.0\t0\t5\n", "89\t7\t113.0\t0\t7\n", "90\t21\t113.0\t0\t21\n", "91\t7\t113.0\t0\t7\n", "92\t29\t113.0\t0\t29\n", "93\t29\t113.0\t0\t29\n", "94\t46\t113.0\t0\t46\n", "95\t47\t113.0\t0\t47\n", "96\t42\t113.0\t0\t42\n", "97\t37\t113.0\t0\t37\n", "98\t38\t113.0\t0\t38\n", "99\t21\t113.0\t0\t21\n", "100\t54\t113.0\t0\t54\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 86898 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.8%\n", " C: 19.8%\n", " G: 18.3%\n", " T: 18.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t47178\t115676.4\t0\t47178\n", "4\t10084\t28919.1\t0\t10084\n", "5\t2000\t7229.8\t0\t2000\n", "6\t648\t1807.4\t0\t648\n", "7\t549\t451.9\t0\t549\n", "8\t534\t451.9\t0\t534\n", "9\t548\t451.9\t0\t548\n", "10\t528\t451.9\t0\t528\n", "11\t625\t451.9\t0\t625\n", "12\t505\t451.9\t0\t505\n", "13\t564\t451.9\t0\t564\n", "14\t608\t451.9\t0\t608\n", "15\t656\t451.9\t0\t656\n", "16\t659\t451.9\t0\t659\n", "17\t661\t451.9\t0\t661\n", "18\t666\t451.9\t0\t666\n", "19\t594\t451.9\t0\t594\n", "20\t635\t451.9\t0\t635\n", "21\t599\t451.9\t0\t599\n", "22\t551\t451.9\t0\t551\n", "23\t522\t451.9\t0\t522\n", "24\t532\t451.9\t0\t532\n", "25\t540\t451.9\t0\t540\n", "26\t486\t451.9\t0\t486\n", "27\t534\t451.9\t0\t534\n", "28\t521\t451.9\t0\t521\n", "29\t552\t451.9\t0\t552\n", "30\t542\t451.9\t0\t542\n", "31\t498\t451.9\t0\t498\n", "32\t542\t451.9\t0\t542\n", "33\t531\t451.9\t0\t531\n", "34\t504\t451.9\t0\t504\n", "35\t497\t451.9\t0\t497\n", "36\t453\t451.9\t0\t453\n", "37\t480\t451.9\t0\t480\n", "38\t388\t451.9\t0\t388\n", "39\t420\t451.9\t0\t420\n", "40\t430\t451.9\t0\t430\n", "41\t441\t451.9\t0\t441\n", "42\t356\t451.9\t0\t356\n", "43\t591\t451.9\t0\t591\n", "44\t115\t451.9\t0\t115\n", "45\t349\t451.9\t0\t349\n", "46\t340\t451.9\t0\t340\n", "47\t269\t451.9\t0\t269\n", "48\t273\t451.9\t0\t273\n", "49\t279\t451.9\t0\t279\n", "50\t258\t451.9\t0\t258\n", "51\t248\t451.9\t0\t248\n", "52\t247\t451.9\t0\t247\n", "53\t252\t451.9\t0\t252\n", "54\t228\t451.9\t0\t228\n", "55\t201\t451.9\t0\t201\n", "56\t215\t451.9\t0\t215\n", "57\t154\t451.9\t0\t154\n", "58\t230\t451.9\t0\t230\n", "59\t131\t451.9\t0\t131\n", "60\t161\t451.9\t0\t161\n", "61\t164\t451.9\t0\t164\n", "62\t171\t451.9\t0\t171\n", "63\t176\t451.9\t0\t176\n", "64\t112\t451.9\t0\t112\n", "65\t108\t451.9\t0\t108\n", "66\t102\t451.9\t0\t102\n", "67\t124\t451.9\t0\t124\n", "68\t166\t451.9\t0\t166\n", "69\t46\t451.9\t0\t46\n", "70\t46\t451.9\t0\t46\n", "71\t86\t451.9\t0\t86\n", "72\t106\t451.9\t0\t106\n", "73\t85\t451.9\t0\t85\n", "74\t85\t451.9\t0\t85\n", "75\t69\t451.9\t0\t69\n", "76\t81\t451.9\t0\t81\n", "77\t64\t451.9\t0\t64\n", "78\t59\t451.9\t0\t59\n", "79\t56\t451.9\t0\t56\n", "80\t58\t451.9\t0\t58\n", "81\t61\t451.9\t0\t61\n", "82\t81\t451.9\t0\t81\n", "83\t66\t451.9\t0\t66\n", "84\t106\t451.9\t0\t106\n", "85\t77\t451.9\t0\t77\n", "86\t85\t451.9\t0\t85\n", "87\t104\t451.9\t0\t104\n", "88\t60\t451.9\t0\t60\n", "89\t68\t451.9\t0\t68\n", "90\t54\t451.9\t0\t54\n", "91\t46\t451.9\t0\t46\n", "92\t38\t451.9\t0\t38\n", "93\t33\t451.9\t0\t33\n", "94\t53\t451.9\t0\t53\n", "95\t47\t451.9\t0\t47\n", "96\t38\t451.9\t0\t38\n", "97\t45\t451.9\t0\t45\n", "98\t48\t451.9\t0\t48\n", "99\t56\t451.9\t0\t56\n", "100\t66\t451.9\t0\t66\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 302_S15_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/302.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 150.61 s (15 us/read; 4.07 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 10,211,834\n", "Reads with adapters: 7,750,124 (75.9%)\n", "Reads written (passing filters): 9,834,992 (96.3%)\n", "\n", "Total basepairs processed: 1,021,183,400 bp\n", "Quality-trimmed: 3,492,057 bp (0.3%)\n", "Total written (filtered): 703,673,362 bp (68.9%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 7600837 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 34.6%\n", " G: 38.6%\n", " T: 26.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t152372\t159559.9\t0\t152372\n", "4\t101561\t39890.0\t0\t101561\n", "5\t84074\t9972.5\t0\t84074\n", "6\t74416\t2493.1\t0\t74416\n", "7\t71987\t623.3\t0\t71987\n", "8\t74619\t155.8\t0\t74619\n", "9\t74628\t155.8\t0\t74628\n", "10\t74392\t155.8\t0\t74392\n", "11\t74747\t155.8\t0\t74747\n", "12\t76459\t155.8\t0\t76459\n", "13\t77428\t155.8\t0\t77428\n", "14\t81537\t155.8\t0\t81537\n", "15\t81576\t155.8\t0\t81576\n", "16\t86658\t155.8\t0\t86658\n", "17\t98205\t155.8\t0\t98205\n", "18\t112696\t155.8\t0\t112696\n", "19\t101997\t155.8\t0\t101997\n", "20\t86423\t155.8\t0\t86423\n", "21\t84458\t155.8\t0\t84458\n", "22\t78913\t155.8\t0\t78913\n", "23\t88304\t155.8\t0\t88304\n", "24\t102264\t155.8\t0\t102264\n", "25\t106760\t155.8\t0\t106760\n", "26\t121297\t155.8\t0\t121297\n", "27\t129947\t155.8\t0\t129947\n", "28\t117049\t155.8\t0\t117049\n", "29\t109408\t155.8\t0\t109408\n", "30\t109174\t155.8\t0\t109174\n", "31\t121645\t155.8\t0\t121645\n", "32\t123822\t155.8\t0\t123822\n", "33\t117530\t155.8\t0\t117530\n", "34\t113551\t155.8\t0\t113551\n", "35\t130041\t155.8\t0\t130041\n", "36\t143382\t155.8\t0\t143382\n", "37\t139937\t155.8\t0\t139937\n", "38\t128254\t155.8\t0\t128254\n", "39\t109776\t155.8\t0\t109776\n", "40\t109515\t155.8\t0\t109515\n", "41\t126736\t155.8\t0\t126736\n", "42\t142009\t155.8\t0\t142009\n", "43\t127247\t155.8\t0\t127247\n", "44\t102429\t155.8\t0\t102429\n", "45\t126930\t155.8\t0\t126930\n", "46\t153570\t155.8\t0\t153570\n", "47\t145932\t155.8\t0\t145932\n", "48\t138827\t155.8\t0\t138827\n", "49\t118511\t155.8\t0\t118511\n", "50\t111467\t155.8\t0\t111467\n", "51\t111761\t155.8\t0\t111761\n", "52\t119128\t155.8\t0\t119128\n", "53\t116774\t155.8\t0\t116774\n", "54\t105004\t155.8\t0\t105004\n", "55\t110762\t155.8\t0\t110762\n", "56\t92543\t155.8\t0\t92543\n", "57\t106417\t155.8\t0\t106417\n", "58\t123306\t155.8\t0\t123306\n", "59\t98961\t155.8\t0\t98961\n", "60\t82248\t155.8\t0\t82248\n", "61\t79030\t155.8\t0\t79030\n", "62\t66339\t155.8\t0\t66339\n", "63\t63160\t155.8\t0\t63160\n", "64\t75232\t155.8\t0\t75232\n", "65\t71415\t155.8\t0\t71415\n", "66\t56409\t155.8\t0\t56409\n", "67\t58556\t155.8\t0\t58556\n", "68\t58510\t155.8\t0\t58510\n", "69\t60726\t155.8\t0\t60726\n", "70\t63794\t155.8\t0\t63794\n", "71\t61292\t155.8\t0\t61292\n", "72\t46439\t155.8\t0\t46439\n", "73\t40618\t155.8\t0\t40618\n", "74\t39727\t155.8\t0\t39727\n", "75\t35685\t155.8\t0\t35685\n", "76\t27554\t155.8\t0\t27554\n", "77\t26995\t155.8\t0\t26995\n", "78\t32489\t155.8\t0\t32489\n", "79\t28554\t155.8\t0\t28554\n", "80\t26040\t155.8\t0\t26040\n", "81\t24985\t155.8\t0\t24985\n", "82\t23589\t155.8\t0\t23589\n", "83\t23369\t155.8\t0\t23369\n", "84\t27363\t155.8\t0\t27363\n", "85\t31394\t155.8\t0\t31394\n", "86\t30195\t155.8\t0\t30195\n", "87\t20163\t155.8\t0\t20163\n", "88\t16962\t155.8\t0\t16962\n", "89\t17626\t155.8\t0\t17626\n", "90\t18653\t155.8\t0\t18653\n", "91\t18487\t155.8\t0\t18487\n", "92\t18741\t155.8\t0\t18741\n", "93\t20080\t155.8\t0\t20080\n", "94\t18294\t155.8\t0\t18294\n", "95\t15000\t155.8\t0\t15000\n", "96\t10862\t155.8\t0\t10862\n", "97\t6507\t155.8\t0\t6507\n", "98\t3590\t155.8\t0\t3590\n", "99\t3162\t155.8\t0\t3162\n", "100\t1887\t155.8\t0\t1887\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 33973 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 60.9%\n", " C: 16.7%\n", " G: 0.0%\n", " T: 22.2%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10787\t159559.9\t0\t10787\n", "4\t2875\t39890.0\t0\t2875\n", "5\t1087\t9972.5\t0\t1087\n", "6\t670\t2493.1\t0\t670\n", "7\t306\t623.3\t0\t306\n", "8\t233\t155.8\t0\t233\n", "9\t255\t155.8\t0\t255\n", "10\t261\t155.8\t0\t261\n", "11\t190\t155.8\t0\t190\n", "12\t199\t155.8\t0\t199\n", "13\t193\t155.8\t0\t193\n", "14\t190\t155.8\t0\t190\n", "15\t187\t155.8\t0\t187\n", "16\t176\t155.8\t0\t176\n", "17\t182\t155.8\t0\t182\n", "18\t216\t155.8\t0\t216\n", "19\t247\t155.8\t0\t247\n", "20\t267\t155.8\t0\t267\n", "21\t222\t155.8\t0\t222\n", "22\t176\t155.8\t0\t176\n", "23\t175\t155.8\t0\t175\n", "24\t182\t155.8\t0\t182\n", "25\t249\t155.8\t0\t249\n", "26\t374\t155.8\t0\t374\n", "27\t317\t155.8\t0\t317\n", "28\t380\t155.8\t0\t380\n", "29\t522\t155.8\t0\t522\n", "30\t886\t155.8\t0\t886\n", "31\t1020\t155.8\t0\t1020\n", "32\t1440\t155.8\t0\t1440\n", "33\t1432\t155.8\t0\t1432\n", "34\t1545\t155.8\t0\t1545\n", "35\t1797\t155.8\t0\t1797\n", "36\t1553\t155.8\t0\t1553\n", "37\t615\t155.8\t0\t615\n", "38\t59\t155.8\t0\t59\n", "39\t67\t155.8\t0\t67\n", "40\t55\t155.8\t0\t55\n", "41\t63\t155.8\t0\t63\n", "42\t60\t155.8\t0\t60\n", "43\t51\t155.8\t0\t51\n", "44\t68\t155.8\t0\t68\n", "45\t44\t155.8\t0\t44\n", "46\t53\t155.8\t0\t53\n", "47\t46\t155.8\t0\t46\n", "48\t70\t155.8\t0\t70\n", "49\t62\t155.8\t0\t62\n", "50\t52\t155.8\t0\t52\n", "51\t48\t155.8\t0\t48\n", "52\t43\t155.8\t0\t43\n", "53\t42\t155.8\t0\t42\n", "54\t42\t155.8\t0\t42\n", "55\t52\t155.8\t0\t52\n", "56\t52\t155.8\t0\t52\n", "57\t43\t155.8\t0\t43\n", "58\t32\t155.8\t0\t32\n", "59\t38\t155.8\t0\t38\n", "60\t35\t155.8\t0\t35\n", "61\t38\t155.8\t0\t38\n", "62\t36\t155.8\t0\t36\n", "63\t30\t155.8\t0\t30\n", "64\t42\t155.8\t0\t42\n", "65\t38\t155.8\t0\t38\n", "66\t31\t155.8\t0\t31\n", "67\t22\t155.8\t0\t22\n", "68\t20\t155.8\t0\t20\n", "69\t34\t155.8\t0\t34\n", "70\t26\t155.8\t0\t26\n", "71\t19\t155.8\t0\t19\n", "72\t13\t155.8\t0\t13\n", "73\t9\t155.8\t0\t9\n", "74\t18\t155.8\t0\t18\n", "75\t12\t155.8\t0\t12\n", "76\t19\t155.8\t0\t19\n", "77\t12\t155.8\t0\t12\n", "78\t10\t155.8\t0\t10\n", "79\t16\t155.8\t0\t16\n", "80\t16\t155.8\t0\t16\n", "81\t21\t155.8\t0\t21\n", "82\t20\t155.8\t0\t20\n", "83\t21\t155.8\t0\t21\n", "84\t12\t155.8\t0\t12\n", "85\t22\t155.8\t0\t22\n", "86\t20\t155.8\t0\t20\n", "87\t10\t155.8\t0\t10\n", "88\t23\t155.8\t0\t23\n", "89\t27\t155.8\t0\t27\n", "90\t21\t155.8\t0\t21\n", "91\t32\t155.8\t0\t32\n", "92\t55\t155.8\t0\t55\n", "93\t58\t155.8\t0\t58\n", "94\t62\t155.8\t0\t62\n", "95\t100\t155.8\t0\t100\n", "96\t123\t155.8\t0\t123\n", "97\t98\t155.8\t0\t98\n", "98\t66\t155.8\t0\t66\n", "99\t47\t155.8\t0\t47\n", "100\t91\t155.8\t0\t91\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 115314 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.4%\n", " C: 19.5%\n", " G: 17.1%\n", " T: 19.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t70876\t159559.9\t0\t70876\n", "4\t16164\t39890.0\t0\t16164\n", "5\t3371\t9972.5\t0\t3371\n", "6\t717\t2493.1\t0\t717\n", "7\t425\t623.3\t0\t425\n", "8\t565\t623.3\t0\t565\n", "9\t530\t623.3\t0\t530\n", "10\t512\t623.3\t0\t512\n", "11\t553\t623.3\t0\t553\n", "12\t562\t623.3\t0\t562\n", "13\t513\t623.3\t0\t513\n", "14\t571\t623.3\t0\t571\n", "15\t560\t623.3\t0\t560\n", "16\t546\t623.3\t0\t546\n", "17\t592\t623.3\t0\t592\n", "18\t578\t623.3\t0\t578\n", "19\t516\t623.3\t0\t516\n", "20\t564\t623.3\t0\t564\n", "21\t516\t623.3\t0\t516\n", "22\t533\t623.3\t0\t533\n", "23\t480\t623.3\t0\t480\n", "24\t470\t623.3\t0\t470\n", "25\t509\t623.3\t0\t509\n", "26\t456\t623.3\t0\t456\n", "27\t521\t623.3\t0\t521\n", "28\t463\t623.3\t0\t463\n", "29\t461\t623.3\t0\t461\n", "30\t501\t623.3\t0\t501\n", "31\t432\t623.3\t0\t432\n", "32\t425\t623.3\t0\t425\n", "33\t488\t623.3\t0\t488\n", "34\t461\t623.3\t0\t461\n", "35\t439\t623.3\t0\t439\n", "36\t387\t623.3\t0\t387\n", "37\t328\t623.3\t0\t328\n", "38\t356\t623.3\t0\t356\n", "39\t355\t623.3\t0\t355\n", "40\t310\t623.3\t0\t310\n", "41\t366\t623.3\t0\t366\n", "42\t270\t623.3\t0\t270\n", "43\t441\t623.3\t0\t441\n", "44\t104\t623.3\t0\t104\n", "45\t262\t623.3\t0\t262\n", "46\t267\t623.3\t0\t267\n", "47\t244\t623.3\t0\t244\n", "48\t198\t623.3\t0\t198\n", "49\t217\t623.3\t0\t217\n", "50\t184\t623.3\t0\t184\n", "51\t199\t623.3\t0\t199\n", "52\t210\t623.3\t0\t210\n", "53\t218\t623.3\t0\t218\n", "54\t156\t623.3\t0\t156\n", "55\t190\t623.3\t0\t190\n", "56\t163\t623.3\t0\t163\n", "57\t124\t623.3\t0\t124\n", "58\t162\t623.3\t0\t162\n", "59\t102\t623.3\t0\t102\n", "60\t157\t623.3\t0\t157\n", "61\t166\t623.3\t0\t166\n", "62\t121\t623.3\t0\t121\n", "63\t110\t623.3\t0\t110\n", "64\t109\t623.3\t0\t109\n", "65\t89\t623.3\t0\t89\n", "66\t88\t623.3\t0\t88\n", "67\t99\t623.3\t0\t99\n", "68\t118\t623.3\t0\t118\n", "69\t67\t623.3\t0\t67\n", "70\t65\t623.3\t0\t65\n", "71\t66\t623.3\t0\t66\n", "72\t76\t623.3\t0\t76\n", "73\t105\t623.3\t0\t105\n", "74\t85\t623.3\t0\t85\n", "75\t80\t623.3\t0\t80\n", "76\t98\t623.3\t0\t98\n", "77\t72\t623.3\t0\t72\n", "78\t83\t623.3\t0\t83\n", "79\t98\t623.3\t0\t98\n", "80\t102\t623.3\t0\t102\n", "81\t108\t623.3\t0\t108\n", "82\t116\t623.3\t0\t116\n", "83\t113\t623.3\t0\t113\n", "84\t91\t623.3\t0\t91\n", "85\t90\t623.3\t0\t90\n", "86\t61\t623.3\t0\t61\n", "87\t105\t623.3\t0\t105\n", "88\t87\t623.3\t0\t87\n", "89\t73\t623.3\t0\t73\n", "90\t74\t623.3\t0\t74\n", "91\t59\t623.3\t0\t59\n", "92\t50\t623.3\t0\t50\n", "93\t65\t623.3\t0\t65\n", "94\t56\t623.3\t0\t56\n", "95\t52\t623.3\t0\t52\n", "96\t47\t623.3\t0\t47\n", "97\t68\t623.3\t0\t68\n", "98\t87\t623.3\t0\t87\n", "99\t74\t623.3\t0\t74\n", "100\t101\t623.3\t0\t101\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 303_S17_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/303.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 106.74 s (14 us/read; 4.40 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,834,141\n", "Reads with adapters: 5,013,666 (64.0%)\n", "Reads written (passing filters): 7,583,861 (96.8%)\n", "\n", "Total basepairs processed: 783,414,100 bp\n", "Quality-trimmed: 2,306,906 bp (0.3%)\n", "Total written (filtered): 592,266,925 bp (75.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4840634 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.4%\n", " G: 38.4%\n", " T: 28.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t155543\t122408.5\t0\t155543\n", "4\t93846\t30602.1\t0\t93846\n", "5\t71049\t7650.5\t0\t71049\n", "6\t61540\t1912.6\t0\t61540\n", "7\t57272\t478.2\t0\t57272\n", "8\t58031\t119.5\t0\t58031\n", "9\t57466\t119.5\t0\t57466\n", "10\t56446\t119.5\t0\t56446\n", "11\t57037\t119.5\t0\t57037\n", "12\t56803\t119.5\t0\t56803\n", "13\t56889\t119.5\t0\t56889\n", "14\t60315\t119.5\t0\t60315\n", "15\t59358\t119.5\t0\t59358\n", "16\t62512\t119.5\t0\t62512\n", "17\t69096\t119.5\t0\t69096\n", "18\t77414\t119.5\t0\t77414\n", "19\t70715\t119.5\t0\t70715\n", "20\t59474\t119.5\t0\t59474\n", "21\t57967\t119.5\t0\t57967\n", "22\t53827\t119.5\t0\t53827\n", "23\t59208\t119.5\t0\t59208\n", "24\t68463\t119.5\t0\t68463\n", "25\t70994\t119.5\t0\t70994\n", "26\t79568\t119.5\t0\t79568\n", "27\t85584\t119.5\t0\t85584\n", "28\t77139\t119.5\t0\t77139\n", "29\t73682\t119.5\t0\t73682\n", "30\t72644\t119.5\t0\t72644\n", "31\t79528\t119.5\t0\t79528\n", "32\t79406\t119.5\t0\t79406\n", "33\t75017\t119.5\t0\t75017\n", "34\t72204\t119.5\t0\t72204\n", "35\t80513\t119.5\t0\t80513\n", "36\t88507\t119.5\t0\t88507\n", "37\t88041\t119.5\t0\t88041\n", "38\t77962\t119.5\t0\t77962\n", "39\t71105\t119.5\t0\t71105\n", "40\t68066\t119.5\t0\t68066\n", "41\t76700\t119.5\t0\t76700\n", "42\t84911\t119.5\t0\t84911\n", "43\t75956\t119.5\t0\t75956\n", "44\t62062\t119.5\t0\t62062\n", "45\t76044\t119.5\t0\t76044\n", "46\t91256\t119.5\t0\t91256\n", "47\t81405\t119.5\t0\t81405\n", "48\t81746\t119.5\t0\t81746\n", "49\t69746\t119.5\t0\t69746\n", "50\t69328\t119.5\t0\t69328\n", "51\t61383\t119.5\t0\t61383\n", "52\t61152\t119.5\t0\t61152\n", "53\t55405\t119.5\t0\t55405\n", "54\t60416\t119.5\t0\t60416\n", "55\t67872\t119.5\t0\t67872\n", "56\t59296\t119.5\t0\t59296\n", "57\t54246\t119.5\t0\t54246\n", "58\t58985\t119.5\t0\t58985\n", "59\t52077\t119.5\t0\t52077\n", "60\t44401\t119.5\t0\t44401\n", "61\t42168\t119.5\t0\t42168\n", "62\t35261\t119.5\t0\t35261\n", "63\t32940\t119.5\t0\t32940\n", "64\t37792\t119.5\t0\t37792\n", "65\t37368\t119.5\t0\t37368\n", "66\t31643\t119.5\t0\t31643\n", "67\t31625\t119.5\t0\t31625\n", "68\t31141\t119.5\t0\t31141\n", "69\t31832\t119.5\t0\t31832\n", "70\t32418\t119.5\t0\t32418\n", "71\t31335\t119.5\t0\t31335\n", "72\t24641\t119.5\t0\t24641\n", "73\t21910\t119.5\t0\t21910\n", "74\t22129\t119.5\t0\t22129\n", "75\t19800\t119.5\t0\t19800\n", "76\t16329\t119.5\t0\t16329\n", "77\t15197\t119.5\t0\t15197\n", "78\t17452\t119.5\t0\t17452\n", "79\t16293\t119.5\t0\t16293\n", "80\t15752\t119.5\t0\t15752\n", "81\t15066\t119.5\t0\t15066\n", "82\t13891\t119.5\t0\t13891\n", "83\t14950\t119.5\t0\t14950\n", "84\t16468\t119.5\t0\t16468\n", "85\t18417\t119.5\t0\t18417\n", "86\t17782\t119.5\t0\t17782\n", "87\t12819\t119.5\t0\t12819\n", "88\t11703\t119.5\t0\t11703\n", "89\t11955\t119.5\t0\t11955\n", "90\t12523\t119.5\t0\t12523\n", "91\t12760\t119.5\t0\t12760\n", "92\t13115\t119.5\t0\t13115\n", "93\t14377\t119.5\t0\t14377\n", "94\t13376\t119.5\t0\t13376\n", "95\t10928\t119.5\t0\t10928\n", "96\t8020\t119.5\t0\t8020\n", "97\t5098\t119.5\t0\t5098\n", "98\t2952\t119.5\t0\t2952\n", "99\t3230\t119.5\t0\t3230\n", "100\t1560\t119.5\t0\t1560\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 56392 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 71.2%\n", " C: 12.7%\n", " G: 0.0%\n", " T: 16.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13133\t122408.5\t0\t13133\n", "4\t3258\t30602.1\t0\t3258\n", "5\t1039\t7650.5\t0\t1039\n", "6\t605\t1912.6\t0\t605\n", "7\t193\t478.2\t0\t193\n", "8\t174\t119.5\t0\t174\n", "9\t151\t119.5\t0\t151\n", "10\t159\t119.5\t0\t159\n", "11\t138\t119.5\t0\t138\n", "12\t140\t119.5\t0\t140\n", "13\t152\t119.5\t0\t152\n", "14\t141\t119.5\t0\t141\n", "15\t141\t119.5\t0\t141\n", "16\t181\t119.5\t0\t181\n", "17\t190\t119.5\t0\t190\n", "18\t308\t119.5\t0\t308\n", "19\t407\t119.5\t0\t407\n", "20\t621\t119.5\t0\t621\n", "21\t407\t119.5\t0\t407\n", "22\t318\t119.5\t0\t318\n", "23\t217\t119.5\t0\t217\n", "24\t267\t119.5\t0\t267\n", "25\t305\t119.5\t0\t305\n", "26\t646\t119.5\t0\t646\n", "27\t654\t119.5\t0\t654\n", "28\t820\t119.5\t0\t820\n", "29\t1078\t119.5\t0\t1078\n", "30\t1923\t119.5\t0\t1923\n", "31\t2297\t119.5\t0\t2297\n", "32\t3206\t119.5\t0\t3206\n", "33\t3633\t119.5\t0\t3633\n", "34\t4108\t119.5\t0\t4108\n", "35\t5163\t119.5\t0\t5163\n", "36\t5744\t119.5\t0\t5744\n", "37\t2433\t119.5\t0\t2433\n", "38\t108\t119.5\t0\t108\n", "39\t67\t119.5\t0\t67\n", "40\t56\t119.5\t0\t56\n", "41\t35\t119.5\t0\t35\n", "42\t42\t119.5\t0\t42\n", "43\t56\t119.5\t0\t56\n", "44\t43\t119.5\t0\t43\n", "45\t42\t119.5\t0\t42\n", "46\t52\t119.5\t0\t52\n", "47\t38\t119.5\t0\t38\n", "48\t55\t119.5\t0\t55\n", "49\t53\t119.5\t0\t53\n", "50\t40\t119.5\t0\t40\n", "51\t49\t119.5\t0\t49\n", "52\t36\t119.5\t0\t36\n", "53\t41\t119.5\t0\t41\n", "54\t20\t119.5\t0\t20\n", "55\t27\t119.5\t0\t27\n", "56\t36\t119.5\t0\t36\n", "57\t21\t119.5\t0\t21\n", "58\t25\t119.5\t0\t25\n", "59\t31\t119.5\t0\t31\n", "60\t26\t119.5\t0\t26\n", "61\t29\t119.5\t0\t29\n", "62\t22\t119.5\t0\t22\n", "63\t38\t119.5\t0\t38\n", "64\t25\t119.5\t0\t25\n", "65\t17\t119.5\t0\t17\n", "66\t22\t119.5\t0\t22\n", "67\t19\t119.5\t0\t19\n", "68\t17\t119.5\t0\t17\n", "69\t23\t119.5\t0\t23\n", "70\t6\t119.5\t0\t6\n", "71\t8\t119.5\t0\t8\n", "72\t10\t119.5\t0\t10\n", "73\t15\t119.5\t0\t15\n", "74\t11\t119.5\t0\t11\n", "75\t10\t119.5\t0\t10\n", "76\t10\t119.5\t0\t10\n", "77\t2\t119.5\t0\t2\n", "78\t12\t119.5\t0\t12\n", "79\t16\t119.5\t0\t16\n", "80\t10\t119.5\t0\t10\n", "81\t17\t119.5\t0\t17\n", "82\t12\t119.5\t0\t12\n", "83\t8\t119.5\t0\t8\n", "84\t8\t119.5\t0\t8\n", "85\t11\t119.5\t0\t11\n", "86\t15\t119.5\t0\t15\n", "87\t14\t119.5\t0\t14\n", "88\t8\t119.5\t0\t8\n", "89\t16\t119.5\t0\t16\n", "90\t15\t119.5\t0\t15\n", "91\t16\t119.5\t0\t16\n", "92\t38\t119.5\t0\t38\n", "93\t43\t119.5\t0\t43\n", "94\t68\t119.5\t0\t68\n", "95\t62\t119.5\t0\t62\n", "96\t81\t119.5\t0\t81\n", "97\t77\t119.5\t0\t77\n", "98\t51\t119.5\t0\t51\n", "99\t55\t119.5\t0\t55\n", "100\t106\t119.5\t0\t106\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 116640 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.5%\n", " C: 20.4%\n", " G: 17.6%\n", " T: 19.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t81954\t122408.5\t0\t81954\n", "4\t17256\t30602.1\t0\t17256\n", "5\t3029\t7650.5\t0\t3029\n", "6\t425\t1912.6\t0\t425\n", "7\t271\t478.2\t0\t271\n", "8\t279\t478.2\t0\t279\n", "9\t265\t478.2\t0\t265\n", "10\t288\t478.2\t0\t288\n", "11\t256\t478.2\t0\t256\n", "12\t282\t478.2\t0\t282\n", "13\t245\t478.2\t0\t245\n", "14\t272\t478.2\t0\t272\n", "15\t290\t478.2\t0\t290\n", "16\t292\t478.2\t0\t292\n", "17\t293\t478.2\t0\t293\n", "18\t287\t478.2\t0\t287\n", "19\t256\t478.2\t0\t256\n", "20\t261\t478.2\t0\t261\n", "21\t261\t478.2\t0\t261\n", "22\t237\t478.2\t0\t237\n", "23\t233\t478.2\t0\t233\n", "24\t216\t478.2\t0\t216\n", "25\t232\t478.2\t0\t232\n", "26\t217\t478.2\t0\t217\n", "27\t198\t478.2\t0\t198\n", "28\t242\t478.2\t0\t242\n", "29\t223\t478.2\t0\t223\n", "30\t230\t478.2\t0\t230\n", "31\t222\t478.2\t0\t222\n", "32\t242\t478.2\t0\t242\n", "33\t231\t478.2\t0\t231\n", "34\t217\t478.2\t0\t217\n", "35\t216\t478.2\t0\t216\n", "36\t167\t478.2\t0\t167\n", "37\t203\t478.2\t0\t203\n", "38\t181\t478.2\t0\t181\n", "39\t188\t478.2\t0\t188\n", "40\t208\t478.2\t0\t208\n", "41\t187\t478.2\t0\t187\n", "42\t141\t478.2\t0\t141\n", "43\t209\t478.2\t0\t209\n", "44\t74\t478.2\t0\t74\n", "45\t139\t478.2\t0\t139\n", "46\t144\t478.2\t0\t144\n", "47\t122\t478.2\t0\t122\n", "48\t116\t478.2\t0\t116\n", "49\t130\t478.2\t0\t130\n", "50\t129\t478.2\t0\t129\n", "51\t125\t478.2\t0\t125\n", "52\t124\t478.2\t0\t124\n", "53\t122\t478.2\t0\t122\n", "54\t107\t478.2\t0\t107\n", "55\t124\t478.2\t0\t124\n", "56\t118\t478.2\t0\t118\n", "57\t91\t478.2\t0\t91\n", "58\t94\t478.2\t0\t94\n", "59\t86\t478.2\t0\t86\n", "60\t104\t478.2\t0\t104\n", "61\t111\t478.2\t0\t111\n", "62\t70\t478.2\t0\t70\n", "63\t55\t478.2\t0\t55\n", "64\t86\t478.2\t0\t86\n", "65\t73\t478.2\t0\t73\n", "66\t61\t478.2\t0\t61\n", "67\t69\t478.2\t0\t69\n", "68\t108\t478.2\t0\t108\n", "69\t62\t478.2\t0\t62\n", "70\t51\t478.2\t0\t51\n", "71\t61\t478.2\t0\t61\n", "72\t65\t478.2\t0\t65\n", "73\t80\t478.2\t0\t80\n", "74\t79\t478.2\t0\t79\n", "75\t65\t478.2\t0\t65\n", "76\t92\t478.2\t0\t92\n", "77\t100\t478.2\t0\t100\n", "78\t91\t478.2\t0\t91\n", "79\t104\t478.2\t0\t104\n", "80\t100\t478.2\t0\t100\n", "81\t98\t478.2\t0\t98\n", "82\t139\t478.2\t0\t139\n", "83\t109\t478.2\t0\t109\n", "84\t104\t478.2\t0\t104\n", "85\t107\t478.2\t0\t107\n", "86\t78\t478.2\t0\t78\n", "87\t108\t478.2\t0\t108\n", "88\t91\t478.2\t0\t91\n", "89\t91\t478.2\t0\t91\n", "90\t79\t478.2\t0\t79\n", "91\t50\t478.2\t0\t50\n", "92\t56\t478.2\t0\t56\n", "93\t65\t478.2\t0\t65\n", "94\t75\t478.2\t0\t75\n", "95\t51\t478.2\t0\t51\n", "96\t70\t478.2\t0\t70\n", "97\t61\t478.2\t0\t61\n", "98\t75\t478.2\t0\t75\n", "99\t93\t478.2\t0\t93\n", "100\t106\t478.2\t0\t106\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 304_S24_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/304.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 129.09 s (14 us/read; 4.19 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 9,009,527\n", "Reads with adapters: 7,641,641 (84.8%)\n", "Reads written (passing filters): 8,289,824 (92.0%)\n", "\n", "Total basepairs processed: 900,952,700 bp\n", "Quality-trimmed: 3,693,647 bp (0.4%)\n", "Total written (filtered): 544,398,566 bp (60.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 7514186 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 35.4%\n", " G: 40.6%\n", " T: 24.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t94123\t140773.9\t0\t94123\n", "4\t66443\t35193.5\t0\t66443\n", "5\t56116\t8798.4\t0\t56116\n", "6\t53530\t2199.6\t0\t53530\n", "7\t53422\t549.9\t0\t53422\n", "8\t55579\t137.5\t0\t55579\n", "9\t56317\t137.5\t0\t56317\n", "10\t56857\t137.5\t0\t56857\n", "11\t58468\t137.5\t0\t58468\n", "12\t61277\t137.5\t0\t61277\n", "13\t65615\t137.5\t0\t65615\n", "14\t68401\t137.5\t0\t68401\n", "15\t67238\t137.5\t0\t67238\n", "16\t72622\t137.5\t0\t72622\n", "17\t81624\t137.5\t0\t81624\n", "18\t92741\t137.5\t0\t92741\n", "19\t85333\t137.5\t0\t85333\n", "20\t73525\t137.5\t0\t73525\n", "21\t71434\t137.5\t0\t71434\n", "22\t67678\t137.5\t0\t67678\n", "23\t75334\t137.5\t0\t75334\n", "24\t85978\t137.5\t0\t85978\n", "25\t91070\t137.5\t0\t91070\n", "26\t102690\t137.5\t0\t102690\n", "27\t109287\t137.5\t0\t109287\n", "28\t101648\t137.5\t0\t101648\n", "29\t94730\t137.5\t0\t94730\n", "30\t99542\t137.5\t0\t99542\n", "31\t113809\t137.5\t0\t113809\n", "32\t106223\t137.5\t0\t106223\n", "33\t105120\t137.5\t0\t105120\n", "34\t101186\t137.5\t0\t101186\n", "35\t117293\t137.5\t0\t117293\n", "36\t127551\t137.5\t0\t127551\n", "37\t125996\t137.5\t0\t125996\n", "38\t114585\t137.5\t0\t114585\n", "39\t108358\t137.5\t0\t108358\n", "40\t107771\t137.5\t0\t107771\n", "41\t119487\t137.5\t0\t119487\n", "42\t125268\t137.5\t0\t125268\n", "43\t115694\t137.5\t0\t115694\n", "44\t96738\t137.5\t0\t96738\n", "45\t123041\t137.5\t0\t123041\n", "46\t148481\t137.5\t0\t148481\n", "47\t132578\t137.5\t0\t132578\n", "48\t134034\t137.5\t0\t134034\n", "49\t108505\t137.5\t0\t108505\n", "50\t108043\t137.5\t0\t108043\n", "51\t98096\t137.5\t0\t98096\n", "52\t104961\t137.5\t0\t104961\n", "53\t110314\t137.5\t0\t110314\n", "54\t120733\t137.5\t0\t120733\n", "55\t124963\t137.5\t0\t124963\n", "56\t102803\t137.5\t0\t102803\n", "57\t108196\t137.5\t0\t108196\n", "58\t124012\t137.5\t0\t124012\n", "59\t114240\t137.5\t0\t114240\n", "60\t93208\t137.5\t0\t93208\n", "61\t87668\t137.5\t0\t87668\n", "62\t75717\t137.5\t0\t75717\n", "63\t77263\t137.5\t0\t77263\n", "64\t89182\t137.5\t0\t89182\n", "65\t80135\t137.5\t0\t80135\n", "66\t65340\t137.5\t0\t65340\n", "67\t71191\t137.5\t0\t71191\n", "68\t73495\t137.5\t0\t73495\n", "69\t78537\t137.5\t0\t78537\n", "70\t87321\t137.5\t0\t87321\n", "71\t82685\t137.5\t0\t82685\n", "72\t61324\t137.5\t0\t61324\n", "73\t50061\t137.5\t0\t50061\n", "74\t48140\t137.5\t0\t48140\n", "75\t44241\t137.5\t0\t44241\n", "76\t34894\t137.5\t0\t34894\n", "77\t39380\t137.5\t0\t39380\n", "78\t50146\t137.5\t0\t50146\n", "79\t42460\t137.5\t0\t42460\n", "80\t39288\t137.5\t0\t39288\n", "81\t38744\t137.5\t0\t38744\n", "82\t36626\t137.5\t0\t36626\n", "83\t35131\t137.5\t0\t35131\n", "84\t43579\t137.5\t0\t43579\n", "85\t52698\t137.5\t0\t52698\n", "86\t51844\t137.5\t0\t51844\n", "87\t34604\t137.5\t0\t34604\n", "88\t28225\t137.5\t0\t28225\n", "89\t30713\t137.5\t0\t30713\n", "90\t34725\t137.5\t0\t34725\n", "91\t38378\t137.5\t0\t38378\n", "92\t42810\t137.5\t0\t42810\n", "93\t48096\t137.5\t0\t48096\n", "94\t43277\t137.5\t0\t43277\n", "95\t36322\t137.5\t0\t36322\n", "96\t27386\t137.5\t0\t27386\n", "97\t17221\t137.5\t0\t17221\n", "98\t10256\t137.5\t0\t10256\n", "99\t17386\t137.5\t0\t17386\n", "100\t7788\t137.5\t0\t7788\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 57805 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 77.8%\n", " C: 10.8%\n", " G: 0.0%\n", " T: 11.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t7953\t140773.9\t0\t7953\n", "4\t2259\t35193.5\t0\t2259\n", "5\t1189\t8798.4\t0\t1189\n", "6\t957\t2199.6\t0\t957\n", "7\t520\t549.9\t0\t520\n", "8\t438\t137.5\t0\t438\n", "9\t469\t137.5\t0\t469\n", "10\t452\t137.5\t0\t452\n", "11\t354\t137.5\t0\t354\n", "12\t368\t137.5\t0\t368\n", "13\t375\t137.5\t0\t375\n", "14\t363\t137.5\t0\t363\n", "15\t393\t137.5\t0\t393\n", "16\t420\t137.5\t0\t420\n", "17\t489\t137.5\t0\t489\n", "18\t678\t137.5\t0\t678\n", "19\t912\t137.5\t0\t912\n", "20\t1218\t137.5\t0\t1218\n", "21\t842\t137.5\t0\t842\n", "22\t676\t137.5\t0\t676\n", "23\t531\t137.5\t0\t531\n", "24\t576\t137.5\t0\t576\n", "25\t710\t137.5\t0\t710\n", "26\t1211\t137.5\t0\t1211\n", "27\t1147\t137.5\t0\t1147\n", "28\t1282\t137.5\t0\t1282\n", "29\t1636\t137.5\t0\t1636\n", "30\t2486\t137.5\t0\t2486\n", "31\t3136\t137.5\t0\t3136\n", "32\t4236\t137.5\t0\t4236\n", "33\t3990\t137.5\t0\t3990\n", "34\t4176\t137.5\t0\t4176\n", "35\t4853\t137.5\t0\t4853\n", "36\t4202\t137.5\t0\t4202\n", "37\t1123\t137.5\t0\t1123\n", "38\t73\t137.5\t0\t73\n", "39\t32\t137.5\t0\t32\n", "40\t29\t137.5\t0\t29\n", "41\t28\t137.5\t0\t28\n", "42\t29\t137.5\t0\t29\n", "43\t32\t137.5\t0\t32\n", "44\t21\t137.5\t0\t21\n", "45\t33\t137.5\t0\t33\n", "46\t30\t137.5\t0\t30\n", "47\t29\t137.5\t0\t29\n", "48\t27\t137.5\t0\t27\n", "49\t39\t137.5\t0\t39\n", "50\t28\t137.5\t0\t28\n", "51\t28\t137.5\t0\t28\n", "52\t24\t137.5\t0\t24\n", "53\t24\t137.5\t0\t24\n", "54\t14\t137.5\t0\t14\n", "55\t15\t137.5\t0\t15\n", "56\t28\t137.5\t0\t28\n", "57\t20\t137.5\t0\t20\n", "58\t16\t137.5\t0\t16\n", "59\t10\t137.5\t0\t10\n", "60\t23\t137.5\t0\t23\n", "61\t27\t137.5\t0\t27\n", "62\t14\t137.5\t0\t14\n", "63\t20\t137.5\t0\t20\n", "64\t22\t137.5\t0\t22\n", "65\t15\t137.5\t0\t15\n", "66\t16\t137.5\t0\t16\n", "67\t15\t137.5\t0\t15\n", "68\t20\t137.5\t0\t20\n", "69\t13\t137.5\t0\t13\n", "70\t11\t137.5\t0\t11\n", "71\t5\t137.5\t0\t5\n", "72\t7\t137.5\t0\t7\n", "73\t3\t137.5\t0\t3\n", "74\t5\t137.5\t0\t5\n", "75\t2\t137.5\t0\t2\n", "76\t6\t137.5\t0\t6\n", "77\t5\t137.5\t0\t5\n", "78\t5\t137.5\t0\t5\n", "79\t2\t137.5\t0\t2\n", "80\t7\t137.5\t0\t7\n", "81\t3\t137.5\t0\t3\n", "82\t3\t137.5\t0\t3\n", "83\t8\t137.5\t0\t8\n", "84\t6\t137.5\t0\t6\n", "85\t4\t137.5\t0\t4\n", "86\t7\t137.5\t0\t7\n", "87\t4\t137.5\t0\t4\n", "88\t6\t137.5\t0\t6\n", "89\t8\t137.5\t0\t8\n", "90\t9\t137.5\t0\t9\n", "91\t10\t137.5\t0\t10\n", "92\t19\t137.5\t0\t19\n", "93\t21\t137.5\t0\t21\n", "94\t31\t137.5\t0\t31\n", "95\t42\t137.5\t0\t42\n", "96\t41\t137.5\t0\t41\n", "97\t29\t137.5\t0\t29\n", "98\t28\t137.5\t0\t28\n", "99\t26\t137.5\t0\t26\n", "100\t28\t137.5\t0\t28\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 69650 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.7%\n", " C: 19.4%\n", " G: 18.1%\n", " T: 16.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t39611\t140773.9\t0\t39611\n", "4\t8502\t35193.5\t0\t8502\n", "5\t1694\t8798.4\t0\t1694\n", "6\t446\t2199.6\t0\t446\n", "7\t360\t549.9\t0\t360\n", "8\t396\t549.9\t0\t396\n", "9\t347\t549.9\t0\t347\n", "10\t368\t549.9\t0\t368\n", "11\t347\t549.9\t0\t347\n", "12\t412\t549.9\t0\t412\n", "13\t359\t549.9\t0\t359\n", "14\t378\t549.9\t0\t378\n", "15\t418\t549.9\t0\t418\n", "16\t419\t549.9\t0\t419\n", "17\t382\t549.9\t0\t382\n", "18\t416\t549.9\t0\t416\n", "19\t395\t549.9\t0\t395\n", "20\t378\t549.9\t0\t378\n", "21\t368\t549.9\t0\t368\n", "22\t377\t549.9\t0\t377\n", "23\t371\t549.9\t0\t371\n", "24\t311\t549.9\t0\t311\n", "25\t363\t549.9\t0\t363\n", "26\t346\t549.9\t0\t346\n", "27\t410\t549.9\t0\t410\n", "28\t358\t549.9\t0\t358\n", "29\t337\t549.9\t0\t337\n", "30\t338\t549.9\t0\t338\n", "31\t326\t549.9\t0\t326\n", "32\t353\t549.9\t0\t353\n", "33\t332\t549.9\t0\t332\n", "34\t333\t549.9\t0\t333\n", "35\t302\t549.9\t0\t302\n", "36\t348\t549.9\t0\t348\n", "37\t296\t549.9\t0\t296\n", "38\t274\t549.9\t0\t274\n", "39\t303\t549.9\t0\t303\n", "40\t315\t549.9\t0\t315\n", "41\t233\t549.9\t0\t233\n", "42\t240\t549.9\t0\t240\n", "43\t408\t549.9\t0\t408\n", "44\t77\t549.9\t0\t77\n", "45\t212\t549.9\t0\t212\n", "46\t241\t549.9\t0\t241\n", "47\t225\t549.9\t0\t225\n", "48\t184\t549.9\t0\t184\n", "49\t206\t549.9\t0\t206\n", "50\t200\t549.9\t0\t200\n", "51\t174\t549.9\t0\t174\n", "52\t204\t549.9\t0\t204\n", "53\t239\t549.9\t0\t239\n", "54\t153\t549.9\t0\t153\n", "55\t214\t549.9\t0\t214\n", "56\t160\t549.9\t0\t160\n", "57\t131\t549.9\t0\t131\n", "58\t171\t549.9\t0\t171\n", "59\t87\t549.9\t0\t87\n", "60\t151\t549.9\t0\t151\n", "61\t160\t549.9\t0\t160\n", "62\t110\t549.9\t0\t110\n", "63\t115\t549.9\t0\t115\n", "64\t173\t549.9\t0\t173\n", "65\t62\t549.9\t0\t62\n", "66\t118\t549.9\t0\t118\n", "67\t140\t549.9\t0\t140\n", "68\t160\t549.9\t0\t160\n", "69\t50\t549.9\t0\t50\n", "70\t38\t549.9\t0\t38\n", "71\t87\t549.9\t0\t87\n", "72\t76\t549.9\t0\t76\n", "73\t91\t549.9\t0\t91\n", "74\t103\t549.9\t0\t103\n", "75\t94\t549.9\t0\t94\n", "76\t108\t549.9\t0\t108\n", "77\t107\t549.9\t0\t107\n", "78\t72\t549.9\t0\t72\n", "79\t85\t549.9\t0\t85\n", "80\t85\t549.9\t0\t85\n", "81\t90\t549.9\t0\t90\n", "82\t141\t549.9\t0\t141\n", "83\t90\t549.9\t0\t90\n", "84\t67\t549.9\t0\t67\n", "85\t89\t549.9\t0\t89\n", "86\t71\t549.9\t0\t71\n", "87\t80\t549.9\t0\t80\n", "88\t101\t549.9\t0\t101\n", "89\t82\t549.9\t0\t82\n", "90\t74\t549.9\t0\t74\n", "91\t54\t549.9\t0\t54\n", "92\t40\t549.9\t0\t40\n", "93\t38\t549.9\t0\t38\n", "94\t57\t549.9\t0\t57\n", "95\t40\t549.9\t0\t40\n", "96\t40\t549.9\t0\t40\n", "97\t45\t549.9\t0\t45\n", "98\t30\t549.9\t0\t30\n", "99\t45\t549.9\t0\t45\n", "100\t43\t549.9\t0\t43\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 305_S1_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/305.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 85.39 s (14 us/read; 4.34 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,179,940\n", "Reads with adapters: 3,988,249 (64.5%)\n", "Reads written (passing filters): 5,956,268 (96.4%)\n", "\n", "Total basepairs processed: 617,994,000 bp\n", "Quality-trimmed: 1,684,650 bp (0.3%)\n", "Total written (filtered): 460,767,518 bp (74.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3827596 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 32.3%\n", " G: 41.2%\n", " T: 26.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t112794\t96561.6\t0\t112794\n", "4\t65573\t24140.4\t0\t65573\n", "5\t50340\t6035.1\t0\t50340\n", "6\t43474\t1508.8\t0\t43474\n", "7\t40633\t377.2\t0\t40633\n", "8\t41776\t94.3\t0\t41776\n", "9\t40949\t94.3\t0\t40949\n", "10\t41330\t94.3\t0\t41330\n", "11\t42106\t94.3\t0\t42106\n", "12\t43202\t94.3\t0\t43202\n", "13\t49630\t94.3\t0\t49630\n", "14\t49556\t94.3\t0\t49556\n", "15\t46022\t94.3\t0\t46022\n", "16\t48352\t94.3\t0\t48352\n", "17\t51637\t94.3\t0\t51637\n", "18\t58537\t94.3\t0\t58537\n", "19\t55129\t94.3\t0\t55129\n", "20\t46779\t94.3\t0\t46779\n", "21\t44286\t94.3\t0\t44286\n", "22\t41849\t94.3\t0\t41849\n", "23\t45462\t94.3\t0\t45462\n", "24\t51725\t94.3\t0\t51725\n", "25\t54215\t94.3\t0\t54215\n", "26\t60673\t94.3\t0\t60673\n", "27\t65365\t94.3\t0\t65365\n", "28\t60632\t94.3\t0\t60632\n", "29\t56384\t94.3\t0\t56384\n", "30\t57712\t94.3\t0\t57712\n", "31\t62564\t94.3\t0\t62564\n", "32\t60678\t94.3\t0\t60678\n", "33\t56968\t94.3\t0\t56968\n", "34\t56077\t94.3\t0\t56077\n", "35\t62057\t94.3\t0\t62057\n", "36\t70485\t94.3\t0\t70485\n", "37\t75400\t94.3\t0\t75400\n", "38\t63455\t94.3\t0\t63455\n", "39\t55994\t94.3\t0\t55994\n", "40\t54230\t94.3\t0\t54230\n", "41\t60427\t94.3\t0\t60427\n", "42\t67768\t94.3\t0\t67768\n", "43\t59199\t94.3\t0\t59199\n", "44\t48100\t94.3\t0\t48100\n", "45\t56553\t94.3\t0\t56553\n", "46\t64836\t94.3\t0\t64836\n", "47\t62311\t94.3\t0\t62311\n", "48\t61736\t94.3\t0\t61736\n", "49\t53720\t94.3\t0\t53720\n", "50\t50497\t94.3\t0\t50497\n", "51\t46365\t94.3\t0\t46365\n", "52\t49262\t94.3\t0\t49262\n", "53\t48676\t94.3\t0\t48676\n", "54\t50284\t94.3\t0\t50284\n", "55\t46700\t94.3\t0\t46700\n", "56\t44283\t94.3\t0\t44283\n", "57\t42207\t94.3\t0\t42207\n", "58\t48628\t94.3\t0\t48628\n", "59\t43840\t94.3\t0\t43840\n", "60\t36941\t94.3\t0\t36941\n", "61\t34556\t94.3\t0\t34556\n", "62\t29773\t94.3\t0\t29773\n", "63\t28653\t94.3\t0\t28653\n", "64\t30962\t94.3\t0\t30962\n", "65\t30676\t94.3\t0\t30676\n", "66\t28332\t94.3\t0\t28332\n", "67\t27676\t94.3\t0\t27676\n", "68\t27237\t94.3\t0\t27237\n", "69\t28842\t94.3\t0\t28842\n", "70\t29887\t94.3\t0\t29887\n", "71\t28544\t94.3\t0\t28544\n", "72\t23222\t94.3\t0\t23222\n", "73\t21437\t94.3\t0\t21437\n", "74\t21169\t94.3\t0\t21169\n", "75\t18948\t94.3\t0\t18948\n", "76\t16241\t94.3\t0\t16241\n", "77\t14744\t94.3\t0\t14744\n", "78\t16276\t94.3\t0\t16276\n", "79\t16447\t94.3\t0\t16447\n", "80\t16268\t94.3\t0\t16268\n", "81\t14951\t94.3\t0\t14951\n", "82\t13837\t94.3\t0\t13837\n", "83\t14297\t94.3\t0\t14297\n", "84\t15645\t94.3\t0\t15645\n", "85\t16681\t94.3\t0\t16681\n", "86\t16069\t94.3\t0\t16069\n", "87\t12001\t94.3\t0\t12001\n", "88\t10572\t94.3\t0\t10572\n", "89\t10664\t94.3\t0\t10664\n", "90\t10974\t94.3\t0\t10974\n", "91\t10637\t94.3\t0\t10637\n", "92\t10728\t94.3\t0\t10728\n", "93\t11094\t94.3\t0\t11094\n", "94\t11134\t94.3\t0\t11134\n", "95\t9819\t94.3\t0\t9819\n", "96\t7398\t94.3\t0\t7398\n", "97\t5013\t94.3\t0\t5013\n", "98\t2954\t94.3\t0\t2954\n", "99\t5060\t94.3\t0\t5060\n", "100\t1815\t94.3\t0\t1815\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 68206 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 76.3%\n", " C: 11.2%\n", " G: 0.0%\n", " T: 12.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t11022\t96561.6\t0\t11022\n", "4\t2837\t24140.4\t0\t2837\n", "5\t1341\t6035.1\t0\t1341\n", "6\t967\t1508.8\t0\t967\n", "7\t345\t377.2\t0\t345\n", "8\t268\t94.3\t0\t268\n", "9\t275\t94.3\t0\t275\n", "10\t243\t94.3\t0\t243\n", "11\t239\t94.3\t0\t239\n", "12\t210\t94.3\t0\t210\n", "13\t194\t94.3\t0\t194\n", "14\t192\t94.3\t0\t192\n", "15\t238\t94.3\t0\t238\n", "16\t216\t94.3\t0\t216\n", "17\t250\t94.3\t0\t250\n", "18\t341\t94.3\t0\t341\n", "19\t472\t94.3\t0\t472\n", "20\t701\t94.3\t0\t701\n", "21\t480\t94.3\t0\t480\n", "22\t382\t94.3\t0\t382\n", "23\t304\t94.3\t0\t304\n", "24\t368\t94.3\t0\t368\n", "25\t444\t94.3\t0\t444\n", "26\t856\t94.3\t0\t856\n", "27\t930\t94.3\t0\t930\n", "28\t1254\t94.3\t0\t1254\n", "29\t1630\t94.3\t0\t1630\n", "30\t3059\t94.3\t0\t3059\n", "31\t3591\t94.3\t0\t3591\n", "32\t4647\t94.3\t0\t4647\n", "33\t5067\t94.3\t0\t5067\n", "34\t5162\t94.3\t0\t5162\n", "35\t7039\t94.3\t0\t7039\n", "36\t7926\t94.3\t0\t7926\n", "37\t2937\t94.3\t0\t2937\n", "38\t101\t94.3\t0\t101\n", "39\t42\t94.3\t0\t42\n", "40\t30\t94.3\t0\t30\n", "41\t42\t94.3\t0\t42\n", "42\t36\t94.3\t0\t36\n", "43\t33\t94.3\t0\t33\n", "44\t42\t94.3\t0\t42\n", "45\t35\t94.3\t0\t35\n", "46\t40\t94.3\t0\t40\n", "47\t36\t94.3\t0\t36\n", "48\t29\t94.3\t0\t29\n", "49\t37\t94.3\t0\t37\n", "50\t23\t94.3\t0\t23\n", "51\t29\t94.3\t0\t29\n", "52\t31\t94.3\t0\t31\n", "53\t29\t94.3\t0\t29\n", "54\t33\t94.3\t0\t33\n", "55\t32\t94.3\t0\t32\n", "56\t32\t94.3\t0\t32\n", "57\t32\t94.3\t0\t32\n", "58\t32\t94.3\t0\t32\n", "59\t29\t94.3\t0\t29\n", "60\t21\t94.3\t0\t21\n", "61\t31\t94.3\t0\t31\n", "62\t25\t94.3\t0\t25\n", "63\t17\t94.3\t0\t17\n", "64\t23\t94.3\t0\t23\n", "65\t41\t94.3\t0\t41\n", "66\t28\t94.3\t0\t28\n", "67\t24\t94.3\t0\t24\n", "68\t15\t94.3\t0\t15\n", "69\t16\t94.3\t0\t16\n", "70\t14\t94.3\t0\t14\n", "71\t12\t94.3\t0\t12\n", "72\t16\t94.3\t0\t16\n", "73\t13\t94.3\t0\t13\n", "74\t8\t94.3\t0\t8\n", "75\t12\t94.3\t0\t12\n", "76\t8\t94.3\t0\t8\n", "77\t16\t94.3\t0\t16\n", "78\t7\t94.3\t0\t7\n", "79\t8\t94.3\t0\t8\n", "80\t7\t94.3\t0\t7\n", "81\t8\t94.3\t0\t8\n", "82\t14\t94.3\t0\t14\n", "83\t11\t94.3\t0\t11\n", "84\t11\t94.3\t0\t11\n", "85\t11\t94.3\t0\t11\n", "86\t8\t94.3\t0\t8\n", "87\t16\t94.3\t0\t16\n", "88\t13\t94.3\t0\t13\n", "89\t8\t94.3\t0\t8\n", "90\t9\t94.3\t0\t9\n", "91\t8\t94.3\t0\t8\n", "92\t22\t94.3\t0\t22\n", "93\t37\t94.3\t0\t37\n", "94\t59\t94.3\t0\t59\n", "95\t56\t94.3\t0\t56\n", "96\t59\t94.3\t0\t59\n", "97\t65\t94.3\t0\t65\n", "98\t63\t94.3\t0\t63\n", "99\t43\t94.3\t0\t43\n", "100\t91\t94.3\t0\t91\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 92447 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.1%\n", " C: 19.5%\n", " G: 18.0%\n", " T: 21.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t63053\t96561.6\t0\t63053\n", "4\t13894\t24140.4\t0\t13894\n", "5\t2250\t6035.1\t0\t2250\n", "6\t368\t1508.8\t0\t368\n", "7\t244\t377.2\t0\t244\n", "8\t248\t377.2\t0\t248\n", "9\t236\t377.2\t0\t236\n", "10\t243\t377.2\t0\t243\n", "11\t229\t377.2\t0\t229\n", "12\t243\t377.2\t0\t243\n", "13\t273\t377.2\t0\t273\n", "14\t210\t377.2\t0\t210\n", "15\t270\t377.2\t0\t270\n", "16\t244\t377.2\t0\t244\n", "17\t283\t377.2\t0\t283\n", "18\t304\t377.2\t0\t304\n", "19\t249\t377.2\t0\t249\n", "20\t253\t377.2\t0\t253\n", "21\t250\t377.2\t0\t250\n", "22\t235\t377.2\t0\t235\n", "23\t229\t377.2\t0\t229\n", "24\t221\t377.2\t0\t221\n", "25\t199\t377.2\t0\t199\n", "26\t201\t377.2\t0\t201\n", "27\t226\t377.2\t0\t226\n", "28\t202\t377.2\t0\t202\n", "29\t231\t377.2\t0\t231\n", "30\t192\t377.2\t0\t192\n", "31\t205\t377.2\t0\t205\n", "32\t220\t377.2\t0\t220\n", "33\t198\t377.2\t0\t198\n", "34\t225\t377.2\t0\t225\n", "35\t182\t377.2\t0\t182\n", "36\t167\t377.2\t0\t167\n", "37\t155\t377.2\t0\t155\n", "38\t187\t377.2\t0\t187\n", "39\t193\t377.2\t0\t193\n", "40\t187\t377.2\t0\t187\n", "41\t135\t377.2\t0\t135\n", "42\t127\t377.2\t0\t127\n", "43\t214\t377.2\t0\t214\n", "44\t67\t377.2\t0\t67\n", "45\t152\t377.2\t0\t152\n", "46\t133\t377.2\t0\t133\n", "47\t116\t377.2\t0\t116\n", "48\t116\t377.2\t0\t116\n", "49\t120\t377.2\t0\t120\n", "50\t128\t377.2\t0\t128\n", "51\t118\t377.2\t0\t118\n", "52\t114\t377.2\t0\t114\n", "53\t124\t377.2\t0\t124\n", "54\t100\t377.2\t0\t100\n", "55\t132\t377.2\t0\t132\n", "56\t114\t377.2\t0\t114\n", "57\t91\t377.2\t0\t91\n", "58\t109\t377.2\t0\t109\n", "59\t94\t377.2\t0\t94\n", "60\t102\t377.2\t0\t102\n", "61\t99\t377.2\t0\t99\n", "62\t84\t377.2\t0\t84\n", "63\t61\t377.2\t0\t61\n", "64\t102\t377.2\t0\t102\n", "65\t77\t377.2\t0\t77\n", "66\t90\t377.2\t0\t90\n", "67\t103\t377.2\t0\t103\n", "68\t111\t377.2\t0\t111\n", "69\t62\t377.2\t0\t62\n", "70\t84\t377.2\t0\t84\n", "71\t87\t377.2\t0\t87\n", "72\t64\t377.2\t0\t64\n", "73\t73\t377.2\t0\t73\n", "74\t80\t377.2\t0\t80\n", "75\t60\t377.2\t0\t60\n", "76\t73\t377.2\t0\t73\n", "77\t78\t377.2\t0\t78\n", "78\t65\t377.2\t0\t65\n", "79\t52\t377.2\t0\t52\n", "80\t65\t377.2\t0\t65\n", "81\t77\t377.2\t0\t77\n", "82\t75\t377.2\t0\t75\n", "83\t72\t377.2\t0\t72\n", "84\t85\t377.2\t0\t85\n", "85\t60\t377.2\t0\t60\n", "86\t84\t377.2\t0\t84\n", "87\t83\t377.2\t0\t83\n", "88\t86\t377.2\t0\t86\n", "89\t55\t377.2\t0\t55\n", "90\t53\t377.2\t0\t53\n", "91\t43\t377.2\t0\t43\n", "92\t38\t377.2\t0\t38\n", "93\t33\t377.2\t0\t33\n", "94\t48\t377.2\t0\t48\n", "95\t40\t377.2\t0\t40\n", "96\t40\t377.2\t0\t40\n", "97\t44\t377.2\t0\t44\n", "98\t77\t377.2\t0\t77\n", "99\t80\t377.2\t0\t80\n", "100\t99\t377.2\t0\t99\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 306_S44_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/306.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 108.11 s (14 us/read; 4.42 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,965,794\n", "Reads with adapters: 4,272,677 (53.6%)\n", "Reads written (passing filters): 7,630,183 (95.8%)\n", "\n", "Total basepairs processed: 796,579,400 bp\n", "Quality-trimmed: 2,657,204 bp (0.3%)\n", "Total written (filtered): 625,250,566 bp (78.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4086846 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.7%\n", " G: 34.7%\n", " T: 35.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t171365\t124465.5\t0\t171365\n", "4\t93209\t31116.4\t0\t93209\n", "5\t63450\t7779.1\t0\t63450\n", "6\t50086\t1944.8\t0\t50086\n", "7\t44435\t486.2\t0\t44435\n", "8\t43490\t121.5\t0\t43490\n", "9\t42804\t121.5\t0\t42804\n", "10\t41587\t121.5\t0\t41587\n", "11\t42514\t121.5\t0\t42514\n", "12\t42531\t121.5\t0\t42531\n", "13\t45460\t121.5\t0\t45460\n", "14\t47732\t121.5\t0\t47732\n", "15\t45908\t121.5\t0\t45908\n", "16\t49521\t121.5\t0\t49521\n", "17\t53740\t121.5\t0\t53740\n", "18\t57987\t121.5\t0\t57987\n", "19\t52613\t121.5\t0\t52613\n", "20\t44891\t121.5\t0\t44891\n", "21\t42723\t121.5\t0\t42723\n", "22\t40381\t121.5\t0\t40381\n", "23\t44694\t121.5\t0\t44694\n", "24\t51196\t121.5\t0\t51196\n", "25\t52075\t121.5\t0\t52075\n", "26\t57573\t121.5\t0\t57573\n", "27\t63054\t121.5\t0\t63054\n", "28\t59413\t121.5\t0\t59413\n", "29\t56701\t121.5\t0\t56701\n", "30\t57392\t121.5\t0\t57392\n", "31\t61309\t121.5\t0\t61309\n", "32\t60550\t121.5\t0\t60550\n", "33\t57085\t121.5\t0\t57085\n", "34\t56177\t121.5\t0\t56177\n", "35\t61783\t121.5\t0\t61783\n", "36\t68901\t121.5\t0\t68901\n", "37\t72379\t121.5\t0\t72379\n", "38\t63910\t121.5\t0\t63910\n", "39\t55810\t121.5\t0\t55810\n", "40\t53061\t121.5\t0\t53061\n", "41\t57388\t121.5\t0\t57388\n", "42\t61240\t121.5\t0\t61240\n", "43\t57371\t121.5\t0\t57371\n", "44\t49727\t121.5\t0\t49727\n", "45\t56667\t121.5\t0\t56667\n", "46\t65378\t121.5\t0\t65378\n", "47\t62847\t121.5\t0\t62847\n", "48\t62166\t121.5\t0\t62166\n", "49\t55365\t121.5\t0\t55365\n", "50\t52366\t121.5\t0\t52366\n", "51\t49033\t121.5\t0\t49033\n", "52\t52295\t121.5\t0\t52295\n", "53\t54415\t121.5\t0\t54415\n", "54\t51774\t121.5\t0\t51774\n", "55\t52514\t121.5\t0\t52514\n", "56\t45857\t121.5\t0\t45857\n", "57\t46077\t121.5\t0\t46077\n", "58\t50732\t121.5\t0\t50732\n", "59\t49023\t121.5\t0\t49023\n", "60\t42881\t121.5\t0\t42881\n", "61\t39004\t121.5\t0\t39004\n", "62\t34441\t121.5\t0\t34441\n", "63\t34708\t121.5\t0\t34708\n", "64\t38377\t121.5\t0\t38377\n", "65\t33841\t121.5\t0\t33841\n", "66\t30242\t121.5\t0\t30242\n", "67\t31772\t121.5\t0\t31772\n", "68\t31481\t121.5\t0\t31481\n", "69\t31853\t121.5\t0\t31853\n", "70\t34211\t121.5\t0\t34211\n", "71\t31650\t121.5\t0\t31650\n", "72\t25087\t121.5\t0\t25087\n", "73\t20562\t121.5\t0\t20562\n", "74\t18982\t121.5\t0\t18982\n", "75\t18031\t121.5\t0\t18031\n", "76\t16476\t121.5\t0\t16476\n", "77\t17790\t121.5\t0\t17790\n", "78\t20419\t121.5\t0\t20419\n", "79\t18527\t121.5\t0\t18527\n", "80\t17754\t121.5\t0\t17754\n", "81\t18024\t121.5\t0\t18024\n", "82\t18102\t121.5\t0\t18102\n", "83\t18426\t121.5\t0\t18426\n", "84\t20068\t121.5\t0\t20068\n", "85\t22651\t121.5\t0\t22651\n", "86\t23502\t121.5\t0\t23502\n", "87\t21523\t121.5\t0\t21523\n", "88\t20759\t121.5\t0\t20759\n", "89\t19179\t121.5\t0\t19179\n", "90\t18274\t121.5\t0\t18274\n", "91\t17484\t121.5\t0\t17484\n", "92\t15710\t121.5\t0\t15710\n", "93\t14349\t121.5\t0\t14349\n", "94\t11844\t121.5\t0\t11844\n", "95\t9838\t121.5\t0\t9838\n", "96\t7544\t121.5\t0\t7544\n", "97\t5600\t121.5\t0\t5600\n", "98\t4522\t121.5\t0\t4522\n", "99\t4682\t121.5\t0\t4682\n", "100\t4951\t121.5\t0\t4951\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 40729 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.5%\n", " C: 28.8%\n", " G: 0.0%\n", " T: 27.5%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t18621\t124465.5\t0\t18621\n", "4\t4848\t31116.4\t0\t4848\n", "5\t2385\t7779.1\t0\t2385\n", "6\t1125\t1944.8\t0\t1125\n", "7\t120\t486.2\t0\t120\n", "8\t115\t121.5\t0\t115\n", "9\t88\t121.5\t0\t88\n", "10\t96\t121.5\t0\t96\n", "11\t94\t121.5\t0\t94\n", "12\t97\t121.5\t0\t97\n", "13\t83\t121.5\t0\t83\n", "14\t104\t121.5\t0\t104\n", "15\t110\t121.5\t0\t110\n", "16\t120\t121.5\t0\t120\n", "17\t164\t121.5\t0\t164\n", "18\t326\t121.5\t0\t326\n", "19\t524\t121.5\t0\t524\n", "20\t590\t121.5\t0\t590\n", "21\t342\t121.5\t0\t342\n", "22\t237\t121.5\t0\t237\n", "23\t172\t121.5\t0\t172\n", "24\t126\t121.5\t0\t126\n", "25\t128\t121.5\t0\t128\n", "26\t145\t121.5\t0\t145\n", "27\t156\t121.5\t0\t156\n", "28\t164\t121.5\t0\t164\n", "29\t234\t121.5\t0\t234\n", "30\t385\t121.5\t0\t385\n", "31\t509\t121.5\t0\t509\n", "32\t652\t121.5\t0\t652\n", "33\t750\t121.5\t0\t750\n", "34\t945\t121.5\t0\t945\n", "35\t1066\t121.5\t0\t1066\n", "36\t859\t121.5\t0\t859\n", "37\t458\t121.5\t0\t458\n", "38\t114\t121.5\t0\t114\n", "39\t97\t121.5\t0\t97\n", "40\t73\t121.5\t0\t73\n", "41\t84\t121.5\t0\t84\n", "42\t53\t121.5\t0\t53\n", "43\t72\t121.5\t0\t72\n", "44\t70\t121.5\t0\t70\n", "45\t69\t121.5\t0\t69\n", "46\t65\t121.5\t0\t65\n", "47\t42\t121.5\t0\t42\n", "48\t75\t121.5\t0\t75\n", "49\t67\t121.5\t0\t67\n", "50\t69\t121.5\t0\t69\n", "51\t70\t121.5\t0\t70\n", "52\t81\t121.5\t0\t81\n", "53\t73\t121.5\t0\t73\n", "54\t59\t121.5\t0\t59\n", "55\t54\t121.5\t0\t54\n", "56\t52\t121.5\t0\t52\n", "57\t61\t121.5\t0\t61\n", "58\t44\t121.5\t0\t44\n", "59\t57\t121.5\t0\t57\n", "60\t44\t121.5\t0\t44\n", "61\t45\t121.5\t0\t45\n", "62\t37\t121.5\t0\t37\n", "63\t43\t121.5\t0\t43\n", "64\t69\t121.5\t0\t69\n", "65\t52\t121.5\t0\t52\n", "66\t47\t121.5\t0\t47\n", "67\t38\t121.5\t0\t38\n", "68\t39\t121.5\t0\t39\n", "69\t36\t121.5\t0\t36\n", "70\t42\t121.5\t0\t42\n", "71\t34\t121.5\t0\t34\n", "72\t58\t121.5\t0\t58\n", "73\t46\t121.5\t0\t46\n", "74\t28\t121.5\t0\t28\n", "75\t45\t121.5\t0\t45\n", "76\t34\t121.5\t0\t34\n", "77\t23\t121.5\t0\t23\n", "78\t27\t121.5\t0\t27\n", "79\t22\t121.5\t0\t22\n", "80\t44\t121.5\t0\t44\n", "81\t25\t121.5\t0\t25\n", "82\t29\t121.5\t0\t29\n", "83\t24\t121.5\t0\t24\n", "84\t26\t121.5\t0\t26\n", "85\t30\t121.5\t0\t30\n", "86\t24\t121.5\t0\t24\n", "87\t27\t121.5\t0\t27\n", "88\t21\t121.5\t0\t21\n", "89\t37\t121.5\t0\t37\n", "90\t39\t121.5\t0\t39\n", "91\t47\t121.5\t0\t47\n", "92\t50\t121.5\t0\t50\n", "93\t71\t121.5\t0\t71\n", "94\t96\t121.5\t0\t96\n", "95\t113\t121.5\t0\t113\n", "96\t148\t121.5\t0\t148\n", "97\t201\t121.5\t0\t201\n", "98\t156\t121.5\t0\t156\n", "99\t78\t121.5\t0\t78\n", "100\t195\t121.5\t0\t195\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 145102 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 38.5%\n", " C: 19.1%\n", " G: 17.4%\n", " T: 25.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t107062\t124465.5\t0\t107062\n", "4\t25766\t31116.4\t0\t25766\n", "5\t3347\t7779.1\t0\t3347\n", "6\t334\t1944.8\t0\t334\n", "7\t82\t486.2\t0\t82\n", "8\t77\t486.2\t0\t77\n", "9\t76\t486.2\t0\t76\n", "10\t75\t486.2\t0\t75\n", "11\t79\t486.2\t0\t79\n", "12\t85\t486.2\t0\t85\n", "13\t105\t486.2\t0\t105\n", "14\t107\t486.2\t0\t107\n", "15\t110\t486.2\t0\t110\n", "16\t99\t486.2\t0\t99\n", "17\t110\t486.2\t0\t110\n", "18\t100\t486.2\t0\t100\n", "19\t105\t486.2\t0\t105\n", "20\t93\t486.2\t0\t93\n", "21\t103\t486.2\t0\t103\n", "22\t90\t486.2\t0\t90\n", "23\t96\t486.2\t0\t96\n", "24\t80\t486.2\t0\t80\n", "25\t79\t486.2\t0\t79\n", "26\t101\t486.2\t0\t101\n", "27\t91\t486.2\t0\t91\n", "28\t120\t486.2\t0\t120\n", "29\t101\t486.2\t0\t101\n", "30\t89\t486.2\t0\t89\n", "31\t89\t486.2\t0\t89\n", "32\t97\t486.2\t0\t97\n", "33\t115\t486.2\t0\t115\n", "34\t92\t486.2\t0\t92\n", "35\t99\t486.2\t0\t99\n", "36\t79\t486.2\t0\t79\n", "37\t88\t486.2\t0\t88\n", "38\t96\t486.2\t0\t96\n", "39\t144\t486.2\t0\t144\n", "40\t109\t486.2\t0\t109\n", "41\t105\t486.2\t0\t105\n", "42\t81\t486.2\t0\t81\n", "43\t100\t486.2\t0\t100\n", "44\t79\t486.2\t0\t79\n", "45\t83\t486.2\t0\t83\n", "46\t127\t486.2\t0\t127\n", "47\t112\t486.2\t0\t112\n", "48\t72\t486.2\t0\t72\n", "49\t80\t486.2\t0\t80\n", "50\t84\t486.2\t0\t84\n", "51\t65\t486.2\t0\t65\n", "52\t83\t486.2\t0\t83\n", "53\t106\t486.2\t0\t106\n", "54\t81\t486.2\t0\t81\n", "55\t92\t486.2\t0\t92\n", "56\t84\t486.2\t0\t84\n", "57\t145\t486.2\t0\t145\n", "58\t99\t486.2\t0\t99\n", "59\t100\t486.2\t0\t100\n", "60\t204\t486.2\t0\t204\n", "61\t121\t486.2\t0\t121\n", "62\t85\t486.2\t0\t85\n", "63\t93\t486.2\t0\t93\n", "64\t188\t486.2\t0\t188\n", "65\t64\t486.2\t0\t64\n", "66\t92\t486.2\t0\t92\n", "67\t92\t486.2\t0\t92\n", "68\t79\t486.2\t0\t79\n", "69\t53\t486.2\t0\t53\n", "70\t63\t486.2\t0\t63\n", "71\t68\t486.2\t0\t68\n", "72\t62\t486.2\t0\t62\n", "73\t84\t486.2\t0\t84\n", "74\t84\t486.2\t0\t84\n", "75\t68\t486.2\t0\t68\n", "76\t71\t486.2\t0\t71\n", "77\t81\t486.2\t0\t81\n", "78\t74\t486.2\t0\t74\n", "79\t71\t486.2\t0\t71\n", "80\t76\t486.2\t0\t76\n", "81\t77\t486.2\t0\t77\n", "82\t113\t486.2\t0\t113\n", "83\t102\t486.2\t0\t102\n", "84\t107\t486.2\t0\t107\n", "85\t90\t486.2\t0\t90\n", "86\t79\t486.2\t0\t79\n", "87\t116\t486.2\t0\t116\n", "88\t228\t486.2\t0\t228\n", "89\t117\t486.2\t0\t117\n", "90\t93\t486.2\t0\t93\n", "91\t49\t486.2\t0\t49\n", "92\t44\t486.2\t0\t44\n", "93\t30\t486.2\t0\t30\n", "94\t39\t486.2\t0\t39\n", "95\t31\t486.2\t0\t31\n", "96\t32\t486.2\t0\t32\n", "97\t68\t486.2\t0\t68\n", "98\t75\t486.2\t0\t75\n", "99\t91\t486.2\t0\t91\n", "100\t100\t486.2\t0\t100\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 307_S45_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/307.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 103.96 s (14 us/read; 4.30 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,454,922\n", "Reads with adapters: 3,659,105 (49.1%)\n", "Reads written (passing filters): 7,296,222 (97.9%)\n", "\n", "Total basepairs processed: 745,492,200 bp\n", "Quality-trimmed: 1,758,899 bp (0.2%)\n", "Total written (filtered): 624,159,558 bp (83.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3475558 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.7%\n", " G: 36.8%\n", " T: 33.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t182174\t116483.2\t0\t182174\n", "4\t101529\t29120.8\t0\t101529\n", "5\t70849\t7280.2\t0\t70849\n", "6\t57977\t1820.0\t0\t57977\n", "7\t49338\t455.0\t0\t49338\n", "8\t48956\t113.8\t0\t48956\n", "9\t48084\t113.8\t0\t48084\n", "10\t47304\t113.8\t0\t47304\n", "11\t48137\t113.8\t0\t48137\n", "12\t48667\t113.8\t0\t48667\n", "13\t51161\t113.8\t0\t51161\n", "14\t52246\t113.8\t0\t52246\n", "15\t51622\t113.8\t0\t51622\n", "16\t54854\t113.8\t0\t54854\n", "17\t58833\t113.8\t0\t58833\n", "18\t65401\t113.8\t0\t65401\n", "19\t57499\t113.8\t0\t57499\n", "20\t49269\t113.8\t0\t49269\n", "21\t46193\t113.8\t0\t46193\n", "22\t43960\t113.8\t0\t43960\n", "23\t48395\t113.8\t0\t48395\n", "24\t55171\t113.8\t0\t55171\n", "25\t56091\t113.8\t0\t56091\n", "26\t62781\t113.8\t0\t62781\n", "27\t67013\t113.8\t0\t67013\n", "28\t61955\t113.8\t0\t61955\n", "29\t57686\t113.8\t0\t57686\n", "30\t57822\t113.8\t0\t57822\n", "31\t61380\t113.8\t0\t61380\n", "32\t62896\t113.8\t0\t62896\n", "33\t56963\t113.8\t0\t56963\n", "34\t54998\t113.8\t0\t54998\n", "35\t59039\t113.8\t0\t59039\n", "36\t65459\t113.8\t0\t65459\n", "37\t67137\t113.8\t0\t67137\n", "38\t57661\t113.8\t0\t57661\n", "39\t48240\t113.8\t0\t48240\n", "40\t45692\t113.8\t0\t45692\n", "41\t48119\t113.8\t0\t48119\n", "42\t50684\t113.8\t0\t50684\n", "43\t46745\t113.8\t0\t46745\n", "44\t39873\t113.8\t0\t39873\n", "45\t45195\t113.8\t0\t45195\n", "46\t51532\t113.8\t0\t51532\n", "47\t48261\t113.8\t0\t48261\n", "48\t46664\t113.8\t0\t46664\n", "49\t39006\t113.8\t0\t39006\n", "50\t36576\t113.8\t0\t36576\n", "51\t32942\t113.8\t0\t32942\n", "52\t35089\t113.8\t0\t35089\n", "53\t36546\t113.8\t0\t36546\n", "54\t33878\t113.8\t0\t33878\n", "55\t36912\t113.8\t0\t36912\n", "56\t36086\t113.8\t0\t36086\n", "57\t31690\t113.8\t0\t31690\n", "58\t30981\t113.8\t0\t30981\n", "59\t25972\t113.8\t0\t25972\n", "60\t22858\t113.8\t0\t22858\n", "61\t21438\t113.8\t0\t21438\n", "62\t18975\t113.8\t0\t18975\n", "63\t18197\t113.8\t0\t18197\n", "64\t19170\t113.8\t0\t19170\n", "65\t18409\t113.8\t0\t18409\n", "66\t16731\t113.8\t0\t16731\n", "67\t16321\t113.8\t0\t16321\n", "68\t15598\t113.8\t0\t15598\n", "69\t15604\t113.8\t0\t15604\n", "70\t15839\t113.8\t0\t15839\n", "71\t14702\t113.8\t0\t14702\n", "72\t12389\t113.8\t0\t12389\n", "73\t11273\t113.8\t0\t11273\n", "74\t10969\t113.8\t0\t10969\n", "75\t9888\t113.8\t0\t9888\n", "76\t8853\t113.8\t0\t8853\n", "77\t8557\t113.8\t0\t8557\n", "78\t8994\t113.8\t0\t8994\n", "79\t8749\t113.8\t0\t8749\n", "80\t8956\t113.8\t0\t8956\n", "81\t8628\t113.8\t0\t8628\n", "82\t8734\t113.8\t0\t8734\n", "83\t9011\t113.8\t0\t9011\n", "84\t9403\t113.8\t0\t9403\n", "85\t9871\t113.8\t0\t9871\n", "86\t9989\t113.8\t0\t9989\n", "87\t9208\t113.8\t0\t9208\n", "88\t9343\t113.8\t0\t9343\n", "89\t8795\t113.8\t0\t8795\n", "90\t8373\t113.8\t0\t8373\n", "91\t8104\t113.8\t0\t8104\n", "92\t7623\t113.8\t0\t7623\n", "93\t6907\t113.8\t0\t6907\n", "94\t5818\t113.8\t0\t5818\n", "95\t5027\t113.8\t0\t5027\n", "96\t3958\t113.8\t0\t3958\n", "97\t2952\t113.8\t0\t2952\n", "98\t2416\t113.8\t0\t2416\n", "99\t2527\t113.8\t0\t2527\n", "100\t3218\t113.8\t0\t3218\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 32628 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.8%\n", " C: 28.8%\n", " G: 0.0%\n", " T: 30.9%\n", " none/other: 0.5%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t17305\t116483.2\t0\t17305\n", "4\t4384\t29120.8\t0\t4384\n", "5\t1936\t7280.2\t0\t1936\n", "6\t686\t1820.0\t0\t686\n", "7\t108\t455.0\t0\t108\n", "8\t97\t113.8\t0\t97\n", "9\t73\t113.8\t0\t73\n", "10\t90\t113.8\t0\t90\n", "11\t76\t113.8\t0\t76\n", "12\t77\t113.8\t0\t77\n", "13\t92\t113.8\t0\t92\n", "14\t55\t113.8\t0\t55\n", "15\t75\t113.8\t0\t75\n", "16\t83\t113.8\t0\t83\n", "17\t95\t113.8\t0\t95\n", "18\t86\t113.8\t0\t86\n", "19\t118\t113.8\t0\t118\n", "20\t169\t113.8\t0\t169\n", "21\t106\t113.8\t0\t106\n", "22\t97\t113.8\t0\t97\n", "23\t94\t113.8\t0\t94\n", "24\t65\t113.8\t0\t65\n", "25\t86\t113.8\t0\t86\n", "26\t93\t113.8\t0\t93\n", "27\t108\t113.8\t0\t108\n", "28\t119\t113.8\t0\t119\n", "29\t125\t113.8\t0\t125\n", "30\t194\t113.8\t0\t194\n", "31\t234\t113.8\t0\t234\n", "32\t266\t113.8\t0\t266\n", "33\t308\t113.8\t0\t308\n", "34\t303\t113.8\t0\t303\n", "35\t404\t113.8\t0\t404\n", "36\t450\t113.8\t0\t450\n", "37\t237\t113.8\t0\t237\n", "38\t81\t113.8\t0\t81\n", "39\t71\t113.8\t0\t71\n", "40\t78\t113.8\t0\t78\n", "41\t63\t113.8\t0\t63\n", "42\t51\t113.8\t0\t51\n", "43\t56\t113.8\t0\t56\n", "44\t71\t113.8\t0\t71\n", "45\t81\t113.8\t0\t81\n", "46\t58\t113.8\t0\t58\n", "47\t55\t113.8\t0\t55\n", "48\t68\t113.8\t0\t68\n", "49\t74\t113.8\t0\t74\n", "50\t68\t113.8\t0\t68\n", "51\t55\t113.8\t0\t55\n", "52\t52\t113.8\t0\t52\n", "53\t58\t113.8\t0\t58\n", "54\t68\t113.8\t0\t68\n", "55\t59\t113.8\t0\t59\n", "56\t45\t113.8\t0\t45\n", "57\t55\t113.8\t0\t55\n", "58\t53\t113.8\t0\t53\n", "59\t42\t113.8\t0\t42\n", "60\t35\t113.8\t0\t35\n", "61\t55\t113.8\t0\t55\n", "62\t50\t113.8\t0\t50\n", "63\t48\t113.8\t0\t48\n", "64\t42\t113.8\t0\t42\n", "65\t51\t113.8\t0\t51\n", "66\t50\t113.8\t0\t50\n", "67\t35\t113.8\t0\t35\n", "68\t50\t113.8\t0\t50\n", "69\t40\t113.8\t0\t40\n", "70\t30\t113.8\t0\t30\n", "71\t37\t113.8\t0\t37\n", "72\t39\t113.8\t0\t39\n", "73\t19\t113.8\t0\t19\n", "74\t37\t113.8\t0\t37\n", "75\t31\t113.8\t0\t31\n", "76\t29\t113.8\t0\t29\n", "77\t24\t113.8\t0\t24\n", "78\t26\t113.8\t0\t26\n", "79\t27\t113.8\t0\t27\n", "80\t34\t113.8\t0\t34\n", "81\t38\t113.8\t0\t38\n", "82\t25\t113.8\t0\t25\n", "83\t32\t113.8\t0\t32\n", "84\t23\t113.8\t0\t23\n", "85\t34\t113.8\t0\t34\n", "86\t30\t113.8\t0\t30\n", "87\t31\t113.8\t0\t31\n", "88\t28\t113.8\t0\t28\n", "89\t32\t113.8\t0\t32\n", "90\t28\t113.8\t0\t28\n", "91\t43\t113.8\t0\t43\n", "92\t66\t113.8\t0\t66\n", "93\t96\t113.8\t0\t96\n", "94\t131\t113.8\t0\t131\n", "95\t152\t113.8\t0\t152\n", "96\t177\t113.8\t0\t177\n", "97\t195\t113.8\t0\t195\n", "98\t152\t113.8\t0\t152\n", "99\t96\t113.8\t0\t96\n", "100\t174\t113.8\t0\t174\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 150919 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 38.5%\n", " C: 18.3%\n", " G: 15.9%\n", " T: 27.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t111195\t116483.2\t0\t111195\n", "4\t28014\t29120.8\t0\t28014\n", "5\t3180\t7280.2\t0\t3180\n", "6\t330\t1820.0\t0\t330\n", "7\t99\t455.0\t0\t99\n", "8\t96\t455.0\t0\t96\n", "9\t84\t455.0\t0\t84\n", "10\t100\t455.0\t0\t100\n", "11\t92\t455.0\t0\t92\n", "12\t95\t455.0\t0\t95\n", "13\t131\t455.0\t0\t131\n", "14\t110\t455.0\t0\t110\n", "15\t114\t455.0\t0\t114\n", "16\t137\t455.0\t0\t137\n", "17\t111\t455.0\t0\t111\n", "18\t107\t455.0\t0\t107\n", "19\t100\t455.0\t0\t100\n", "20\t103\t455.0\t0\t103\n", "21\t111\t455.0\t0\t111\n", "22\t86\t455.0\t0\t86\n", "23\t80\t455.0\t0\t80\n", "24\t81\t455.0\t0\t81\n", "25\t98\t455.0\t0\t98\n", "26\t82\t455.0\t0\t82\n", "27\t90\t455.0\t0\t90\n", "28\t94\t455.0\t0\t94\n", "29\t100\t455.0\t0\t100\n", "30\t96\t455.0\t0\t96\n", "31\t90\t455.0\t0\t90\n", "32\t138\t455.0\t0\t138\n", "33\t101\t455.0\t0\t101\n", "34\t108\t455.0\t0\t108\n", "35\t86\t455.0\t0\t86\n", "36\t85\t455.0\t0\t85\n", "37\t90\t455.0\t0\t90\n", "38\t73\t455.0\t0\t73\n", "39\t78\t455.0\t0\t78\n", "40\t106\t455.0\t0\t106\n", "41\t80\t455.0\t0\t80\n", "42\t66\t455.0\t0\t66\n", "43\t79\t455.0\t0\t79\n", "44\t74\t455.0\t0\t74\n", "45\t90\t455.0\t0\t90\n", "46\t81\t455.0\t0\t81\n", "47\t87\t455.0\t0\t87\n", "48\t75\t455.0\t0\t75\n", "49\t80\t455.0\t0\t80\n", "50\t63\t455.0\t0\t63\n", "51\t84\t455.0\t0\t84\n", "52\t82\t455.0\t0\t82\n", "53\t71\t455.0\t0\t71\n", "54\t78\t455.0\t0\t78\n", "55\t70\t455.0\t0\t70\n", "56\t83\t455.0\t0\t83\n", "57\t99\t455.0\t0\t99\n", "58\t93\t455.0\t0\t93\n", "59\t60\t455.0\t0\t60\n", "60\t100\t455.0\t0\t100\n", "61\t89\t455.0\t0\t89\n", "62\t85\t455.0\t0\t85\n", "63\t63\t455.0\t0\t63\n", "64\t66\t455.0\t0\t66\n", "65\t78\t455.0\t0\t78\n", "66\t94\t455.0\t0\t94\n", "67\t84\t455.0\t0\t84\n", "68\t80\t455.0\t0\t80\n", "69\t56\t455.0\t0\t56\n", "70\t49\t455.0\t0\t49\n", "71\t66\t455.0\t0\t66\n", "72\t69\t455.0\t0\t69\n", "73\t61\t455.0\t0\t61\n", "74\t87\t455.0\t0\t87\n", "75\t78\t455.0\t0\t78\n", "76\t84\t455.0\t0\t84\n", "77\t87\t455.0\t0\t87\n", "78\t84\t455.0\t0\t84\n", "79\t73\t455.0\t0\t73\n", "80\t80\t455.0\t0\t80\n", "81\t83\t455.0\t0\t83\n", "82\t90\t455.0\t0\t90\n", "83\t92\t455.0\t0\t92\n", "84\t89\t455.0\t0\t89\n", "85\t99\t455.0\t0\t99\n", "86\t77\t455.0\t0\t77\n", "87\t106\t455.0\t0\t106\n", "88\t155\t455.0\t0\t155\n", "89\t135\t455.0\t0\t135\n", "90\t88\t455.0\t0\t88\n", "91\t51\t455.0\t0\t51\n", "92\t40\t455.0\t0\t40\n", "93\t32\t455.0\t0\t32\n", "94\t60\t455.0\t0\t60\n", "95\t65\t455.0\t0\t65\n", "96\t44\t455.0\t0\t44\n", "97\t85\t455.0\t0\t85\n", "98\t98\t455.0\t0\t98\n", "99\t116\t455.0\t0\t116\n", "100\t135\t455.0\t0\t135\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 308_S5_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/308.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 111.33 s (14 us/read; 4.41 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,178,700\n", "Reads with adapters: 4,914,353 (60.1%)\n", "Reads written (passing filters): 8,014,531 (98.0%)\n", "\n", "Total basepairs processed: 817,870,000 bp\n", "Quality-trimmed: 2,023,498 bp (0.2%)\n", "Total written (filtered): 643,150,462 bp (78.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4698173 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.1%\n", " G: 38.7%\n", " T: 28.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t172841\t127792.2\t0\t172841\n", "4\t102142\t31948.0\t0\t102142\n", "5\t75260\t7987.0\t0\t75260\n", "6\t64975\t1996.8\t0\t64975\n", "7\t60862\t499.2\t0\t60862\n", "8\t61594\t124.8\t0\t61594\n", "9\t61045\t124.8\t0\t61045\n", "10\t59636\t124.8\t0\t59636\n", "11\t60202\t124.8\t0\t60202\n", "12\t60684\t124.8\t0\t60684\n", "13\t61331\t124.8\t0\t61331\n", "14\t64041\t124.8\t0\t64041\n", "15\t62954\t124.8\t0\t62954\n", "16\t66420\t124.8\t0\t66420\n", "17\t73773\t124.8\t0\t73773\n", "18\t81371\t124.8\t0\t81371\n", "19\t75266\t124.8\t0\t75266\n", "20\t62841\t124.8\t0\t62841\n", "21\t58720\t124.8\t0\t58720\n", "22\t55395\t124.8\t0\t55395\n", "23\t61265\t124.8\t0\t61265\n", "24\t70279\t124.8\t0\t70279\n", "25\t74191\t124.8\t0\t74191\n", "26\t80775\t124.8\t0\t80775\n", "27\t81445\t124.8\t0\t81445\n", "28\t75632\t124.8\t0\t75632\n", "29\t73294\t124.8\t0\t73294\n", "30\t75674\t124.8\t0\t75674\n", "31\t82149\t124.8\t0\t82149\n", "32\t80349\t124.8\t0\t80349\n", "33\t75410\t124.8\t0\t75410\n", "34\t73189\t124.8\t0\t73189\n", "35\t80509\t124.8\t0\t80509\n", "36\t88450\t124.8\t0\t88450\n", "37\t90916\t124.8\t0\t90916\n", "38\t79874\t124.8\t0\t79874\n", "39\t71329\t124.8\t0\t71329\n", "40\t68105\t124.8\t0\t68105\n", "41\t73299\t124.8\t0\t73299\n", "42\t79200\t124.8\t0\t79200\n", "43\t71726\t124.8\t0\t71726\n", "44\t60535\t124.8\t0\t60535\n", "45\t74048\t124.8\t0\t74048\n", "46\t87062\t124.8\t0\t87062\n", "47\t76230\t124.8\t0\t76230\n", "48\t73304\t124.8\t0\t73304\n", "49\t60516\t124.8\t0\t60516\n", "50\t60872\t124.8\t0\t60872\n", "51\t55956\t124.8\t0\t55956\n", "52\t59170\t124.8\t0\t59170\n", "53\t60465\t124.8\t0\t60465\n", "54\t56257\t124.8\t0\t56257\n", "55\t60112\t124.8\t0\t60112\n", "56\t58177\t124.8\t0\t58177\n", "57\t48478\t124.8\t0\t48478\n", "58\t47507\t124.8\t0\t47507\n", "59\t41793\t124.8\t0\t41793\n", "60\t38597\t124.8\t0\t38597\n", "61\t36856\t124.8\t0\t36856\n", "62\t30314\t124.8\t0\t30314\n", "63\t28102\t124.8\t0\t28102\n", "64\t31388\t124.8\t0\t31388\n", "65\t32070\t124.8\t0\t32070\n", "66\t28315\t124.8\t0\t28315\n", "67\t27661\t124.8\t0\t27661\n", "68\t27524\t124.8\t0\t27524\n", "69\t28674\t124.8\t0\t28674\n", "70\t28548\t124.8\t0\t28548\n", "71\t27090\t124.8\t0\t27090\n", "72\t22366\t124.8\t0\t22366\n", "73\t20278\t124.8\t0\t20278\n", "74\t20061\t124.8\t0\t20061\n", "75\t17704\t124.8\t0\t17704\n", "76\t15588\t124.8\t0\t15588\n", "77\t13897\t124.8\t0\t13897\n", "78\t14411\t124.8\t0\t14411\n", "79\t13952\t124.8\t0\t13952\n", "80\t13360\t124.8\t0\t13360\n", "81\t12221\t124.8\t0\t12221\n", "82\t11780\t124.8\t0\t11780\n", "83\t11560\t124.8\t0\t11560\n", "84\t12420\t124.8\t0\t12420\n", "85\t12644\t124.8\t0\t12644\n", "86\t11311\t124.8\t0\t11311\n", "87\t8048\t124.8\t0\t8048\n", "88\t7326\t124.8\t0\t7326\n", "89\t7483\t124.8\t0\t7483\n", "90\t7513\t124.8\t0\t7513\n", "91\t8027\t124.8\t0\t8027\n", "92\t7664\t124.8\t0\t7664\n", "93\t7537\t124.8\t0\t7537\n", "94\t6792\t124.8\t0\t6792\n", "95\t5677\t124.8\t0\t5677\n", "96\t4397\t124.8\t0\t4397\n", "97\t2841\t124.8\t0\t2841\n", "98\t1856\t124.8\t0\t1856\n", "99\t3100\t124.8\t0\t3100\n", "100\t2325\t124.8\t0\t2325\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 39613 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 56.9%\n", " C: 19.9%\n", " G: 0.0%\n", " T: 23.1%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t15392\t127792.2\t0\t15392\n", "4\t4346\t31948.0\t0\t4346\n", "5\t2072\t7987.0\t0\t2072\n", "6\t1610\t1996.8\t0\t1610\n", "7\t761\t499.2\t0\t761\n", "8\t627\t124.8\t0\t627\n", "9\t554\t124.8\t0\t554\n", "10\t584\t124.8\t0\t584\n", "11\t484\t124.8\t0\t484\n", "12\t473\t124.8\t0\t473\n", "13\t424\t124.8\t0\t424\n", "14\t434\t124.8\t0\t434\n", "15\t351\t124.8\t0\t351\n", "16\t305\t124.8\t0\t305\n", "17\t332\t124.8\t0\t332\n", "18\t453\t124.8\t0\t453\n", "19\t531\t124.8\t0\t531\n", "20\t853\t124.8\t0\t853\n", "21\t543\t124.8\t0\t543\n", "22\t379\t124.8\t0\t379\n", "23\t246\t124.8\t0\t246\n", "24\t288\t124.8\t0\t288\n", "25\t262\t124.8\t0\t262\n", "26\t354\t124.8\t0\t354\n", "27\t283\t124.8\t0\t283\n", "28\t261\t124.8\t0\t261\n", "29\t308\t124.8\t0\t308\n", "30\t411\t124.8\t0\t411\n", "31\t406\t124.8\t0\t406\n", "32\t608\t124.8\t0\t608\n", "33\t584\t124.8\t0\t584\n", "34\t562\t124.8\t0\t562\n", "35\t711\t124.8\t0\t711\n", "36\t688\t124.8\t0\t688\n", "37\t305\t124.8\t0\t305\n", "38\t49\t124.8\t0\t49\n", "39\t40\t124.8\t0\t40\n", "40\t43\t124.8\t0\t43\n", "41\t43\t124.8\t0\t43\n", "42\t41\t124.8\t0\t41\n", "43\t42\t124.8\t0\t42\n", "44\t44\t124.8\t0\t44\n", "45\t48\t124.8\t0\t48\n", "46\t36\t124.8\t0\t36\n", "47\t47\t124.8\t0\t47\n", "48\t33\t124.8\t0\t33\n", "49\t40\t124.8\t0\t40\n", "50\t42\t124.8\t0\t42\n", "51\t34\t124.8\t0\t34\n", "52\t39\t124.8\t0\t39\n", "53\t39\t124.8\t0\t39\n", "54\t37\t124.8\t0\t37\n", "55\t37\t124.8\t0\t37\n", "56\t30\t124.8\t0\t30\n", "57\t30\t124.8\t0\t30\n", "58\t25\t124.8\t0\t25\n", "59\t29\t124.8\t0\t29\n", "60\t28\t124.8\t0\t28\n", "61\t28\t124.8\t0\t28\n", "62\t34\t124.8\t0\t34\n", "63\t25\t124.8\t0\t25\n", "64\t19\t124.8\t0\t19\n", "65\t15\t124.8\t0\t15\n", "66\t23\t124.8\t0\t23\n", "67\t23\t124.8\t0\t23\n", "68\t14\t124.8\t0\t14\n", "69\t18\t124.8\t0\t18\n", "70\t20\t124.8\t0\t20\n", "71\t20\t124.8\t0\t20\n", "72\t18\t124.8\t0\t18\n", "73\t13\t124.8\t0\t13\n", "74\t16\t124.8\t0\t16\n", "75\t9\t124.8\t0\t9\n", "76\t8\t124.8\t0\t8\n", "77\t15\t124.8\t0\t15\n", "78\t10\t124.8\t0\t10\n", "79\t13\t124.8\t0\t13\n", "80\t3\t124.8\t0\t3\n", "81\t10\t124.8\t0\t10\n", "82\t12\t124.8\t0\t12\n", "83\t24\t124.8\t0\t24\n", "84\t10\t124.8\t0\t10\n", "85\t7\t124.8\t0\t7\n", "86\t8\t124.8\t0\t8\n", "87\t10\t124.8\t0\t10\n", "88\t16\t124.8\t0\t16\n", "89\t13\t124.8\t0\t13\n", "90\t21\t124.8\t0\t21\n", "91\t15\t124.8\t0\t15\n", "92\t19\t124.8\t0\t19\n", "93\t38\t124.8\t0\t38\n", "94\t35\t124.8\t0\t35\n", "95\t66\t124.8\t0\t66\n", "96\t55\t124.8\t0\t55\n", "97\t83\t124.8\t0\t83\n", "98\t56\t124.8\t0\t56\n", "99\t35\t124.8\t0\t35\n", "100\t75\t124.8\t0\t75\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 176567 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.8%\n", " C: 17.7%\n", " G: 15.6%\n", " T: 25.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t103829\t127792.2\t0\t103829\n", "4\t26638\t31948.0\t0\t26638\n", "5\t8039\t7987.0\t0\t8039\n", "6\t996\t1996.8\t0\t996\n", "7\t778\t499.2\t0\t778\n", "8\t793\t499.2\t0\t793\n", "9\t699\t499.2\t0\t699\n", "10\t743\t499.2\t0\t743\n", "11\t781\t499.2\t0\t781\n", "12\t791\t499.2\t0\t791\n", "13\t736\t499.2\t0\t736\n", "14\t772\t499.2\t0\t772\n", "15\t860\t499.2\t0\t860\n", "16\t755\t499.2\t0\t755\n", "17\t844\t499.2\t0\t844\n", "18\t751\t499.2\t0\t751\n", "19\t715\t499.2\t0\t715\n", "20\t726\t499.2\t0\t726\n", "21\t675\t499.2\t0\t675\n", "22\t697\t499.2\t0\t697\n", "23\t717\t499.2\t0\t717\n", "24\t643\t499.2\t0\t643\n", "25\t666\t499.2\t0\t666\n", "26\t610\t499.2\t0\t610\n", "27\t638\t499.2\t0\t638\n", "28\t658\t499.2\t0\t658\n", "29\t635\t499.2\t0\t635\n", "30\t612\t499.2\t0\t612\n", "31\t634\t499.2\t0\t634\n", "32\t698\t499.2\t0\t698\n", "33\t596\t499.2\t0\t596\n", "34\t676\t499.2\t0\t676\n", "35\t638\t499.2\t0\t638\n", "36\t497\t499.2\t0\t497\n", "37\t585\t499.2\t0\t585\n", "38\t571\t499.2\t0\t571\n", "39\t489\t499.2\t0\t489\n", "40\t560\t499.2\t0\t560\n", "41\t542\t499.2\t0\t542\n", "42\t418\t499.2\t0\t418\n", "43\t735\t499.2\t0\t735\n", "44\t160\t499.2\t0\t160\n", "45\t443\t499.2\t0\t443\n", "46\t404\t499.2\t0\t404\n", "47\t397\t499.2\t0\t397\n", "48\t359\t499.2\t0\t359\n", "49\t355\t499.2\t0\t355\n", "50\t352\t499.2\t0\t352\n", "51\t339\t499.2\t0\t339\n", "52\t327\t499.2\t0\t327\n", "53\t306\t499.2\t0\t306\n", "54\t310\t499.2\t0\t310\n", "55\t307\t499.2\t0\t307\n", "56\t333\t499.2\t0\t333\n", "57\t268\t499.2\t0\t268\n", "58\t384\t499.2\t0\t384\n", "59\t251\t499.2\t0\t251\n", "60\t350\t499.2\t0\t350\n", "61\t381\t499.2\t0\t381\n", "62\t318\t499.2\t0\t318\n", "63\t214\t499.2\t0\t214\n", "64\t280\t499.2\t0\t280\n", "65\t284\t499.2\t0\t284\n", "66\t263\t499.2\t0\t263\n", "67\t202\t499.2\t0\t202\n", "68\t208\t499.2\t0\t208\n", "69\t122\t499.2\t0\t122\n", "70\t106\t499.2\t0\t106\n", "71\t127\t499.2\t0\t127\n", "72\t181\t499.2\t0\t181\n", "73\t165\t499.2\t0\t165\n", "74\t174\t499.2\t0\t174\n", "75\t126\t499.2\t0\t126\n", "76\t162\t499.2\t0\t162\n", "77\t190\t499.2\t0\t190\n", "78\t157\t499.2\t0\t157\n", "79\t171\t499.2\t0\t171\n", "80\t163\t499.2\t0\t163\n", "81\t136\t499.2\t0\t136\n", "82\t169\t499.2\t0\t169\n", "83\t153\t499.2\t0\t153\n", "84\t145\t499.2\t0\t145\n", "85\t143\t499.2\t0\t143\n", "86\t113\t499.2\t0\t113\n", "87\t154\t499.2\t0\t154\n", "88\t257\t499.2\t0\t257\n", "89\t202\t499.2\t0\t202\n", "90\t135\t499.2\t0\t135\n", "91\t83\t499.2\t0\t83\n", "92\t67\t499.2\t0\t67\n", "93\t57\t499.2\t0\t57\n", "94\t80\t499.2\t0\t80\n", "95\t70\t499.2\t0\t70\n", "96\t68\t499.2\t0\t68\n", "97\t124\t499.2\t0\t124\n", "98\t88\t499.2\t0\t88\n", "99\t127\t499.2\t0\t127\n", "100\t121\t499.2\t0\t121\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 309_S20_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/309.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 120.51 s (14 us/read; 4.28 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,601,123\n", "Reads with adapters: 5,587,494 (65.0%)\n", "Reads written (passing filters): 8,376,279 (97.4%)\n", "\n", "Total basepairs processed: 860,112,300 bp\n", "Quality-trimmed: 2,298,255 bp (0.3%)\n", "Total written (filtered): 654,485,376 bp (76.1%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5428630 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 34.0%\n", " G: 39.5%\n", " T: 26.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t173531\t134392.5\t0\t173531\n", "4\t105288\t33598.1\t0\t105288\n", "5\t82215\t8399.5\t0\t82215\n", "6\t70809\t2099.9\t0\t70809\n", "7\t67380\t525.0\t0\t67380\n", "8\t68295\t131.2\t0\t68295\n", "9\t68029\t131.2\t0\t68029\n", "10\t67821\t131.2\t0\t67821\n", "11\t68003\t131.2\t0\t68003\n", "12\t69817\t131.2\t0\t69817\n", "13\t74753\t131.2\t0\t74753\n", "14\t76826\t131.2\t0\t76826\n", "15\t72954\t131.2\t0\t72954\n", "16\t77894\t131.2\t0\t77894\n", "17\t85491\t131.2\t0\t85491\n", "18\t97201\t131.2\t0\t97201\n", "19\t86073\t131.2\t0\t86073\n", "20\t72490\t131.2\t0\t72490\n", "21\t68725\t131.2\t0\t68725\n", "22\t63382\t131.2\t0\t63382\n", "23\t69682\t131.2\t0\t69682\n", "24\t79913\t131.2\t0\t79913\n", "25\t84198\t131.2\t0\t84198\n", "26\t95156\t131.2\t0\t95156\n", "27\t101034\t131.2\t0\t101034\n", "28\t90052\t131.2\t0\t90052\n", "29\t81664\t131.2\t0\t81664\n", "30\t83085\t131.2\t0\t83085\n", "31\t94397\t131.2\t0\t94397\n", "32\t86536\t131.2\t0\t86536\n", "33\t87070\t131.2\t0\t87070\n", "34\t80702\t131.2\t0\t80702\n", "35\t93545\t131.2\t0\t93545\n", "36\t104871\t131.2\t0\t104871\n", "37\t99382\t131.2\t0\t99382\n", "38\t87551\t131.2\t0\t87551\n", "39\t77250\t131.2\t0\t77250\n", "40\t76602\t131.2\t0\t76602\n", "41\t87904\t131.2\t0\t87904\n", "42\t96616\t131.2\t0\t96616\n", "43\t85501\t131.2\t0\t85501\n", "44\t65243\t131.2\t0\t65243\n", "45\t80158\t131.2\t0\t80158\n", "46\t93530\t131.2\t0\t93530\n", "47\t87713\t131.2\t0\t87713\n", "48\t83109\t131.2\t0\t83109\n", "49\t68900\t131.2\t0\t68900\n", "50\t68620\t131.2\t0\t68620\n", "51\t60128\t131.2\t0\t60128\n", "52\t68148\t131.2\t0\t68148\n", "53\t74610\t131.2\t0\t74610\n", "54\t66481\t131.2\t0\t66481\n", "55\t69728\t131.2\t0\t69728\n", "56\t62367\t131.2\t0\t62367\n", "57\t65400\t131.2\t0\t65400\n", "58\t58817\t131.2\t0\t58817\n", "59\t54109\t131.2\t0\t54109\n", "60\t47181\t131.2\t0\t47181\n", "61\t45559\t131.2\t0\t45559\n", "62\t38388\t131.2\t0\t38388\n", "63\t35959\t131.2\t0\t35959\n", "64\t41023\t131.2\t0\t41023\n", "65\t39790\t131.2\t0\t39790\n", "66\t33525\t131.2\t0\t33525\n", "67\t33456\t131.2\t0\t33456\n", "68\t33141\t131.2\t0\t33141\n", "69\t34202\t131.2\t0\t34202\n", "70\t35606\t131.2\t0\t35606\n", "71\t34463\t131.2\t0\t34463\n", "72\t26293\t131.2\t0\t26293\n", "73\t23755\t131.2\t0\t23755\n", "74\t23311\t131.2\t0\t23311\n", "75\t20840\t131.2\t0\t20840\n", "76\t17446\t131.2\t0\t17446\n", "77\t15902\t131.2\t0\t15902\n", "78\t18341\t131.2\t0\t18341\n", "79\t17136\t131.2\t0\t17136\n", "80\t15909\t131.2\t0\t15909\n", "81\t15055\t131.2\t0\t15055\n", "82\t14403\t131.2\t0\t14403\n", "83\t14519\t131.2\t0\t14519\n", "84\t16331\t131.2\t0\t16331\n", "85\t17952\t131.2\t0\t17952\n", "86\t17029\t131.2\t0\t17029\n", "87\t11924\t131.2\t0\t11924\n", "88\t10823\t131.2\t0\t10823\n", "89\t10985\t131.2\t0\t10985\n", "90\t11274\t131.2\t0\t11274\n", "91\t11035\t131.2\t0\t11035\n", "92\t10897\t131.2\t0\t10897\n", "93\t11266\t131.2\t0\t11266\n", "94\t10800\t131.2\t0\t10800\n", "95\t9037\t131.2\t0\t9037\n", "96\t6467\t131.2\t0\t6467\n", "97\t4004\t131.2\t0\t4004\n", "98\t2437\t131.2\t0\t2437\n", "99\t2823\t131.2\t0\t2823\n", "100\t1594\t131.2\t0\t1594\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 34999 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 48.9%\n", " C: 26.6%\n", " G: 0.0%\n", " T: 24.4%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t16169\t134392.5\t0\t16169\n", "4\t3676\t33598.1\t0\t3676\n", "5\t1302\t8399.5\t0\t1302\n", "6\t773\t2099.9\t0\t773\n", "7\t209\t525.0\t0\t209\n", "8\t356\t131.2\t0\t356\n", "9\t135\t131.2\t0\t135\n", "10\t113\t131.2\t0\t113\n", "11\t120\t131.2\t0\t120\n", "12\t100\t131.2\t0\t100\n", "13\t95\t131.2\t0\t95\n", "14\t118\t131.2\t0\t118\n", "15\t104\t131.2\t0\t104\n", "16\t120\t131.2\t0\t120\n", "17\t138\t131.2\t0\t138\n", "18\t170\t131.2\t0\t170\n", "19\t158\t131.2\t0\t158\n", "20\t255\t131.2\t0\t255\n", "21\t209\t131.2\t0\t209\n", "22\t154\t131.2\t0\t154\n", "23\t112\t131.2\t0\t112\n", "24\t138\t131.2\t0\t138\n", "25\t170\t131.2\t0\t170\n", "26\t242\t131.2\t0\t242\n", "27\t247\t131.2\t0\t247\n", "28\t266\t131.2\t0\t266\n", "29\t354\t131.2\t0\t354\n", "30\t547\t131.2\t0\t547\n", "31\t619\t131.2\t0\t619\n", "32\t846\t131.2\t0\t846\n", "33\t775\t131.2\t0\t775\n", "34\t797\t131.2\t0\t797\n", "35\t953\t131.2\t0\t953\n", "36\t847\t131.2\t0\t847\n", "37\t347\t131.2\t0\t347\n", "38\t90\t131.2\t0\t90\n", "39\t63\t131.2\t0\t63\n", "40\t78\t131.2\t0\t78\n", "41\t64\t131.2\t0\t64\n", "42\t68\t131.2\t0\t68\n", "43\t85\t131.2\t0\t85\n", "44\t71\t131.2\t0\t71\n", "45\t74\t131.2\t0\t74\n", "46\t89\t131.2\t0\t89\n", "47\t82\t131.2\t0\t82\n", "48\t71\t131.2\t0\t71\n", "49\t93\t131.2\t0\t93\n", "50\t81\t131.2\t0\t81\n", "51\t55\t131.2\t0\t55\n", "52\t71\t131.2\t0\t71\n", "53\t72\t131.2\t0\t72\n", "54\t47\t131.2\t0\t47\n", "55\t68\t131.2\t0\t68\n", "56\t49\t131.2\t0\t49\n", "57\t46\t131.2\t0\t46\n", "58\t47\t131.2\t0\t47\n", "59\t48\t131.2\t0\t48\n", "60\t49\t131.2\t0\t49\n", "61\t54\t131.2\t0\t54\n", "62\t50\t131.2\t0\t50\n", "63\t47\t131.2\t0\t47\n", "64\t46\t131.2\t0\t46\n", "65\t38\t131.2\t0\t38\n", "66\t34\t131.2\t0\t34\n", "67\t45\t131.2\t0\t45\n", "68\t28\t131.2\t0\t28\n", "69\t22\t131.2\t0\t22\n", "70\t30\t131.2\t0\t30\n", "71\t23\t131.2\t0\t23\n", "72\t24\t131.2\t0\t24\n", "73\t11\t131.2\t0\t11\n", "74\t15\t131.2\t0\t15\n", "75\t14\t131.2\t0\t14\n", "76\t12\t131.2\t0\t12\n", "77\t12\t131.2\t0\t12\n", "78\t22\t131.2\t0\t22\n", "79\t21\t131.2\t0\t21\n", "80\t13\t131.2\t0\t13\n", "81\t14\t131.2\t0\t14\n", "82\t14\t131.2\t0\t14\n", "83\t17\t131.2\t0\t17\n", "84\t21\t131.2\t0\t21\n", "85\t34\t131.2\t0\t34\n", "86\t24\t131.2\t0\t24\n", "87\t17\t131.2\t0\t17\n", "88\t15\t131.2\t0\t15\n", "89\t19\t131.2\t0\t19\n", "90\t18\t131.2\t0\t18\n", "91\t32\t131.2\t0\t32\n", "92\t39\t131.2\t0\t39\n", "93\t80\t131.2\t0\t80\n", "94\t97\t131.2\t0\t97\n", "95\t98\t131.2\t0\t98\n", "96\t176\t131.2\t0\t176\n", "97\t116\t131.2\t0\t116\n", "98\t93\t131.2\t0\t93\n", "99\t83\t131.2\t0\t83\n", "100\t136\t131.2\t0\t136\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 123865 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.6%\n", " C: 19.2%\n", " G: 18.7%\n", " T: 19.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t89506\t134392.5\t0\t89506\n", "4\t19022\t33598.1\t0\t19022\n", "5\t3269\t8399.5\t0\t3269\n", "6\t389\t2099.9\t0\t389\n", "7\t155\t525.0\t0\t155\n", "8\t177\t525.0\t0\t177\n", "9\t158\t525.0\t0\t158\n", "10\t154\t525.0\t0\t154\n", "11\t154\t525.0\t0\t154\n", "12\t191\t525.0\t0\t191\n", "13\t203\t525.0\t0\t203\n", "14\t196\t525.0\t0\t196\n", "15\t207\t525.0\t0\t207\n", "16\t231\t525.0\t0\t231\n", "17\t195\t525.0\t0\t195\n", "18\t195\t525.0\t0\t195\n", "19\t188\t525.0\t0\t188\n", "20\t202\t525.0\t0\t202\n", "21\t201\t525.0\t0\t201\n", "22\t185\t525.0\t0\t185\n", "23\t162\t525.0\t0\t162\n", "24\t187\t525.0\t0\t187\n", "25\t161\t525.0\t0\t161\n", "26\t156\t525.0\t0\t156\n", "27\t173\t525.0\t0\t173\n", "28\t182\t525.0\t0\t182\n", "29\t162\t525.0\t0\t162\n", "30\t182\t525.0\t0\t182\n", "31\t145\t525.0\t0\t145\n", "32\t161\t525.0\t0\t161\n", "33\t149\t525.0\t0\t149\n", "34\t178\t525.0\t0\t178\n", "35\t156\t525.0\t0\t156\n", "36\t130\t525.0\t0\t130\n", "37\t143\t525.0\t0\t143\n", "38\t132\t525.0\t0\t132\n", "39\t148\t525.0\t0\t148\n", "40\t182\t525.0\t0\t182\n", "41\t133\t525.0\t0\t133\n", "42\t96\t525.0\t0\t96\n", "43\t153\t525.0\t0\t153\n", "44\t79\t525.0\t0\t79\n", "45\t109\t525.0\t0\t109\n", "46\t107\t525.0\t0\t107\n", "47\t118\t525.0\t0\t118\n", "48\t99\t525.0\t0\t99\n", "49\t113\t525.0\t0\t113\n", "50\t92\t525.0\t0\t92\n", "51\t97\t525.0\t0\t97\n", "52\t100\t525.0\t0\t100\n", "53\t83\t525.0\t0\t83\n", "54\t103\t525.0\t0\t103\n", "55\t76\t525.0\t0\t76\n", "56\t92\t525.0\t0\t92\n", "57\t72\t525.0\t0\t72\n", "58\t101\t525.0\t0\t101\n", "59\t73\t525.0\t0\t73\n", "60\t78\t525.0\t0\t78\n", "61\t86\t525.0\t0\t86\n", "62\t70\t525.0\t0\t70\n", "63\t83\t525.0\t0\t83\n", "64\t82\t525.0\t0\t82\n", "65\t85\t525.0\t0\t85\n", "66\t72\t525.0\t0\t72\n", "67\t82\t525.0\t0\t82\n", "68\t84\t525.0\t0\t84\n", "69\t77\t525.0\t0\t77\n", "70\t93\t525.0\t0\t93\n", "71\t72\t525.0\t0\t72\n", "72\t84\t525.0\t0\t84\n", "73\t79\t525.0\t0\t79\n", "74\t97\t525.0\t0\t97\n", "75\t94\t525.0\t0\t94\n", "76\t174\t525.0\t0\t174\n", "77\t120\t525.0\t0\t120\n", "78\t116\t525.0\t0\t116\n", "79\t118\t525.0\t0\t118\n", "80\t124\t525.0\t0\t124\n", "81\t116\t525.0\t0\t116\n", "82\t138\t525.0\t0\t138\n", "83\t103\t525.0\t0\t103\n", "84\t124\t525.0\t0\t124\n", "85\t117\t525.0\t0\t117\n", "86\t94\t525.0\t0\t94\n", "87\t97\t525.0\t0\t97\n", "88\t98\t525.0\t0\t98\n", "89\t76\t525.0\t0\t76\n", "90\t92\t525.0\t0\t92\n", "91\t75\t525.0\t0\t75\n", "92\t67\t525.0\t0\t67\n", "93\t68\t525.0\t0\t68\n", "94\t75\t525.0\t0\t75\n", "95\t95\t525.0\t0\t95\n", "96\t56\t525.0\t0\t56\n", "97\t100\t525.0\t0\t100\n", "98\t104\t525.0\t0\t104\n", "99\t110\t525.0\t0\t110\n", "100\t127\t525.0\t0\t127\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 311_S2_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/311.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 102.81 s (15 us/read; 4.13 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,073,914\n", "Reads with adapters: 4,420,404 (62.5%)\n", "Reads written (passing filters): 6,870,080 (97.1%)\n", "\n", "Total basepairs processed: 707,391,400 bp\n", "Quality-trimmed: 1,818,770 bp (0.3%)\n", "Total written (filtered): 542,247,927 bp (76.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4276772 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 32.9%\n", " G: 39.1%\n", " T: 27.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t144301\t110529.9\t0\t144301\n", "4\t86204\t27632.5\t0\t86204\n", "5\t65506\t6908.1\t0\t65506\n", "6\t56358\t1727.0\t0\t56358\n", "7\t52452\t431.8\t0\t52452\n", "8\t52723\t107.9\t0\t52723\n", "9\t52294\t107.9\t0\t52294\n", "10\t52610\t107.9\t0\t52610\n", "11\t53221\t107.9\t0\t53221\n", "12\t54617\t107.9\t0\t54617\n", "13\t62682\t107.9\t0\t62682\n", "14\t63009\t107.9\t0\t63009\n", "15\t57395\t107.9\t0\t57395\n", "16\t60040\t107.9\t0\t60040\n", "17\t65209\t107.9\t0\t65209\n", "18\t75005\t107.9\t0\t75005\n", "19\t67964\t107.9\t0\t67964\n", "20\t57354\t107.9\t0\t57354\n", "21\t54091\t107.9\t0\t54091\n", "22\t50110\t107.9\t0\t50110\n", "23\t53884\t107.9\t0\t53884\n", "24\t60940\t107.9\t0\t60940\n", "25\t63722\t107.9\t0\t63722\n", "26\t69944\t107.9\t0\t69944\n", "27\t73330\t107.9\t0\t73330\n", "28\t67865\t107.9\t0\t67865\n", "29\t62784\t107.9\t0\t62784\n", "30\t62020\t107.9\t0\t62020\n", "31\t68029\t107.9\t0\t68029\n", "32\t64177\t107.9\t0\t64177\n", "33\t62136\t107.9\t0\t62136\n", "34\t62071\t107.9\t0\t62071\n", "35\t69063\t107.9\t0\t69063\n", "36\t75229\t107.9\t0\t75229\n", "37\t75727\t107.9\t0\t75727\n", "38\t64429\t107.9\t0\t64429\n", "39\t61716\t107.9\t0\t61716\n", "40\t60181\t107.9\t0\t60181\n", "41\t67343\t107.9\t0\t67343\n", "42\t73578\t107.9\t0\t73578\n", "43\t65122\t107.9\t0\t65122\n", "44\t52098\t107.9\t0\t52098\n", "45\t60969\t107.9\t0\t60969\n", "46\t73478\t107.9\t0\t73478\n", "47\t74021\t107.9\t0\t74021\n", "48\t67450\t107.9\t0\t67450\n", "49\t58718\t107.9\t0\t58718\n", "50\t54260\t107.9\t0\t54260\n", "51\t49672\t107.9\t0\t49672\n", "52\t47956\t107.9\t0\t47956\n", "53\t47084\t107.9\t0\t47084\n", "54\t53722\t107.9\t0\t53722\n", "55\t58811\t107.9\t0\t58811\n", "56\t49455\t107.9\t0\t49455\n", "57\t47635\t107.9\t0\t47635\n", "58\t49761\t107.9\t0\t49761\n", "59\t44663\t107.9\t0\t44663\n", "60\t39078\t107.9\t0\t39078\n", "61\t37319\t107.9\t0\t37319\n", "62\t32215\t107.9\t0\t32215\n", "63\t29714\t107.9\t0\t29714\n", "64\t33192\t107.9\t0\t33192\n", "65\t32350\t107.9\t0\t32350\n", "66\t28246\t107.9\t0\t28246\n", "67\t27996\t107.9\t0\t27996\n", "68\t27872\t107.9\t0\t27872\n", "69\t28553\t107.9\t0\t28553\n", "70\t29889\t107.9\t0\t29889\n", "71\t28835\t107.9\t0\t28835\n", "72\t22826\t107.9\t0\t22826\n", "73\t20513\t107.9\t0\t20513\n", "74\t20100\t107.9\t0\t20100\n", "75\t17832\t107.9\t0\t17832\n", "76\t14846\t107.9\t0\t14846\n", "77\t13728\t107.9\t0\t13728\n", "78\t15747\t107.9\t0\t15747\n", "79\t15327\t107.9\t0\t15327\n", "80\t14612\t107.9\t0\t14612\n", "81\t13981\t107.9\t0\t13981\n", "82\t13039\t107.9\t0\t13039\n", "83\t13245\t107.9\t0\t13245\n", "84\t14579\t107.9\t0\t14579\n", "85\t16048\t107.9\t0\t16048\n", "86\t15517\t107.9\t0\t15517\n", "87\t11454\t107.9\t0\t11454\n", "88\t10062\t107.9\t0\t10062\n", "89\t9918\t107.9\t0\t9918\n", "90\t9988\t107.9\t0\t9988\n", "91\t9896\t107.9\t0\t9896\n", "92\t9638\t107.9\t0\t9638\n", "93\t9610\t107.9\t0\t9610\n", "94\t9319\t107.9\t0\t9319\n", "95\t7914\t107.9\t0\t7914\n", "96\t5720\t107.9\t0\t5720\n", "97\t3678\t107.9\t0\t3678\n", "98\t2191\t107.9\t0\t2191\n", "99\t2714\t107.9\t0\t2714\n", "100\t1283\t107.9\t0\t1283\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 42337 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 65.5%\n", " C: 16.4%\n", " G: 0.0%\n", " T: 18.0%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t12249\t110529.9\t0\t12249\n", "4\t2898\t27632.5\t0\t2898\n", "5\t1141\t6908.1\t0\t1141\n", "6\t729\t1727.0\t0\t729\n", "7\t145\t431.8\t0\t145\n", "8\t116\t107.9\t0\t116\n", "9\t106\t107.9\t0\t106\n", "10\t107\t107.9\t0\t107\n", "11\t101\t107.9\t0\t101\n", "12\t78\t107.9\t0\t78\n", "13\t87\t107.9\t0\t87\n", "14\t104\t107.9\t0\t104\n", "15\t110\t107.9\t0\t110\n", "16\t110\t107.9\t0\t110\n", "17\t128\t107.9\t0\t128\n", "18\t175\t107.9\t0\t175\n", "19\t214\t107.9\t0\t214\n", "20\t366\t107.9\t0\t366\n", "21\t245\t107.9\t0\t245\n", "22\t203\t107.9\t0\t203\n", "23\t160\t107.9\t0\t160\n", "24\t146\t107.9\t0\t146\n", "25\t206\t107.9\t0\t206\n", "26\t361\t107.9\t0\t361\n", "27\t427\t107.9\t0\t427\n", "28\t477\t107.9\t0\t477\n", "29\t703\t107.9\t0\t703\n", "30\t1314\t107.9\t0\t1314\n", "31\t1507\t107.9\t0\t1507\n", "32\t2182\t107.9\t0\t2182\n", "33\t2297\t107.9\t0\t2297\n", "34\t2503\t107.9\t0\t2503\n", "35\t3235\t107.9\t0\t3235\n", "36\t3297\t107.9\t0\t3297\n", "37\t1386\t107.9\t0\t1386\n", "38\t78\t107.9\t0\t78\n", "39\t65\t107.9\t0\t65\n", "40\t46\t107.9\t0\t46\n", "41\t37\t107.9\t0\t37\n", "42\t28\t107.9\t0\t28\n", "43\t43\t107.9\t0\t43\n", "44\t69\t107.9\t0\t69\n", "45\t40\t107.9\t0\t40\n", "46\t56\t107.9\t0\t56\n", "47\t39\t107.9\t0\t39\n", "48\t51\t107.9\t0\t51\n", "49\t49\t107.9\t0\t49\n", "50\t55\t107.9\t0\t55\n", "51\t36\t107.9\t0\t36\n", "52\t46\t107.9\t0\t46\n", "53\t37\t107.9\t0\t37\n", "54\t32\t107.9\t0\t32\n", "55\t38\t107.9\t0\t38\n", "56\t28\t107.9\t0\t28\n", "57\t34\t107.9\t0\t34\n", "58\t38\t107.9\t0\t38\n", "59\t29\t107.9\t0\t29\n", "60\t32\t107.9\t0\t32\n", "61\t29\t107.9\t0\t29\n", "62\t37\t107.9\t0\t37\n", "63\t33\t107.9\t0\t33\n", "64\t29\t107.9\t0\t29\n", "65\t25\t107.9\t0\t25\n", "66\t20\t107.9\t0\t20\n", "67\t35\t107.9\t0\t35\n", "68\t20\t107.9\t0\t20\n", "69\t22\t107.9\t0\t22\n", "70\t23\t107.9\t0\t23\n", "71\t14\t107.9\t0\t14\n", "72\t15\t107.9\t0\t15\n", "73\t11\t107.9\t0\t11\n", "74\t17\t107.9\t0\t17\n", "75\t9\t107.9\t0\t9\n", "76\t7\t107.9\t0\t7\n", "77\t16\t107.9\t0\t16\n", "78\t21\t107.9\t0\t21\n", "79\t31\t107.9\t0\t31\n", "80\t9\t107.9\t0\t9\n", "81\t18\t107.9\t0\t18\n", "82\t18\t107.9\t0\t18\n", "83\t21\t107.9\t0\t21\n", "84\t48\t107.9\t0\t48\n", "85\t40\t107.9\t0\t40\n", "86\t34\t107.9\t0\t34\n", "87\t24\t107.9\t0\t24\n", "88\t30\t107.9\t0\t30\n", "89\t21\t107.9\t0\t21\n", "90\t38\t107.9\t0\t38\n", "91\t47\t107.9\t0\t47\n", "92\t56\t107.9\t0\t56\n", "93\t77\t107.9\t0\t77\n", "94\t144\t107.9\t0\t144\n", "95\t150\t107.9\t0\t150\n", "96\t156\t107.9\t0\t156\n", "97\t126\t107.9\t0\t126\n", "98\t102\t107.9\t0\t102\n", "99\t52\t107.9\t0\t52\n", "100\t93\t107.9\t0\t93\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 101295 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.8%\n", " C: 19.7%\n", " G: 17.9%\n", " T: 20.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t73100\t110529.9\t0\t73100\n", "4\t16145\t27632.5\t0\t16145\n", "5\t3095\t6908.1\t0\t3095\n", "6\t318\t1727.0\t0\t318\n", "7\t134\t431.8\t0\t134\n", "8\t138\t431.8\t0\t138\n", "9\t137\t431.8\t0\t137\n", "10\t139\t431.8\t0\t139\n", "11\t132\t431.8\t0\t132\n", "12\t150\t431.8\t0\t150\n", "13\t131\t431.8\t0\t131\n", "14\t168\t431.8\t0\t168\n", "15\t161\t431.8\t0\t161\n", "16\t124\t431.8\t0\t124\n", "17\t156\t431.8\t0\t156\n", "18\t149\t431.8\t0\t149\n", "19\t152\t431.8\t0\t152\n", "20\t139\t431.8\t0\t139\n", "21\t131\t431.8\t0\t131\n", "22\t158\t431.8\t0\t158\n", "23\t129\t431.8\t0\t129\n", "24\t108\t431.8\t0\t108\n", "25\t100\t431.8\t0\t100\n", "26\t147\t431.8\t0\t147\n", "27\t146\t431.8\t0\t146\n", "28\t116\t431.8\t0\t116\n", "29\t120\t431.8\t0\t120\n", "30\t124\t431.8\t0\t124\n", "31\t98\t431.8\t0\t98\n", "32\t126\t431.8\t0\t126\n", "33\t109\t431.8\t0\t109\n", "34\t128\t431.8\t0\t128\n", "35\t116\t431.8\t0\t116\n", "36\t105\t431.8\t0\t105\n", "37\t102\t431.8\t0\t102\n", "38\t75\t431.8\t0\t75\n", "39\t102\t431.8\t0\t102\n", "40\t82\t431.8\t0\t82\n", "41\t66\t431.8\t0\t66\n", "42\t70\t431.8\t0\t70\n", "43\t111\t431.8\t0\t111\n", "44\t40\t431.8\t0\t40\n", "45\t94\t431.8\t0\t94\n", "46\t77\t431.8\t0\t77\n", "47\t94\t431.8\t0\t94\n", "48\t64\t431.8\t0\t64\n", "49\t82\t431.8\t0\t82\n", "50\t91\t431.8\t0\t91\n", "51\t90\t431.8\t0\t90\n", "52\t61\t431.8\t0\t61\n", "53\t71\t431.8\t0\t71\n", "54\t89\t431.8\t0\t89\n", "55\t86\t431.8\t0\t86\n", "56\t87\t431.8\t0\t87\n", "57\t81\t431.8\t0\t81\n", "58\t68\t431.8\t0\t68\n", "59\t63\t431.8\t0\t63\n", "60\t55\t431.8\t0\t55\n", "61\t60\t431.8\t0\t60\n", "62\t64\t431.8\t0\t64\n", "63\t47\t431.8\t0\t47\n", "64\t78\t431.8\t0\t78\n", "65\t55\t431.8\t0\t55\n", "66\t46\t431.8\t0\t46\n", "67\t59\t431.8\t0\t59\n", "68\t68\t431.8\t0\t68\n", "69\t35\t431.8\t0\t35\n", "70\t41\t431.8\t0\t41\n", "71\t73\t431.8\t0\t73\n", "72\t59\t431.8\t0\t59\n", "73\t78\t431.8\t0\t78\n", "74\t71\t431.8\t0\t71\n", "75\t77\t431.8\t0\t77\n", "76\t82\t431.8\t0\t82\n", "77\t87\t431.8\t0\t87\n", "78\t73\t431.8\t0\t73\n", "79\t67\t431.8\t0\t67\n", "80\t71\t431.8\t0\t71\n", "81\t88\t431.8\t0\t88\n", "82\t87\t431.8\t0\t87\n", "83\t98\t431.8\t0\t98\n", "84\t81\t431.8\t0\t81\n", "85\t87\t431.8\t0\t87\n", "86\t79\t431.8\t0\t79\n", "87\t88\t431.8\t0\t88\n", "88\t98\t431.8\t0\t98\n", "89\t52\t431.8\t0\t52\n", "90\t69\t431.8\t0\t69\n", "91\t55\t431.8\t0\t55\n", "92\t55\t431.8\t0\t55\n", "93\t55\t431.8\t0\t55\n", "94\t68\t431.8\t0\t68\n", "95\t62\t431.8\t0\t62\n", "96\t59\t431.8\t0\t59\n", "97\t47\t431.8\t0\t47\n", "98\t75\t431.8\t0\t75\n", "99\t74\t431.8\t0\t74\n", "100\t97\t431.8\t0\t97\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 312_S28_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/312.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 98.36 s (14 us/read; 4.36 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,147,390\n", "Reads with adapters: 4,471,169 (62.6%)\n", "Reads written (passing filters): 6,899,004 (96.5%)\n", "\n", "Total basepairs processed: 714,739,000 bp\n", "Quality-trimmed: 1,707,798 bp (0.2%)\n", "Total written (filtered): 547,259,901 bp (76.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4329447 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.0%\n", " G: 40.3%\n", " T: 26.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t139165\t111678.0\t0\t139165\n", "4\t86575\t27919.5\t0\t86575\n", "5\t66905\t6979.9\t0\t66905\n", "6\t58164\t1745.0\t0\t58164\n", "7\t53550\t436.2\t0\t53550\n", "8\t52698\t109.1\t0\t52698\n", "9\t53751\t109.1\t0\t53751\n", "10\t53302\t109.1\t0\t53302\n", "11\t55383\t109.1\t0\t55383\n", "12\t55350\t109.1\t0\t55350\n", "13\t60692\t109.1\t0\t60692\n", "14\t61107\t109.1\t0\t61107\n", "15\t58893\t109.1\t0\t58893\n", "16\t62020\t109.1\t0\t62020\n", "17\t68610\t109.1\t0\t68610\n", "18\t77108\t109.1\t0\t77108\n", "19\t67993\t109.1\t0\t67993\n", "20\t57411\t109.1\t0\t57411\n", "21\t55206\t109.1\t0\t55206\n", "22\t52058\t109.1\t0\t52058\n", "23\t57233\t109.1\t0\t57233\n", "24\t65331\t109.1\t0\t65331\n", "25\t68706\t109.1\t0\t68706\n", "26\t76411\t109.1\t0\t76411\n", "27\t78985\t109.1\t0\t78985\n", "28\t71209\t109.1\t0\t71209\n", "29\t65127\t109.1\t0\t65127\n", "30\t64111\t109.1\t0\t64111\n", "31\t71093\t109.1\t0\t71093\n", "32\t70486\t109.1\t0\t70486\n", "33\t66935\t109.1\t0\t66935\n", "34\t65959\t109.1\t0\t65959\n", "35\t73119\t109.1\t0\t73119\n", "36\t80618\t109.1\t0\t80618\n", "37\t81718\t109.1\t0\t81718\n", "38\t67096\t109.1\t0\t67096\n", "39\t63117\t109.1\t0\t63117\n", "40\t60353\t109.1\t0\t60353\n", "41\t69601\t109.1\t0\t69601\n", "42\t79541\t109.1\t0\t79541\n", "43\t69863\t109.1\t0\t69863\n", "44\t54445\t109.1\t0\t54445\n", "45\t63602\t109.1\t0\t63602\n", "46\t72840\t109.1\t0\t72840\n", "47\t65915\t109.1\t0\t65915\n", "48\t59096\t109.1\t0\t59096\n", "49\t50495\t109.1\t0\t50495\n", "50\t50309\t109.1\t0\t50309\n", "51\t43263\t109.1\t0\t43263\n", "52\t48205\t109.1\t0\t48205\n", "53\t50970\t109.1\t0\t50970\n", "54\t48712\t109.1\t0\t48712\n", "55\t49730\t109.1\t0\t49730\n", "56\t43080\t109.1\t0\t43080\n", "57\t46201\t109.1\t0\t46201\n", "58\t51409\t109.1\t0\t51409\n", "59\t41590\t109.1\t0\t41590\n", "60\t34711\t109.1\t0\t34711\n", "61\t33166\t109.1\t0\t33166\n", "62\t28371\t109.1\t0\t28371\n", "63\t26495\t109.1\t0\t26495\n", "64\t30169\t109.1\t0\t30169\n", "65\t29915\t109.1\t0\t29915\n", "66\t25920\t109.1\t0\t25920\n", "67\t25801\t109.1\t0\t25801\n", "68\t25305\t109.1\t0\t25305\n", "69\t26024\t109.1\t0\t26024\n", "70\t27700\t109.1\t0\t27700\n", "71\t27058\t109.1\t0\t27058\n", "72\t21525\t109.1\t0\t21525\n", "73\t19314\t109.1\t0\t19314\n", "74\t19288\t109.1\t0\t19288\n", "75\t17338\t109.1\t0\t17338\n", "76\t14599\t109.1\t0\t14599\n", "77\t13810\t109.1\t0\t13810\n", "78\t15378\t109.1\t0\t15378\n", "79\t15244\t109.1\t0\t15244\n", "80\t14949\t109.1\t0\t14949\n", "81\t14407\t109.1\t0\t14407\n", "82\t14075\t109.1\t0\t14075\n", "83\t15205\t109.1\t0\t15205\n", "84\t17329\t109.1\t0\t17329\n", "85\t19679\t109.1\t0\t19679\n", "86\t18414\t109.1\t0\t18414\n", "87\t12956\t109.1\t0\t12956\n", "88\t11798\t109.1\t0\t11798\n", "89\t12482\t109.1\t0\t12482\n", "90\t12986\t109.1\t0\t12986\n", "91\t12568\t109.1\t0\t12568\n", "92\t12380\t109.1\t0\t12380\n", "93\t13737\t109.1\t0\t13737\n", "94\t13019\t109.1\t0\t13019\n", "95\t11391\t109.1\t0\t11391\n", "96\t8387\t109.1\t0\t8387\n", "97\t5095\t109.1\t0\t5095\n", "98\t3084\t109.1\t0\t3084\n", "99\t3493\t109.1\t0\t3493\n", "100\t2467\t109.1\t0\t2467\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 46444 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 69.1%\n", " C: 11.5%\n", " G: 0.0%\n", " T: 19.3%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t11234\t111678.0\t0\t11234\n", "4\t2591\t27919.5\t0\t2591\n", "5\t931\t6979.9\t0\t931\n", "6\t467\t1745.0\t0\t467\n", "7\t117\t436.2\t0\t117\n", "8\t135\t109.1\t0\t135\n", "9\t90\t109.1\t0\t90\n", "10\t87\t109.1\t0\t87\n", "11\t65\t109.1\t0\t65\n", "12\t80\t109.1\t0\t80\n", "13\t103\t109.1\t0\t103\n", "14\t80\t109.1\t0\t80\n", "15\t86\t109.1\t0\t86\n", "16\t98\t109.1\t0\t98\n", "17\t145\t109.1\t0\t145\n", "18\t235\t109.1\t0\t235\n", "19\t327\t109.1\t0\t327\n", "20\t533\t109.1\t0\t533\n", "21\t473\t109.1\t0\t473\n", "22\t333\t109.1\t0\t333\n", "23\t277\t109.1\t0\t277\n", "24\t263\t109.1\t0\t263\n", "25\t296\t109.1\t0\t296\n", "26\t500\t109.1\t0\t500\n", "27\t488\t109.1\t0\t488\n", "28\t599\t109.1\t0\t599\n", "29\t869\t109.1\t0\t869\n", "30\t1564\t109.1\t0\t1564\n", "31\t1978\t109.1\t0\t1978\n", "32\t2891\t109.1\t0\t2891\n", "33\t2906\t109.1\t0\t2906\n", "34\t3025\t109.1\t0\t3025\n", "35\t3822\t109.1\t0\t3822\n", "36\t3707\t109.1\t0\t3707\n", "37\t1519\t109.1\t0\t1519\n", "38\t107\t109.1\t0\t107\n", "39\t91\t109.1\t0\t91\n", "40\t64\t109.1\t0\t64\n", "41\t65\t109.1\t0\t65\n", "42\t58\t109.1\t0\t58\n", "43\t50\t109.1\t0\t50\n", "44\t71\t109.1\t0\t71\n", "45\t45\t109.1\t0\t45\n", "46\t47\t109.1\t0\t47\n", "47\t56\t109.1\t0\t56\n", "48\t41\t109.1\t0\t41\n", "49\t59\t109.1\t0\t59\n", "50\t78\t109.1\t0\t78\n", "51\t53\t109.1\t0\t53\n", "52\t39\t109.1\t0\t39\n", "53\t66\t109.1\t0\t66\n", "54\t55\t109.1\t0\t55\n", "55\t44\t109.1\t0\t44\n", "56\t36\t109.1\t0\t36\n", "57\t30\t109.1\t0\t30\n", "58\t37\t109.1\t0\t37\n", "59\t39\t109.1\t0\t39\n", "60\t38\t109.1\t0\t38\n", "61\t48\t109.1\t0\t48\n", "62\t32\t109.1\t0\t32\n", "63\t40\t109.1\t0\t40\n", "64\t37\t109.1\t0\t37\n", "65\t37\t109.1\t0\t37\n", "66\t34\t109.1\t0\t34\n", "67\t33\t109.1\t0\t33\n", "68\t27\t109.1\t0\t27\n", "69\t25\t109.1\t0\t25\n", "70\t24\t109.1\t0\t24\n", "71\t24\t109.1\t0\t24\n", "72\t16\t109.1\t0\t16\n", "73\t14\t109.1\t0\t14\n", "74\t20\t109.1\t0\t20\n", "75\t15\t109.1\t0\t15\n", "76\t14\t109.1\t0\t14\n", "77\t14\t109.1\t0\t14\n", "78\t22\t109.1\t0\t22\n", "79\t24\t109.1\t0\t24\n", "80\t24\t109.1\t0\t24\n", "81\t30\t109.1\t0\t30\n", "82\t21\t109.1\t0\t21\n", "83\t37\t109.1\t0\t37\n", "84\t36\t109.1\t0\t36\n", "85\t35\t109.1\t0\t35\n", "86\t21\t109.1\t0\t21\n", "87\t28\t109.1\t0\t28\n", "88\t42\t109.1\t0\t42\n", "89\t40\t109.1\t0\t40\n", "90\t46\t109.1\t0\t46\n", "91\t47\t109.1\t0\t47\n", "92\t70\t109.1\t0\t70\n", "93\t126\t109.1\t0\t126\n", "94\t138\t109.1\t0\t138\n", "95\t214\t109.1\t0\t214\n", "96\t212\t109.1\t0\t212\n", "97\t166\t109.1\t0\t166\n", "98\t156\t109.1\t0\t156\n", "99\t101\t109.1\t0\t101\n", "100\t171\t109.1\t0\t171\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 95278 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.0%\n", " C: 19.3%\n", " G: 18.1%\n", " T: 21.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t70839\t111678.0\t0\t70839\n", "4\t14872\t27919.5\t0\t14872\n", "5\t2276\t6979.9\t0\t2276\n", "6\t287\t1745.0\t0\t287\n", "7\t86\t436.2\t0\t86\n", "8\t85\t436.2\t0\t85\n", "9\t93\t436.2\t0\t93\n", "10\t92\t436.2\t0\t92\n", "11\t76\t436.2\t0\t76\n", "12\t84\t436.2\t0\t84\n", "13\t77\t436.2\t0\t77\n", "14\t99\t436.2\t0\t99\n", "15\t99\t436.2\t0\t99\n", "16\t102\t436.2\t0\t102\n", "17\t129\t436.2\t0\t129\n", "18\t119\t436.2\t0\t119\n", "19\t107\t436.2\t0\t107\n", "20\t102\t436.2\t0\t102\n", "21\t97\t436.2\t0\t97\n", "22\t97\t436.2\t0\t97\n", "23\t86\t436.2\t0\t86\n", "24\t93\t436.2\t0\t93\n", "25\t87\t436.2\t0\t87\n", "26\t83\t436.2\t0\t83\n", "27\t83\t436.2\t0\t83\n", "28\t99\t436.2\t0\t99\n", "29\t99\t436.2\t0\t99\n", "30\t104\t436.2\t0\t104\n", "31\t82\t436.2\t0\t82\n", "32\t100\t436.2\t0\t100\n", "33\t107\t436.2\t0\t107\n", "34\t84\t436.2\t0\t84\n", "35\t82\t436.2\t0\t82\n", "36\t66\t436.2\t0\t66\n", "37\t72\t436.2\t0\t72\n", "38\t54\t436.2\t0\t54\n", "39\t61\t436.2\t0\t61\n", "40\t75\t436.2\t0\t75\n", "41\t87\t436.2\t0\t87\n", "42\t82\t436.2\t0\t82\n", "43\t72\t436.2\t0\t72\n", "44\t39\t436.2\t0\t39\n", "45\t67\t436.2\t0\t67\n", "46\t70\t436.2\t0\t70\n", "47\t80\t436.2\t0\t80\n", "48\t74\t436.2\t0\t74\n", "49\t63\t436.2\t0\t63\n", "50\t54\t436.2\t0\t54\n", "51\t62\t436.2\t0\t62\n", "52\t60\t436.2\t0\t60\n", "53\t61\t436.2\t0\t61\n", "54\t38\t436.2\t0\t38\n", "55\t68\t436.2\t0\t68\n", "56\t77\t436.2\t0\t77\n", "57\t41\t436.2\t0\t41\n", "58\t59\t436.2\t0\t59\n", "59\t47\t436.2\t0\t47\n", "60\t50\t436.2\t0\t50\n", "61\t52\t436.2\t0\t52\n", "62\t56\t436.2\t0\t56\n", "63\t40\t436.2\t0\t40\n", "64\t70\t436.2\t0\t70\n", "65\t61\t436.2\t0\t61\n", "66\t55\t436.2\t0\t55\n", "67\t48\t436.2\t0\t48\n", "68\t71\t436.2\t0\t71\n", "69\t62\t436.2\t0\t62\n", "70\t40\t436.2\t0\t40\n", "71\t58\t436.2\t0\t58\n", "72\t51\t436.2\t0\t51\n", "73\t61\t436.2\t0\t61\n", "74\t63\t436.2\t0\t63\n", "75\t55\t436.2\t0\t55\n", "76\t53\t436.2\t0\t53\n", "77\t64\t436.2\t0\t64\n", "78\t77\t436.2\t0\t77\n", "79\t61\t436.2\t0\t61\n", "80\t70\t436.2\t0\t70\n", "81\t77\t436.2\t0\t77\n", "82\t87\t436.2\t0\t87\n", "83\t82\t436.2\t0\t82\n", "84\t109\t436.2\t0\t109\n", "85\t95\t436.2\t0\t95\n", "86\t98\t436.2\t0\t98\n", "87\t99\t436.2\t0\t99\n", "88\t108\t436.2\t0\t108\n", "89\t72\t436.2\t0\t72\n", "90\t61\t436.2\t0\t61\n", "91\t63\t436.2\t0\t63\n", "92\t46\t436.2\t0\t46\n", "93\t53\t436.2\t0\t53\n", "94\t71\t436.2\t0\t71\n", "95\t41\t436.2\t0\t41\n", "96\t47\t436.2\t0\t47\n", "97\t55\t436.2\t0\t55\n", "98\t67\t436.2\t0\t67\n", "99\t98\t436.2\t0\t98\n", "100\t95\t436.2\t0\t95\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 313_S36_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/313.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 93.87 s (13 us/read; 4.45 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,960,546\n", "Reads with adapters: 4,321,905 (62.1%)\n", "Reads written (passing filters): 6,811,884 (97.9%)\n", "\n", "Total basepairs processed: 696,054,600 bp\n", "Quality-trimmed: 1,757,249 bp (0.3%)\n", "Total written (filtered): 541,157,382 bp (77.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4184694 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.6%\n", " G: 39.6%\n", " T: 26.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t144903\t108758.5\t0\t144903\n", "4\t84845\t27189.6\t0\t84845\n", "5\t65639\t6797.4\t0\t65639\n", "6\t56475\t1699.4\t0\t56475\n", "7\t53513\t424.8\t0\t53513\n", "8\t53627\t106.2\t0\t53627\n", "9\t53268\t106.2\t0\t53268\n", "10\t53195\t106.2\t0\t53195\n", "11\t53398\t106.2\t0\t53398\n", "12\t54950\t106.2\t0\t54950\n", "13\t59366\t106.2\t0\t59366\n", "14\t59963\t106.2\t0\t59963\n", "15\t57058\t106.2\t0\t57058\n", "16\t60136\t106.2\t0\t60136\n", "17\t66135\t106.2\t0\t66135\n", "18\t73335\t106.2\t0\t73335\n", "19\t66541\t106.2\t0\t66541\n", "20\t56673\t106.2\t0\t56673\n", "21\t53512\t106.2\t0\t53512\n", "22\t50280\t106.2\t0\t50280\n", "23\t54982\t106.2\t0\t54982\n", "24\t62410\t106.2\t0\t62410\n", "25\t65547\t106.2\t0\t65547\n", "26\t73435\t106.2\t0\t73435\n", "27\t77725\t106.2\t0\t77725\n", "28\t70069\t106.2\t0\t70069\n", "29\t65540\t106.2\t0\t65540\n", "30\t65870\t106.2\t0\t65870\n", "31\t71688\t106.2\t0\t71688\n", "32\t71910\t106.2\t0\t71910\n", "33\t67101\t106.2\t0\t67101\n", "34\t65164\t106.2\t0\t65164\n", "35\t71872\t106.2\t0\t71872\n", "36\t79589\t106.2\t0\t79589\n", "37\t80651\t106.2\t0\t80651\n", "38\t70033\t106.2\t0\t70033\n", "39\t63764\t106.2\t0\t63764\n", "40\t60949\t106.2\t0\t60949\n", "41\t68581\t106.2\t0\t68581\n", "42\t76302\t106.2\t0\t76302\n", "43\t66297\t106.2\t0\t66297\n", "44\t52027\t106.2\t0\t52027\n", "45\t63092\t106.2\t0\t63092\n", "46\t73977\t106.2\t0\t73977\n", "47\t67106\t106.2\t0\t67106\n", "48\t65867\t106.2\t0\t65867\n", "49\t56141\t106.2\t0\t56141\n", "50\t54417\t106.2\t0\t54417\n", "51\t46752\t106.2\t0\t46752\n", "52\t55278\t106.2\t0\t55278\n", "53\t59743\t106.2\t0\t59743\n", "54\t49219\t106.2\t0\t49219\n", "55\t48113\t106.2\t0\t48113\n", "56\t40171\t106.2\t0\t40171\n", "57\t44302\t106.2\t0\t44302\n", "58\t48128\t106.2\t0\t48128\n", "59\t39899\t106.2\t0\t39899\n", "60\t33835\t106.2\t0\t33835\n", "61\t33068\t106.2\t0\t33068\n", "62\t28038\t106.2\t0\t28038\n", "63\t26289\t106.2\t0\t26289\n", "64\t30298\t106.2\t0\t30298\n", "65\t29040\t106.2\t0\t29040\n", "66\t23942\t106.2\t0\t23942\n", "67\t24642\t106.2\t0\t24642\n", "68\t24391\t106.2\t0\t24391\n", "69\t25233\t106.2\t0\t25233\n", "70\t26673\t106.2\t0\t26673\n", "71\t25258\t106.2\t0\t25258\n", "72\t19268\t106.2\t0\t19268\n", "73\t16777\t106.2\t0\t16777\n", "74\t16406\t106.2\t0\t16406\n", "75\t14650\t106.2\t0\t14650\n", "76\t11839\t106.2\t0\t11839\n", "77\t11436\t106.2\t0\t11436\n", "78\t13294\t106.2\t0\t13294\n", "79\t11917\t106.2\t0\t11917\n", "80\t10973\t106.2\t0\t10973\n", "81\t10048\t106.2\t0\t10048\n", "82\t9782\t106.2\t0\t9782\n", "83\t9415\t106.2\t0\t9415\n", "84\t10719\t106.2\t0\t10719\n", "85\t11790\t106.2\t0\t11790\n", "86\t10928\t106.2\t0\t10928\n", "87\t7691\t106.2\t0\t7691\n", "88\t6668\t106.2\t0\t6668\n", "89\t6860\t106.2\t0\t6860\n", "90\t7171\t106.2\t0\t7171\n", "91\t7054\t106.2\t0\t7054\n", "92\t7100\t106.2\t0\t7100\n", "93\t7363\t106.2\t0\t7363\n", "94\t6998\t106.2\t0\t6998\n", "95\t5908\t106.2\t0\t5908\n", "96\t4345\t106.2\t0\t4345\n", "97\t2821\t106.2\t0\t2821\n", "98\t1527\t106.2\t0\t1527\n", "99\t1708\t106.2\t0\t1708\n", "100\t1008\t106.2\t0\t1008\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28699 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 46.5%\n", " C: 28.2%\n", " G: 0.0%\n", " T: 25.3%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t14300\t108758.5\t0\t14300\n", "4\t3395\t27189.6\t0\t3395\n", "5\t1255\t6797.4\t0\t1255\n", "6\t900\t1699.4\t0\t900\n", "7\t143\t424.8\t0\t143\n", "8\t106\t106.2\t0\t106\n", "9\t97\t106.2\t0\t97\n", "10\t101\t106.2\t0\t101\n", "11\t78\t106.2\t0\t78\n", "12\t77\t106.2\t0\t77\n", "13\t94\t106.2\t0\t94\n", "14\t95\t106.2\t0\t95\n", "15\t75\t106.2\t0\t75\n", "16\t94\t106.2\t0\t94\n", "17\t97\t106.2\t0\t97\n", "18\t133\t106.2\t0\t133\n", "19\t169\t106.2\t0\t169\n", "20\t211\t106.2\t0\t211\n", "21\t136\t106.2\t0\t136\n", "22\t83\t106.2\t0\t83\n", "23\t117\t106.2\t0\t117\n", "24\t98\t106.2\t0\t98\n", "25\t111\t106.2\t0\t111\n", "26\t158\t106.2\t0\t158\n", "27\t135\t106.2\t0\t135\n", "28\t165\t106.2\t0\t165\n", "29\t215\t106.2\t0\t215\n", "30\t336\t106.2\t0\t336\n", "31\t412\t106.2\t0\t412\n", "32\t617\t106.2\t0\t617\n", "33\t522\t106.2\t0\t522\n", "34\t545\t106.2\t0\t545\n", "35\t640\t106.2\t0\t640\n", "36\t566\t106.2\t0\t566\n", "37\t209\t106.2\t0\t209\n", "38\t55\t106.2\t0\t55\n", "39\t53\t106.2\t0\t53\n", "40\t59\t106.2\t0\t59\n", "41\t38\t106.2\t0\t38\n", "42\t53\t106.2\t0\t53\n", "43\t55\t106.2\t0\t55\n", "44\t46\t106.2\t0\t46\n", "45\t53\t106.2\t0\t53\n", "46\t42\t106.2\t0\t42\n", "47\t37\t106.2\t0\t37\n", "48\t40\t106.2\t0\t40\n", "49\t51\t106.2\t0\t51\n", "50\t48\t106.2\t0\t48\n", "51\t46\t106.2\t0\t46\n", "52\t33\t106.2\t0\t33\n", "53\t33\t106.2\t0\t33\n", "54\t43\t106.2\t0\t43\n", "55\t49\t106.2\t0\t49\n", "56\t26\t106.2\t0\t26\n", "57\t28\t106.2\t0\t28\n", "58\t42\t106.2\t0\t42\n", "59\t29\t106.2\t0\t29\n", "60\t44\t106.2\t0\t44\n", "61\t30\t106.2\t0\t30\n", "62\t34\t106.2\t0\t34\n", "63\t33\t106.2\t0\t33\n", "64\t29\t106.2\t0\t29\n", "65\t30\t106.2\t0\t30\n", "66\t28\t106.2\t0\t28\n", "67\t20\t106.2\t0\t20\n", "68\t27\t106.2\t0\t27\n", "69\t20\t106.2\t0\t20\n", "70\t14\t106.2\t0\t14\n", "71\t7\t106.2\t0\t7\n", "72\t19\t106.2\t0\t19\n", "73\t8\t106.2\t0\t8\n", "74\t11\t106.2\t0\t11\n", "75\t13\t106.2\t0\t13\n", "76\t13\t106.2\t0\t13\n", "77\t9\t106.2\t0\t9\n", "78\t4\t106.2\t0\t4\n", "79\t12\t106.2\t0\t12\n", "80\t9\t106.2\t0\t9\n", "81\t16\t106.2\t0\t16\n", "82\t8\t106.2\t0\t8\n", "83\t12\t106.2\t0\t12\n", "84\t12\t106.2\t0\t12\n", "85\t8\t106.2\t0\t8\n", "86\t14\t106.2\t0\t14\n", "87\t8\t106.2\t0\t8\n", "88\t8\t106.2\t0\t8\n", "89\t13\t106.2\t0\t13\n", "90\t16\t106.2\t0\t16\n", "91\t30\t106.2\t0\t30\n", "92\t42\t106.2\t0\t42\n", "93\t51\t106.2\t0\t51\n", "94\t76\t106.2\t0\t76\n", "95\t103\t106.2\t0\t103\n", "96\t105\t106.2\t0\t105\n", "97\t103\t106.2\t0\t103\n", "98\t80\t106.2\t0\t80\n", "99\t55\t106.2\t0\t55\n", "100\t81\t106.2\t0\t81\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 108512 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.1%\n", " C: 20.1%\n", " G: 18.9%\n", " T: 19.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t77896\t108758.5\t0\t77896\n", "4\t16171\t27189.6\t0\t16171\n", "5\t2733\t6797.4\t0\t2733\n", "6\t384\t1699.4\t0\t384\n", "7\t151\t424.8\t0\t151\n", "8\t168\t424.8\t0\t168\n", "9\t156\t424.8\t0\t156\n", "10\t201\t424.8\t0\t201\n", "11\t183\t424.8\t0\t183\n", "12\t180\t424.8\t0\t180\n", "13\t179\t424.8\t0\t179\n", "14\t198\t424.8\t0\t198\n", "15\t197\t424.8\t0\t197\n", "16\t207\t424.8\t0\t207\n", "17\t207\t424.8\t0\t207\n", "18\t169\t424.8\t0\t169\n", "19\t200\t424.8\t0\t200\n", "20\t202\t424.8\t0\t202\n", "21\t188\t424.8\t0\t188\n", "22\t211\t424.8\t0\t211\n", "23\t146\t424.8\t0\t146\n", "24\t154\t424.8\t0\t154\n", "25\t158\t424.8\t0\t158\n", "26\t135\t424.8\t0\t135\n", "27\t162\t424.8\t0\t162\n", "28\t169\t424.8\t0\t169\n", "29\t179\t424.8\t0\t179\n", "30\t145\t424.8\t0\t145\n", "31\t137\t424.8\t0\t137\n", "32\t185\t424.8\t0\t185\n", "33\t159\t424.8\t0\t159\n", "34\t128\t424.8\t0\t128\n", "35\t173\t424.8\t0\t173\n", "36\t149\t424.8\t0\t149\n", "37\t158\t424.8\t0\t158\n", "38\t166\t424.8\t0\t166\n", "39\t150\t424.8\t0\t150\n", "40\t171\t424.8\t0\t171\n", "41\t143\t424.8\t0\t143\n", "42\t106\t424.8\t0\t106\n", "43\t159\t424.8\t0\t159\n", "44\t86\t424.8\t0\t86\n", "45\t121\t424.8\t0\t121\n", "46\t127\t424.8\t0\t127\n", "47\t148\t424.8\t0\t148\n", "48\t89\t424.8\t0\t89\n", "49\t87\t424.8\t0\t87\n", "50\t94\t424.8\t0\t94\n", "51\t101\t424.8\t0\t101\n", "52\t99\t424.8\t0\t99\n", "53\t97\t424.8\t0\t97\n", "54\t72\t424.8\t0\t72\n", "55\t84\t424.8\t0\t84\n", "56\t85\t424.8\t0\t85\n", "57\t58\t424.8\t0\t58\n", "58\t102\t424.8\t0\t102\n", "59\t64\t424.8\t0\t64\n", "60\t104\t424.8\t0\t104\n", "61\t113\t424.8\t0\t113\n", "62\t95\t424.8\t0\t95\n", "63\t94\t424.8\t0\t94\n", "64\t99\t424.8\t0\t99\n", "65\t81\t424.8\t0\t81\n", "66\t74\t424.8\t0\t74\n", "67\t78\t424.8\t0\t78\n", "68\t61\t424.8\t0\t61\n", "69\t69\t424.8\t0\t69\n", "70\t67\t424.8\t0\t67\n", "71\t74\t424.8\t0\t74\n", "72\t94\t424.8\t0\t94\n", "73\t113\t424.8\t0\t113\n", "74\t90\t424.8\t0\t90\n", "75\t79\t424.8\t0\t79\n", "76\t67\t424.8\t0\t67\n", "77\t109\t424.8\t0\t109\n", "78\t76\t424.8\t0\t76\n", "79\t96\t424.8\t0\t96\n", "80\t89\t424.8\t0\t89\n", "81\t104\t424.8\t0\t104\n", "82\t154\t424.8\t0\t154\n", "83\t116\t424.8\t0\t116\n", "84\t123\t424.8\t0\t123\n", "85\t92\t424.8\t0\t92\n", "86\t87\t424.8\t0\t87\n", "87\t88\t424.8\t0\t88\n", "88\t110\t424.8\t0\t110\n", "89\t86\t424.8\t0\t86\n", "90\t75\t424.8\t0\t75\n", "91\t71\t424.8\t0\t71\n", "92\t69\t424.8\t0\t69\n", "93\t39\t424.8\t0\t39\n", "94\t58\t424.8\t0\t58\n", "95\t55\t424.8\t0\t55\n", "96\t59\t424.8\t0\t59\n", "97\t95\t424.8\t0\t95\n", "98\t91\t424.8\t0\t91\n", "99\t108\t424.8\t0\t108\n", "100\t83\t424.8\t0\t83\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 314_S49_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/314.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 69.21 s (13 us/read; 4.65 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,366,881\n", "Reads with adapters: 2,249,690 (41.9%)\n", "Reads written (passing filters): 5,277,805 (98.3%)\n", "\n", "Total basepairs processed: 536,688,100 bp\n", "Quality-trimmed: 985,896 bp (0.2%)\n", "Total written (filtered): 465,217,595 bp (86.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2109423 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.1%\n", " G: 40.8%\n", " T: 31.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t131776\t83857.5\t0\t131776\n", "4\t63854\t20964.4\t0\t63854\n", "5\t43699\t5241.1\t0\t43699\n", "6\t36798\t1310.3\t0\t36798\n", "7\t30524\t327.6\t0\t30524\n", "8\t29602\t81.9\t0\t29602\n", "9\t30661\t81.9\t0\t30661\n", "10\t30702\t81.9\t0\t30702\n", "11\t31177\t81.9\t0\t31177\n", "12\t32314\t81.9\t0\t32314\n", "13\t39712\t81.9\t0\t39712\n", "14\t39689\t81.9\t0\t39689\n", "15\t33940\t81.9\t0\t33940\n", "16\t36142\t81.9\t0\t36142\n", "17\t37213\t81.9\t0\t37213\n", "18\t40920\t81.9\t0\t40920\n", "19\t34844\t81.9\t0\t34844\n", "20\t27857\t81.9\t0\t27857\n", "21\t26465\t81.9\t0\t26465\n", "22\t25251\t81.9\t0\t25251\n", "23\t27192\t81.9\t0\t27192\n", "24\t31273\t81.9\t0\t31273\n", "25\t31584\t81.9\t0\t31584\n", "26\t34906\t81.9\t0\t34906\n", "27\t37171\t81.9\t0\t37171\n", "28\t34631\t81.9\t0\t34631\n", "29\t33300\t81.9\t0\t33300\n", "30\t33699\t81.9\t0\t33699\n", "31\t36750\t81.9\t0\t36750\n", "32\t35519\t81.9\t0\t35519\n", "33\t33326\t81.9\t0\t33326\n", "34\t31865\t81.9\t0\t31865\n", "35\t34745\t81.9\t0\t34745\n", "36\t39755\t81.9\t0\t39755\n", "37\t42237\t81.9\t0\t42237\n", "38\t34480\t81.9\t0\t34480\n", "39\t30108\t81.9\t0\t30108\n", "40\t29574\t81.9\t0\t29574\n", "41\t34165\t81.9\t0\t34165\n", "42\t38060\t81.9\t0\t38060\n", "43\t33045\t81.9\t0\t33045\n", "44\t25031\t81.9\t0\t25031\n", "45\t29538\t81.9\t0\t29538\n", "46\t33090\t81.9\t0\t33090\n", "47\t27248\t81.9\t0\t27248\n", "48\t25711\t81.9\t0\t25711\n", "49\t22342\t81.9\t0\t22342\n", "50\t21657\t81.9\t0\t21657\n", "51\t18115\t81.9\t0\t18115\n", "52\t18734\t81.9\t0\t18734\n", "53\t16828\t81.9\t0\t16828\n", "54\t16171\t81.9\t0\t16171\n", "55\t17975\t81.9\t0\t17975\n", "56\t16874\t81.9\t0\t16874\n", "57\t16303\t81.9\t0\t16303\n", "58\t16117\t81.9\t0\t16117\n", "59\t14468\t81.9\t0\t14468\n", "60\t12380\t81.9\t0\t12380\n", "61\t11215\t81.9\t0\t11215\n", "62\t10141\t81.9\t0\t10141\n", "63\t9598\t81.9\t0\t9598\n", "64\t10130\t81.9\t0\t10130\n", "65\t9779\t81.9\t0\t9779\n", "66\t8196\t81.9\t0\t8196\n", "67\t8819\t81.9\t0\t8819\n", "68\t8997\t81.9\t0\t8997\n", "69\t9579\t81.9\t0\t9579\n", "70\t10728\t81.9\t0\t10728\n", "71\t10127\t81.9\t0\t10127\n", "72\t7533\t81.9\t0\t7533\n", "73\t6635\t81.9\t0\t6635\n", "74\t6412\t81.9\t0\t6412\n", "75\t5903\t81.9\t0\t5903\n", "76\t4997\t81.9\t0\t4997\n", "77\t5235\t81.9\t0\t5235\n", "78\t5914\t81.9\t0\t5914\n", "79\t5615\t81.9\t0\t5615\n", "80\t5221\t81.9\t0\t5221\n", "81\t5164\t81.9\t0\t5164\n", "82\t5088\t81.9\t0\t5088\n", "83\t5039\t81.9\t0\t5039\n", "84\t5407\t81.9\t0\t5407\n", "85\t6089\t81.9\t0\t6089\n", "86\t6062\t81.9\t0\t6062\n", "87\t5047\t81.9\t0\t5047\n", "88\t4882\t81.9\t0\t4882\n", "89\t4562\t81.9\t0\t4562\n", "90\t4595\t81.9\t0\t4595\n", "91\t4525\t81.9\t0\t4525\n", "92\t4402\t81.9\t0\t4402\n", "93\t4522\t81.9\t0\t4522\n", "94\t3919\t81.9\t0\t3919\n", "95\t3383\t81.9\t0\t3383\n", "96\t2474\t81.9\t0\t2474\n", "97\t1613\t81.9\t0\t1613\n", "98\t1028\t81.9\t0\t1028\n", "99\t1059\t81.9\t0\t1059\n", "100\t682\t81.9\t0\t682\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 38308 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.7%\n", " C: 35.4%\n", " G: 0.0%\n", " T: 22.8%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t17922\t83857.5\t0\t17922\n", "4\t4691\t20964.4\t0\t4691\n", "5\t2417\t5241.1\t0\t2417\n", "6\t1263\t1310.3\t0\t1263\n", "7\t68\t327.6\t0\t68\n", "8\t53\t81.9\t0\t53\n", "9\t40\t81.9\t0\t40\n", "10\t50\t81.9\t0\t50\n", "11\t40\t81.9\t0\t40\n", "12\t49\t81.9\t0\t49\n", "13\t47\t81.9\t0\t47\n", "14\t32\t81.9\t0\t32\n", "15\t45\t81.9\t0\t45\n", "16\t66\t81.9\t0\t66\n", "17\t74\t81.9\t0\t74\n", "18\t79\t81.9\t0\t79\n", "19\t115\t81.9\t0\t115\n", "20\t122\t81.9\t0\t122\n", "21\t124\t81.9\t0\t124\n", "22\t89\t81.9\t0\t89\n", "23\t67\t81.9\t0\t67\n", "24\t77\t81.9\t0\t77\n", "25\t71\t81.9\t0\t71\n", "26\t147\t81.9\t0\t147\n", "27\t132\t81.9\t0\t132\n", "28\t196\t81.9\t0\t196\n", "29\t296\t81.9\t0\t296\n", "30\t477\t81.9\t0\t477\n", "31\t648\t81.9\t0\t648\n", "32\t909\t81.9\t0\t909\n", "33\t1022\t81.9\t0\t1022\n", "34\t1184\t81.9\t0\t1184\n", "35\t1444\t81.9\t0\t1444\n", "36\t1334\t81.9\t0\t1334\n", "37\t651\t81.9\t0\t651\n", "38\t78\t81.9\t0\t78\n", "39\t59\t81.9\t0\t59\n", "40\t43\t81.9\t0\t43\n", "41\t38\t81.9\t0\t38\n", "42\t29\t81.9\t0\t29\n", "43\t31\t81.9\t0\t31\n", "44\t33\t81.9\t0\t33\n", "45\t27\t81.9\t0\t27\n", "46\t32\t81.9\t0\t32\n", "47\t33\t81.9\t0\t33\n", "48\t32\t81.9\t0\t32\n", "49\t20\t81.9\t0\t20\n", "50\t25\t81.9\t0\t25\n", "51\t32\t81.9\t0\t32\n", "52\t36\t81.9\t0\t36\n", "53\t25\t81.9\t0\t25\n", "54\t25\t81.9\t0\t25\n", "55\t21\t81.9\t0\t21\n", "56\t23\t81.9\t0\t23\n", "57\t21\t81.9\t0\t21\n", "58\t26\t81.9\t0\t26\n", "59\t21\t81.9\t0\t21\n", "60\t24\t81.9\t0\t24\n", "61\t18\t81.9\t0\t18\n", "62\t31\t81.9\t0\t31\n", "63\t16\t81.9\t0\t16\n", "64\t18\t81.9\t0\t18\n", "65\t26\t81.9\t0\t26\n", "66\t14\t81.9\t0\t14\n", "67\t12\t81.9\t0\t12\n", "68\t18\t81.9\t0\t18\n", "69\t25\t81.9\t0\t25\n", "70\t17\t81.9\t0\t17\n", "71\t18\t81.9\t0\t18\n", "72\t19\t81.9\t0\t19\n", "73\t17\t81.9\t0\t17\n", "74\t19\t81.9\t0\t19\n", "75\t19\t81.9\t0\t19\n", "76\t12\t81.9\t0\t12\n", "77\t16\t81.9\t0\t16\n", "78\t22\t81.9\t0\t22\n", "79\t17\t81.9\t0\t17\n", "80\t11\t81.9\t0\t11\n", "81\t19\t81.9\t0\t19\n", "82\t13\t81.9\t0\t13\n", "83\t30\t81.9\t0\t30\n", "84\t20\t81.9\t0\t20\n", "85\t27\t81.9\t0\t27\n", "86\t25\t81.9\t0\t25\n", "87\t22\t81.9\t0\t22\n", "88\t18\t81.9\t0\t18\n", "89\t27\t81.9\t0\t27\n", "90\t29\t81.9\t0\t29\n", "91\t39\t81.9\t0\t39\n", "92\t55\t81.9\t0\t55\n", "93\t77\t81.9\t0\t77\n", "94\t89\t81.9\t0\t89\n", "95\t134\t81.9\t0\t134\n", "96\t118\t81.9\t0\t118\n", "97\t114\t81.9\t0\t114\n", "98\t108\t81.9\t0\t108\n", "99\t59\t81.9\t0\t59\n", "100\t145\t81.9\t0\t145\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 101959 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.5%\n", " C: 21.1%\n", " G: 15.1%\n", " T: 24.2%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t77979\t83857.5\t0\t77979\n", "4\t16650\t20964.4\t0\t16650\n", "5\t1954\t5241.1\t0\t1954\n", "6\t216\t1310.3\t0\t216\n", "7\t56\t327.6\t0\t56\n", "8\t51\t327.6\t0\t51\n", "9\t46\t327.6\t0\t46\n", "10\t50\t327.6\t0\t50\n", "11\t58\t327.6\t0\t58\n", "12\t60\t327.6\t0\t60\n", "13\t63\t327.6\t0\t63\n", "14\t79\t327.6\t0\t79\n", "15\t80\t327.6\t0\t80\n", "16\t82\t327.6\t0\t82\n", "17\t95\t327.6\t0\t95\n", "18\t67\t327.6\t0\t67\n", "19\t75\t327.6\t0\t75\n", "20\t72\t327.6\t0\t72\n", "21\t69\t327.6\t0\t69\n", "22\t61\t327.6\t0\t61\n", "23\t55\t327.6\t0\t55\n", "24\t46\t327.6\t0\t46\n", "25\t46\t327.6\t0\t46\n", "26\t42\t327.6\t0\t42\n", "27\t54\t327.6\t0\t54\n", "28\t79\t327.6\t0\t79\n", "29\t63\t327.6\t0\t63\n", "30\t59\t327.6\t0\t59\n", "31\t80\t327.6\t0\t80\n", "32\t72\t327.6\t0\t72\n", "33\t60\t327.6\t0\t60\n", "34\t36\t327.6\t0\t36\n", "35\t46\t327.6\t0\t46\n", "36\t55\t327.6\t0\t55\n", "37\t43\t327.6\t0\t43\n", "38\t71\t327.6\t0\t71\n", "39\t61\t327.6\t0\t61\n", "40\t79\t327.6\t0\t79\n", "41\t56\t327.6\t0\t56\n", "42\t42\t327.6\t0\t42\n", "43\t68\t327.6\t0\t68\n", "44\t60\t327.6\t0\t60\n", "45\t49\t327.6\t0\t49\n", "46\t66\t327.6\t0\t66\n", "47\t54\t327.6\t0\t54\n", "48\t35\t327.6\t0\t35\n", "49\t46\t327.6\t0\t46\n", "50\t57\t327.6\t0\t57\n", "51\t53\t327.6\t0\t53\n", "52\t48\t327.6\t0\t48\n", "53\t52\t327.6\t0\t52\n", "54\t49\t327.6\t0\t49\n", "55\t61\t327.6\t0\t61\n", "56\t38\t327.6\t0\t38\n", "57\t41\t327.6\t0\t41\n", "58\t44\t327.6\t0\t44\n", "59\t36\t327.6\t0\t36\n", "60\t37\t327.6\t0\t37\n", "61\t34\t327.6\t0\t34\n", "62\t29\t327.6\t0\t29\n", "63\t47\t327.6\t0\t47\n", "64\t40\t327.6\t0\t40\n", "65\t29\t327.6\t0\t29\n", "66\t44\t327.6\t0\t44\n", "67\t46\t327.6\t0\t46\n", "68\t35\t327.6\t0\t35\n", "69\t55\t327.6\t0\t55\n", "70\t69\t327.6\t0\t69\n", "71\t38\t327.6\t0\t38\n", "72\t49\t327.6\t0\t49\n", "73\t36\t327.6\t0\t36\n", "74\t32\t327.6\t0\t32\n", "75\t44\t327.6\t0\t44\n", "76\t57\t327.6\t0\t57\n", "77\t55\t327.6\t0\t55\n", "78\t49\t327.6\t0\t49\n", "79\t60\t327.6\t0\t60\n", "80\t57\t327.6\t0\t57\n", "81\t53\t327.6\t0\t53\n", "82\t73\t327.6\t0\t73\n", "83\t59\t327.6\t0\t59\n", "84\t80\t327.6\t0\t80\n", "85\t57\t327.6\t0\t57\n", "86\t77\t327.6\t0\t77\n", "87\t77\t327.6\t0\t77\n", "88\t82\t327.6\t0\t82\n", "89\t55\t327.6\t0\t55\n", "90\t54\t327.6\t0\t54\n", "91\t34\t327.6\t0\t34\n", "92\t13\t327.6\t0\t13\n", "93\t33\t327.6\t0\t33\n", "94\t43\t327.6\t0\t43\n", "95\t23\t327.6\t0\t23\n", "96\t43\t327.6\t0\t43\n", "97\t57\t327.6\t0\t57\n", "98\t59\t327.6\t0\t59\n", "99\t76\t327.6\t0\t76\n", "100\t104\t327.6\t0\t104\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 315_S26_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/315.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 129.93 s (14 us/read; 4.17 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 9,029,499\n", "Reads with adapters: 7,442,365 (82.4%)\n", "Reads written (passing filters): 8,512,680 (94.3%)\n", "\n", "Total basepairs processed: 902,949,900 bp\n", "Quality-trimmed: 3,088,376 bp (0.3%)\n", "Total written (filtered): 582,563,122 bp (64.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 7320050 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 34.6%\n", " G: 40.5%\n", " T: 24.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t111931\t141085.9\t0\t111931\n", "4\t79809\t35271.5\t0\t79809\n", "5\t69522\t8817.9\t0\t69522\n", "6\t64499\t2204.5\t0\t64499\n", "7\t65163\t551.1\t0\t65163\n", "8\t66889\t137.8\t0\t66889\n", "9\t67963\t137.8\t0\t67963\n", "10\t68365\t137.8\t0\t68365\n", "11\t69595\t137.8\t0\t69595\n", "12\t72652\t137.8\t0\t72652\n", "13\t78716\t137.8\t0\t78716\n", "14\t80702\t137.8\t0\t80702\n", "15\t78826\t137.8\t0\t78826\n", "16\t84739\t137.8\t0\t84739\n", "17\t94909\t137.8\t0\t94909\n", "18\t106179\t137.8\t0\t106179\n", "19\t98410\t137.8\t0\t98410\n", "20\t83176\t137.8\t0\t83176\n", "21\t80463\t137.8\t0\t80463\n", "22\t75806\t137.8\t0\t75806\n", "23\t83314\t137.8\t0\t83314\n", "24\t95907\t137.8\t0\t95907\n", "25\t101418\t137.8\t0\t101418\n", "26\t116091\t137.8\t0\t116091\n", "27\t122761\t137.8\t0\t122761\n", "28\t112352\t137.8\t0\t112352\n", "29\t103429\t137.8\t0\t103429\n", "30\t106215\t137.8\t0\t106215\n", "31\t119564\t137.8\t0\t119564\n", "32\t111937\t137.8\t0\t111937\n", "33\t110051\t137.8\t0\t110051\n", "34\t107746\t137.8\t0\t107746\n", "35\t122883\t137.8\t0\t122883\n", "36\t134224\t137.8\t0\t134224\n", "37\t134831\t137.8\t0\t134831\n", "38\t116466\t137.8\t0\t116466\n", "39\t108479\t137.8\t0\t108479\n", "40\t105500\t137.8\t0\t105500\n", "41\t116949\t137.8\t0\t116949\n", "42\t125078\t137.8\t0\t125078\n", "43\t113142\t137.8\t0\t113142\n", "44\t91387\t137.8\t0\t91387\n", "45\t112824\t137.8\t0\t112824\n", "46\t134855\t137.8\t0\t134855\n", "47\t131145\t137.8\t0\t131145\n", "48\t124204\t137.8\t0\t124204\n", "49\t101250\t137.8\t0\t101250\n", "50\t97674\t137.8\t0\t97674\n", "51\t99753\t137.8\t0\t99753\n", "52\t103990\t137.8\t0\t103990\n", "53\t92690\t137.8\t0\t92690\n", "54\t99416\t137.8\t0\t99416\n", "55\t102344\t137.8\t0\t102344\n", "56\t105295\t137.8\t0\t105295\n", "57\t107902\t137.8\t0\t107902\n", "58\t107727\t137.8\t0\t107727\n", "59\t94885\t137.8\t0\t94885\n", "60\t83444\t137.8\t0\t83444\n", "61\t77875\t137.8\t0\t77875\n", "62\t63617\t137.8\t0\t63617\n", "63\t59576\t137.8\t0\t59576\n", "64\t68273\t137.8\t0\t68273\n", "65\t69439\t137.8\t0\t69439\n", "66\t62444\t137.8\t0\t62444\n", "67\t61712\t137.8\t0\t61712\n", "68\t60581\t137.8\t0\t60581\n", "69\t62331\t137.8\t0\t62331\n", "70\t64789\t137.8\t0\t64789\n", "71\t61599\t137.8\t0\t61599\n", "72\t49576\t137.8\t0\t49576\n", "73\t46510\t137.8\t0\t46510\n", "74\t46818\t137.8\t0\t46818\n", "75\t40803\t137.8\t0\t40803\n", "76\t35129\t137.8\t0\t35129\n", "77\t31367\t137.8\t0\t31367\n", "78\t35035\t137.8\t0\t35035\n", "79\t33977\t137.8\t0\t33977\n", "80\t33881\t137.8\t0\t33881\n", "81\t30927\t137.8\t0\t30927\n", "82\t29254\t137.8\t0\t29254\n", "83\t31633\t137.8\t0\t31633\n", "84\t36674\t137.8\t0\t36674\n", "85\t41790\t137.8\t0\t41790\n", "86\t37857\t137.8\t0\t37857\n", "87\t24579\t137.8\t0\t24579\n", "88\t21575\t137.8\t0\t21575\n", "89\t24078\t137.8\t0\t24078\n", "90\t26154\t137.8\t0\t26154\n", "91\t27239\t137.8\t0\t27239\n", "92\t28127\t137.8\t0\t28127\n", "93\t31661\t137.8\t0\t31661\n", "94\t30055\t137.8\t0\t30055\n", "95\t25437\t137.8\t0\t25437\n", "96\t18494\t137.8\t0\t18494\n", "97\t11475\t137.8\t0\t11475\n", "98\t6753\t137.8\t0\t6753\n", "99\t8599\t137.8\t0\t8599\n", "100\t4921\t137.8\t0\t4921\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 45616 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 73.0%\n", " C: 13.0%\n", " G: 0.0%\n", " T: 14.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t8652\t141085.9\t0\t8652\n", "4\t2329\t35271.5\t0\t2329\n", "5\t1080\t8817.9\t0\t1080\n", "6\t762\t2204.5\t0\t762\n", "7\t381\t551.1\t0\t381\n", "8\t298\t137.8\t0\t298\n", "9\t281\t137.8\t0\t281\n", "10\t305\t137.8\t0\t305\n", "11\t277\t137.8\t0\t277\n", "12\t270\t137.8\t0\t270\n", "13\t278\t137.8\t0\t278\n", "14\t254\t137.8\t0\t254\n", "15\t266\t137.8\t0\t266\n", "16\t253\t137.8\t0\t253\n", "17\t311\t137.8\t0\t311\n", "18\t423\t137.8\t0\t423\n", "19\t565\t137.8\t0\t565\n", "20\t983\t137.8\t0\t983\n", "21\t670\t137.8\t0\t670\n", "22\t529\t137.8\t0\t529\n", "23\t362\t137.8\t0\t362\n", "24\t383\t137.8\t0\t383\n", "25\t424\t137.8\t0\t424\n", "26\t872\t137.8\t0\t872\n", "27\t766\t137.8\t0\t766\n", "28\t777\t137.8\t0\t777\n", "29\t980\t137.8\t0\t980\n", "30\t1692\t137.8\t0\t1692\n", "31\t1937\t137.8\t0\t1937\n", "32\t2829\t137.8\t0\t2829\n", "33\t2607\t137.8\t0\t2607\n", "34\t2698\t137.8\t0\t2698\n", "35\t3460\t137.8\t0\t3460\n", "36\t3464\t137.8\t0\t3464\n", "37\t1059\t137.8\t0\t1059\n", "38\t58\t137.8\t0\t58\n", "39\t69\t137.8\t0\t69\n", "40\t63\t137.8\t0\t63\n", "41\t50\t137.8\t0\t50\n", "42\t54\t137.8\t0\t54\n", "43\t44\t137.8\t0\t44\n", "44\t43\t137.8\t0\t43\n", "45\t56\t137.8\t0\t56\n", "46\t54\t137.8\t0\t54\n", "47\t57\t137.8\t0\t57\n", "48\t50\t137.8\t0\t50\n", "49\t60\t137.8\t0\t60\n", "50\t61\t137.8\t0\t61\n", "51\t63\t137.8\t0\t63\n", "52\t50\t137.8\t0\t50\n", "53\t58\t137.8\t0\t58\n", "54\t59\t137.8\t0\t59\n", "55\t59\t137.8\t0\t59\n", "56\t44\t137.8\t0\t44\n", "57\t57\t137.8\t0\t57\n", "58\t52\t137.8\t0\t52\n", "59\t34\t137.8\t0\t34\n", "60\t28\t137.8\t0\t28\n", "61\t39\t137.8\t0\t39\n", "62\t35\t137.8\t0\t35\n", "63\t32\t137.8\t0\t32\n", "64\t38\t137.8\t0\t38\n", "65\t42\t137.8\t0\t42\n", "66\t31\t137.8\t0\t31\n", "67\t32\t137.8\t0\t32\n", "68\t24\t137.8\t0\t24\n", "69\t20\t137.8\t0\t20\n", "70\t24\t137.8\t0\t24\n", "71\t17\t137.8\t0\t17\n", "72\t17\t137.8\t0\t17\n", "73\t8\t137.8\t0\t8\n", "74\t7\t137.8\t0\t7\n", "75\t10\t137.8\t0\t10\n", "76\t3\t137.8\t0\t3\n", "77\t7\t137.8\t0\t7\n", "78\t5\t137.8\t0\t5\n", "79\t3\t137.8\t0\t3\n", "80\t7\t137.8\t0\t7\n", "81\t3\t137.8\t0\t3\n", "82\t9\t137.8\t0\t9\n", "83\t9\t137.8\t0\t9\n", "84\t6\t137.8\t0\t6\n", "85\t13\t137.8\t0\t13\n", "86\t11\t137.8\t0\t11\n", "87\t11\t137.8\t0\t11\n", "88\t17\t137.8\t0\t17\n", "89\t9\t137.8\t0\t9\n", "90\t9\t137.8\t0\t9\n", "91\t15\t137.8\t0\t15\n", "92\t32\t137.8\t0\t32\n", "93\t31\t137.8\t0\t31\n", "94\t49\t137.8\t0\t49\n", "95\t48\t137.8\t0\t48\n", "96\t62\t137.8\t0\t62\n", "97\t59\t137.8\t0\t59\n", "98\t36\t137.8\t0\t36\n", "99\t22\t137.8\t0\t22\n", "100\t64\t137.8\t0\t64\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 76699 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.6%\n", " C: 18.7%\n", " G: 19.9%\n", " T: 16.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t47673\t141085.9\t0\t47673\n", "4\t10230\t35271.5\t0\t10230\n", "5\t2051\t8817.9\t0\t2051\n", "6\t428\t2204.5\t0\t428\n", "7\t322\t551.1\t0\t322\n", "8\t308\t551.1\t0\t308\n", "9\t270\t551.1\t0\t270\n", "10\t263\t551.1\t0\t263\n", "11\t319\t551.1\t0\t319\n", "12\t282\t551.1\t0\t282\n", "13\t344\t551.1\t0\t344\n", "14\t291\t551.1\t0\t291\n", "15\t345\t551.1\t0\t345\n", "16\t377\t551.1\t0\t377\n", "17\t340\t551.1\t0\t340\n", "18\t339\t551.1\t0\t339\n", "19\t328\t551.1\t0\t328\n", "20\t316\t551.1\t0\t316\n", "21\t300\t551.1\t0\t300\n", "22\t286\t551.1\t0\t286\n", "23\t282\t551.1\t0\t282\n", "24\t267\t551.1\t0\t267\n", "25\t266\t551.1\t0\t266\n", "26\t291\t551.1\t0\t291\n", "27\t283\t551.1\t0\t283\n", "28\t279\t551.1\t0\t279\n", "29\t300\t551.1\t0\t300\n", "30\t301\t551.1\t0\t301\n", "31\t276\t551.1\t0\t276\n", "32\t279\t551.1\t0\t279\n", "33\t284\t551.1\t0\t284\n", "34\t261\t551.1\t0\t261\n", "35\t239\t551.1\t0\t239\n", "36\t246\t551.1\t0\t246\n", "37\t241\t551.1\t0\t241\n", "38\t226\t551.1\t0\t226\n", "39\t197\t551.1\t0\t197\n", "40\t215\t551.1\t0\t215\n", "41\t202\t551.1\t0\t202\n", "42\t167\t551.1\t0\t167\n", "43\t290\t551.1\t0\t290\n", "44\t86\t551.1\t0\t86\n", "45\t187\t551.1\t0\t187\n", "46\t195\t551.1\t0\t195\n", "47\t179\t551.1\t0\t179\n", "48\t166\t551.1\t0\t166\n", "49\t179\t551.1\t0\t179\n", "50\t181\t551.1\t0\t181\n", "51\t147\t551.1\t0\t147\n", "52\t150\t551.1\t0\t150\n", "53\t154\t551.1\t0\t154\n", "54\t160\t551.1\t0\t160\n", "55\t154\t551.1\t0\t154\n", "56\t139\t551.1\t0\t139\n", "57\t123\t551.1\t0\t123\n", "58\t118\t551.1\t0\t118\n", "59\t100\t551.1\t0\t100\n", "60\t103\t551.1\t0\t103\n", "61\t116\t551.1\t0\t116\n", "62\t100\t551.1\t0\t100\n", "63\t84\t551.1\t0\t84\n", "64\t96\t551.1\t0\t96\n", "65\t83\t551.1\t0\t83\n", "66\t102\t551.1\t0\t102\n", "67\t92\t551.1\t0\t92\n", "68\t114\t551.1\t0\t114\n", "69\t45\t551.1\t0\t45\n", "70\t50\t551.1\t0\t50\n", "71\t60\t551.1\t0\t60\n", "72\t87\t551.1\t0\t87\n", "73\t74\t551.1\t0\t74\n", "74\t82\t551.1\t0\t82\n", "75\t82\t551.1\t0\t82\n", "76\t90\t551.1\t0\t90\n", "77\t110\t551.1\t0\t110\n", "78\t83\t551.1\t0\t83\n", "79\t91\t551.1\t0\t91\n", "80\t98\t551.1\t0\t98\n", "81\t90\t551.1\t0\t90\n", "82\t131\t551.1\t0\t131\n", "83\t113\t551.1\t0\t113\n", "84\t105\t551.1\t0\t105\n", "85\t103\t551.1\t0\t103\n", "86\t71\t551.1\t0\t71\n", "87\t84\t551.1\t0\t84\n", "88\t90\t551.1\t0\t90\n", "89\t80\t551.1\t0\t80\n", "90\t79\t551.1\t0\t79\n", "91\t62\t551.1\t0\t62\n", "92\t62\t551.1\t0\t62\n", "93\t58\t551.1\t0\t58\n", "94\t66\t551.1\t0\t66\n", "95\t65\t551.1\t0\t65\n", "96\t64\t551.1\t0\t64\n", "97\t83\t551.1\t0\t83\n", "98\t88\t551.1\t0\t88\n", "99\t68\t551.1\t0\t68\n", "100\t73\t551.1\t0\t73\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 316_S9_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/316.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 129.86 s (13 us/read; 4.53 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 9,796,267\n", "Reads with adapters: 6,848,041 (69.9%)\n", "Reads written (passing filters): 9,498,546 (97.0%)\n", "\n", "Total basepairs processed: 979,626,700 bp\n", "Quality-trimmed: 2,588,400 bp (0.3%)\n", "Total written (filtered): 725,929,947 bp (74.1%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 6671506 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 34.7%\n", " G: 40.6%\n", " T: 24.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t184207\t153066.7\t0\t184207\n", "4\t117267\t38266.7\t0\t117267\n", "5\t95455\t9566.7\t0\t95455\n", "6\t85395\t2391.7\t0\t85395\n", "7\t83900\t597.9\t0\t83900\n", "8\t85474\t149.5\t0\t85474\n", "9\t85086\t149.5\t0\t85086\n", "10\t84949\t149.5\t0\t84949\n", "11\t86973\t149.5\t0\t86973\n", "12\t88001\t149.5\t0\t88001\n", "13\t93495\t149.5\t0\t93495\n", "14\t95608\t149.5\t0\t95608\n", "15\t93179\t149.5\t0\t93179\n", "16\t98589\t149.5\t0\t98589\n", "17\t109195\t149.5\t0\t109195\n", "18\t120701\t149.5\t0\t120701\n", "19\t108610\t149.5\t0\t108610\n", "20\t92293\t149.5\t0\t92293\n", "21\t87600\t149.5\t0\t87600\n", "22\t82132\t149.5\t0\t82132\n", "23\t89869\t149.5\t0\t89869\n", "24\t102337\t149.5\t0\t102337\n", "25\t107931\t149.5\t0\t107931\n", "26\t121473\t149.5\t0\t121473\n", "27\t126403\t149.5\t0\t126403\n", "28\t112924\t149.5\t0\t112924\n", "29\t104227\t149.5\t0\t104227\n", "30\t102087\t149.5\t0\t102087\n", "31\t111284\t149.5\t0\t111284\n", "32\t113717\t149.5\t0\t113717\n", "33\t108628\t149.5\t0\t108628\n", "34\t107103\t149.5\t0\t107103\n", "35\t118109\t149.5\t0\t118109\n", "36\t127541\t149.5\t0\t127541\n", "37\t126394\t149.5\t0\t126394\n", "38\t108380\t149.5\t0\t108380\n", "39\t99902\t149.5\t0\t99902\n", "40\t95819\t149.5\t0\t95819\n", "41\t107473\t149.5\t0\t107473\n", "42\t115051\t149.5\t0\t115051\n", "43\t101444\t149.5\t0\t101444\n", "44\t81800\t149.5\t0\t81800\n", "45\t97459\t149.5\t0\t97459\n", "46\t112091\t149.5\t0\t112091\n", "47\t102944\t149.5\t0\t102944\n", "48\t97101\t149.5\t0\t97101\n", "49\t82757\t149.5\t0\t82757\n", "50\t81364\t149.5\t0\t81364\n", "51\t72760\t149.5\t0\t72760\n", "52\t74310\t149.5\t0\t74310\n", "53\t77118\t149.5\t0\t77118\n", "54\t76974\t149.5\t0\t76974\n", "55\t72753\t149.5\t0\t72753\n", "56\t75631\t149.5\t0\t75631\n", "57\t76762\t149.5\t0\t76762\n", "58\t81386\t149.5\t0\t81386\n", "59\t72275\t149.5\t0\t72275\n", "60\t58963\t149.5\t0\t58963\n", "61\t54610\t149.5\t0\t54610\n", "62\t45005\t149.5\t0\t45005\n", "63\t41719\t149.5\t0\t41719\n", "64\t46782\t149.5\t0\t46782\n", "65\t46461\t149.5\t0\t46461\n", "66\t41350\t149.5\t0\t41350\n", "67\t41078\t149.5\t0\t41078\n", "68\t40017\t149.5\t0\t40017\n", "69\t41196\t149.5\t0\t41196\n", "70\t42865\t149.5\t0\t42865\n", "71\t40749\t149.5\t0\t40749\n", "72\t32465\t149.5\t0\t32465\n", "73\t29904\t149.5\t0\t29904\n", "74\t29946\t149.5\t0\t29946\n", "75\t26677\t149.5\t0\t26677\n", "76\t22616\t149.5\t0\t22616\n", "77\t20356\t149.5\t0\t20356\n", "78\t22369\t149.5\t0\t22369\n", "79\t21699\t149.5\t0\t21699\n", "80\t20779\t149.5\t0\t20779\n", "81\t19007\t149.5\t0\t19007\n", "82\t17895\t149.5\t0\t17895\n", "83\t18799\t149.5\t0\t18799\n", "84\t21451\t149.5\t0\t21451\n", "85\t23651\t149.5\t0\t23651\n", "86\t22281\t149.5\t0\t22281\n", "87\t14803\t149.5\t0\t14803\n", "88\t13486\t149.5\t0\t13486\n", "89\t14101\t149.5\t0\t14101\n", "90\t15041\t149.5\t0\t15041\n", "91\t15133\t149.5\t0\t15133\n", "92\t15072\t149.5\t0\t15072\n", "93\t16515\t149.5\t0\t16515\n", "94\t15859\t149.5\t0\t15859\n", "95\t13426\t149.5\t0\t13426\n", "96\t9676\t149.5\t0\t9676\n", "97\t5918\t149.5\t0\t5918\n", "98\t3421\t149.5\t0\t3421\n", "99\t4732\t149.5\t0\t4732\n", "100\t1943\t149.5\t0\t1943\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 50823 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 53.5%\n", " C: 26.3%\n", " G: 0.0%\n", " T: 20.1%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t19166\t153066.7\t0\t19166\n", "4\t4535\t38266.7\t0\t4535\n", "5\t1782\t9566.7\t0\t1782\n", "6\t1443\t2391.7\t0\t1443\n", "7\t161\t597.9\t0\t161\n", "8\t164\t149.5\t0\t164\n", "9\t138\t149.5\t0\t138\n", "10\t137\t149.5\t0\t137\n", "11\t123\t149.5\t0\t123\n", "12\t111\t149.5\t0\t111\n", "13\t126\t149.5\t0\t126\n", "14\t125\t149.5\t0\t125\n", "15\t107\t149.5\t0\t107\n", "16\t135\t149.5\t0\t135\n", "17\t151\t149.5\t0\t151\n", "18\t165\t149.5\t0\t165\n", "19\t218\t149.5\t0\t218\n", "20\t292\t149.5\t0\t292\n", "21\t241\t149.5\t0\t241\n", "22\t223\t149.5\t0\t223\n", "23\t179\t149.5\t0\t179\n", "24\t192\t149.5\t0\t192\n", "25\t227\t149.5\t0\t227\n", "26\t403\t149.5\t0\t403\n", "27\t384\t149.5\t0\t384\n", "28\t455\t149.5\t0\t455\n", "29\t674\t149.5\t0\t674\n", "30\t1081\t149.5\t0\t1081\n", "31\t1324\t149.5\t0\t1324\n", "32\t2076\t149.5\t0\t2076\n", "33\t1781\t149.5\t0\t1781\n", "34\t1725\t149.5\t0\t1725\n", "35\t2192\t149.5\t0\t2192\n", "36\t2157\t149.5\t0\t2157\n", "37\t831\t149.5\t0\t831\n", "38\t109\t149.5\t0\t109\n", "39\t110\t149.5\t0\t110\n", "40\t104\t149.5\t0\t104\n", "41\t91\t149.5\t0\t91\n", "42\t92\t149.5\t0\t92\n", "43\t124\t149.5\t0\t124\n", "44\t113\t149.5\t0\t113\n", "45\t98\t149.5\t0\t98\n", "46\t107\t149.5\t0\t107\n", "47\t112\t149.5\t0\t112\n", "48\t100\t149.5\t0\t100\n", "49\t124\t149.5\t0\t124\n", "50\t119\t149.5\t0\t119\n", "51\t99\t149.5\t0\t99\n", "52\t85\t149.5\t0\t85\n", "53\t91\t149.5\t0\t91\n", "54\t74\t149.5\t0\t74\n", "55\t89\t149.5\t0\t89\n", "56\t92\t149.5\t0\t92\n", "57\t84\t149.5\t0\t84\n", "58\t74\t149.5\t0\t74\n", "59\t82\t149.5\t0\t82\n", "60\t70\t149.5\t0\t70\n", "61\t52\t149.5\t0\t52\n", "62\t71\t149.5\t0\t71\n", "63\t64\t149.5\t0\t64\n", "64\t59\t149.5\t0\t59\n", "65\t65\t149.5\t0\t65\n", "66\t50\t149.5\t0\t50\n", "67\t37\t149.5\t0\t37\n", "68\t43\t149.5\t0\t43\n", "69\t34\t149.5\t0\t34\n", "70\t26\t149.5\t0\t26\n", "71\t19\t149.5\t0\t19\n", "72\t22\t149.5\t0\t22\n", "73\t18\t149.5\t0\t18\n", "74\t18\t149.5\t0\t18\n", "75\t19\t149.5\t0\t19\n", "76\t18\t149.5\t0\t18\n", "77\t20\t149.5\t0\t20\n", "78\t38\t149.5\t0\t38\n", "79\t37\t149.5\t0\t37\n", "80\t45\t149.5\t0\t45\n", "81\t44\t149.5\t0\t44\n", "82\t68\t149.5\t0\t68\n", "83\t102\t149.5\t0\t102\n", "84\t94\t149.5\t0\t94\n", "85\t111\t149.5\t0\t111\n", "86\t84\t149.5\t0\t84\n", "87\t106\t149.5\t0\t106\n", "88\t76\t149.5\t0\t76\n", "89\t82\t149.5\t0\t82\n", "90\t55\t149.5\t0\t55\n", "91\t87\t149.5\t0\t87\n", "92\t139\t149.5\t0\t139\n", "93\t194\t149.5\t0\t194\n", "94\t259\t149.5\t0\t259\n", "95\t262\t149.5\t0\t262\n", "96\t249\t149.5\t0\t249\n", "97\t258\t149.5\t0\t258\n", "98\t129\t149.5\t0\t129\n", "99\t64\t149.5\t0\t64\n", "100\t138\t149.5\t0\t138\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 125712 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.0%\n", " C: 18.1%\n", " G: 20.8%\n", " T: 20.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t91120\t153066.7\t0\t91120\n", "4\t19172\t38266.7\t0\t19172\n", "5\t3137\t9566.7\t0\t3137\n", "6\t401\t2391.7\t0\t401\n", "7\t185\t597.9\t0\t185\n", "8\t168\t597.9\t0\t168\n", "9\t124\t597.9\t0\t124\n", "10\t168\t597.9\t0\t168\n", "11\t183\t597.9\t0\t183\n", "12\t170\t597.9\t0\t170\n", "13\t172\t597.9\t0\t172\n", "14\t184\t597.9\t0\t184\n", "15\t214\t597.9\t0\t214\n", "16\t161\t597.9\t0\t161\n", "17\t213\t597.9\t0\t213\n", "18\t216\t597.9\t0\t216\n", "19\t196\t597.9\t0\t196\n", "20\t174\t597.9\t0\t174\n", "21\t186\t597.9\t0\t186\n", "22\t161\t597.9\t0\t161\n", "23\t175\t597.9\t0\t175\n", "24\t149\t597.9\t0\t149\n", "25\t151\t597.9\t0\t151\n", "26\t146\t597.9\t0\t146\n", "27\t151\t597.9\t0\t151\n", "28\t170\t597.9\t0\t170\n", "29\t167\t597.9\t0\t167\n", "30\t153\t597.9\t0\t153\n", "31\t151\t597.9\t0\t151\n", "32\t179\t597.9\t0\t179\n", "33\t178\t597.9\t0\t178\n", "34\t167\t597.9\t0\t167\n", "35\t153\t597.9\t0\t153\n", "36\t142\t597.9\t0\t142\n", "37\t126\t597.9\t0\t126\n", "38\t147\t597.9\t0\t147\n", "39\t130\t597.9\t0\t130\n", "40\t139\t597.9\t0\t139\n", "41\t133\t597.9\t0\t133\n", "42\t92\t597.9\t0\t92\n", "43\t162\t597.9\t0\t162\n", "44\t86\t597.9\t0\t86\n", "45\t133\t597.9\t0\t133\n", "46\t147\t597.9\t0\t147\n", "47\t128\t597.9\t0\t128\n", "48\t122\t597.9\t0\t122\n", "49\t111\t597.9\t0\t111\n", "50\t99\t597.9\t0\t99\n", "51\t114\t597.9\t0\t114\n", "52\t121\t597.9\t0\t121\n", "53\t115\t597.9\t0\t115\n", "54\t90\t597.9\t0\t90\n", "55\t76\t597.9\t0\t76\n", "56\t100\t597.9\t0\t100\n", "57\t87\t597.9\t0\t87\n", "58\t71\t597.9\t0\t71\n", "59\t72\t597.9\t0\t72\n", "60\t93\t597.9\t0\t93\n", "61\t70\t597.9\t0\t70\n", "62\t85\t597.9\t0\t85\n", "63\t79\t597.9\t0\t79\n", "64\t81\t597.9\t0\t81\n", "65\t80\t597.9\t0\t80\n", "66\t81\t597.9\t0\t81\n", "67\t92\t597.9\t0\t92\n", "68\t97\t597.9\t0\t97\n", "69\t72\t597.9\t0\t72\n", "70\t72\t597.9\t0\t72\n", "71\t75\t597.9\t0\t75\n", "72\t97\t597.9\t0\t97\n", "73\t94\t597.9\t0\t94\n", "74\t125\t597.9\t0\t125\n", "75\t110\t597.9\t0\t110\n", "76\t127\t597.9\t0\t127\n", "77\t125\t597.9\t0\t125\n", "78\t137\t597.9\t0\t137\n", "79\t120\t597.9\t0\t120\n", "80\t112\t597.9\t0\t112\n", "81\t139\t597.9\t0\t139\n", "82\t157\t597.9\t0\t157\n", "83\t121\t597.9\t0\t121\n", "84\t133\t597.9\t0\t133\n", "85\t130\t597.9\t0\t130\n", "86\t96\t597.9\t0\t96\n", "87\t106\t597.9\t0\t106\n", "88\t122\t597.9\t0\t122\n", "89\t121\t597.9\t0\t121\n", "90\t97\t597.9\t0\t97\n", "91\t80\t597.9\t0\t80\n", "92\t71\t597.9\t0\t71\n", "93\t61\t597.9\t0\t61\n", "94\t96\t597.9\t0\t96\n", "95\t91\t597.9\t0\t91\n", "96\t69\t597.9\t0\t69\n", "97\t84\t597.9\t0\t84\n", "98\t100\t597.9\t0\t100\n", "99\t133\t597.9\t0\t133\n", "100\t143\t597.9\t0\t143\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 317_S33_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/317.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 75.83 s (13 us/read; 4.63 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,855,264\n", "Reads with adapters: 3,667,881 (62.6%)\n", "Reads written (passing filters): 5,632,419 (96.2%)\n", "\n", "Total basepairs processed: 585,526,400 bp\n", "Quality-trimmed: 1,433,815 bp (0.2%)\n", "Total written (filtered): 446,864,955 bp (76.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3537767 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 35.0%\n", " G: 40.1%\n", " T: 24.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t121048\t91488.5\t0\t121048\n", "4\t71078\t22872.1\t0\t71078\n", "5\t55015\t5718.0\t0\t55015\n", "6\t47741\t1429.5\t0\t47741\n", "7\t45950\t357.4\t0\t45950\n", "8\t45832\t89.3\t0\t45832\n", "9\t45979\t89.3\t0\t45979\n", "10\t45379\t89.3\t0\t45379\n", "11\t46013\t89.3\t0\t46013\n", "12\t46590\t89.3\t0\t46590\n", "13\t49494\t89.3\t0\t49494\n", "14\t50683\t89.3\t0\t50683\n", "15\t49308\t89.3\t0\t49308\n", "16\t50495\t89.3\t0\t50495\n", "17\t54324\t89.3\t0\t54324\n", "18\t61114\t89.3\t0\t61114\n", "19\t58810\t89.3\t0\t58810\n", "20\t47423\t89.3\t0\t47423\n", "21\t45182\t89.3\t0\t45182\n", "22\t41784\t89.3\t0\t41784\n", "23\t45799\t89.3\t0\t45799\n", "24\t53142\t89.3\t0\t53142\n", "25\t57319\t89.3\t0\t57319\n", "26\t62177\t89.3\t0\t62177\n", "27\t58880\t89.3\t0\t58880\n", "28\t53892\t89.3\t0\t53892\n", "29\t50986\t89.3\t0\t50986\n", "30\t50687\t89.3\t0\t50687\n", "31\t55593\t89.3\t0\t55593\n", "32\t55727\t89.3\t0\t55727\n", "33\t53298\t89.3\t0\t53298\n", "34\t52030\t89.3\t0\t52030\n", "35\t57919\t89.3\t0\t57919\n", "36\t62577\t89.3\t0\t62577\n", "37\t62076\t89.3\t0\t62076\n", "38\t53323\t89.3\t0\t53323\n", "39\t48395\t89.3\t0\t48395\n", "40\t46101\t89.3\t0\t46101\n", "41\t51801\t89.3\t0\t51801\n", "42\t56626\t89.3\t0\t56626\n", "43\t49569\t89.3\t0\t49569\n", "44\t38673\t89.3\t0\t38673\n", "45\t47248\t89.3\t0\t47248\n", "46\t54309\t89.3\t0\t54309\n", "47\t51204\t89.3\t0\t51204\n", "48\t48500\t89.3\t0\t48500\n", "49\t42214\t89.3\t0\t42214\n", "50\t41772\t89.3\t0\t41772\n", "51\t35876\t89.3\t0\t35876\n", "52\t36910\t89.3\t0\t36910\n", "53\t32680\t89.3\t0\t32680\n", "54\t38367\t89.3\t0\t38367\n", "55\t44586\t89.3\t0\t44586\n", "56\t43240\t89.3\t0\t43240\n", "57\t39121\t89.3\t0\t39121\n", "58\t41094\t89.3\t0\t41094\n", "59\t33723\t89.3\t0\t33723\n", "60\t29660\t89.3\t0\t29660\n", "61\t28579\t89.3\t0\t28579\n", "62\t24119\t89.3\t0\t24119\n", "63\t22864\t89.3\t0\t22864\n", "64\t26552\t89.3\t0\t26552\n", "65\t26325\t89.3\t0\t26325\n", "66\t22542\t89.3\t0\t22542\n", "67\t22804\t89.3\t0\t22804\n", "68\t23074\t89.3\t0\t23074\n", "69\t24059\t89.3\t0\t24059\n", "70\t25202\t89.3\t0\t25202\n", "71\t24852\t89.3\t0\t24852\n", "72\t19344\t89.3\t0\t19344\n", "73\t17782\t89.3\t0\t17782\n", "74\t18072\t89.3\t0\t18072\n", "75\t16217\t89.3\t0\t16217\n", "76\t13256\t89.3\t0\t13256\n", "77\t12577\t89.3\t0\t12577\n", "78\t14677\t89.3\t0\t14677\n", "79\t13698\t89.3\t0\t13698\n", "80\t13274\t89.3\t0\t13274\n", "81\t12676\t89.3\t0\t12676\n", "82\t11951\t89.3\t0\t11951\n", "83\t12693\t89.3\t0\t12693\n", "84\t14791\t89.3\t0\t14791\n", "85\t17121\t89.3\t0\t17121\n", "86\t15921\t89.3\t0\t15921\n", "87\t10653\t89.3\t0\t10653\n", "88\t9646\t89.3\t0\t9646\n", "89\t10298\t89.3\t0\t10298\n", "90\t11026\t89.3\t0\t11026\n", "91\t11878\t89.3\t0\t11878\n", "92\t12407\t89.3\t0\t12407\n", "93\t14183\t89.3\t0\t14183\n", "94\t13631\t89.3\t0\t13631\n", "95\t11350\t89.3\t0\t11350\n", "96\t8265\t89.3\t0\t8265\n", "97\t5056\t89.3\t0\t5056\n", "98\t2899\t89.3\t0\t2899\n", "99\t3293\t89.3\t0\t3293\n", "100\t1824\t89.3\t0\t1824\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 38176 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 57.2%\n", " C: 22.7%\n", " G: 0.0%\n", " T: 20.1%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13958\t91488.5\t0\t13958\n", "4\t3324\t22872.1\t0\t3324\n", "5\t1281\t5718.0\t0\t1281\n", "6\t906\t1429.5\t0\t906\n", "7\t251\t357.4\t0\t251\n", "8\t219\t89.3\t0\t219\n", "9\t179\t89.3\t0\t179\n", "10\t225\t89.3\t0\t225\n", "11\t174\t89.3\t0\t174\n", "12\t160\t89.3\t0\t160\n", "13\t145\t89.3\t0\t145\n", "14\t159\t89.3\t0\t159\n", "15\t154\t89.3\t0\t154\n", "16\t180\t89.3\t0\t180\n", "17\t198\t89.3\t0\t198\n", "18\t228\t89.3\t0\t228\n", "19\t297\t89.3\t0\t297\n", "20\t364\t89.3\t0\t364\n", "21\t332\t89.3\t0\t332\n", "22\t269\t89.3\t0\t269\n", "23\t216\t89.3\t0\t216\n", "24\t222\t89.3\t0\t222\n", "25\t274\t89.3\t0\t274\n", "26\t431\t89.3\t0\t431\n", "27\t414\t89.3\t0\t414\n", "28\t452\t89.3\t0\t452\n", "29\t570\t89.3\t0\t570\n", "30\t896\t89.3\t0\t896\n", "31\t1053\t89.3\t0\t1053\n", "32\t1495\t89.3\t0\t1495\n", "33\t1331\t89.3\t0\t1331\n", "34\t1353\t89.3\t0\t1353\n", "35\t1563\t89.3\t0\t1563\n", "36\t1543\t89.3\t0\t1543\n", "37\t523\t89.3\t0\t523\n", "38\t74\t89.3\t0\t74\n", "39\t56\t89.3\t0\t56\n", "40\t49\t89.3\t0\t49\n", "41\t56\t89.3\t0\t56\n", "42\t44\t89.3\t0\t44\n", "43\t56\t89.3\t0\t56\n", "44\t43\t89.3\t0\t43\n", "45\t75\t89.3\t0\t75\n", "46\t62\t89.3\t0\t62\n", "47\t58\t89.3\t0\t58\n", "48\t52\t89.3\t0\t52\n", "49\t66\t89.3\t0\t66\n", "50\t64\t89.3\t0\t64\n", "51\t56\t89.3\t0\t56\n", "52\t60\t89.3\t0\t60\n", "53\t46\t89.3\t0\t46\n", "54\t39\t89.3\t0\t39\n", "55\t53\t89.3\t0\t53\n", "56\t46\t89.3\t0\t46\n", "57\t54\t89.3\t0\t54\n", "58\t48\t89.3\t0\t48\n", "59\t35\t89.3\t0\t35\n", "60\t34\t89.3\t0\t34\n", "61\t35\t89.3\t0\t35\n", "62\t24\t89.3\t0\t24\n", "63\t37\t89.3\t0\t37\n", "64\t40\t89.3\t0\t40\n", "65\t27\t89.3\t0\t27\n", "66\t22\t89.3\t0\t22\n", "67\t23\t89.3\t0\t23\n", "68\t16\t89.3\t0\t16\n", "69\t18\t89.3\t0\t18\n", "70\t17\t89.3\t0\t17\n", "71\t20\t89.3\t0\t20\n", "72\t22\t89.3\t0\t22\n", "73\t14\t89.3\t0\t14\n", "74\t16\t89.3\t0\t16\n", "75\t22\t89.3\t0\t22\n", "76\t17\t89.3\t0\t17\n", "77\t10\t89.3\t0\t10\n", "78\t19\t89.3\t0\t19\n", "79\t20\t89.3\t0\t20\n", "80\t19\t89.3\t0\t19\n", "81\t28\t89.3\t0\t28\n", "82\t18\t89.3\t0\t18\n", "83\t41\t89.3\t0\t41\n", "84\t29\t89.3\t0\t29\n", "85\t46\t89.3\t0\t46\n", "86\t31\t89.3\t0\t31\n", "87\t29\t89.3\t0\t29\n", "88\t33\t89.3\t0\t33\n", "89\t38\t89.3\t0\t38\n", "90\t34\t89.3\t0\t34\n", "91\t20\t89.3\t0\t20\n", "92\t65\t89.3\t0\t65\n", "93\t84\t89.3\t0\t84\n", "94\t100\t89.3\t0\t100\n", "95\t134\t89.3\t0\t134\n", "96\t139\t89.3\t0\t139\n", "97\t107\t89.3\t0\t107\n", "98\t75\t89.3\t0\t75\n", "99\t32\t89.3\t0\t32\n", "100\t90\t89.3\t0\t90\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 91938 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.3%\n", " C: 20.1%\n", " G: 20.0%\n", " T: 19.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t65987\t91488.5\t0\t65987\n", "4\t13839\t22872.1\t0\t13839\n", "5\t2305\t5718.0\t0\t2305\n", "6\t299\t1429.5\t0\t299\n", "7\t120\t357.4\t0\t120\n", "8\t138\t357.4\t0\t138\n", "9\t107\t357.4\t0\t107\n", "10\t134\t357.4\t0\t134\n", "11\t155\t357.4\t0\t155\n", "12\t158\t357.4\t0\t158\n", "13\t141\t357.4\t0\t141\n", "14\t170\t357.4\t0\t170\n", "15\t173\t357.4\t0\t173\n", "16\t211\t357.4\t0\t211\n", "17\t158\t357.4\t0\t158\n", "18\t173\t357.4\t0\t173\n", "19\t137\t357.4\t0\t137\n", "20\t142\t357.4\t0\t142\n", "21\t149\t357.4\t0\t149\n", "22\t136\t357.4\t0\t136\n", "23\t139\t357.4\t0\t139\n", "24\t130\t357.4\t0\t130\n", "25\t133\t357.4\t0\t133\n", "26\t114\t357.4\t0\t114\n", "27\t129\t357.4\t0\t129\n", "28\t115\t357.4\t0\t115\n", "29\t145\t357.4\t0\t145\n", "30\t108\t357.4\t0\t108\n", "31\t139\t357.4\t0\t139\n", "32\t138\t357.4\t0\t138\n", "33\t117\t357.4\t0\t117\n", "34\t113\t357.4\t0\t113\n", "35\t132\t357.4\t0\t132\n", "36\t104\t357.4\t0\t104\n", "37\t118\t357.4\t0\t118\n", "38\t115\t357.4\t0\t115\n", "39\t122\t357.4\t0\t122\n", "40\t120\t357.4\t0\t120\n", "41\t109\t357.4\t0\t109\n", "42\t90\t357.4\t0\t90\n", "43\t125\t357.4\t0\t125\n", "44\t58\t357.4\t0\t58\n", "45\t102\t357.4\t0\t102\n", "46\t105\t357.4\t0\t105\n", "47\t86\t357.4\t0\t86\n", "48\t99\t357.4\t0\t99\n", "49\t97\t357.4\t0\t97\n", "50\t79\t357.4\t0\t79\n", "51\t94\t357.4\t0\t94\n", "52\t96\t357.4\t0\t96\n", "53\t101\t357.4\t0\t101\n", "54\t99\t357.4\t0\t99\n", "55\t79\t357.4\t0\t79\n", "56\t103\t357.4\t0\t103\n", "57\t86\t357.4\t0\t86\n", "58\t84\t357.4\t0\t84\n", "59\t73\t357.4\t0\t73\n", "60\t92\t357.4\t0\t92\n", "61\t77\t357.4\t0\t77\n", "62\t80\t357.4\t0\t80\n", "63\t75\t357.4\t0\t75\n", "64\t61\t357.4\t0\t61\n", "65\t71\t357.4\t0\t71\n", "66\t81\t357.4\t0\t81\n", "67\t81\t357.4\t0\t81\n", "68\t93\t357.4\t0\t93\n", "69\t48\t357.4\t0\t48\n", "70\t32\t357.4\t0\t32\n", "71\t73\t357.4\t0\t73\n", "72\t101\t357.4\t0\t101\n", "73\t86\t357.4\t0\t86\n", "74\t85\t357.4\t0\t85\n", "75\t91\t357.4\t0\t91\n", "76\t84\t357.4\t0\t84\n", "77\t84\t357.4\t0\t84\n", "78\t93\t357.4\t0\t93\n", "79\t81\t357.4\t0\t81\n", "80\t78\t357.4\t0\t78\n", "81\t70\t357.4\t0\t70\n", "82\t91\t357.4\t0\t91\n", "83\t95\t357.4\t0\t95\n", "84\t94\t357.4\t0\t94\n", "85\t81\t357.4\t0\t81\n", "86\t58\t357.4\t0\t58\n", "87\t88\t357.4\t0\t88\n", "88\t113\t357.4\t0\t113\n", "89\t84\t357.4\t0\t84\n", "90\t71\t357.4\t0\t71\n", "91\t66\t357.4\t0\t66\n", "92\t47\t357.4\t0\t47\n", "93\t47\t357.4\t0\t47\n", "94\t64\t357.4\t0\t64\n", "95\t52\t357.4\t0\t52\n", "96\t43\t357.4\t0\t43\n", "97\t62\t357.4\t0\t62\n", "98\t63\t357.4\t0\t63\n", "99\t82\t357.4\t0\t82\n", "100\t92\t357.4\t0\t92\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 318_S6_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/318.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 82.50 s (13 us/read; 4.60 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,322,897\n", "Reads with adapters: 4,147,316 (65.6%)\n", "Reads written (passing filters): 6,174,885 (97.7%)\n", "\n", "Total basepairs processed: 632,289,700 bp\n", "Quality-trimmed: 1,648,618 bp (0.3%)\n", "Total written (filtered): 481,577,955 bp (76.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4030067 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.9%\n", " G: 38.8%\n", " T: 27.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t131487\t98795.3\t0\t131487\n", "4\t79054\t24698.8\t0\t79054\n", "5\t61676\t6174.7\t0\t61676\n", "6\t53530\t1543.7\t0\t53530\n", "7\t50059\t385.9\t0\t50059\n", "8\t50671\t96.5\t0\t50671\n", "9\t50936\t96.5\t0\t50936\n", "10\t49859\t96.5\t0\t49859\n", "11\t50560\t96.5\t0\t50560\n", "12\t51745\t96.5\t0\t51745\n", "13\t55528\t96.5\t0\t55528\n", "14\t57071\t96.5\t0\t57071\n", "15\t54746\t96.5\t0\t54746\n", "16\t57898\t96.5\t0\t57898\n", "17\t63976\t96.5\t0\t63976\n", "18\t70216\t96.5\t0\t70216\n", "19\t63529\t96.5\t0\t63529\n", "20\t54554\t96.5\t0\t54554\n", "21\t51386\t96.5\t0\t51386\n", "22\t48712\t96.5\t0\t48712\n", "23\t52505\t96.5\t0\t52505\n", "24\t59210\t96.5\t0\t59210\n", "25\t61510\t96.5\t0\t61510\n", "26\t68889\t96.5\t0\t68889\n", "27\t73930\t96.5\t0\t73930\n", "28\t67048\t96.5\t0\t67048\n", "29\t63577\t96.5\t0\t63577\n", "30\t65425\t96.5\t0\t65425\n", "31\t69997\t96.5\t0\t69997\n", "32\t67810\t96.5\t0\t67810\n", "33\t64243\t96.5\t0\t64243\n", "34\t63489\t96.5\t0\t63489\n", "35\t69443\t96.5\t0\t69443\n", "36\t75384\t96.5\t0\t75384\n", "37\t76817\t96.5\t0\t76817\n", "38\t67676\t96.5\t0\t67676\n", "39\t61917\t96.5\t0\t61917\n", "40\t59589\t96.5\t0\t59589\n", "41\t64539\t96.5\t0\t64539\n", "42\t70265\t96.5\t0\t70265\n", "43\t61750\t96.5\t0\t61750\n", "44\t52213\t96.5\t0\t52213\n", "45\t60447\t96.5\t0\t60447\n", "46\t69395\t96.5\t0\t69395\n", "47\t66848\t96.5\t0\t66848\n", "48\t63684\t96.5\t0\t63684\n", "49\t53320\t96.5\t0\t53320\n", "50\t51576\t96.5\t0\t51576\n", "51\t48073\t96.5\t0\t48073\n", "52\t53047\t96.5\t0\t53047\n", "53\t55570\t96.5\t0\t55570\n", "54\t51701\t96.5\t0\t51701\n", "55\t50432\t96.5\t0\t50432\n", "56\t45147\t96.5\t0\t45147\n", "57\t41606\t96.5\t0\t41606\n", "58\t44574\t96.5\t0\t44574\n", "59\t41075\t96.5\t0\t41075\n", "60\t35727\t96.5\t0\t35727\n", "61\t33250\t96.5\t0\t33250\n", "62\t28024\t96.5\t0\t28024\n", "63\t25687\t96.5\t0\t25687\n", "64\t27919\t96.5\t0\t27919\n", "65\t27898\t96.5\t0\t27898\n", "66\t25314\t96.5\t0\t25314\n", "67\t24603\t96.5\t0\t24603\n", "68\t23577\t96.5\t0\t23577\n", "69\t24554\t96.5\t0\t24554\n", "70\t24684\t96.5\t0\t24684\n", "71\t23174\t96.5\t0\t23174\n", "72\t18693\t96.5\t0\t18693\n", "73\t16797\t96.5\t0\t16797\n", "74\t16978\t96.5\t0\t16978\n", "75\t14811\t96.5\t0\t14811\n", "76\t12855\t96.5\t0\t12855\n", "77\t11403\t96.5\t0\t11403\n", "78\t12202\t96.5\t0\t12202\n", "79\t11613\t96.5\t0\t11613\n", "80\t11039\t96.5\t0\t11039\n", "81\t10305\t96.5\t0\t10305\n", "82\t9799\t96.5\t0\t9799\n", "83\t9923\t96.5\t0\t9923\n", "84\t10943\t96.5\t0\t10943\n", "85\t11234\t96.5\t0\t11234\n", "86\t10449\t96.5\t0\t10449\n", "87\t7615\t96.5\t0\t7615\n", "88\t6837\t96.5\t0\t6837\n", "89\t6895\t96.5\t0\t6895\n", "90\t7173\t96.5\t0\t7173\n", "91\t7391\t96.5\t0\t7391\n", "92\t7131\t96.5\t0\t7131\n", "93\t7347\t96.5\t0\t7347\n", "94\t6610\t96.5\t0\t6610\n", "95\t5618\t96.5\t0\t5618\n", "96\t4132\t96.5\t0\t4132\n", "97\t2939\t96.5\t0\t2939\n", "98\t1895\t96.5\t0\t1895\n", "99\t2268\t96.5\t0\t2268\n", "100\t1847\t96.5\t0\t1847\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 23378 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 53.9%\n", " C: 19.6%\n", " G: 0.0%\n", " T: 26.4%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9763\t98795.3\t0\t9763\n", "4\t2370\t24698.8\t0\t2370\n", "5\t633\t6174.7\t0\t633\n", "6\t369\t1543.7\t0\t369\n", "7\t76\t385.9\t0\t76\n", "8\t53\t96.5\t0\t53\n", "9\t50\t96.5\t0\t50\n", "10\t67\t96.5\t0\t67\n", "11\t60\t96.5\t0\t60\n", "12\t67\t96.5\t0\t67\n", "13\t75\t96.5\t0\t75\n", "14\t68\t96.5\t0\t68\n", "15\t81\t96.5\t0\t81\n", "16\t91\t96.5\t0\t91\n", "17\t97\t96.5\t0\t97\n", "18\t225\t96.5\t0\t225\n", "19\t290\t96.5\t0\t290\n", "20\t596\t96.5\t0\t596\n", "21\t373\t96.5\t0\t373\n", "22\t208\t96.5\t0\t208\n", "23\t128\t96.5\t0\t128\n", "24\t97\t96.5\t0\t97\n", "25\t114\t96.5\t0\t114\n", "26\t138\t96.5\t0\t138\n", "27\t147\t96.5\t0\t147\n", "28\t156\t96.5\t0\t156\n", "29\t210\t96.5\t0\t210\n", "30\t403\t96.5\t0\t403\n", "31\t401\t96.5\t0\t401\n", "32\t587\t96.5\t0\t587\n", "33\t642\t96.5\t0\t642\n", "34\t646\t96.5\t0\t646\n", "35\t872\t96.5\t0\t872\n", "36\t858\t96.5\t0\t858\n", "37\t350\t96.5\t0\t350\n", "38\t63\t96.5\t0\t63\n", "39\t61\t96.5\t0\t61\n", "40\t58\t96.5\t0\t58\n", "41\t53\t96.5\t0\t53\n", "42\t69\t96.5\t0\t69\n", "43\t48\t96.5\t0\t48\n", "44\t62\t96.5\t0\t62\n", "45\t47\t96.5\t0\t47\n", "46\t61\t96.5\t0\t61\n", "47\t54\t96.5\t0\t54\n", "48\t58\t96.5\t0\t58\n", "49\t40\t96.5\t0\t40\n", "50\t54\t96.5\t0\t54\n", "51\t62\t96.5\t0\t62\n", "52\t34\t96.5\t0\t34\n", "53\t58\t96.5\t0\t58\n", "54\t29\t96.5\t0\t29\n", "55\t36\t96.5\t0\t36\n", "56\t34\t96.5\t0\t34\n", "57\t37\t96.5\t0\t37\n", "58\t34\t96.5\t0\t34\n", "59\t40\t96.5\t0\t40\n", "60\t33\t96.5\t0\t33\n", "61\t20\t96.5\t0\t20\n", "62\t37\t96.5\t0\t37\n", "63\t31\t96.5\t0\t31\n", "64\t32\t96.5\t0\t32\n", "65\t28\t96.5\t0\t28\n", "66\t23\t96.5\t0\t23\n", "67\t26\t96.5\t0\t26\n", "68\t28\t96.5\t0\t28\n", "69\t22\t96.5\t0\t22\n", "70\t20\t96.5\t0\t20\n", "71\t8\t96.5\t0\t8\n", "72\t15\t96.5\t0\t15\n", "73\t5\t96.5\t0\t5\n", "74\t14\t96.5\t0\t14\n", "75\t8\t96.5\t0\t8\n", "76\t17\t96.5\t0\t17\n", "77\t8\t96.5\t0\t8\n", "78\t9\t96.5\t0\t9\n", "79\t5\t96.5\t0\t5\n", "80\t8\t96.5\t0\t8\n", "81\t9\t96.5\t0\t9\n", "82\t14\t96.5\t0\t14\n", "83\t6\t96.5\t0\t6\n", "84\t11\t96.5\t0\t11\n", "85\t10\t96.5\t0\t10\n", "86\t7\t96.5\t0\t7\n", "87\t9\t96.5\t0\t9\n", "88\t14\t96.5\t0\t14\n", "89\t12\t96.5\t0\t12\n", "90\t10\t96.5\t0\t10\n", "91\t14\t96.5\t0\t14\n", "92\t21\t96.5\t0\t21\n", "93\t26\t96.5\t0\t26\n", "94\t38\t96.5\t0\t38\n", "95\t54\t96.5\t0\t54\n", "96\t68\t96.5\t0\t68\n", "97\t60\t96.5\t0\t60\n", "98\t38\t96.5\t0\t38\n", "99\t50\t96.5\t0\t50\n", "100\t57\t96.5\t0\t57\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 93871 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.1%\n", " C: 18.8%\n", " G: 17.7%\n", " T: 21.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t67510\t98795.3\t0\t67510\n", "4\t15540\t24698.8\t0\t15540\n", "5\t2530\t6174.7\t0\t2530\n", "6\t226\t1543.7\t0\t226\n", "7\t76\t385.9\t0\t76\n", "8\t77\t385.9\t0\t77\n", "9\t91\t385.9\t0\t91\n", "10\t94\t385.9\t0\t94\n", "11\t70\t385.9\t0\t70\n", "12\t91\t385.9\t0\t91\n", "13\t90\t385.9\t0\t90\n", "14\t96\t385.9\t0\t96\n", "15\t95\t385.9\t0\t95\n", "16\t117\t385.9\t0\t117\n", "17\t120\t385.9\t0\t120\n", "18\t85\t385.9\t0\t85\n", "19\t108\t385.9\t0\t108\n", "20\t86\t385.9\t0\t86\n", "21\t113\t385.9\t0\t113\n", "22\t94\t385.9\t0\t94\n", "23\t79\t385.9\t0\t79\n", "24\t89\t385.9\t0\t89\n", "25\t93\t385.9\t0\t93\n", "26\t95\t385.9\t0\t95\n", "27\t101\t385.9\t0\t101\n", "28\t91\t385.9\t0\t91\n", "29\t108\t385.9\t0\t108\n", "30\t115\t385.9\t0\t115\n", "31\t111\t385.9\t0\t111\n", "32\t109\t385.9\t0\t109\n", "33\t134\t385.9\t0\t134\n", "34\t93\t385.9\t0\t93\n", "35\t91\t385.9\t0\t91\n", "36\t100\t385.9\t0\t100\n", "37\t102\t385.9\t0\t102\n", "38\t91\t385.9\t0\t91\n", "39\t116\t385.9\t0\t116\n", "40\t109\t385.9\t0\t109\n", "41\t107\t385.9\t0\t107\n", "42\t93\t385.9\t0\t93\n", "43\t117\t385.9\t0\t117\n", "44\t66\t385.9\t0\t66\n", "45\t88\t385.9\t0\t88\n", "46\t67\t385.9\t0\t67\n", "47\t81\t385.9\t0\t81\n", "48\t59\t385.9\t0\t59\n", "49\t89\t385.9\t0\t89\n", "50\t86\t385.9\t0\t86\n", "51\t75\t385.9\t0\t75\n", "52\t57\t385.9\t0\t57\n", "53\t67\t385.9\t0\t67\n", "54\t71\t385.9\t0\t71\n", "55\t62\t385.9\t0\t62\n", "56\t66\t385.9\t0\t66\n", "57\t67\t385.9\t0\t67\n", "58\t85\t385.9\t0\t85\n", "59\t61\t385.9\t0\t61\n", "60\t71\t385.9\t0\t71\n", "61\t64\t385.9\t0\t64\n", "62\t84\t385.9\t0\t84\n", "63\t57\t385.9\t0\t57\n", "64\t90\t385.9\t0\t90\n", "65\t72\t385.9\t0\t72\n", "66\t73\t385.9\t0\t73\n", "67\t60\t385.9\t0\t60\n", "68\t60\t385.9\t0\t60\n", "69\t74\t385.9\t0\t74\n", "70\t62\t385.9\t0\t62\n", "71\t55\t385.9\t0\t55\n", "72\t88\t385.9\t0\t88\n", "73\t77\t385.9\t0\t77\n", "74\t84\t385.9\t0\t84\n", "75\t58\t385.9\t0\t58\n", "76\t83\t385.9\t0\t83\n", "77\t94\t385.9\t0\t94\n", "78\t115\t385.9\t0\t115\n", "79\t104\t385.9\t0\t104\n", "80\t76\t385.9\t0\t76\n", "81\t118\t385.9\t0\t118\n", "82\t129\t385.9\t0\t129\n", "83\t111\t385.9\t0\t111\n", "84\t109\t385.9\t0\t109\n", "85\t75\t385.9\t0\t75\n", "86\t92\t385.9\t0\t92\n", "87\t93\t385.9\t0\t93\n", "88\t135\t385.9\t0\t135\n", "89\t96\t385.9\t0\t96\n", "90\t83\t385.9\t0\t83\n", "91\t68\t385.9\t0\t68\n", "92\t54\t385.9\t0\t54\n", "93\t51\t385.9\t0\t51\n", "94\t45\t385.9\t0\t45\n", "95\t58\t385.9\t0\t58\n", "96\t47\t385.9\t0\t47\n", "97\t64\t385.9\t0\t64\n", "98\t60\t385.9\t0\t60\n", "99\t98\t385.9\t0\t98\n", "100\t84\t385.9\t0\t84\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 319_S52_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/319.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 104.34 s (13 us/read; 4.57 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,954,995\n", "Reads with adapters: 4,201,397 (52.8%)\n", "Reads written (passing filters): 7,780,353 (97.8%)\n", "\n", "Total basepairs processed: 795,499,500 bp\n", "Quality-trimmed: 1,868,419 bp (0.2%)\n", "Total written (filtered): 651,838,049 bp (81.9%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4023152 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.3%\n", " G: 38.2%\n", " T: 32.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t185929\t124296.8\t0\t185929\n", "4\t107853\t31074.2\t0\t107853\n", "5\t78257\t7768.5\t0\t78257\n", "6\t63126\t1942.1\t0\t63126\n", "7\t54370\t485.5\t0\t54370\n", "8\t52215\t121.4\t0\t52215\n", "9\t52076\t121.4\t0\t52076\n", "10\t51735\t121.4\t0\t51735\n", "11\t54516\t121.4\t0\t54516\n", "12\t54893\t121.4\t0\t54893\n", "13\t61362\t121.4\t0\t61362\n", "14\t62235\t121.4\t0\t62235\n", "15\t58465\t121.4\t0\t58465\n", "16\t61891\t121.4\t0\t61891\n", "17\t67249\t121.4\t0\t67249\n", "18\t73971\t121.4\t0\t73971\n", "19\t62586\t121.4\t0\t62586\n", "20\t52538\t121.4\t0\t52538\n", "21\t50176\t121.4\t0\t50176\n", "22\t47828\t121.4\t0\t47828\n", "23\t53533\t121.4\t0\t53533\n", "24\t61648\t121.4\t0\t61648\n", "25\t63876\t121.4\t0\t63876\n", "26\t71797\t121.4\t0\t71797\n", "27\t76280\t121.4\t0\t76280\n", "28\t68700\t121.4\t0\t68700\n", "29\t63931\t121.4\t0\t63931\n", "30\t64168\t121.4\t0\t64168\n", "31\t68704\t121.4\t0\t68704\n", "32\t70312\t121.4\t0\t70312\n", "33\t65883\t121.4\t0\t65883\n", "34\t63974\t121.4\t0\t63974\n", "35\t71097\t121.4\t0\t71097\n", "36\t79246\t121.4\t0\t79246\n", "37\t82957\t121.4\t0\t82957\n", "38\t68652\t121.4\t0\t68652\n", "39\t59615\t121.4\t0\t59615\n", "40\t55937\t121.4\t0\t55937\n", "41\t60074\t121.4\t0\t60074\n", "42\t63698\t121.4\t0\t63698\n", "43\t56845\t121.4\t0\t56845\n", "44\t47151\t121.4\t0\t47151\n", "45\t55711\t121.4\t0\t55711\n", "46\t65182\t121.4\t0\t65182\n", "47\t58287\t121.4\t0\t58287\n", "48\t57140\t121.4\t0\t57140\n", "49\t49688\t121.4\t0\t49688\n", "50\t48058\t121.4\t0\t48058\n", "51\t42511\t121.4\t0\t42511\n", "52\t42016\t121.4\t0\t42016\n", "53\t41211\t121.4\t0\t41211\n", "54\t41146\t121.4\t0\t41146\n", "55\t49114\t121.4\t0\t49114\n", "56\t45357\t121.4\t0\t45357\n", "57\t39804\t121.4\t0\t39804\n", "58\t36145\t121.4\t0\t36145\n", "59\t32469\t121.4\t0\t32469\n", "60\t29098\t121.4\t0\t29098\n", "61\t26380\t121.4\t0\t26380\n", "62\t22103\t121.4\t0\t22103\n", "63\t20962\t121.4\t0\t20962\n", "64\t23066\t121.4\t0\t23066\n", "65\t22674\t121.4\t0\t22674\n", "66\t19662\t121.4\t0\t19662\n", "67\t19524\t121.4\t0\t19524\n", "68\t18681\t121.4\t0\t18681\n", "69\t19069\t121.4\t0\t19069\n", "70\t19865\t121.4\t0\t19865\n", "71\t19196\t121.4\t0\t19196\n", "72\t15121\t121.4\t0\t15121\n", "73\t14077\t121.4\t0\t14077\n", "74\t14022\t121.4\t0\t14022\n", "75\t12433\t121.4\t0\t12433\n", "76\t11126\t121.4\t0\t11126\n", "77\t10287\t121.4\t0\t10287\n", "78\t11093\t121.4\t0\t11093\n", "79\t10933\t121.4\t0\t10933\n", "80\t11149\t121.4\t0\t11149\n", "81\t10556\t121.4\t0\t10556\n", "82\t10115\t121.4\t0\t10115\n", "83\t10650\t121.4\t0\t10650\n", "84\t11642\t121.4\t0\t11642\n", "85\t12178\t121.4\t0\t12178\n", "86\t11818\t121.4\t0\t11818\n", "87\t9888\t121.4\t0\t9888\n", "88\t9490\t121.4\t0\t9490\n", "89\t9248\t121.4\t0\t9248\n", "90\t8951\t121.4\t0\t8951\n", "91\t8438\t121.4\t0\t8438\n", "92\t7909\t121.4\t0\t7909\n", "93\t7605\t121.4\t0\t7605\n", "94\t6788\t121.4\t0\t6788\n", "95\t6048\t121.4\t0\t6048\n", "96\t4475\t121.4\t0\t4475\n", "97\t3378\t121.4\t0\t3378\n", "98\t2594\t121.4\t0\t2594\n", "99\t2805\t121.4\t0\t2805\n", "100\t2867\t121.4\t0\t2867\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 36204 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.8%\n", " C: 28.5%\n", " G: 0.0%\n", " T: 26.3%\n", " none/other: 0.4%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t15980\t124296.8\t0\t15980\n", "4\t4658\t31074.2\t0\t4658\n", "5\t2274\t7768.5\t0\t2274\n", "6\t437\t1942.1\t0\t437\n", "7\t99\t485.5\t0\t99\n", "8\t83\t121.4\t0\t83\n", "9\t69\t121.4\t0\t69\n", "10\t89\t121.4\t0\t89\n", "11\t57\t121.4\t0\t57\n", "12\t99\t121.4\t0\t99\n", "13\t72\t121.4\t0\t72\n", "14\t77\t121.4\t0\t77\n", "15\t70\t121.4\t0\t70\n", "16\t93\t121.4\t0\t93\n", "17\t92\t121.4\t0\t92\n", "18\t139\t121.4\t0\t139\n", "19\t169\t121.4\t0\t169\n", "20\t381\t121.4\t0\t381\n", "21\t199\t121.4\t0\t199\n", "22\t137\t121.4\t0\t137\n", "23\t123\t121.4\t0\t123\n", "24\t122\t121.4\t0\t122\n", "25\t108\t121.4\t0\t108\n", "26\t138\t121.4\t0\t138\n", "27\t154\t121.4\t0\t154\n", "28\t152\t121.4\t0\t152\n", "29\t230\t121.4\t0\t230\n", "30\t380\t121.4\t0\t380\n", "31\t470\t121.4\t0\t470\n", "32\t681\t121.4\t0\t681\n", "33\t755\t121.4\t0\t755\n", "34\t814\t121.4\t0\t814\n", "35\t1042\t121.4\t0\t1042\n", "36\t1074\t121.4\t0\t1074\n", "37\t618\t121.4\t0\t618\n", "38\t88\t121.4\t0\t88\n", "39\t80\t121.4\t0\t80\n", "40\t56\t121.4\t0\t56\n", "41\t86\t121.4\t0\t86\n", "42\t59\t121.4\t0\t59\n", "43\t64\t121.4\t0\t64\n", "44\t53\t121.4\t0\t53\n", "45\t54\t121.4\t0\t54\n", "46\t55\t121.4\t0\t55\n", "47\t50\t121.4\t0\t50\n", "48\t60\t121.4\t0\t60\n", "49\t56\t121.4\t0\t56\n", "50\t61\t121.4\t0\t61\n", "51\t75\t121.4\t0\t75\n", "52\t65\t121.4\t0\t65\n", "53\t54\t121.4\t0\t54\n", "54\t38\t121.4\t0\t38\n", "55\t48\t121.4\t0\t48\n", "56\t50\t121.4\t0\t50\n", "57\t31\t121.4\t0\t31\n", "58\t46\t121.4\t0\t46\n", "59\t42\t121.4\t0\t42\n", "60\t36\t121.4\t0\t36\n", "61\t38\t121.4\t0\t38\n", "62\t32\t121.4\t0\t32\n", "63\t24\t121.4\t0\t24\n", "64\t46\t121.4\t0\t46\n", "65\t25\t121.4\t0\t25\n", "66\t33\t121.4\t0\t33\n", "67\t27\t121.4\t0\t27\n", "68\t20\t121.4\t0\t20\n", "69\t30\t121.4\t0\t30\n", "70\t33\t121.4\t0\t33\n", "71\t34\t121.4\t0\t34\n", "72\t28\t121.4\t0\t28\n", "73\t31\t121.4\t0\t31\n", "74\t29\t121.4\t0\t29\n", "75\t21\t121.4\t0\t21\n", "76\t27\t121.4\t0\t27\n", "77\t25\t121.4\t0\t25\n", "78\t27\t121.4\t0\t27\n", "79\t41\t121.4\t0\t41\n", "80\t31\t121.4\t0\t31\n", "81\t37\t121.4\t0\t37\n", "82\t17\t121.4\t0\t17\n", "83\t27\t121.4\t0\t27\n", "84\t16\t121.4\t0\t16\n", "85\t23\t121.4\t0\t23\n", "86\t37\t121.4\t0\t37\n", "87\t37\t121.4\t0\t37\n", "88\t36\t121.4\t0\t36\n", "89\t44\t121.4\t0\t44\n", "90\t29\t121.4\t0\t29\n", "91\t51\t121.4\t0\t51\n", "92\t77\t121.4\t0\t77\n", "93\t131\t121.4\t0\t131\n", "94\t174\t121.4\t0\t174\n", "95\t261\t121.4\t0\t261\n", "96\t255\t121.4\t0\t255\n", "97\t254\t121.4\t0\t254\n", "98\t218\t121.4\t0\t218\n", "99\t146\t121.4\t0\t146\n", "100\t290\t121.4\t0\t290\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 142041 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 38.8%\n", " C: 18.7%\n", " G: 15.8%\n", " T: 26.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t105242\t124296.8\t0\t105242\n", "4\t25303\t31074.2\t0\t25303\n", "5\t2972\t7768.5\t0\t2972\n", "6\t324\t1942.1\t0\t324\n", "7\t87\t485.5\t0\t87\n", "8\t94\t485.5\t0\t94\n", "9\t70\t485.5\t0\t70\n", "10\t113\t485.5\t0\t113\n", "11\t109\t485.5\t0\t109\n", "12\t118\t485.5\t0\t118\n", "13\t119\t485.5\t0\t119\n", "14\t164\t485.5\t0\t164\n", "15\t131\t485.5\t0\t131\n", "16\t90\t485.5\t0\t90\n", "17\t144\t485.5\t0\t144\n", "18\t115\t485.5\t0\t115\n", "19\t130\t485.5\t0\t130\n", "20\t99\t485.5\t0\t99\n", "21\t82\t485.5\t0\t82\n", "22\t76\t485.5\t0\t76\n", "23\t96\t485.5\t0\t96\n", "24\t79\t485.5\t0\t79\n", "25\t79\t485.5\t0\t79\n", "26\t62\t485.5\t0\t62\n", "27\t117\t485.5\t0\t117\n", "28\t85\t485.5\t0\t85\n", "29\t77\t485.5\t0\t77\n", "30\t84\t485.5\t0\t84\n", "31\t97\t485.5\t0\t97\n", "32\t94\t485.5\t0\t94\n", "33\t106\t485.5\t0\t106\n", "34\t91\t485.5\t0\t91\n", "35\t75\t485.5\t0\t75\n", "36\t62\t485.5\t0\t62\n", "37\t92\t485.5\t0\t92\n", "38\t86\t485.5\t0\t86\n", "39\t100\t485.5\t0\t100\n", "40\t98\t485.5\t0\t98\n", "41\t89\t485.5\t0\t89\n", "42\t56\t485.5\t0\t56\n", "43\t80\t485.5\t0\t80\n", "44\t86\t485.5\t0\t86\n", "45\t87\t485.5\t0\t87\n", "46\t72\t485.5\t0\t72\n", "47\t91\t485.5\t0\t91\n", "48\t78\t485.5\t0\t78\n", "49\t93\t485.5\t0\t93\n", "50\t92\t485.5\t0\t92\n", "51\t69\t485.5\t0\t69\n", "52\t64\t485.5\t0\t64\n", "53\t76\t485.5\t0\t76\n", "54\t62\t485.5\t0\t62\n", "55\t76\t485.5\t0\t76\n", "56\t55\t485.5\t0\t55\n", "57\t93\t485.5\t0\t93\n", "58\t99\t485.5\t0\t99\n", "59\t80\t485.5\t0\t80\n", "60\t91\t485.5\t0\t91\n", "61\t69\t485.5\t0\t69\n", "62\t59\t485.5\t0\t59\n", "63\t66\t485.5\t0\t66\n", "64\t85\t485.5\t0\t85\n", "65\t69\t485.5\t0\t69\n", "66\t66\t485.5\t0\t66\n", "67\t74\t485.5\t0\t74\n", "68\t74\t485.5\t0\t74\n", "69\t80\t485.5\t0\t80\n", "70\t63\t485.5\t0\t63\n", "71\t95\t485.5\t0\t95\n", "72\t83\t485.5\t0\t83\n", "73\t76\t485.5\t0\t76\n", "74\t98\t485.5\t0\t98\n", "75\t72\t485.5\t0\t72\n", "76\t64\t485.5\t0\t64\n", "77\t80\t485.5\t0\t80\n", "78\t57\t485.5\t0\t57\n", "79\t66\t485.5\t0\t66\n", "80\t94\t485.5\t0\t94\n", "81\t88\t485.5\t0\t88\n", "82\t67\t485.5\t0\t67\n", "83\t96\t485.5\t0\t96\n", "84\t69\t485.5\t0\t69\n", "85\t88\t485.5\t0\t88\n", "86\t100\t485.5\t0\t100\n", "87\t104\t485.5\t0\t104\n", "88\t192\t485.5\t0\t192\n", "89\t88\t485.5\t0\t88\n", "90\t102\t485.5\t0\t102\n", "91\t71\t485.5\t0\t71\n", "92\t42\t485.5\t0\t42\n", "93\t62\t485.5\t0\t62\n", "94\t75\t485.5\t0\t75\n", "95\t47\t485.5\t0\t47\n", "96\t57\t485.5\t0\t57\n", "97\t71\t485.5\t0\t71\n", "98\t116\t485.5\t0\t116\n", "99\t127\t485.5\t0\t127\n", "100\t138\t485.5\t0\t138\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 321_S29_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/321.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 89.59 s (14 us/read; 4.17 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,233,571\n", "Reads with adapters: 4,017,529 (64.4%)\n", "Reads written (passing filters): 6,027,317 (96.7%)\n", "\n", "Total basepairs processed: 623,357,100 bp\n", "Quality-trimmed: 1,823,708 bp (0.3%)\n", "Total written (filtered): 475,886,663 bp (76.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3895332 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 32.4%\n", " G: 40.2%\n", " T: 27.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t126064\t97399.5\t0\t126064\n", "4\t77127\t24349.9\t0\t77127\n", "5\t59602\t6087.5\t0\t59602\n", "6\t52444\t1521.9\t0\t52444\n", "7\t49382\t380.5\t0\t49382\n", "8\t48937\t95.1\t0\t48937\n", "9\t49140\t95.1\t0\t49140\n", "10\t49142\t95.1\t0\t49142\n", "11\t50575\t95.1\t0\t50575\n", "12\t52210\t95.1\t0\t52210\n", "13\t60135\t95.1\t0\t60135\n", "14\t59464\t95.1\t0\t59464\n", "15\t56017\t95.1\t0\t56017\n", "16\t57797\t95.1\t0\t57797\n", "17\t63095\t95.1\t0\t63095\n", "18\t71645\t95.1\t0\t71645\n", "19\t63811\t95.1\t0\t63811\n", "20\t53739\t95.1\t0\t53739\n", "21\t51857\t95.1\t0\t51857\n", "22\t47880\t95.1\t0\t47880\n", "23\t51934\t95.1\t0\t51934\n", "24\t59837\t95.1\t0\t59837\n", "25\t62169\t95.1\t0\t62169\n", "26\t69702\t95.1\t0\t69702\n", "27\t73802\t95.1\t0\t73802\n", "28\t67447\t95.1\t0\t67447\n", "29\t62242\t95.1\t0\t62242\n", "30\t62297\t95.1\t0\t62297\n", "31\t67658\t95.1\t0\t67658\n", "32\t65709\t95.1\t0\t65709\n", "33\t62938\t95.1\t0\t62938\n", "34\t60834\t95.1\t0\t60834\n", "35\t66754\t95.1\t0\t66754\n", "36\t73558\t95.1\t0\t73558\n", "37\t75642\t95.1\t0\t75642\n", "38\t63365\t95.1\t0\t63365\n", "39\t58062\t95.1\t0\t58062\n", "40\t55645\t95.1\t0\t55645\n", "41\t61260\t95.1\t0\t61260\n", "42\t65954\t95.1\t0\t65954\n", "43\t58352\t95.1\t0\t58352\n", "44\t46415\t95.1\t0\t46415\n", "45\t54573\t95.1\t0\t54573\n", "46\t62967\t95.1\t0\t62967\n", "47\t58256\t95.1\t0\t58256\n", "48\t54501\t95.1\t0\t54501\n", "49\t49057\t95.1\t0\t49057\n", "50\t47975\t95.1\t0\t47975\n", "51\t43346\t95.1\t0\t43346\n", "52\t45977\t95.1\t0\t45977\n", "53\t43060\t95.1\t0\t43060\n", "54\t41787\t95.1\t0\t41787\n", "55\t39604\t95.1\t0\t39604\n", "56\t38127\t95.1\t0\t38127\n", "57\t35723\t95.1\t0\t35723\n", "58\t37414\t95.1\t0\t37414\n", "59\t33635\t95.1\t0\t33635\n", "60\t30361\t95.1\t0\t30361\n", "61\t28898\t95.1\t0\t28898\n", "62\t24257\t95.1\t0\t24257\n", "63\t22987\t95.1\t0\t22987\n", "64\t25617\t95.1\t0\t25617\n", "65\t25123\t95.1\t0\t25123\n", "66\t22252\t95.1\t0\t22252\n", "67\t22575\t95.1\t0\t22575\n", "68\t22348\t95.1\t0\t22348\n", "69\t22961\t95.1\t0\t22961\n", "70\t23985\t95.1\t0\t23985\n", "71\t22907\t95.1\t0\t22907\n", "72\t17905\t95.1\t0\t17905\n", "73\t16954\t95.1\t0\t16954\n", "74\t16790\t95.1\t0\t16790\n", "75\t15262\t95.1\t0\t15262\n", "76\t12778\t95.1\t0\t12778\n", "77\t11998\t95.1\t0\t11998\n", "78\t13219\t95.1\t0\t13219\n", "79\t13121\t95.1\t0\t13121\n", "80\t12715\t95.1\t0\t12715\n", "81\t12037\t95.1\t0\t12037\n", "82\t11458\t95.1\t0\t11458\n", "83\t12319\t95.1\t0\t12319\n", "84\t13925\t95.1\t0\t13925\n", "85\t15338\t95.1\t0\t15338\n", "86\t14753\t95.1\t0\t14753\n", "87\t10682\t95.1\t0\t10682\n", "88\t9670\t95.1\t0\t9670\n", "89\t10013\t95.1\t0\t10013\n", "90\t10326\t95.1\t0\t10326\n", "91\t10709\t95.1\t0\t10709\n", "92\t10971\t95.1\t0\t10971\n", "93\t11871\t95.1\t0\t11871\n", "94\t11267\t95.1\t0\t11267\n", "95\t9597\t95.1\t0\t9597\n", "96\t7024\t95.1\t0\t7024\n", "97\t4298\t95.1\t0\t4298\n", "98\t2470\t95.1\t0\t2470\n", "99\t2302\t95.1\t0\t2302\n", "100\t1648\t95.1\t0\t1648\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 34055 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 58.5%\n", " C: 20.0%\n", " G: 0.0%\n", " T: 21.4%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t11324\t97399.5\t0\t11324\n", "4\t2755\t24349.9\t0\t2755\n", "5\t1216\t6087.5\t0\t1216\n", "6\t860\t1521.9\t0\t860\n", "7\t164\t380.5\t0\t164\n", "8\t114\t95.1\t0\t114\n", "9\t124\t95.1\t0\t124\n", "10\t137\t95.1\t0\t137\n", "11\t156\t95.1\t0\t156\n", "12\t117\t95.1\t0\t117\n", "13\t115\t95.1\t0\t115\n", "14\t120\t95.1\t0\t120\n", "15\t124\t95.1\t0\t124\n", "16\t135\t95.1\t0\t135\n", "17\t139\t95.1\t0\t139\n", "18\t215\t95.1\t0\t215\n", "19\t263\t95.1\t0\t263\n", "20\t371\t95.1\t0\t371\n", "21\t289\t95.1\t0\t289\n", "22\t230\t95.1\t0\t230\n", "23\t168\t95.1\t0\t168\n", "24\t175\t95.1\t0\t175\n", "25\t187\t95.1\t0\t187\n", "26\t358\t95.1\t0\t358\n", "27\t344\t95.1\t0\t344\n", "28\t421\t95.1\t0\t421\n", "29\t499\t95.1\t0\t499\n", "30\t832\t95.1\t0\t832\n", "31\t916\t95.1\t0\t916\n", "32\t1516\t95.1\t0\t1516\n", "33\t1357\t95.1\t0\t1357\n", "34\t1439\t95.1\t0\t1439\n", "35\t1869\t95.1\t0\t1869\n", "36\t1872\t95.1\t0\t1872\n", "37\t718\t95.1\t0\t718\n", "38\t81\t95.1\t0\t81\n", "39\t70\t95.1\t0\t70\n", "40\t73\t95.1\t0\t73\n", "41\t46\t95.1\t0\t46\n", "42\t59\t95.1\t0\t59\n", "43\t49\t95.1\t0\t49\n", "44\t56\t95.1\t0\t56\n", "45\t50\t95.1\t0\t50\n", "46\t56\t95.1\t0\t56\n", "47\t55\t95.1\t0\t55\n", "48\t47\t95.1\t0\t47\n", "49\t43\t95.1\t0\t43\n", "50\t51\t95.1\t0\t51\n", "51\t47\t95.1\t0\t47\n", "52\t45\t95.1\t0\t45\n", "53\t42\t95.1\t0\t42\n", "54\t47\t95.1\t0\t47\n", "55\t43\t95.1\t0\t43\n", "56\t34\t95.1\t0\t34\n", "57\t41\t95.1\t0\t41\n", "58\t50\t95.1\t0\t50\n", "59\t32\t95.1\t0\t32\n", "60\t39\t95.1\t0\t39\n", "61\t26\t95.1\t0\t26\n", "62\t36\t95.1\t0\t36\n", "63\t30\t95.1\t0\t30\n", "64\t34\t95.1\t0\t34\n", "65\t26\t95.1\t0\t26\n", "66\t28\t95.1\t0\t28\n", "67\t37\t95.1\t0\t37\n", "68\t38\t95.1\t0\t38\n", "69\t20\t95.1\t0\t20\n", "70\t22\t95.1\t0\t22\n", "71\t14\t95.1\t0\t14\n", "72\t16\t95.1\t0\t16\n", "73\t16\t95.1\t0\t16\n", "74\t8\t95.1\t0\t8\n", "75\t13\t95.1\t0\t13\n", "76\t7\t95.1\t0\t7\n", "77\t7\t95.1\t0\t7\n", "78\t13\t95.1\t0\t13\n", "79\t20\t95.1\t0\t20\n", "80\t18\t95.1\t0\t18\n", "81\t10\t95.1\t0\t10\n", "82\t9\t95.1\t0\t9\n", "83\t14\t95.1\t0\t14\n", "84\t18\t95.1\t0\t18\n", "85\t20\t95.1\t0\t20\n", "86\t17\t95.1\t0\t17\n", "87\t14\t95.1\t0\t14\n", "88\t12\t95.1\t0\t12\n", "89\t29\t95.1\t0\t29\n", "90\t14\t95.1\t0\t14\n", "91\t23\t95.1\t0\t23\n", "92\t33\t95.1\t0\t33\n", "93\t51\t95.1\t0\t51\n", "94\t63\t95.1\t0\t63\n", "95\t99\t95.1\t0\t99\n", "96\t100\t95.1\t0\t100\n", "97\t107\t95.1\t0\t107\n", "98\t63\t95.1\t0\t63\n", "99\t49\t95.1\t0\t49\n", "100\t86\t95.1\t0\t86\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 88142 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.0%\n", " C: 19.8%\n", " G: 18.0%\n", " T: 21.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t64134\t97399.5\t0\t64134\n", "4\t13462\t24349.9\t0\t13462\n", "5\t2448\t6087.5\t0\t2448\n", "6\t286\t1521.9\t0\t286\n", "7\t105\t380.5\t0\t105\n", "8\t105\t380.5\t0\t105\n", "9\t122\t380.5\t0\t122\n", "10\t126\t380.5\t0\t126\n", "11\t101\t380.5\t0\t101\n", "12\t114\t380.5\t0\t114\n", "13\t128\t380.5\t0\t128\n", "14\t131\t380.5\t0\t131\n", "15\t137\t380.5\t0\t137\n", "16\t154\t380.5\t0\t154\n", "17\t151\t380.5\t0\t151\n", "18\t127\t380.5\t0\t127\n", "19\t123\t380.5\t0\t123\n", "20\t128\t380.5\t0\t128\n", "21\t139\t380.5\t0\t139\n", "22\t118\t380.5\t0\t118\n", "23\t119\t380.5\t0\t119\n", "24\t105\t380.5\t0\t105\n", "25\t105\t380.5\t0\t105\n", "26\t99\t380.5\t0\t99\n", "27\t109\t380.5\t0\t109\n", "28\t95\t380.5\t0\t95\n", "29\t107\t380.5\t0\t107\n", "30\t136\t380.5\t0\t136\n", "31\t76\t380.5\t0\t76\n", "32\t139\t380.5\t0\t139\n", "33\t102\t380.5\t0\t102\n", "34\t98\t380.5\t0\t98\n", "35\t94\t380.5\t0\t94\n", "36\t112\t380.5\t0\t112\n", "37\t94\t380.5\t0\t94\n", "38\t70\t380.5\t0\t70\n", "39\t84\t380.5\t0\t84\n", "40\t87\t380.5\t0\t87\n", "41\t83\t380.5\t0\t83\n", "42\t79\t380.5\t0\t79\n", "43\t112\t380.5\t0\t112\n", "44\t55\t380.5\t0\t55\n", "45\t74\t380.5\t0\t74\n", "46\t72\t380.5\t0\t72\n", "47\t75\t380.5\t0\t75\n", "48\t60\t380.5\t0\t60\n", "49\t61\t380.5\t0\t61\n", "50\t60\t380.5\t0\t60\n", "51\t56\t380.5\t0\t56\n", "52\t64\t380.5\t0\t64\n", "53\t55\t380.5\t0\t55\n", "54\t79\t380.5\t0\t79\n", "55\t60\t380.5\t0\t60\n", "56\t65\t380.5\t0\t65\n", "57\t52\t380.5\t0\t52\n", "58\t77\t380.5\t0\t77\n", "59\t45\t380.5\t0\t45\n", "60\t59\t380.5\t0\t59\n", "61\t59\t380.5\t0\t59\n", "62\t59\t380.5\t0\t59\n", "63\t74\t380.5\t0\t74\n", "64\t50\t380.5\t0\t50\n", "65\t62\t380.5\t0\t62\n", "66\t53\t380.5\t0\t53\n", "67\t59\t380.5\t0\t59\n", "68\t76\t380.5\t0\t76\n", "69\t47\t380.5\t0\t47\n", "70\t51\t380.5\t0\t51\n", "71\t54\t380.5\t0\t54\n", "72\t47\t380.5\t0\t47\n", "73\t58\t380.5\t0\t58\n", "74\t70\t380.5\t0\t70\n", "75\t64\t380.5\t0\t64\n", "76\t69\t380.5\t0\t69\n", "77\t78\t380.5\t0\t78\n", "78\t67\t380.5\t0\t67\n", "79\t76\t380.5\t0\t76\n", "80\t75\t380.5\t0\t75\n", "81\t85\t380.5\t0\t85\n", "82\t98\t380.5\t0\t98\n", "83\t72\t380.5\t0\t72\n", "84\t85\t380.5\t0\t85\n", "85\t77\t380.5\t0\t77\n", "86\t61\t380.5\t0\t61\n", "87\t75\t380.5\t0\t75\n", "88\t95\t380.5\t0\t95\n", "89\t75\t380.5\t0\t75\n", "90\t56\t380.5\t0\t56\n", "91\t50\t380.5\t0\t50\n", "92\t40\t380.5\t0\t40\n", "93\t41\t380.5\t0\t41\n", "94\t56\t380.5\t0\t56\n", "95\t68\t380.5\t0\t68\n", "96\t54\t380.5\t0\t54\n", "97\t56\t380.5\t0\t56\n", "98\t72\t380.5\t0\t72\n", "99\t72\t380.5\t0\t72\n", "100\t93\t380.5\t0\t93\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 322_S8_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/322.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 104.95 s (14 us/read; 4.36 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,624,640\n", "Reads with adapters: 4,938,384 (64.8%)\n", "Reads written (passing filters): 7,301,694 (95.8%)\n", "\n", "Total basepairs processed: 762,464,000 bp\n", "Quality-trimmed: 1,864,695 bp (0.2%)\n", "Total written (filtered): 570,596,920 bp (74.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4788897 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.8%\n", " G: 38.7%\n", " T: 27.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t149691\t119135.0\t0\t149691\n", "4\t91998\t29783.8\t0\t91998\n", "5\t71365\t7445.9\t0\t71365\n", "6\t61829\t1861.5\t0\t61829\n", "7\t58706\t465.4\t0\t58706\n", "8\t58162\t116.3\t0\t58162\n", "9\t59067\t116.3\t0\t59067\n", "10\t57275\t116.3\t0\t57275\n", "11\t57561\t116.3\t0\t57561\n", "12\t59114\t116.3\t0\t59114\n", "13\t60610\t116.3\t0\t60610\n", "14\t62654\t116.3\t0\t62654\n", "15\t61744\t116.3\t0\t61744\n", "16\t65556\t116.3\t0\t65556\n", "17\t71802\t116.3\t0\t71802\n", "18\t79477\t116.3\t0\t79477\n", "19\t72519\t116.3\t0\t72519\n", "20\t63182\t116.3\t0\t63182\n", "21\t58631\t116.3\t0\t58631\n", "22\t54983\t116.3\t0\t54983\n", "23\t59931\t116.3\t0\t59931\n", "24\t68008\t116.3\t0\t68008\n", "25\t70825\t116.3\t0\t70825\n", "26\t79385\t116.3\t0\t79385\n", "27\t84012\t116.3\t0\t84012\n", "28\t76515\t116.3\t0\t76515\n", "29\t71767\t116.3\t0\t71767\n", "30\t71629\t116.3\t0\t71629\n", "31\t76432\t116.3\t0\t76432\n", "32\t74490\t116.3\t0\t74490\n", "33\t71403\t116.3\t0\t71403\n", "34\t70215\t116.3\t0\t70215\n", "35\t77790\t116.3\t0\t77790\n", "36\t85531\t116.3\t0\t85531\n", "37\t87151\t116.3\t0\t87151\n", "38\t74884\t116.3\t0\t74884\n", "39\t67779\t116.3\t0\t67779\n", "40\t65567\t116.3\t0\t65567\n", "41\t74206\t116.3\t0\t74206\n", "42\t81825\t116.3\t0\t81825\n", "43\t71431\t116.3\t0\t71431\n", "44\t59031\t116.3\t0\t59031\n", "45\t68089\t116.3\t0\t68089\n", "46\t77558\t116.3\t0\t77558\n", "47\t70472\t116.3\t0\t70472\n", "48\t67982\t116.3\t0\t67982\n", "49\t59490\t116.3\t0\t59490\n", "50\t58123\t116.3\t0\t58123\n", "51\t49131\t116.3\t0\t49131\n", "52\t51044\t116.3\t0\t51044\n", "53\t52578\t116.3\t0\t52578\n", "54\t54778\t116.3\t0\t54778\n", "55\t55830\t116.3\t0\t55830\n", "56\t52778\t116.3\t0\t52778\n", "57\t51807\t116.3\t0\t51807\n", "58\t56624\t116.3\t0\t56624\n", "59\t52976\t116.3\t0\t52976\n", "60\t46387\t116.3\t0\t46387\n", "61\t40562\t116.3\t0\t40562\n", "62\t33485\t116.3\t0\t33485\n", "63\t31483\t116.3\t0\t31483\n", "64\t34908\t116.3\t0\t34908\n", "65\t34960\t116.3\t0\t34960\n", "66\t31475\t116.3\t0\t31475\n", "67\t31723\t116.3\t0\t31723\n", "68\t31574\t116.3\t0\t31574\n", "69\t32373\t116.3\t0\t32373\n", "70\t33465\t116.3\t0\t33465\n", "71\t32140\t116.3\t0\t32140\n", "72\t26547\t116.3\t0\t26547\n", "73\t24107\t116.3\t0\t24107\n", "74\t24215\t116.3\t0\t24215\n", "75\t21695\t116.3\t0\t21695\n", "76\t18937\t116.3\t0\t18937\n", "77\t17682\t116.3\t0\t17682\n", "78\t19480\t116.3\t0\t19480\n", "79\t19061\t116.3\t0\t19061\n", "80\t19058\t116.3\t0\t19058\n", "81\t17866\t116.3\t0\t17866\n", "82\t17188\t116.3\t0\t17188\n", "83\t18485\t116.3\t0\t18485\n", "84\t21314\t116.3\t0\t21314\n", "85\t23484\t116.3\t0\t23484\n", "86\t22367\t116.3\t0\t22367\n", "87\t16625\t116.3\t0\t16625\n", "88\t15025\t116.3\t0\t15025\n", "89\t15710\t116.3\t0\t15710\n", "90\t16815\t116.3\t0\t16815\n", "91\t17355\t116.3\t0\t17355\n", "92\t18164\t116.3\t0\t18164\n", "93\t19969\t116.3\t0\t19969\n", "94\t19971\t116.3\t0\t19971\n", "95\t16910\t116.3\t0\t16910\n", "96\t12704\t116.3\t0\t12704\n", "97\t7929\t116.3\t0\t7929\n", "98\t4472\t116.3\t0\t4472\n", "99\t3835\t116.3\t0\t3835\n", "100\t2399\t116.3\t0\t2399\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 46808 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 66.0%\n", " C: 16.7%\n", " G: 0.0%\n", " T: 17.2%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13542\t119135.0\t0\t13542\n", "4\t3280\t29783.8\t0\t3280\n", "5\t1155\t7445.9\t0\t1155\n", "6\t730\t1861.5\t0\t730\n", "7\t227\t465.4\t0\t227\n", "8\t180\t116.3\t0\t180\n", "9\t138\t116.3\t0\t138\n", "10\t145\t116.3\t0\t145\n", "11\t149\t116.3\t0\t149\n", "12\t127\t116.3\t0\t127\n", "13\t145\t116.3\t0\t145\n", "14\t165\t116.3\t0\t165\n", "15\t125\t116.3\t0\t125\n", "16\t168\t116.3\t0\t168\n", "17\t193\t116.3\t0\t193\n", "18\t244\t116.3\t0\t244\n", "19\t329\t116.3\t0\t329\n", "20\t525\t116.3\t0\t525\n", "21\t335\t116.3\t0\t335\n", "22\t293\t116.3\t0\t293\n", "23\t250\t116.3\t0\t250\n", "24\t247\t116.3\t0\t247\n", "25\t291\t116.3\t0\t291\n", "26\t530\t116.3\t0\t530\n", "27\t495\t116.3\t0\t495\n", "28\t586\t116.3\t0\t586\n", "29\t830\t116.3\t0\t830\n", "30\t1571\t116.3\t0\t1571\n", "31\t1770\t116.3\t0\t1770\n", "32\t2658\t116.3\t0\t2658\n", "33\t2505\t116.3\t0\t2505\n", "34\t2730\t116.3\t0\t2730\n", "35\t3375\t116.3\t0\t3375\n", "36\t3389\t116.3\t0\t3389\n", "37\t1262\t116.3\t0\t1262\n", "38\t84\t116.3\t0\t84\n", "39\t71\t116.3\t0\t71\n", "40\t45\t116.3\t0\t45\n", "41\t38\t116.3\t0\t38\n", "42\t42\t116.3\t0\t42\n", "43\t33\t116.3\t0\t33\n", "44\t52\t116.3\t0\t52\n", "45\t47\t116.3\t0\t47\n", "46\t42\t116.3\t0\t42\n", "47\t57\t116.3\t0\t57\n", "48\t45\t116.3\t0\t45\n", "49\t50\t116.3\t0\t50\n", "50\t56\t116.3\t0\t56\n", "51\t44\t116.3\t0\t44\n", "52\t42\t116.3\t0\t42\n", "53\t46\t116.3\t0\t46\n", "54\t28\t116.3\t0\t28\n", "55\t31\t116.3\t0\t31\n", "56\t42\t116.3\t0\t42\n", "57\t27\t116.3\t0\t27\n", "58\t29\t116.3\t0\t29\n", "59\t30\t116.3\t0\t30\n", "60\t24\t116.3\t0\t24\n", "61\t27\t116.3\t0\t27\n", "62\t26\t116.3\t0\t26\n", "63\t25\t116.3\t0\t25\n", "64\t16\t116.3\t0\t16\n", "65\t22\t116.3\t0\t22\n", "66\t29\t116.3\t0\t29\n", "67\t33\t116.3\t0\t33\n", "68\t23\t116.3\t0\t23\n", "69\t23\t116.3\t0\t23\n", "70\t30\t116.3\t0\t30\n", "71\t17\t116.3\t0\t17\n", "72\t14\t116.3\t0\t14\n", "73\t12\t116.3\t0\t12\n", "74\t17\t116.3\t0\t17\n", "75\t13\t116.3\t0\t13\n", "76\t9\t116.3\t0\t9\n", "77\t14\t116.3\t0\t14\n", "78\t18\t116.3\t0\t18\n", "79\t13\t116.3\t0\t13\n", "80\t5\t116.3\t0\t5\n", "81\t12\t116.3\t0\t12\n", "82\t13\t116.3\t0\t13\n", "83\t11\t116.3\t0\t11\n", "84\t9\t116.3\t0\t9\n", "85\t8\t116.3\t0\t8\n", "86\t18\t116.3\t0\t18\n", "87\t19\t116.3\t0\t19\n", "88\t12\t116.3\t0\t12\n", "89\t17\t116.3\t0\t17\n", "90\t15\t116.3\t0\t15\n", "91\t16\t116.3\t0\t16\n", "92\t30\t116.3\t0\t30\n", "93\t31\t116.3\t0\t31\n", "94\t68\t116.3\t0\t68\n", "95\t78\t116.3\t0\t78\n", "96\t61\t116.3\t0\t61\n", "97\t91\t116.3\t0\t91\n", "98\t69\t116.3\t0\t69\n", "99\t67\t116.3\t0\t67\n", "100\t88\t116.3\t0\t88\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 102679 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.4%\n", " C: 20.0%\n", " G: 18.4%\n", " T: 20.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t74414\t119135.0\t0\t74414\n", "4\t15682\t29783.8\t0\t15682\n", "5\t2461\t7445.9\t0\t2461\n", "6\t310\t1861.5\t0\t310\n", "7\t113\t465.4\t0\t113\n", "8\t145\t465.4\t0\t145\n", "9\t133\t465.4\t0\t133\n", "10\t125\t465.4\t0\t125\n", "11\t132\t465.4\t0\t132\n", "12\t142\t465.4\t0\t142\n", "13\t160\t465.4\t0\t160\n", "14\t173\t465.4\t0\t173\n", "15\t148\t465.4\t0\t148\n", "16\t134\t465.4\t0\t134\n", "17\t166\t465.4\t0\t166\n", "18\t192\t465.4\t0\t192\n", "19\t148\t465.4\t0\t148\n", "20\t174\t465.4\t0\t174\n", "21\t147\t465.4\t0\t147\n", "22\t138\t465.4\t0\t138\n", "23\t107\t465.4\t0\t107\n", "24\t126\t465.4\t0\t126\n", "25\t111\t465.4\t0\t111\n", "26\t112\t465.4\t0\t112\n", "27\t145\t465.4\t0\t145\n", "28\t153\t465.4\t0\t153\n", "29\t132\t465.4\t0\t132\n", "30\t116\t465.4\t0\t116\n", "31\t109\t465.4\t0\t109\n", "32\t128\t465.4\t0\t128\n", "33\t128\t465.4\t0\t128\n", "34\t134\t465.4\t0\t134\n", "35\t154\t465.4\t0\t154\n", "36\t123\t465.4\t0\t123\n", "37\t89\t465.4\t0\t89\n", "38\t122\t465.4\t0\t122\n", "39\t144\t465.4\t0\t144\n", "40\t103\t465.4\t0\t103\n", "41\t109\t465.4\t0\t109\n", "42\t96\t465.4\t0\t96\n", "43\t148\t465.4\t0\t148\n", "44\t72\t465.4\t0\t72\n", "45\t106\t465.4\t0\t106\n", "46\t107\t465.4\t0\t107\n", "47\t104\t465.4\t0\t104\n", "48\t109\t465.4\t0\t109\n", "49\t97\t465.4\t0\t97\n", "50\t96\t465.4\t0\t96\n", "51\t75\t465.4\t0\t75\n", "52\t87\t465.4\t0\t87\n", "53\t90\t465.4\t0\t90\n", "54\t103\t465.4\t0\t103\n", "55\t96\t465.4\t0\t96\n", "56\t94\t465.4\t0\t94\n", "57\t81\t465.4\t0\t81\n", "58\t58\t465.4\t0\t58\n", "59\t55\t465.4\t0\t55\n", "60\t102\t465.4\t0\t102\n", "61\t72\t465.4\t0\t72\n", "62\t78\t465.4\t0\t78\n", "63\t70\t465.4\t0\t70\n", "64\t64\t465.4\t0\t64\n", "65\t88\t465.4\t0\t88\n", "66\t75\t465.4\t0\t75\n", "67\t80\t465.4\t0\t80\n", "68\t83\t465.4\t0\t83\n", "69\t46\t465.4\t0\t46\n", "70\t68\t465.4\t0\t68\n", "71\t57\t465.4\t0\t57\n", "72\t83\t465.4\t0\t83\n", "73\t87\t465.4\t0\t87\n", "74\t113\t465.4\t0\t113\n", "75\t94\t465.4\t0\t94\n", "76\t98\t465.4\t0\t98\n", "77\t94\t465.4\t0\t94\n", "78\t78\t465.4\t0\t78\n", "79\t93\t465.4\t0\t93\n", "80\t93\t465.4\t0\t93\n", "81\t94\t465.4\t0\t94\n", "82\t126\t465.4\t0\t126\n", "83\t102\t465.4\t0\t102\n", "84\t87\t465.4\t0\t87\n", "85\t87\t465.4\t0\t87\n", "86\t101\t465.4\t0\t101\n", "87\t112\t465.4\t0\t112\n", "88\t125\t465.4\t0\t125\n", "89\t77\t465.4\t0\t77\n", "90\t87\t465.4\t0\t87\n", "91\t63\t465.4\t0\t63\n", "92\t54\t465.4\t0\t54\n", "93\t53\t465.4\t0\t53\n", "94\t61\t465.4\t0\t61\n", "95\t71\t465.4\t0\t71\n", "96\t49\t465.4\t0\t49\n", "97\t69\t465.4\t0\t69\n", "98\t82\t465.4\t0\t82\n", "99\t103\t465.4\t0\t103\n", "100\t104\t465.4\t0\t104\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 323_S39_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/323.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 148.57 s (15 us/read; 4.11 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 10,167,458\n", "Reads with adapters: 8,188,464 (80.5%)\n", "Reads written (passing filters): 9,545,280 (93.9%)\n", "\n", "Total basepairs processed: 1,016,745,800 bp\n", "Quality-trimmed: 3,720,094 bp (0.4%)\n", "Total written (filtered): 659,149,011 bp (64.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 7890595 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 35.7%\n", " G: 39.2%\n", " T: 25.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t132295\t158866.5\t0\t132295\n", "4\t89825\t39716.6\t0\t89825\n", "5\t75636\t9929.2\t0\t75636\n", "6\t68097\t2482.3\t0\t68097\n", "7\t68855\t620.6\t0\t68855\n", "8\t69919\t155.1\t0\t69919\n", "9\t71581\t155.1\t0\t71581\n", "10\t70495\t155.1\t0\t70495\n", "11\t72556\t155.1\t0\t72556\n", "12\t75116\t155.1\t0\t75116\n", "13\t76600\t155.1\t0\t76600\n", "14\t80671\t155.1\t0\t80671\n", "15\t80725\t155.1\t0\t80725\n", "16\t86089\t155.1\t0\t86089\n", "17\t98347\t155.1\t0\t98347\n", "18\t110876\t155.1\t0\t110876\n", "19\t100796\t155.1\t0\t100796\n", "20\t85432\t155.1\t0\t85432\n", "21\t83651\t155.1\t0\t83651\n", "22\t77726\t155.1\t0\t77726\n", "23\t86070\t155.1\t0\t86070\n", "24\t100133\t155.1\t0\t100133\n", "25\t105439\t155.1\t0\t105439\n", "26\t120178\t155.1\t0\t120178\n", "27\t127967\t155.1\t0\t127967\n", "28\t115707\t155.1\t0\t115707\n", "29\t105887\t155.1\t0\t105887\n", "30\t109471\t155.1\t0\t109471\n", "31\t124268\t155.1\t0\t124268\n", "32\t116105\t155.1\t0\t116105\n", "33\t115969\t155.1\t0\t115969\n", "34\t113460\t155.1\t0\t113460\n", "35\t129121\t155.1\t0\t129121\n", "36\t139667\t155.1\t0\t139667\n", "37\t135722\t155.1\t0\t135722\n", "38\t120654\t155.1\t0\t120654\n", "39\t115856\t155.1\t0\t115856\n", "40\t111641\t155.1\t0\t111641\n", "41\t124553\t155.1\t0\t124553\n", "42\t135385\t155.1\t0\t135385\n", "43\t122615\t155.1\t0\t122615\n", "44\t99219\t155.1\t0\t99219\n", "45\t123641\t155.1\t0\t123641\n", "46\t148637\t155.1\t0\t148637\n", "47\t146432\t155.1\t0\t146432\n", "48\t141437\t155.1\t0\t141437\n", "49\t114231\t155.1\t0\t114231\n", "50\t112429\t155.1\t0\t112429\n", "51\t106759\t155.1\t0\t106759\n", "52\t112048\t155.1\t0\t112048\n", "53\t113593\t155.1\t0\t113593\n", "54\t131916\t155.1\t0\t131916\n", "55\t108869\t155.1\t0\t108869\n", "56\t98208\t155.1\t0\t98208\n", "57\t96392\t155.1\t0\t96392\n", "58\t106098\t155.1\t0\t106098\n", "59\t101851\t155.1\t0\t101851\n", "60\t90770\t155.1\t0\t90770\n", "61\t85312\t155.1\t0\t85312\n", "62\t68812\t155.1\t0\t68812\n", "63\t65225\t155.1\t0\t65225\n", "64\t75268\t155.1\t0\t75268\n", "65\t78253\t155.1\t0\t78253\n", "66\t68077\t155.1\t0\t68077\n", "67\t68581\t155.1\t0\t68581\n", "68\t66770\t155.1\t0\t66770\n", "69\t69339\t155.1\t0\t69339\n", "70\t71055\t155.1\t0\t71055\n", "71\t68764\t155.1\t0\t68764\n", "72\t55362\t155.1\t0\t55362\n", "73\t52210\t155.1\t0\t52210\n", "74\t54162\t155.1\t0\t54162\n", "75\t46867\t155.1\t0\t46867\n", "76\t40463\t155.1\t0\t40463\n", "77\t35803\t155.1\t0\t35803\n", "78\t40235\t155.1\t0\t40235\n", "79\t38681\t155.1\t0\t38681\n", "80\t38086\t155.1\t0\t38086\n", "81\t34821\t155.1\t0\t34821\n", "82\t33867\t155.1\t0\t33867\n", "83\t36627\t155.1\t0\t36627\n", "84\t42757\t155.1\t0\t42757\n", "85\t48473\t155.1\t0\t48473\n", "86\t45105\t155.1\t0\t45105\n", "87\t29172\t155.1\t0\t29172\n", "88\t25679\t155.1\t0\t25679\n", "89\t28726\t155.1\t0\t28726\n", "90\t32368\t155.1\t0\t32368\n", "91\t34749\t155.1\t0\t34749\n", "92\t36515\t155.1\t0\t36515\n", "93\t40615\t155.1\t0\t40615\n", "94\t36450\t155.1\t0\t36450\n", "95\t30672\t155.1\t0\t30672\n", "96\t23164\t155.1\t0\t23164\n", "97\t14241\t155.1\t0\t14241\n", "98\t7939\t155.1\t0\t7939\n", "99\t12892\t155.1\t0\t12892\n", "100\t4752\t155.1\t0\t4752\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 192968 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 86.6%\n", " C: 5.6%\n", " G: 0.0%\n", " T: 7.8%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10560\t158866.5\t0\t10560\n", "4\t2661\t39716.6\t0\t2661\n", "5\t957\t9929.2\t0\t957\n", "6\t579\t2482.3\t0\t579\n", "7\t345\t620.6\t0\t345\n", "8\t327\t155.1\t0\t327\n", "9\t303\t155.1\t0\t303\n", "10\t312\t155.1\t0\t312\n", "11\t251\t155.1\t0\t251\n", "12\t244\t155.1\t0\t244\n", "13\t289\t155.1\t0\t289\n", "14\t273\t155.1\t0\t273\n", "15\t330\t155.1\t0\t330\n", "16\t391\t155.1\t0\t391\n", "17\t562\t155.1\t0\t562\n", "18\t876\t155.1\t0\t876\n", "19\t1425\t155.1\t0\t1425\n", "20\t2454\t155.1\t0\t2454\n", "21\t1730\t155.1\t0\t1730\n", "22\t1328\t155.1\t0\t1328\n", "23\t965\t155.1\t0\t965\n", "24\t1120\t155.1\t0\t1120\n", "25\t1530\t155.1\t0\t1530\n", "26\t3255\t155.1\t0\t3255\n", "27\t3513\t155.1\t0\t3513\n", "28\t4582\t155.1\t0\t4582\n", "29\t6082\t155.1\t0\t6082\n", "30\t11255\t155.1\t0\t11255\n", "31\t12582\t155.1\t0\t12582\n", "32\t16810\t155.1\t0\t16810\n", "33\t18777\t155.1\t0\t18777\n", "34\t19228\t155.1\t0\t19228\n", "35\t25442\t155.1\t0\t25442\n", "36\t28310\t155.1\t0\t28310\n", "37\t10463\t155.1\t0\t10463\n", "38\t288\t155.1\t0\t288\n", "39\t110\t155.1\t0\t110\n", "40\t71\t155.1\t0\t71\n", "41\t64\t155.1\t0\t64\n", "42\t62\t155.1\t0\t62\n", "43\t75\t155.1\t0\t75\n", "44\t66\t155.1\t0\t66\n", "45\t73\t155.1\t0\t73\n", "46\t54\t155.1\t0\t54\n", "47\t69\t155.1\t0\t69\n", "48\t89\t155.1\t0\t89\n", "49\t80\t155.1\t0\t80\n", "50\t75\t155.1\t0\t75\n", "51\t64\t155.1\t0\t64\n", "52\t55\t155.1\t0\t55\n", "53\t62\t155.1\t0\t62\n", "54\t52\t155.1\t0\t52\n", "55\t59\t155.1\t0\t59\n", "56\t49\t155.1\t0\t49\n", "57\t66\t155.1\t0\t66\n", "58\t48\t155.1\t0\t48\n", "59\t48\t155.1\t0\t48\n", "60\t53\t155.1\t0\t53\n", "61\t58\t155.1\t0\t58\n", "62\t45\t155.1\t0\t45\n", "63\t29\t155.1\t0\t29\n", "64\t45\t155.1\t0\t45\n", "65\t40\t155.1\t0\t40\n", "66\t25\t155.1\t0\t25\n", "67\t27\t155.1\t0\t27\n", "68\t29\t155.1\t0\t29\n", "69\t21\t155.1\t0\t21\n", "70\t21\t155.1\t0\t21\n", "71\t12\t155.1\t0\t12\n", "72\t23\t155.1\t0\t23\n", "73\t13\t155.1\t0\t13\n", "74\t9\t155.1\t0\t9\n", "75\t14\t155.1\t0\t14\n", "76\t16\t155.1\t0\t16\n", "77\t15\t155.1\t0\t15\n", "78\t15\t155.1\t0\t15\n", "79\t20\t155.1\t0\t20\n", "80\t7\t155.1\t0\t7\n", "81\t13\t155.1\t0\t13\n", "82\t10\t155.1\t0\t10\n", "83\t17\t155.1\t0\t17\n", "84\t15\t155.1\t0\t15\n", "85\t21\t155.1\t0\t21\n", "86\t14\t155.1\t0\t14\n", "87\t13\t155.1\t0\t13\n", "88\t18\t155.1\t0\t18\n", "89\t8\t155.1\t0\t8\n", "90\t17\t155.1\t0\t17\n", "91\t16\t155.1\t0\t16\n", "92\t36\t155.1\t0\t36\n", "93\t50\t155.1\t0\t50\n", "94\t51\t155.1\t0\t51\n", "95\t71\t155.1\t0\t71\n", "96\t71\t155.1\t0\t71\n", "97\t89\t155.1\t0\t89\n", "98\t36\t155.1\t0\t36\n", "99\t21\t155.1\t0\t21\n", "100\t54\t155.1\t0\t54\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 104901 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.7%\n", " C: 20.6%\n", " G: 21.2%\n", " T: 18.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t62299\t158866.5\t0\t62299\n", "4\t13858\t39716.6\t0\t13858\n", "5\t2389\t9929.2\t0\t2389\n", "6\t515\t2482.3\t0\t515\n", "7\t302\t620.6\t0\t302\n", "8\t348\t620.6\t0\t348\n", "9\t299\t620.6\t0\t299\n", "10\t375\t620.6\t0\t375\n", "11\t300\t620.6\t0\t300\n", "12\t346\t620.6\t0\t346\n", "13\t380\t620.6\t0\t380\n", "14\t345\t620.6\t0\t345\n", "15\t390\t620.6\t0\t390\n", "16\t386\t620.6\t0\t386\n", "17\t348\t620.6\t0\t348\n", "18\t336\t620.6\t0\t336\n", "19\t320\t620.6\t0\t320\n", "20\t372\t620.6\t0\t372\n", "21\t424\t620.6\t0\t424\n", "22\t369\t620.6\t0\t369\n", "23\t363\t620.6\t0\t363\n", "24\t300\t620.6\t0\t300\n", "25\t318\t620.6\t0\t318\n", "26\t326\t620.6\t0\t326\n", "27\t400\t620.6\t0\t400\n", "28\t385\t620.6\t0\t385\n", "29\t359\t620.6\t0\t359\n", "30\t393\t620.6\t0\t393\n", "31\t401\t620.6\t0\t401\n", "32\t415\t620.6\t0\t415\n", "33\t423\t620.6\t0\t423\n", "34\t411\t620.6\t0\t411\n", "35\t454\t620.6\t0\t454\n", "36\t536\t620.6\t0\t536\n", "37\t333\t620.6\t0\t333\n", "38\t383\t620.6\t0\t383\n", "39\t437\t620.6\t0\t437\n", "40\t421\t620.6\t0\t421\n", "41\t356\t620.6\t0\t356\n", "42\t322\t620.6\t0\t322\n", "43\t456\t620.6\t0\t456\n", "44\t127\t620.6\t0\t127\n", "45\t281\t620.6\t0\t281\n", "46\t285\t620.6\t0\t285\n", "47\t277\t620.6\t0\t277\n", "48\t243\t620.6\t0\t243\n", "49\t287\t620.6\t0\t287\n", "50\t246\t620.6\t0\t246\n", "51\t278\t620.6\t0\t278\n", "52\t231\t620.6\t0\t231\n", "53\t239\t620.6\t0\t239\n", "54\t204\t620.6\t0\t204\n", "55\t225\t620.6\t0\t225\n", "56\t267\t620.6\t0\t267\n", "57\t317\t620.6\t0\t317\n", "58\t555\t620.6\t0\t555\n", "59\t310\t620.6\t0\t310\n", "60\t553\t620.6\t0\t553\n", "61\t701\t620.6\t0\t701\n", "62\t657\t620.6\t0\t657\n", "63\t335\t620.6\t0\t335\n", "64\t621\t620.6\t0\t621\n", "65\t636\t620.6\t0\t636\n", "66\t463\t620.6\t0\t463\n", "67\t283\t620.6\t0\t283\n", "68\t235\t620.6\t0\t235\n", "69\t116\t620.6\t0\t116\n", "70\t93\t620.6\t0\t93\n", "71\t163\t620.6\t0\t163\n", "72\t153\t620.6\t0\t153\n", "73\t155\t620.6\t0\t155\n", "74\t126\t620.6\t0\t126\n", "75\t110\t620.6\t0\t110\n", "76\t111\t620.6\t0\t111\n", "77\t113\t620.6\t0\t113\n", "78\t94\t620.6\t0\t94\n", "79\t89\t620.6\t0\t89\n", "80\t106\t620.6\t0\t106\n", "81\t97\t620.6\t0\t97\n", "82\t123\t620.6\t0\t123\n", "83\t99\t620.6\t0\t99\n", "84\t93\t620.6\t0\t93\n", "85\t98\t620.6\t0\t98\n", "86\t82\t620.6\t0\t82\n", "87\t112\t620.6\t0\t112\n", "88\t144\t620.6\t0\t144\n", "89\t101\t620.6\t0\t101\n", "90\t118\t620.6\t0\t118\n", "91\t78\t620.6\t0\t78\n", "92\t66\t620.6\t0\t66\n", "93\t68\t620.6\t0\t68\n", "94\t68\t620.6\t0\t68\n", "95\t59\t620.6\t0\t59\n", "96\t47\t620.6\t0\t47\n", "97\t77\t620.6\t0\t77\n", "98\t59\t620.6\t0\t59\n", "99\t64\t620.6\t0\t64\n", "100\t70\t620.6\t0\t70\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 324_S47_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/324.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 118.99 s (14 us/read; 4.30 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,527,120\n", "Reads with adapters: 6,179,035 (72.5%)\n", "Reads written (passing filters): 8,321,889 (97.6%)\n", "\n", "Total basepairs processed: 852,712,000 bp\n", "Quality-trimmed: 2,889,475 bp (0.3%)\n", "Total written (filtered): 614,216,137 bp (72.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 6056434 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 34.8%\n", " G: 37.9%\n", " T: 27.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t141532\t133236.2\t0\t141532\n", "4\t86591\t33309.1\t0\t86591\n", "5\t70660\t8327.3\t0\t70660\n", "6\t61954\t2081.8\t0\t61954\n", "7\t61933\t520.5\t0\t61933\n", "8\t63099\t130.1\t0\t63099\n", "9\t64428\t130.1\t0\t64428\n", "10\t63558\t130.1\t0\t63558\n", "11\t65798\t130.1\t0\t65798\n", "12\t66436\t130.1\t0\t66436\n", "13\t70749\t130.1\t0\t70749\n", "14\t73364\t130.1\t0\t73364\n", "15\t71498\t130.1\t0\t71498\n", "16\t77231\t130.1\t0\t77231\n", "17\t86606\t130.1\t0\t86606\n", "18\t98963\t130.1\t0\t98963\n", "19\t86983\t130.1\t0\t86983\n", "20\t72049\t130.1\t0\t72049\n", "21\t70324\t130.1\t0\t70324\n", "22\t67536\t130.1\t0\t67536\n", "23\t75704\t130.1\t0\t75704\n", "24\t87258\t130.1\t0\t87258\n", "25\t90641\t130.1\t0\t90641\n", "26\t103190\t130.1\t0\t103190\n", "27\t110159\t130.1\t0\t110159\n", "28\t95619\t130.1\t0\t95619\n", "29\t88081\t130.1\t0\t88081\n", "30\t88568\t130.1\t0\t88568\n", "31\t98478\t130.1\t0\t98478\n", "32\t99328\t130.1\t0\t99328\n", "33\t95788\t130.1\t0\t95788\n", "34\t93202\t130.1\t0\t93202\n", "35\t108751\t130.1\t0\t108751\n", "36\t115285\t130.1\t0\t115285\n", "37\t108043\t130.1\t0\t108043\n", "38\t97286\t130.1\t0\t97286\n", "39\t96373\t130.1\t0\t96373\n", "40\t95476\t130.1\t0\t95476\n", "41\t111237\t130.1\t0\t111237\n", "42\t121982\t130.1\t0\t121982\n", "43\t116783\t130.1\t0\t116783\n", "44\t91138\t130.1\t0\t91138\n", "45\t117341\t130.1\t0\t117341\n", "46\t142497\t130.1\t0\t142497\n", "47\t129951\t130.1\t0\t129951\n", "48\t114232\t130.1\t0\t114232\n", "49\t94351\t130.1\t0\t94351\n", "50\t93512\t130.1\t0\t93512\n", "51\t94911\t130.1\t0\t94911\n", "52\t94957\t130.1\t0\t94957\n", "53\t71038\t130.1\t0\t71038\n", "54\t75916\t130.1\t0\t75916\n", "55\t76910\t130.1\t0\t76910\n", "56\t77000\t130.1\t0\t77000\n", "57\t77900\t130.1\t0\t77900\n", "58\t81292\t130.1\t0\t81292\n", "59\t76597\t130.1\t0\t76597\n", "60\t63268\t130.1\t0\t63268\n", "61\t57714\t130.1\t0\t57714\n", "62\t47701\t130.1\t0\t47701\n", "63\t46996\t130.1\t0\t46996\n", "64\t55849\t130.1\t0\t55849\n", "65\t47909\t130.1\t0\t47909\n", "66\t38008\t130.1\t0\t38008\n", "67\t40660\t130.1\t0\t40660\n", "68\t40121\t130.1\t0\t40121\n", "69\t40687\t130.1\t0\t40687\n", "70\t44893\t130.1\t0\t44893\n", "71\t40961\t130.1\t0\t40961\n", "72\t28991\t130.1\t0\t28991\n", "73\t23318\t130.1\t0\t23318\n", "74\t21922\t130.1\t0\t21922\n", "75\t19555\t130.1\t0\t19555\n", "76\t15261\t130.1\t0\t15261\n", "77\t17052\t130.1\t0\t17052\n", "78\t21645\t130.1\t0\t21645\n", "79\t16944\t130.1\t0\t16944\n", "80\t15135\t130.1\t0\t15135\n", "81\t15243\t130.1\t0\t15243\n", "82\t14025\t130.1\t0\t14025\n", "83\t13072\t130.1\t0\t13072\n", "84\t15098\t130.1\t0\t15098\n", "85\t16964\t130.1\t0\t16964\n", "86\t16523\t130.1\t0\t16523\n", "87\t11967\t130.1\t0\t11967\n", "88\t10229\t130.1\t0\t10229\n", "89\t9701\t130.1\t0\t9701\n", "90\t9359\t130.1\t0\t9359\n", "91\t8653\t130.1\t0\t8653\n", "92\t7923\t130.1\t0\t7923\n", "93\t8132\t130.1\t0\t8132\n", "94\t7518\t130.1\t0\t7518\n", "95\t6333\t130.1\t0\t6333\n", "96\t4598\t130.1\t0\t4598\n", "97\t3289\t130.1\t0\t3289\n", "98\t1939\t130.1\t0\t1939\n", "99\t2123\t130.1\t0\t2123\n", "100\t1088\t130.1\t0\t1088\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29284 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 57.5%\n", " C: 18.7%\n", " G: 0.0%\n", " T: 23.7%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10725\t133236.2\t0\t10725\n", "4\t2612\t33309.1\t0\t2612\n", "5\t968\t8327.3\t0\t968\n", "6\t294\t2081.8\t0\t294\n", "7\t71\t520.5\t0\t71\n", "8\t57\t130.1\t0\t57\n", "9\t53\t130.1\t0\t53\n", "10\t61\t130.1\t0\t61\n", "11\t56\t130.1\t0\t56\n", "12\t51\t130.1\t0\t51\n", "13\t62\t130.1\t0\t62\n", "14\t50\t130.1\t0\t50\n", "15\t59\t130.1\t0\t59\n", "16\t60\t130.1\t0\t60\n", "17\t67\t130.1\t0\t67\n", "18\t131\t130.1\t0\t131\n", "19\t147\t130.1\t0\t147\n", "20\t178\t130.1\t0\t178\n", "21\t134\t130.1\t0\t134\n", "22\t129\t130.1\t0\t129\n", "23\t83\t130.1\t0\t83\n", "24\t87\t130.1\t0\t87\n", "25\t90\t130.1\t0\t90\n", "26\t154\t130.1\t0\t154\n", "27\t178\t130.1\t0\t178\n", "28\t255\t130.1\t0\t255\n", "29\t319\t130.1\t0\t319\n", "30\t579\t130.1\t0\t579\n", "31\t775\t130.1\t0\t775\n", "32\t1081\t130.1\t0\t1081\n", "33\t1292\t130.1\t0\t1292\n", "34\t1646\t130.1\t0\t1646\n", "35\t2018\t130.1\t0\t2018\n", "36\t1778\t130.1\t0\t1778\n", "37\t710\t130.1\t0\t710\n", "38\t78\t130.1\t0\t78\n", "39\t43\t130.1\t0\t43\n", "40\t40\t130.1\t0\t40\n", "41\t43\t130.1\t0\t43\n", "42\t42\t130.1\t0\t42\n", "43\t49\t130.1\t0\t49\n", "44\t45\t130.1\t0\t45\n", "45\t33\t130.1\t0\t33\n", "46\t37\t130.1\t0\t37\n", "47\t40\t130.1\t0\t40\n", "48\t46\t130.1\t0\t46\n", "49\t50\t130.1\t0\t50\n", "50\t55\t130.1\t0\t55\n", "51\t35\t130.1\t0\t35\n", "52\t34\t130.1\t0\t34\n", "53\t28\t130.1\t0\t28\n", "54\t39\t130.1\t0\t39\n", "55\t33\t130.1\t0\t33\n", "56\t27\t130.1\t0\t27\n", "57\t36\t130.1\t0\t36\n", "58\t42\t130.1\t0\t42\n", "59\t43\t130.1\t0\t43\n", "60\t29\t130.1\t0\t29\n", "61\t39\t130.1\t0\t39\n", "62\t32\t130.1\t0\t32\n", "63\t28\t130.1\t0\t28\n", "64\t28\t130.1\t0\t28\n", "65\t29\t130.1\t0\t29\n", "66\t22\t130.1\t0\t22\n", "67\t28\t130.1\t0\t28\n", "68\t14\t130.1\t0\t14\n", "69\t15\t130.1\t0\t15\n", "70\t13\t130.1\t0\t13\n", "71\t16\t130.1\t0\t16\n", "72\t10\t130.1\t0\t10\n", "73\t13\t130.1\t0\t13\n", "74\t8\t130.1\t0\t8\n", "75\t11\t130.1\t0\t11\n", "76\t10\t130.1\t0\t10\n", "77\t11\t130.1\t0\t11\n", "78\t15\t130.1\t0\t15\n", "79\t16\t130.1\t0\t16\n", "80\t14\t130.1\t0\t14\n", "81\t21\t130.1\t0\t21\n", "82\t31\t130.1\t0\t31\n", "83\t26\t130.1\t0\t26\n", "84\t38\t130.1\t0\t38\n", "85\t28\t130.1\t0\t28\n", "86\t26\t130.1\t0\t26\n", "87\t26\t130.1\t0\t26\n", "88\t32\t130.1\t0\t32\n", "89\t27\t130.1\t0\t27\n", "90\t46\t130.1\t0\t46\n", "91\t29\t130.1\t0\t29\n", "92\t44\t130.1\t0\t44\n", "93\t61\t130.1\t0\t61\n", "94\t70\t130.1\t0\t70\n", "95\t82\t130.1\t0\t82\n", "96\t85\t130.1\t0\t85\n", "97\t101\t130.1\t0\t101\n", "98\t65\t130.1\t0\t65\n", "99\t32\t130.1\t0\t32\n", "100\t85\t130.1\t0\t85\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 93317 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.9%\n", " C: 17.5%\n", " G: 17.8%\n", " T: 21.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t67461\t133236.2\t0\t67461\n", "4\t16104\t33309.1\t0\t16104\n", "5\t2417\t8327.3\t0\t2417\n", "6\t292\t2081.8\t0\t292\n", "7\t90\t520.5\t0\t90\n", "8\t113\t520.5\t0\t113\n", "9\t74\t520.5\t0\t74\n", "10\t92\t520.5\t0\t92\n", "11\t114\t520.5\t0\t114\n", "12\t83\t520.5\t0\t83\n", "13\t108\t520.5\t0\t108\n", "14\t101\t520.5\t0\t101\n", "15\t114\t520.5\t0\t114\n", "16\t116\t520.5\t0\t116\n", "17\t128\t520.5\t0\t128\n", "18\t149\t520.5\t0\t149\n", "19\t110\t520.5\t0\t110\n", "20\t125\t520.5\t0\t125\n", "21\t132\t520.5\t0\t132\n", "22\t106\t520.5\t0\t106\n", "23\t91\t520.5\t0\t91\n", "24\t89\t520.5\t0\t89\n", "25\t92\t520.5\t0\t92\n", "26\t108\t520.5\t0\t108\n", "27\t86\t520.5\t0\t86\n", "28\t115\t520.5\t0\t115\n", "29\t83\t520.5\t0\t83\n", "30\t109\t520.5\t0\t109\n", "31\t96\t520.5\t0\t96\n", "32\t96\t520.5\t0\t96\n", "33\t100\t520.5\t0\t100\n", "34\t96\t520.5\t0\t96\n", "35\t84\t520.5\t0\t84\n", "36\t81\t520.5\t0\t81\n", "37\t91\t520.5\t0\t91\n", "38\t89\t520.5\t0\t89\n", "39\t108\t520.5\t0\t108\n", "40\t99\t520.5\t0\t99\n", "41\t96\t520.5\t0\t96\n", "42\t77\t520.5\t0\t77\n", "43\t71\t520.5\t0\t71\n", "44\t68\t520.5\t0\t68\n", "45\t88\t520.5\t0\t88\n", "46\t91\t520.5\t0\t91\n", "47\t75\t520.5\t0\t75\n", "48\t59\t520.5\t0\t59\n", "49\t79\t520.5\t0\t79\n", "50\t62\t520.5\t0\t62\n", "51\t64\t520.5\t0\t64\n", "52\t52\t520.5\t0\t52\n", "53\t66\t520.5\t0\t66\n", "54\t63\t520.5\t0\t63\n", "55\t53\t520.5\t0\t53\n", "56\t54\t520.5\t0\t54\n", "57\t51\t520.5\t0\t51\n", "58\t54\t520.5\t0\t54\n", "59\t50\t520.5\t0\t50\n", "60\t53\t520.5\t0\t53\n", "61\t63\t520.5\t0\t63\n", "62\t30\t520.5\t0\t30\n", "63\t38\t520.5\t0\t38\n", "64\t43\t520.5\t0\t43\n", "65\t30\t520.5\t0\t30\n", "66\t40\t520.5\t0\t40\n", "67\t46\t520.5\t0\t46\n", "68\t57\t520.5\t0\t57\n", "69\t41\t520.5\t0\t41\n", "70\t53\t520.5\t0\t53\n", "71\t42\t520.5\t0\t42\n", "72\t53\t520.5\t0\t53\n", "73\t49\t520.5\t0\t49\n", "74\t63\t520.5\t0\t63\n", "75\t55\t520.5\t0\t55\n", "76\t62\t520.5\t0\t62\n", "77\t74\t520.5\t0\t74\n", "78\t67\t520.5\t0\t67\n", "79\t58\t520.5\t0\t58\n", "80\t52\t520.5\t0\t52\n", "81\t60\t520.5\t0\t60\n", "82\t85\t520.5\t0\t85\n", "83\t65\t520.5\t0\t65\n", "84\t61\t520.5\t0\t61\n", "85\t56\t520.5\t0\t56\n", "86\t52\t520.5\t0\t52\n", "87\t90\t520.5\t0\t90\n", "88\t106\t520.5\t0\t106\n", "89\t71\t520.5\t0\t71\n", "90\t52\t520.5\t0\t52\n", "91\t42\t520.5\t0\t42\n", "92\t39\t520.5\t0\t39\n", "93\t27\t520.5\t0\t27\n", "94\t38\t520.5\t0\t38\n", "95\t30\t520.5\t0\t30\n", "96\t32\t520.5\t0\t32\n", "97\t61\t520.5\t0\t61\n", "98\t60\t520.5\t0\t60\n", "99\t89\t520.5\t0\t89\n", "100\t117\t520.5\t0\t117\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 325_S13_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/325.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 114.68 s (15 us/read; 4.11 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,860,511\n", "Reads with adapters: 5,044,758 (64.2%)\n", "Reads written (passing filters): 7,590,400 (96.6%)\n", "\n", "Total basepairs processed: 786,051,100 bp\n", "Quality-trimmed: 2,144,882 bp (0.3%)\n", "Total written (filtered): 597,055,407 bp (76.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4887840 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.3%\n", " G: 38.8%\n", " T: 27.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t156995\t122820.5\t0\t156995\n", "4\t95569\t30705.1\t0\t95569\n", "5\t73872\t7676.3\t0\t73872\n", "6\t64260\t1919.1\t0\t64260\n", "7\t60477\t479.8\t0\t60477\n", "8\t60911\t119.9\t0\t60911\n", "9\t60926\t119.9\t0\t60926\n", "10\t60007\t119.9\t0\t60007\n", "11\t61159\t119.9\t0\t61159\n", "12\t62480\t119.9\t0\t62480\n", "13\t66761\t119.9\t0\t66761\n", "14\t68568\t119.9\t0\t68568\n", "15\t66071\t119.9\t0\t66071\n", "16\t68634\t119.9\t0\t68634\n", "17\t75660\t119.9\t0\t75660\n", "18\t86376\t119.9\t0\t86376\n", "19\t78721\t119.9\t0\t78721\n", "20\t65838\t119.9\t0\t65838\n", "21\t63281\t119.9\t0\t63281\n", "22\t57807\t119.9\t0\t57807\n", "23\t63811\t119.9\t0\t63811\n", "24\t73020\t119.9\t0\t73020\n", "25\t76024\t119.9\t0\t76024\n", "26\t85500\t119.9\t0\t85500\n", "27\t90207\t119.9\t0\t90207\n", "28\t80797\t119.9\t0\t80797\n", "29\t75787\t119.9\t0\t75787\n", "30\t74287\t119.9\t0\t74287\n", "31\t81508\t119.9\t0\t81508\n", "32\t80735\t119.9\t0\t80735\n", "33\t77940\t119.9\t0\t77940\n", "34\t75255\t119.9\t0\t75255\n", "35\t83894\t119.9\t0\t83894\n", "36\t91428\t119.9\t0\t91428\n", "37\t89942\t119.9\t0\t89942\n", "38\t76724\t119.9\t0\t76724\n", "39\t71972\t119.9\t0\t71972\n", "40\t68293\t119.9\t0\t68293\n", "41\t76611\t119.9\t0\t76611\n", "42\t83212\t119.9\t0\t83212\n", "43\t73607\t119.9\t0\t73607\n", "44\t57189\t119.9\t0\t57189\n", "45\t69051\t119.9\t0\t69051\n", "46\t78982\t119.9\t0\t78982\n", "47\t73462\t119.9\t0\t73462\n", "48\t70868\t119.9\t0\t70868\n", "49\t61804\t119.9\t0\t61804\n", "50\t62825\t119.9\t0\t62825\n", "51\t57012\t119.9\t0\t57012\n", "52\t57884\t119.9\t0\t57884\n", "53\t48463\t119.9\t0\t48463\n", "54\t46711\t119.9\t0\t46711\n", "55\t55434\t119.9\t0\t55434\n", "56\t56577\t119.9\t0\t56577\n", "57\t55361\t119.9\t0\t55361\n", "58\t59162\t119.9\t0\t59162\n", "59\t50184\t119.9\t0\t50184\n", "60\t43086\t119.9\t0\t43086\n", "61\t39784\t119.9\t0\t39784\n", "62\t33124\t119.9\t0\t33124\n", "63\t30771\t119.9\t0\t30771\n", "64\t35514\t119.9\t0\t35514\n", "65\t34945\t119.9\t0\t34945\n", "66\t29296\t119.9\t0\t29296\n", "67\t30022\t119.9\t0\t30022\n", "68\t29583\t119.9\t0\t29583\n", "69\t30318\t119.9\t0\t30318\n", "70\t31761\t119.9\t0\t31761\n", "71\t30744\t119.9\t0\t30744\n", "72\t23975\t119.9\t0\t23975\n", "73\t21860\t119.9\t0\t21860\n", "74\t21745\t119.9\t0\t21745\n", "75\t19380\t119.9\t0\t19380\n", "76\t16073\t119.9\t0\t16073\n", "77\t15502\t119.9\t0\t15502\n", "78\t18301\t119.9\t0\t18301\n", "79\t17101\t119.9\t0\t17101\n", "80\t16463\t119.9\t0\t16463\n", "81\t15605\t119.9\t0\t15605\n", "82\t15094\t119.9\t0\t15094\n", "83\t15715\t119.9\t0\t15715\n", "84\t17737\t119.9\t0\t17737\n", "85\t20142\t119.9\t0\t20142\n", "86\t19430\t119.9\t0\t19430\n", "87\t13661\t119.9\t0\t13661\n", "88\t12822\t119.9\t0\t12822\n", "89\t13338\t119.9\t0\t13338\n", "90\t13841\t119.9\t0\t13841\n", "91\t14267\t119.9\t0\t14267\n", "92\t14444\t119.9\t0\t14444\n", "93\t15889\t119.9\t0\t15889\n", "94\t14933\t119.9\t0\t14933\n", "95\t12392\t119.9\t0\t12392\n", "96\t9272\t119.9\t0\t9272\n", "97\t5598\t119.9\t0\t5598\n", "98\t3225\t119.9\t0\t3225\n", "99\t3224\t119.9\t0\t3224\n", "100\t1967\t119.9\t0\t1967\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 43411 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 61.5%\n", " C: 17.9%\n", " G: 0.0%\n", " T: 20.5%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13447\t122820.5\t0\t13447\n", "4\t3436\t30705.1\t0\t3436\n", "5\t1512\t7676.3\t0\t1512\n", "6\t1104\t1919.1\t0\t1104\n", "7\t475\t479.8\t0\t475\n", "8\t353\t119.9\t0\t353\n", "9\t299\t119.9\t0\t299\n", "10\t352\t119.9\t0\t352\n", "11\t337\t119.9\t0\t337\n", "12\t327\t119.9\t0\t327\n", "13\t312\t119.9\t0\t312\n", "14\t316\t119.9\t0\t316\n", "15\t287\t119.9\t0\t287\n", "16\t306\t119.9\t0\t306\n", "17\t358\t119.9\t0\t358\n", "18\t361\t119.9\t0\t361\n", "19\t450\t119.9\t0\t450\n", "20\t570\t119.9\t0\t570\n", "21\t453\t119.9\t0\t453\n", "22\t396\t119.9\t0\t396\n", "23\t279\t119.9\t0\t279\n", "24\t308\t119.9\t0\t308\n", "25\t379\t119.9\t0\t379\n", "26\t583\t119.9\t0\t583\n", "27\t570\t119.9\t0\t570\n", "28\t548\t119.9\t0\t548\n", "29\t618\t119.9\t0\t618\n", "30\t963\t119.9\t0\t963\n", "31\t1207\t119.9\t0\t1207\n", "32\t1740\t119.9\t0\t1740\n", "33\t1536\t119.9\t0\t1536\n", "34\t1783\t119.9\t0\t1783\n", "35\t2007\t119.9\t0\t2007\n", "36\t1914\t119.9\t0\t1914\n", "37\t825\t119.9\t0\t825\n", "38\t115\t119.9\t0\t115\n", "39\t86\t119.9\t0\t86\n", "40\t71\t119.9\t0\t71\n", "41\t58\t119.9\t0\t58\n", "42\t83\t119.9\t0\t83\n", "43\t53\t119.9\t0\t53\n", "44\t62\t119.9\t0\t62\n", "45\t75\t119.9\t0\t75\n", "46\t54\t119.9\t0\t54\n", "47\t61\t119.9\t0\t61\n", "48\t61\t119.9\t0\t61\n", "49\t62\t119.9\t0\t62\n", "50\t68\t119.9\t0\t68\n", "51\t55\t119.9\t0\t55\n", "52\t57\t119.9\t0\t57\n", "53\t42\t119.9\t0\t42\n", "54\t36\t119.9\t0\t36\n", "55\t56\t119.9\t0\t56\n", "56\t50\t119.9\t0\t50\n", "57\t49\t119.9\t0\t49\n", "58\t45\t119.9\t0\t45\n", "59\t34\t119.9\t0\t34\n", "60\t34\t119.9\t0\t34\n", "61\t47\t119.9\t0\t47\n", "62\t36\t119.9\t0\t36\n", "63\t29\t119.9\t0\t29\n", "64\t28\t119.9\t0\t28\n", "65\t22\t119.9\t0\t22\n", "66\t41\t119.9\t0\t41\n", "67\t21\t119.9\t0\t21\n", "68\t32\t119.9\t0\t32\n", "69\t26\t119.9\t0\t26\n", "70\t25\t119.9\t0\t25\n", "71\t22\t119.9\t0\t22\n", "72\t16\t119.9\t0\t16\n", "73\t28\t119.9\t0\t28\n", "74\t15\t119.9\t0\t15\n", "75\t17\t119.9\t0\t17\n", "76\t15\t119.9\t0\t15\n", "77\t15\t119.9\t0\t15\n", "78\t12\t119.9\t0\t12\n", "79\t11\t119.9\t0\t11\n", "80\t15\t119.9\t0\t15\n", "81\t11\t119.9\t0\t11\n", "82\t8\t119.9\t0\t8\n", "83\t16\t119.9\t0\t16\n", "84\t24\t119.9\t0\t24\n", "85\t12\t119.9\t0\t12\n", "86\t12\t119.9\t0\t12\n", "87\t22\t119.9\t0\t22\n", "88\t10\t119.9\t0\t10\n", "89\t18\t119.9\t0\t18\n", "90\t15\t119.9\t0\t15\n", "91\t22\t119.9\t0\t22\n", "92\t32\t119.9\t0\t32\n", "93\t42\t119.9\t0\t42\n", "94\t64\t119.9\t0\t64\n", "95\t92\t119.9\t0\t92\n", "96\t108\t119.9\t0\t108\n", "97\t91\t119.9\t0\t91\n", "98\t69\t119.9\t0\t69\n", "99\t75\t119.9\t0\t75\n", "100\t117\t119.9\t0\t117\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 113507 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.6%\n", " C: 19.7%\n", " G: 17.9%\n", " T: 19.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t78962\t122820.5\t0\t78962\n", "4\t16294\t30705.1\t0\t16294\n", "5\t2816\t7676.3\t0\t2816\n", "6\t473\t1919.1\t0\t473\n", "7\t273\t479.8\t0\t273\n", "8\t328\t479.8\t0\t328\n", "9\t281\t479.8\t0\t281\n", "10\t281\t479.8\t0\t281\n", "11\t279\t479.8\t0\t279\n", "12\t301\t479.8\t0\t301\n", "13\t333\t479.8\t0\t333\n", "14\t299\t479.8\t0\t299\n", "15\t298\t479.8\t0\t298\n", "16\t318\t479.8\t0\t318\n", "17\t315\t479.8\t0\t315\n", "18\t283\t479.8\t0\t283\n", "19\t334\t479.8\t0\t334\n", "20\t292\t479.8\t0\t292\n", "21\t275\t479.8\t0\t275\n", "22\t279\t479.8\t0\t279\n", "23\t257\t479.8\t0\t257\n", "24\t268\t479.8\t0\t268\n", "25\t246\t479.8\t0\t246\n", "26\t212\t479.8\t0\t212\n", "27\t295\t479.8\t0\t295\n", "28\t276\t479.8\t0\t276\n", "29\t238\t479.8\t0\t238\n", "30\t265\t479.8\t0\t265\n", "31\t188\t479.8\t0\t188\n", "32\t255\t479.8\t0\t255\n", "33\t243\t479.8\t0\t243\n", "34\t245\t479.8\t0\t245\n", "35\t231\t479.8\t0\t231\n", "36\t174\t479.8\t0\t174\n", "37\t185\t479.8\t0\t185\n", "38\t204\t479.8\t0\t204\n", "39\t171\t479.8\t0\t171\n", "40\t197\t479.8\t0\t197\n", "41\t156\t479.8\t0\t156\n", "42\t155\t479.8\t0\t155\n", "43\t211\t479.8\t0\t211\n", "44\t62\t479.8\t0\t62\n", "45\t128\t479.8\t0\t128\n", "46\t132\t479.8\t0\t132\n", "47\t158\t479.8\t0\t158\n", "48\t150\t479.8\t0\t150\n", "49\t126\t479.8\t0\t126\n", "50\t122\t479.8\t0\t122\n", "51\t152\t479.8\t0\t152\n", "52\t135\t479.8\t0\t135\n", "53\t152\t479.8\t0\t152\n", "54\t104\t479.8\t0\t104\n", "55\t110\t479.8\t0\t110\n", "56\t122\t479.8\t0\t122\n", "57\t77\t479.8\t0\t77\n", "58\t138\t479.8\t0\t138\n", "59\t85\t479.8\t0\t85\n", "60\t94\t479.8\t0\t94\n", "61\t83\t479.8\t0\t83\n", "62\t87\t479.8\t0\t87\n", "63\t89\t479.8\t0\t89\n", "64\t69\t479.8\t0\t69\n", "65\t101\t479.8\t0\t101\n", "66\t93\t479.8\t0\t93\n", "67\t91\t479.8\t0\t91\n", "68\t129\t479.8\t0\t129\n", "69\t73\t479.8\t0\t73\n", "70\t71\t479.8\t0\t71\n", "71\t74\t479.8\t0\t74\n", "72\t79\t479.8\t0\t79\n", "73\t97\t479.8\t0\t97\n", "74\t101\t479.8\t0\t101\n", "75\t73\t479.8\t0\t73\n", "76\t94\t479.8\t0\t94\n", "77\t90\t479.8\t0\t90\n", "78\t88\t479.8\t0\t88\n", "79\t91\t479.8\t0\t91\n", "80\t87\t479.8\t0\t87\n", "81\t102\t479.8\t0\t102\n", "82\t102\t479.8\t0\t102\n", "83\t103\t479.8\t0\t103\n", "84\t85\t479.8\t0\t85\n", "85\t88\t479.8\t0\t88\n", "86\t88\t479.8\t0\t88\n", "87\t92\t479.8\t0\t92\n", "88\t106\t479.8\t0\t106\n", "89\t88\t479.8\t0\t88\n", "90\t75\t479.8\t0\t75\n", "91\t64\t479.8\t0\t64\n", "92\t59\t479.8\t0\t59\n", "93\t58\t479.8\t0\t58\n", "94\t96\t479.8\t0\t96\n", "95\t82\t479.8\t0\t82\n", "96\t52\t479.8\t0\t52\n", "97\t64\t479.8\t0\t64\n", "98\t107\t479.8\t0\t107\n", "99\t100\t479.8\t0\t100\n", "100\t103\t479.8\t0\t103\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 326_S38_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/326.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 125.66 s (14 us/read; 4.34 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 9,095,747\n", "Reads with adapters: 5,662,449 (62.3%)\n", "Reads written (passing filters): 8,911,376 (98.0%)\n", "\n", "Total basepairs processed: 909,574,700 bp\n", "Quality-trimmed: 2,341,920 bp (0.3%)\n", "Total written (filtered): 710,309,289 bp (78.1%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5488547 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 32.2%\n", " G: 36.0%\n", " T: 31.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t196451\t142121.0\t0\t196451\n", "4\t120988\t35530.3\t0\t120988\n", "5\t93245\t8882.6\t0\t93245\n", "6\t78195\t2220.6\t0\t78195\n", "7\t72861\t555.2\t0\t72861\n", "8\t74627\t138.8\t0\t74627\n", "9\t73099\t138.8\t0\t73099\n", "10\t71350\t138.8\t0\t71350\n", "11\t71046\t138.8\t0\t71046\n", "12\t71935\t138.8\t0\t71935\n", "13\t72074\t138.8\t0\t72074\n", "14\t75795\t138.8\t0\t75795\n", "15\t74986\t138.8\t0\t74986\n", "16\t80066\t138.8\t0\t80066\n", "17\t90636\t138.8\t0\t90636\n", "18\t102034\t138.8\t0\t102034\n", "19\t90552\t138.8\t0\t90552\n", "20\t76910\t138.8\t0\t76910\n", "21\t72212\t138.8\t0\t72212\n", "22\t67487\t138.8\t0\t67487\n", "23\t73747\t138.8\t0\t73747\n", "24\t84528\t138.8\t0\t84528\n", "25\t87352\t138.8\t0\t87352\n", "26\t97567\t138.8\t0\t97567\n", "27\t105593\t138.8\t0\t105593\n", "28\t96770\t138.8\t0\t96770\n", "29\t89150\t138.8\t0\t89150\n", "30\t92056\t138.8\t0\t92056\n", "31\t100986\t138.8\t0\t100986\n", "32\t96091\t138.8\t0\t96091\n", "33\t92399\t138.8\t0\t92399\n", "34\t86130\t138.8\t0\t86130\n", "35\t95741\t138.8\t0\t95741\n", "36\t107982\t138.8\t0\t107982\n", "37\t101744\t138.8\t0\t101744\n", "38\t92471\t138.8\t0\t92471\n", "39\t79916\t138.8\t0\t79916\n", "40\t77427\t138.8\t0\t77427\n", "41\t83153\t138.8\t0\t83153\n", "42\t90201\t138.8\t0\t90201\n", "43\t81507\t138.8\t0\t81507\n", "44\t67418\t138.8\t0\t67418\n", "45\t80655\t138.8\t0\t80655\n", "46\t94256\t138.8\t0\t94256\n", "47\t88562\t138.8\t0\t88562\n", "48\t85124\t138.8\t0\t85124\n", "49\t69567\t138.8\t0\t69567\n", "50\t66499\t138.8\t0\t66499\n", "51\t63150\t138.8\t0\t63150\n", "52\t61407\t138.8\t0\t61407\n", "53\t67303\t138.8\t0\t67303\n", "54\t71420\t138.8\t0\t71420\n", "55\t60224\t138.8\t0\t60224\n", "56\t56972\t138.8\t0\t56972\n", "57\t57642\t138.8\t0\t57642\n", "58\t61538\t138.8\t0\t61538\n", "59\t57249\t138.8\t0\t57249\n", "60\t47308\t138.8\t0\t47308\n", "61\t43749\t138.8\t0\t43749\n", "62\t36579\t138.8\t0\t36579\n", "63\t36605\t138.8\t0\t36605\n", "64\t40082\t138.8\t0\t40082\n", "65\t36403\t138.8\t0\t36403\n", "66\t29231\t138.8\t0\t29231\n", "67\t30594\t138.8\t0\t30594\n", "68\t30179\t138.8\t0\t30179\n", "69\t31081\t138.8\t0\t31081\n", "70\t33501\t138.8\t0\t33501\n", "71\t30857\t138.8\t0\t30857\n", "72\t22959\t138.8\t0\t22959\n", "73\t19221\t138.8\t0\t19221\n", "74\t17771\t138.8\t0\t17771\n", "75\t16152\t138.8\t0\t16152\n", "76\t13456\t138.8\t0\t13456\n", "77\t13820\t138.8\t0\t13820\n", "78\t16155\t138.8\t0\t16155\n", "79\t13959\t138.8\t0\t13959\n", "80\t12508\t138.8\t0\t12508\n", "81\t12200\t138.8\t0\t12200\n", "82\t11864\t138.8\t0\t11864\n", "83\t11534\t138.8\t0\t11534\n", "84\t12919\t138.8\t0\t12919\n", "85\t14877\t138.8\t0\t14877\n", "86\t14186\t138.8\t0\t14186\n", "87\t10452\t138.8\t0\t10452\n", "88\t9242\t138.8\t0\t9242\n", "89\t9028\t138.8\t0\t9028\n", "90\t8987\t138.8\t0\t8987\n", "91\t9027\t138.8\t0\t9027\n", "92\t8706\t138.8\t0\t8706\n", "93\t8278\t138.8\t0\t8278\n", "94\t7682\t138.8\t0\t7682\n", "95\t6298\t138.8\t0\t6298\n", "96\t4670\t138.8\t0\t4670\n", "97\t2988\t138.8\t0\t2988\n", "98\t1931\t138.8\t0\t1931\n", "99\t1851\t138.8\t0\t1851\n", "100\t1611\t138.8\t0\t1611\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 29717 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 52.0%\n", " C: 20.2%\n", " G: 0.0%\n", " T: 27.6%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t14205\t142121.0\t0\t14205\n", "4\t3343\t35530.3\t0\t3343\n", "5\t1054\t8882.6\t0\t1054\n", "6\t454\t2220.6\t0\t454\n", "7\t184\t555.2\t0\t184\n", "8\t142\t138.8\t0\t142\n", "9\t127\t138.8\t0\t127\n", "10\t125\t138.8\t0\t125\n", "11\t105\t138.8\t0\t105\n", "12\t122\t138.8\t0\t122\n", "13\t116\t138.8\t0\t116\n", "14\t119\t138.8\t0\t119\n", "15\t121\t138.8\t0\t121\n", "16\t135\t138.8\t0\t135\n", "17\t104\t138.8\t0\t104\n", "18\t131\t138.8\t0\t131\n", "19\t179\t138.8\t0\t179\n", "20\t221\t138.8\t0\t221\n", "21\t171\t138.8\t0\t171\n", "22\t129\t138.8\t0\t129\n", "23\t120\t138.8\t0\t120\n", "24\t144\t138.8\t0\t144\n", "25\t136\t138.8\t0\t136\n", "26\t184\t138.8\t0\t184\n", "27\t190\t138.8\t0\t190\n", "28\t217\t138.8\t0\t217\n", "29\t284\t138.8\t0\t284\n", "30\t421\t138.8\t0\t421\n", "31\t496\t138.8\t0\t496\n", "32\t652\t138.8\t0\t652\n", "33\t738\t138.8\t0\t738\n", "34\t796\t138.8\t0\t796\n", "35\t870\t138.8\t0\t870\n", "36\t796\t138.8\t0\t796\n", "37\t314\t138.8\t0\t314\n", "38\t69\t138.8\t0\t69\n", "39\t55\t138.8\t0\t55\n", "40\t54\t138.8\t0\t54\n", "41\t74\t138.8\t0\t74\n", "42\t44\t138.8\t0\t44\n", "43\t48\t138.8\t0\t48\n", "44\t55\t138.8\t0\t55\n", "45\t58\t138.8\t0\t58\n", "46\t65\t138.8\t0\t65\n", "47\t48\t138.8\t0\t48\n", "48\t53\t138.8\t0\t53\n", "49\t48\t138.8\t0\t48\n", "50\t46\t138.8\t0\t46\n", "51\t42\t138.8\t0\t42\n", "52\t46\t138.8\t0\t46\n", "53\t36\t138.8\t0\t36\n", "54\t28\t138.8\t0\t28\n", "55\t41\t138.8\t0\t41\n", "56\t28\t138.8\t0\t28\n", "57\t32\t138.8\t0\t32\n", "58\t31\t138.8\t0\t31\n", "59\t30\t138.8\t0\t30\n", "60\t27\t138.8\t0\t27\n", "61\t39\t138.8\t0\t39\n", "62\t26\t138.8\t0\t26\n", "63\t29\t138.8\t0\t29\n", "64\t22\t138.8\t0\t22\n", "65\t22\t138.8\t0\t22\n", "66\t28\t138.8\t0\t28\n", "67\t18\t138.8\t0\t18\n", "68\t21\t138.8\t0\t21\n", "69\t13\t138.8\t0\t13\n", "70\t13\t138.8\t0\t13\n", "71\t17\t138.8\t0\t17\n", "72\t15\t138.8\t0\t15\n", "73\t13\t138.8\t0\t13\n", "74\t13\t138.8\t0\t13\n", "75\t7\t138.8\t0\t7\n", "76\t6\t138.8\t0\t6\n", "77\t6\t138.8\t0\t6\n", "78\t11\t138.8\t0\t11\n", "79\t10\t138.8\t0\t10\n", "80\t11\t138.8\t0\t11\n", "81\t17\t138.8\t0\t17\n", "82\t8\t138.8\t0\t8\n", "83\t9\t138.8\t0\t9\n", "84\t9\t138.8\t0\t9\n", "85\t3\t138.8\t0\t3\n", "86\t17\t138.8\t0\t17\n", "87\t10\t138.8\t0\t10\n", "88\t9\t138.8\t0\t9\n", "89\t9\t138.8\t0\t9\n", "90\t12\t138.8\t0\t12\n", "91\t17\t138.8\t0\t17\n", "92\t27\t138.8\t0\t27\n", "93\t35\t138.8\t0\t35\n", "94\t59\t138.8\t0\t59\n", "95\t79\t138.8\t0\t79\n", "96\t81\t138.8\t0\t81\n", "97\t69\t138.8\t0\t69\n", "98\t57\t138.8\t0\t57\n", "99\t48\t138.8\t0\t48\n", "100\t99\t138.8\t0\t99\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 144185 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.1%\n", " C: 19.4%\n", " G: 16.2%\n", " T: 20.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t101077\t142121.0\t0\t101077\n", "4\t23122\t35530.3\t0\t23122\n", "5\t4235\t8882.6\t0\t4235\n", "6\t469\t2220.6\t0\t469\n", "7\t234\t555.2\t0\t234\n", "8\t264\t555.2\t0\t264\n", "9\t205\t555.2\t0\t205\n", "10\t236\t555.2\t0\t236\n", "11\t256\t555.2\t0\t256\n", "12\t239\t555.2\t0\t239\n", "13\t221\t555.2\t0\t221\n", "14\t283\t555.2\t0\t283\n", "15\t276\t555.2\t0\t276\n", "16\t255\t555.2\t0\t255\n", "17\t272\t555.2\t0\t272\n", "18\t259\t555.2\t0\t259\n", "19\t221\t555.2\t0\t221\n", "20\t251\t555.2\t0\t251\n", "21\t242\t555.2\t0\t242\n", "22\t209\t555.2\t0\t209\n", "23\t197\t555.2\t0\t197\n", "24\t206\t555.2\t0\t206\n", "25\t213\t555.2\t0\t213\n", "26\t221\t555.2\t0\t221\n", "27\t229\t555.2\t0\t229\n", "28\t199\t555.2\t0\t199\n", "29\t196\t555.2\t0\t196\n", "30\t202\t555.2\t0\t202\n", "31\t210\t555.2\t0\t210\n", "32\t226\t555.2\t0\t226\n", "33\t211\t555.2\t0\t211\n", "34\t185\t555.2\t0\t185\n", "35\t201\t555.2\t0\t201\n", "36\t198\t555.2\t0\t198\n", "37\t199\t555.2\t0\t199\n", "38\t203\t555.2\t0\t203\n", "39\t206\t555.2\t0\t206\n", "40\t241\t555.2\t0\t241\n", "41\t183\t555.2\t0\t183\n", "42\t170\t555.2\t0\t170\n", "43\t213\t555.2\t0\t213\n", "44\t109\t555.2\t0\t109\n", "45\t188\t555.2\t0\t188\n", "46\t192\t555.2\t0\t192\n", "47\t124\t555.2\t0\t124\n", "48\t136\t555.2\t0\t136\n", "49\t143\t555.2\t0\t143\n", "50\t106\t555.2\t0\t106\n", "51\t111\t555.2\t0\t111\n", "52\t124\t555.2\t0\t124\n", "53\t153\t555.2\t0\t153\n", "54\t131\t555.2\t0\t131\n", "55\t141\t555.2\t0\t141\n", "56\t109\t555.2\t0\t109\n", "57\t122\t555.2\t0\t122\n", "58\t114\t555.2\t0\t114\n", "59\t83\t555.2\t0\t83\n", "60\t145\t555.2\t0\t145\n", "61\t155\t555.2\t0\t155\n", "62\t112\t555.2\t0\t112\n", "63\t99\t555.2\t0\t99\n", "64\t155\t555.2\t0\t155\n", "65\t98\t555.2\t0\t98\n", "66\t116\t555.2\t0\t116\n", "67\t109\t555.2\t0\t109\n", "68\t111\t555.2\t0\t111\n", "69\t99\t555.2\t0\t99\n", "70\t77\t555.2\t0\t77\n", "71\t99\t555.2\t0\t99\n", "72\t115\t555.2\t0\t115\n", "73\t119\t555.2\t0\t119\n", "74\t148\t555.2\t0\t148\n", "75\t103\t555.2\t0\t103\n", "76\t150\t555.2\t0\t150\n", "77\t160\t555.2\t0\t160\n", "78\t174\t555.2\t0\t174\n", "79\t131\t555.2\t0\t131\n", "80\t162\t555.2\t0\t162\n", "81\t143\t555.2\t0\t143\n", "82\t211\t555.2\t0\t211\n", "83\t199\t555.2\t0\t199\n", "84\t132\t555.2\t0\t132\n", "85\t140\t555.2\t0\t140\n", "86\t106\t555.2\t0\t106\n", "87\t139\t555.2\t0\t139\n", "88\t154\t555.2\t0\t154\n", "89\t114\t555.2\t0\t114\n", "90\t101\t555.2\t0\t101\n", "91\t86\t555.2\t0\t86\n", "92\t64\t555.2\t0\t64\n", "93\t64\t555.2\t0\t64\n", "94\t77\t555.2\t0\t77\n", "95\t58\t555.2\t0\t58\n", "96\t61\t555.2\t0\t61\n", "97\t118\t555.2\t0\t118\n", "98\t103\t555.2\t0\t103\n", "99\t135\t555.2\t0\t135\n", "100\t122\t555.2\t0\t122\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 327_S37_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/327.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 78.00 s (13 us/read; 4.55 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,909,209\n", "Reads with adapters: 3,547,432 (60.0%)\n", "Reads written (passing filters): 5,777,410 (97.8%)\n", "\n", "Total basepairs processed: 590,920,900 bp\n", "Quality-trimmed: 1,447,576 bp (0.2%)\n", "Total written (filtered): 468,527,525 bp (79.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3418069 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.4%\n", " G: 38.4%\n", " T: 28.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t131751\t92331.4\t0\t131751\n", "4\t76774\t23082.8\t0\t76774\n", "5\t58409\t5770.7\t0\t58409\n", "6\t50470\t1442.7\t0\t50470\n", "7\t48328\t360.7\t0\t48328\n", "8\t48051\t90.2\t0\t48051\n", "9\t47515\t90.2\t0\t47515\n", "10\t47001\t90.2\t0\t47001\n", "11\t47872\t90.2\t0\t47872\n", "12\t48363\t90.2\t0\t48363\n", "13\t51275\t90.2\t0\t51275\n", "14\t52114\t90.2\t0\t52114\n", "15\t50789\t90.2\t0\t50789\n", "16\t53714\t90.2\t0\t53714\n", "17\t59243\t90.2\t0\t59243\n", "18\t65030\t90.2\t0\t65030\n", "19\t58240\t90.2\t0\t58240\n", "20\t48353\t90.2\t0\t48353\n", "21\t46662\t90.2\t0\t46662\n", "22\t43143\t90.2\t0\t43143\n", "23\t47105\t90.2\t0\t47105\n", "24\t53939\t90.2\t0\t53939\n", "25\t55773\t90.2\t0\t55773\n", "26\t62881\t90.2\t0\t62881\n", "27\t66036\t90.2\t0\t66036\n", "28\t59440\t90.2\t0\t59440\n", "29\t55369\t90.2\t0\t55369\n", "30\t54487\t90.2\t0\t54487\n", "31\t59866\t90.2\t0\t59866\n", "32\t59615\t90.2\t0\t59615\n", "33\t56783\t90.2\t0\t56783\n", "34\t54285\t90.2\t0\t54285\n", "35\t60121\t90.2\t0\t60121\n", "36\t65308\t90.2\t0\t65308\n", "37\t64172\t90.2\t0\t64172\n", "38\t55225\t90.2\t0\t55225\n", "39\t50670\t90.2\t0\t50670\n", "40\t48452\t90.2\t0\t48452\n", "41\t53823\t90.2\t0\t53823\n", "42\t58163\t90.2\t0\t58163\n", "43\t51492\t90.2\t0\t51492\n", "44\t41573\t90.2\t0\t41573\n", "45\t49479\t90.2\t0\t49479\n", "46\t56410\t90.2\t0\t56410\n", "47\t50283\t90.2\t0\t50283\n", "48\t47895\t90.2\t0\t47895\n", "49\t41000\t90.2\t0\t41000\n", "50\t40269\t90.2\t0\t40269\n", "51\t37251\t90.2\t0\t37251\n", "52\t36393\t90.2\t0\t36393\n", "53\t35057\t90.2\t0\t35057\n", "54\t34254\t90.2\t0\t34254\n", "55\t36338\t90.2\t0\t36338\n", "56\t35556\t90.2\t0\t35556\n", "57\t32312\t90.2\t0\t32312\n", "58\t35095\t90.2\t0\t35095\n", "59\t31385\t90.2\t0\t31385\n", "60\t25804\t90.2\t0\t25804\n", "61\t24200\t90.2\t0\t24200\n", "62\t20593\t90.2\t0\t20593\n", "63\t18829\t90.2\t0\t18829\n", "64\t20532\t90.2\t0\t20532\n", "65\t20329\t90.2\t0\t20329\n", "66\t18206\t90.2\t0\t18206\n", "67\t17921\t90.2\t0\t17921\n", "68\t17052\t90.2\t0\t17052\n", "69\t17642\t90.2\t0\t17642\n", "70\t18145\t90.2\t0\t18145\n", "71\t17182\t90.2\t0\t17182\n", "72\t13654\t90.2\t0\t13654\n", "73\t12556\t90.2\t0\t12556\n", "74\t12137\t90.2\t0\t12137\n", "75\t10635\t90.2\t0\t10635\n", "76\t9232\t90.2\t0\t9232\n", "77\t8258\t90.2\t0\t8258\n", "78\t9104\t90.2\t0\t9104\n", "79\t8580\t90.2\t0\t8580\n", "80\t8504\t90.2\t0\t8504\n", "81\t7741\t90.2\t0\t7741\n", "82\t7500\t90.2\t0\t7500\n", "83\t7757\t90.2\t0\t7757\n", "84\t8648\t90.2\t0\t8648\n", "85\t9391\t90.2\t0\t9391\n", "86\t8993\t90.2\t0\t8993\n", "87\t6722\t90.2\t0\t6722\n", "88\t6277\t90.2\t0\t6277\n", "89\t6199\t90.2\t0\t6199\n", "90\t6570\t90.2\t0\t6570\n", "91\t6869\t90.2\t0\t6869\n", "92\t7111\t90.2\t0\t7111\n", "93\t7472\t90.2\t0\t7472\n", "94\t7200\t90.2\t0\t7200\n", "95\t6111\t90.2\t0\t6111\n", "96\t4584\t90.2\t0\t4584\n", "97\t2847\t90.2\t0\t2847\n", "98\t1778\t90.2\t0\t1778\n", "99\t1413\t90.2\t0\t1413\n", "100\t1139\t90.2\t0\t1139\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28788 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 47.4%\n", " C: 26.7%\n", " G: 0.0%\n", " T: 25.8%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13537\t92331.4\t0\t13537\n", "4\t3152\t23082.8\t0\t3152\n", "5\t1429\t5770.7\t0\t1429\n", "6\t1082\t1442.7\t0\t1082\n", "7\t210\t360.7\t0\t210\n", "8\t160\t90.2\t0\t160\n", "9\t151\t90.2\t0\t151\n", "10\t153\t90.2\t0\t153\n", "11\t119\t90.2\t0\t119\n", "12\t133\t90.2\t0\t133\n", "13\t140\t90.2\t0\t140\n", "14\t113\t90.2\t0\t113\n", "15\t105\t90.2\t0\t105\n", "16\t133\t90.2\t0\t133\n", "17\t116\t90.2\t0\t116\n", "18\t137\t90.2\t0\t137\n", "19\t170\t90.2\t0\t170\n", "20\t214\t90.2\t0\t214\n", "21\t176\t90.2\t0\t176\n", "22\t134\t90.2\t0\t134\n", "23\t118\t90.2\t0\t118\n", "24\t100\t90.2\t0\t100\n", "25\t128\t90.2\t0\t128\n", "26\t186\t90.2\t0\t186\n", "27\t178\t90.2\t0\t178\n", "28\t195\t90.2\t0\t195\n", "29\t190\t90.2\t0\t190\n", "30\t386\t90.2\t0\t386\n", "31\t385\t90.2\t0\t385\n", "32\t537\t90.2\t0\t537\n", "33\t529\t90.2\t0\t529\n", "34\t490\t90.2\t0\t490\n", "35\t636\t90.2\t0\t636\n", "36\t622\t90.2\t0\t622\n", "37\t264\t90.2\t0\t264\n", "38\t62\t90.2\t0\t62\n", "39\t48\t90.2\t0\t48\n", "40\t47\t90.2\t0\t47\n", "41\t64\t90.2\t0\t64\n", "42\t34\t90.2\t0\t34\n", "43\t51\t90.2\t0\t51\n", "44\t48\t90.2\t0\t48\n", "45\t51\t90.2\t0\t51\n", "46\t38\t90.2\t0\t38\n", "47\t39\t90.2\t0\t39\n", "48\t42\t90.2\t0\t42\n", "49\t49\t90.2\t0\t49\n", "50\t45\t90.2\t0\t45\n", "51\t51\t90.2\t0\t51\n", "52\t42\t90.2\t0\t42\n", "53\t46\t90.2\t0\t46\n", "54\t38\t90.2\t0\t38\n", "55\t50\t90.2\t0\t50\n", "56\t21\t90.2\t0\t21\n", "57\t35\t90.2\t0\t35\n", "58\t27\t90.2\t0\t27\n", "59\t23\t90.2\t0\t23\n", "60\t41\t90.2\t0\t41\n", "61\t24\t90.2\t0\t24\n", "62\t32\t90.2\t0\t32\n", "63\t30\t90.2\t0\t30\n", "64\t19\t90.2\t0\t19\n", "65\t27\t90.2\t0\t27\n", "66\t34\t90.2\t0\t34\n", "67\t27\t90.2\t0\t27\n", "68\t24\t90.2\t0\t24\n", "69\t23\t90.2\t0\t23\n", "70\t14\t90.2\t0\t14\n", "71\t16\t90.2\t0\t16\n", "72\t13\t90.2\t0\t13\n", "73\t10\t90.2\t0\t10\n", "74\t11\t90.2\t0\t11\n", "75\t16\t90.2\t0\t16\n", "76\t14\t90.2\t0\t14\n", "77\t13\t90.2\t0\t13\n", "78\t12\t90.2\t0\t12\n", "79\t9\t90.2\t0\t9\n", "80\t13\t90.2\t0\t13\n", "81\t14\t90.2\t0\t14\n", "82\t7\t90.2\t0\t7\n", "83\t8\t90.2\t0\t8\n", "84\t13\t90.2\t0\t13\n", "85\t15\t90.2\t0\t15\n", "86\t12\t90.2\t0\t12\n", "87\t13\t90.2\t0\t13\n", "88\t13\t90.2\t0\t13\n", "89\t22\t90.2\t0\t22\n", "90\t26\t90.2\t0\t26\n", "91\t19\t90.2\t0\t19\n", "92\t29\t90.2\t0\t29\n", "93\t60\t90.2\t0\t60\n", "94\t80\t90.2\t0\t80\n", "95\t88\t90.2\t0\t88\n", "96\t116\t90.2\t0\t116\n", "97\t128\t90.2\t0\t128\n", "98\t75\t90.2\t0\t75\n", "99\t56\t90.2\t0\t56\n", "100\t113\t90.2\t0\t113\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 100575 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.9%\n", " C: 20.0%\n", " G: 18.4%\n", " T: 19.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t71268\t92331.4\t0\t71268\n", "4\t14847\t23082.8\t0\t14847\n", "5\t2420\t5770.7\t0\t2420\n", "6\t391\t1442.7\t0\t391\n", "7\t184\t360.7\t0\t184\n", "8\t193\t360.7\t0\t193\n", "9\t238\t360.7\t0\t238\n", "10\t240\t360.7\t0\t240\n", "11\t205\t360.7\t0\t205\n", "12\t200\t360.7\t0\t200\n", "13\t239\t360.7\t0\t239\n", "14\t202\t360.7\t0\t202\n", "15\t234\t360.7\t0\t234\n", "16\t252\t360.7\t0\t252\n", "17\t239\t360.7\t0\t239\n", "18\t257\t360.7\t0\t257\n", "19\t197\t360.7\t0\t197\n", "20\t224\t360.7\t0\t224\n", "21\t205\t360.7\t0\t205\n", "22\t190\t360.7\t0\t190\n", "23\t183\t360.7\t0\t183\n", "24\t190\t360.7\t0\t190\n", "25\t166\t360.7\t0\t166\n", "26\t169\t360.7\t0\t169\n", "27\t183\t360.7\t0\t183\n", "28\t176\t360.7\t0\t176\n", "29\t201\t360.7\t0\t201\n", "30\t180\t360.7\t0\t180\n", "31\t172\t360.7\t0\t172\n", "32\t194\t360.7\t0\t194\n", "33\t147\t360.7\t0\t147\n", "34\t170\t360.7\t0\t170\n", "35\t146\t360.7\t0\t146\n", "36\t149\t360.7\t0\t149\n", "37\t147\t360.7\t0\t147\n", "38\t134\t360.7\t0\t134\n", "39\t135\t360.7\t0\t135\n", "40\t166\t360.7\t0\t166\n", "41\t142\t360.7\t0\t142\n", "42\t103\t360.7\t0\t103\n", "43\t171\t360.7\t0\t171\n", "44\t75\t360.7\t0\t75\n", "45\t114\t360.7\t0\t114\n", "46\t127\t360.7\t0\t127\n", "47\t121\t360.7\t0\t121\n", "48\t127\t360.7\t0\t127\n", "49\t102\t360.7\t0\t102\n", "50\t93\t360.7\t0\t93\n", "51\t105\t360.7\t0\t105\n", "52\t103\t360.7\t0\t103\n", "53\t106\t360.7\t0\t106\n", "54\t105\t360.7\t0\t105\n", "55\t86\t360.7\t0\t86\n", "56\t99\t360.7\t0\t99\n", "57\t70\t360.7\t0\t70\n", "58\t85\t360.7\t0\t85\n", "59\t55\t360.7\t0\t55\n", "60\t69\t360.7\t0\t69\n", "61\t80\t360.7\t0\t80\n", "62\t71\t360.7\t0\t71\n", "63\t64\t360.7\t0\t64\n", "64\t77\t360.7\t0\t77\n", "65\t59\t360.7\t0\t59\n", "66\t75\t360.7\t0\t75\n", "67\t85\t360.7\t0\t85\n", "68\t83\t360.7\t0\t83\n", "69\t52\t360.7\t0\t52\n", "70\t73\t360.7\t0\t73\n", "71\t68\t360.7\t0\t68\n", "72\t68\t360.7\t0\t68\n", "73\t72\t360.7\t0\t72\n", "74\t98\t360.7\t0\t98\n", "75\t69\t360.7\t0\t69\n", "76\t76\t360.7\t0\t76\n", "77\t85\t360.7\t0\t85\n", "78\t75\t360.7\t0\t75\n", "79\t82\t360.7\t0\t82\n", "80\t109\t360.7\t0\t109\n", "81\t95\t360.7\t0\t95\n", "82\t116\t360.7\t0\t116\n", "83\t97\t360.7\t0\t97\n", "84\t84\t360.7\t0\t84\n", "85\t83\t360.7\t0\t83\n", "86\t88\t360.7\t0\t88\n", "87\t92\t360.7\t0\t92\n", "88\t93\t360.7\t0\t93\n", "89\t74\t360.7\t0\t74\n", "90\t63\t360.7\t0\t63\n", "91\t60\t360.7\t0\t60\n", "92\t45\t360.7\t0\t45\n", "93\t51\t360.7\t0\t51\n", "94\t52\t360.7\t0\t52\n", "95\t73\t360.7\t0\t73\n", "96\t49\t360.7\t0\t49\n", "97\t64\t360.7\t0\t64\n", "98\t85\t360.7\t0\t85\n", "99\t106\t360.7\t0\t106\n", "100\t93\t360.7\t0\t93\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 328_S12_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/328.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 184.26 s (14 us/read; 4.21 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 12,914,260\n", "Reads with adapters: 10,943,351 (84.7%)\n", "Reads written (passing filters): 11,991,890 (92.9%)\n", "\n", "Total basepairs processed: 1,291,426,000 bp\n", "Quality-trimmed: 4,750,013 bp (0.4%)\n", "Total written (filtered): 782,928,679 bp (60.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 10684585 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 37.1%\n", " G: 40.9%\n", " T: 22.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t120567\t201785.3\t0\t120567\n", "4\t86383\t50446.3\t0\t86383\n", "5\t74162\t12611.6\t0\t74162\n", "6\t70406\t3152.9\t0\t70406\n", "7\t71748\t788.2\t0\t71748\n", "8\t74962\t197.1\t0\t74962\n", "9\t77133\t197.1\t0\t77133\n", "10\t77944\t197.1\t0\t77944\n", "11\t80761\t197.1\t0\t80761\n", "12\t83263\t197.1\t0\t83263\n", "13\t86403\t197.1\t0\t86403\n", "14\t91380\t197.1\t0\t91380\n", "15\t91905\t197.1\t0\t91905\n", "16\t99879\t197.1\t0\t99879\n", "17\t113484\t197.1\t0\t113484\n", "18\t133222\t197.1\t0\t133222\n", "19\t120736\t197.1\t0\t120736\n", "20\t101613\t197.1\t0\t101613\n", "21\t100574\t197.1\t0\t100574\n", "22\t94354\t197.1\t0\t94354\n", "23\t106197\t197.1\t0\t106197\n", "24\t122352\t197.1\t0\t122352\n", "25\t129012\t197.1\t0\t129012\n", "26\t149563\t197.1\t0\t149563\n", "27\t163194\t197.1\t0\t163194\n", "28\t143431\t197.1\t0\t143431\n", "29\t135337\t197.1\t0\t135337\n", "30\t138168\t197.1\t0\t138168\n", "31\t160993\t197.1\t0\t160993\n", "32\t155831\t197.1\t0\t155831\n", "33\t156698\t197.1\t0\t156698\n", "34\t146655\t197.1\t0\t146655\n", "35\t174439\t197.1\t0\t174439\n", "36\t192729\t197.1\t0\t192729\n", "37\t173289\t197.1\t0\t173289\n", "38\t165297\t197.1\t0\t165297\n", "39\t149633\t197.1\t0\t149633\n", "40\t147256\t197.1\t0\t147256\n", "41\t169943\t197.1\t0\t169943\n", "42\t190913\t197.1\t0\t190913\n", "43\t170523\t197.1\t0\t170523\n", "44\t134803\t197.1\t0\t134803\n", "45\t175909\t197.1\t0\t175909\n", "46\t212748\t197.1\t0\t212748\n", "47\t194992\t197.1\t0\t194992\n", "48\t193904\t197.1\t0\t193904\n", "49\t159181\t197.1\t0\t159181\n", "50\t158659\t197.1\t0\t158659\n", "51\t144381\t197.1\t0\t144381\n", "52\t163467\t197.1\t0\t163467\n", "53\t171375\t197.1\t0\t171375\n", "54\t163831\t197.1\t0\t163831\n", "55\t169315\t197.1\t0\t169315\n", "56\t164886\t197.1\t0\t164886\n", "57\t162587\t197.1\t0\t162587\n", "58\t185601\t197.1\t0\t185601\n", "59\t158109\t197.1\t0\t158109\n", "60\t127593\t197.1\t0\t127593\n", "61\t129747\t197.1\t0\t129747\n", "62\t106995\t197.1\t0\t106995\n", "63\t100592\t197.1\t0\t100592\n", "64\t122890\t197.1\t0\t122890\n", "65\t122947\t197.1\t0\t122947\n", "66\t101948\t197.1\t0\t101948\n", "67\t105940\t197.1\t0\t105940\n", "68\t105704\t197.1\t0\t105704\n", "69\t111697\t197.1\t0\t111697\n", "70\t116983\t197.1\t0\t116983\n", "71\t114454\t197.1\t0\t114454\n", "72\t86071\t197.1\t0\t86071\n", "73\t81010\t197.1\t0\t81010\n", "74\t84544\t197.1\t0\t84544\n", "75\t73389\t197.1\t0\t73389\n", "76\t59254\t197.1\t0\t59254\n", "77\t54524\t197.1\t0\t54524\n", "78\t67599\t197.1\t0\t67599\n", "79\t60917\t197.1\t0\t60917\n", "80\t58081\t197.1\t0\t58081\n", "81\t54137\t197.1\t0\t54137\n", "82\t51334\t197.1\t0\t51334\n", "83\t53920\t197.1\t0\t53920\n", "84\t63931\t197.1\t0\t63931\n", "85\t73431\t197.1\t0\t73431\n", "86\t67637\t197.1\t0\t67637\n", "87\t38952\t197.1\t0\t38952\n", "88\t33627\t197.1\t0\t33627\n", "89\t41126\t197.1\t0\t41126\n", "90\t47970\t197.1\t0\t47970\n", "91\t52735\t197.1\t0\t52735\n", "92\t56227\t197.1\t0\t56227\n", "93\t63130\t197.1\t0\t63130\n", "94\t53709\t197.1\t0\t53709\n", "95\t43597\t197.1\t0\t43597\n", "96\t32991\t197.1\t0\t32991\n", "97\t20408\t197.1\t0\t20408\n", "98\t11161\t197.1\t0\t11161\n", "99\t18658\t197.1\t0\t18658\n", "100\t6945\t197.1\t0\t6945\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 125545 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 82.5%\n", " C: 7.7%\n", " G: 0.0%\n", " T: 9.8%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10595\t201785.3\t0\t10595\n", "4\t3496\t50446.3\t0\t3496\n", "5\t1901\t12611.6\t0\t1901\n", "6\t1591\t3152.9\t0\t1591\n", "7\t1120\t788.2\t0\t1120\n", "8\t987\t197.1\t0\t987\n", "9\t1043\t197.1\t0\t1043\n", "10\t983\t197.1\t0\t983\n", "11\t818\t197.1\t0\t818\n", "12\t822\t197.1\t0\t822\n", "13\t753\t197.1\t0\t753\n", "14\t749\t197.1\t0\t749\n", "15\t757\t197.1\t0\t757\n", "16\t778\t197.1\t0\t778\n", "17\t878\t197.1\t0\t878\n", "18\t1174\t197.1\t0\t1174\n", "19\t1373\t197.1\t0\t1373\n", "20\t2117\t197.1\t0\t2117\n", "21\t1480\t197.1\t0\t1480\n", "22\t1132\t197.1\t0\t1132\n", "23\t903\t197.1\t0\t903\n", "24\t994\t197.1\t0\t994\n", "25\t1363\t197.1\t0\t1363\n", "26\t2569\t197.1\t0\t2569\n", "27\t2654\t197.1\t0\t2654\n", "28\t3116\t197.1\t0\t3116\n", "29\t3772\t197.1\t0\t3772\n", "30\t6255\t197.1\t0\t6255\n", "31\t7196\t197.1\t0\t7196\n", "32\t9629\t197.1\t0\t9629\n", "33\t9805\t197.1\t0\t9805\n", "34\t10209\t197.1\t0\t10209\n", "35\t12545\t197.1\t0\t12545\n", "36\t13237\t197.1\t0\t13237\n", "37\t4482\t197.1\t0\t4482\n", "38\t160\t197.1\t0\t160\n", "39\t102\t197.1\t0\t102\n", "40\t58\t197.1\t0\t58\n", "41\t50\t197.1\t0\t50\n", "42\t49\t197.1\t0\t49\n", "43\t57\t197.1\t0\t57\n", "44\t51\t197.1\t0\t51\n", "45\t68\t197.1\t0\t68\n", "46\t56\t197.1\t0\t56\n", "47\t58\t197.1\t0\t58\n", "48\t53\t197.1\t0\t53\n", "49\t71\t197.1\t0\t71\n", "50\t60\t197.1\t0\t60\n", "51\t62\t197.1\t0\t62\n", "52\t57\t197.1\t0\t57\n", "53\t80\t197.1\t0\t80\n", "54\t59\t197.1\t0\t59\n", "55\t49\t197.1\t0\t49\n", "56\t41\t197.1\t0\t41\n", "57\t40\t197.1\t0\t40\n", "58\t49\t197.1\t0\t49\n", "59\t33\t197.1\t0\t33\n", "60\t33\t197.1\t0\t33\n", "61\t39\t197.1\t0\t39\n", "62\t33\t197.1\t0\t33\n", "63\t39\t197.1\t0\t39\n", "64\t35\t197.1\t0\t35\n", "65\t22\t197.1\t0\t22\n", "66\t25\t197.1\t0\t25\n", "67\t34\t197.1\t0\t34\n", "68\t22\t197.1\t0\t22\n", "69\t25\t197.1\t0\t25\n", "70\t22\t197.1\t0\t22\n", "71\t20\t197.1\t0\t20\n", "72\t24\t197.1\t0\t24\n", "73\t13\t197.1\t0\t13\n", "74\t17\t197.1\t0\t17\n", "75\t7\t197.1\t0\t7\n", "76\t10\t197.1\t0\t10\n", "77\t7\t197.1\t0\t7\n", "78\t13\t197.1\t0\t13\n", "79\t5\t197.1\t0\t5\n", "80\t8\t197.1\t0\t8\n", "81\t8\t197.1\t0\t8\n", "82\t21\t197.1\t0\t21\n", "83\t10\t197.1\t0\t10\n", "84\t26\t197.1\t0\t26\n", "85\t18\t197.1\t0\t18\n", "86\t19\t197.1\t0\t19\n", "87\t9\t197.1\t0\t9\n", "88\t12\t197.1\t0\t12\n", "89\t7\t197.1\t0\t7\n", "90\t21\t197.1\t0\t21\n", "91\t21\t197.1\t0\t21\n", "92\t11\t197.1\t0\t11\n", "93\t28\t197.1\t0\t28\n", "94\t54\t197.1\t0\t54\n", "95\t28\t197.1\t0\t28\n", "96\t46\t197.1\t0\t46\n", "97\t38\t197.1\t0\t38\n", "98\t29\t197.1\t0\t29\n", "99\t17\t197.1\t0\t17\n", "100\t30\t197.1\t0\t30\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 133221 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.3%\n", " C: 21.6%\n", " G: 18.7%\n", " T: 15.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t61062\t201785.3\t0\t61062\n", "4\t12304\t50446.3\t0\t12304\n", "5\t2891\t12611.6\t0\t2891\n", "6\t1246\t3152.9\t0\t1246\n", "7\t1052\t788.2\t0\t1052\n", "8\t1097\t788.2\t0\t1097\n", "9\t1067\t788.2\t0\t1067\n", "10\t1063\t788.2\t0\t1063\n", "11\t1097\t788.2\t0\t1097\n", "12\t1095\t788.2\t0\t1095\n", "13\t1200\t788.2\t0\t1200\n", "14\t1106\t788.2\t0\t1106\n", "15\t1358\t788.2\t0\t1358\n", "16\t1262\t788.2\t0\t1262\n", "17\t1291\t788.2\t0\t1291\n", "18\t1273\t788.2\t0\t1273\n", "19\t1171\t788.2\t0\t1171\n", "20\t1235\t788.2\t0\t1235\n", "21\t1151\t788.2\t0\t1151\n", "22\t1132\t788.2\t0\t1132\n", "23\t1139\t788.2\t0\t1139\n", "24\t1044\t788.2\t0\t1044\n", "25\t1100\t788.2\t0\t1100\n", "26\t1032\t788.2\t0\t1032\n", "27\t1050\t788.2\t0\t1050\n", "28\t1025\t788.2\t0\t1025\n", "29\t976\t788.2\t0\t976\n", "30\t1071\t788.2\t0\t1071\n", "31\t991\t788.2\t0\t991\n", "32\t1066\t788.2\t0\t1066\n", "33\t1030\t788.2\t0\t1030\n", "34\t1053\t788.2\t0\t1053\n", "35\t1091\t788.2\t0\t1091\n", "36\t939\t788.2\t0\t939\n", "37\t952\t788.2\t0\t952\n", "38\t959\t788.2\t0\t959\n", "39\t948\t788.2\t0\t948\n", "40\t894\t788.2\t0\t894\n", "41\t924\t788.2\t0\t924\n", "42\t738\t788.2\t0\t738\n", "43\t1338\t788.2\t0\t1338\n", "44\t249\t788.2\t0\t249\n", "45\t755\t788.2\t0\t755\n", "46\t722\t788.2\t0\t722\n", "47\t685\t788.2\t0\t685\n", "48\t642\t788.2\t0\t642\n", "49\t661\t788.2\t0\t661\n", "50\t608\t788.2\t0\t608\n", "51\t629\t788.2\t0\t629\n", "52\t627\t788.2\t0\t627\n", "53\t609\t788.2\t0\t609\n", "54\t550\t788.2\t0\t550\n", "55\t584\t788.2\t0\t584\n", "56\t575\t788.2\t0\t575\n", "57\t394\t788.2\t0\t394\n", "58\t551\t788.2\t0\t551\n", "59\t344\t788.2\t0\t344\n", "60\t412\t788.2\t0\t412\n", "61\t382\t788.2\t0\t382\n", "62\t389\t788.2\t0\t389\n", "63\t257\t788.2\t0\t257\n", "64\t309\t788.2\t0\t309\n", "65\t303\t788.2\t0\t303\n", "66\t341\t788.2\t0\t341\n", "67\t314\t788.2\t0\t314\n", "68\t428\t788.2\t0\t428\n", "69\t102\t788.2\t0\t102\n", "70\t92\t788.2\t0\t92\n", "71\t206\t788.2\t0\t206\n", "72\t195\t788.2\t0\t195\n", "73\t177\t788.2\t0\t177\n", "74\t183\t788.2\t0\t183\n", "75\t128\t788.2\t0\t128\n", "76\t117\t788.2\t0\t117\n", "77\t119\t788.2\t0\t119\n", "78\t109\t788.2\t0\t109\n", "79\t93\t788.2\t0\t93\n", "80\t113\t788.2\t0\t113\n", "81\t117\t788.2\t0\t117\n", "82\t149\t788.2\t0\t149\n", "83\t124\t788.2\t0\t124\n", "84\t128\t788.2\t0\t128\n", "85\t114\t788.2\t0\t114\n", "86\t99\t788.2\t0\t99\n", "87\t94\t788.2\t0\t94\n", "88\t135\t788.2\t0\t135\n", "89\t117\t788.2\t0\t117\n", "90\t81\t788.2\t0\t81\n", "91\t65\t788.2\t0\t65\n", "92\t55\t788.2\t0\t55\n", "93\t45\t788.2\t0\t45\n", "94\t75\t788.2\t0\t75\n", "95\t38\t788.2\t0\t38\n", "96\t47\t788.2\t0\t47\n", "97\t67\t788.2\t0\t67\n", "98\t55\t788.2\t0\t55\n", "99\t88\t788.2\t0\t88\n", "100\t61\t788.2\t0\t61\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 329_S46_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/329.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 111.87 s (13 us/read; 4.58 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,534,119\n", "Reads with adapters: 4,129,947 (48.4%)\n", "Reads written (passing filters): 8,346,864 (97.8%)\n", "\n", "Total basepairs processed: 853,411,900 bp\n", "Quality-trimmed: 2,015,777 bp (0.2%)\n", "Total written (filtered): 718,034,045 bp (84.1%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3924359 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.6%\n", " G: 38.2%\n", " T: 31.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t210170\t133345.6\t0\t210170\n", "4\t119452\t33336.4\t0\t119452\n", "5\t84948\t8334.1\t0\t84948\n", "6\t70374\t2083.5\t0\t70374\n", "7\t60816\t520.9\t0\t60816\n", "8\t58056\t130.2\t0\t58056\n", "9\t58175\t130.2\t0\t58175\n", "10\t57930\t130.2\t0\t57930\n", "11\t57961\t130.2\t0\t57961\n", "12\t59188\t130.2\t0\t59188\n", "13\t64494\t130.2\t0\t64494\n", "14\t64195\t130.2\t0\t64195\n", "15\t61030\t130.2\t0\t61030\n", "16\t64390\t130.2\t0\t64390\n", "17\t69250\t130.2\t0\t69250\n", "18\t77559\t130.2\t0\t77559\n", "19\t66659\t130.2\t0\t66659\n", "20\t55698\t130.2\t0\t55698\n", "21\t53294\t130.2\t0\t53294\n", "22\t50766\t130.2\t0\t50766\n", "23\t54881\t130.2\t0\t54881\n", "24\t62386\t130.2\t0\t62386\n", "25\t64000\t130.2\t0\t64000\n", "26\t70433\t130.2\t0\t70433\n", "27\t73076\t130.2\t0\t73076\n", "28\t65032\t130.2\t0\t65032\n", "29\t59399\t130.2\t0\t59399\n", "30\t58500\t130.2\t0\t58500\n", "31\t63904\t130.2\t0\t63904\n", "32\t63882\t130.2\t0\t63882\n", "33\t59745\t130.2\t0\t59745\n", "34\t57182\t130.2\t0\t57182\n", "35\t64002\t130.2\t0\t64002\n", "36\t70644\t130.2\t0\t70644\n", "37\t71481\t130.2\t0\t71481\n", "38\t58793\t130.2\t0\t58793\n", "39\t53155\t130.2\t0\t53155\n", "40\t51606\t130.2\t0\t51606\n", "41\t59582\t130.2\t0\t59582\n", "42\t67712\t130.2\t0\t67712\n", "43\t56333\t130.2\t0\t56333\n", "44\t44076\t130.2\t0\t44076\n", "45\t52026\t130.2\t0\t52026\n", "46\t63304\t130.2\t0\t63304\n", "47\t60953\t130.2\t0\t60953\n", "48\t51792\t130.2\t0\t51792\n", "49\t42975\t130.2\t0\t42975\n", "50\t41078\t130.2\t0\t41078\n", "51\t39709\t130.2\t0\t39709\n", "52\t37406\t130.2\t0\t37406\n", "53\t32259\t130.2\t0\t32259\n", "54\t32080\t130.2\t0\t32080\n", "55\t36506\t130.2\t0\t36506\n", "56\t36101\t130.2\t0\t36101\n", "57\t32983\t130.2\t0\t32983\n", "58\t31530\t130.2\t0\t31530\n", "59\t27357\t130.2\t0\t27357\n", "60\t24660\t130.2\t0\t24660\n", "61\t23343\t130.2\t0\t23343\n", "62\t20143\t130.2\t0\t20143\n", "63\t18736\t130.2\t0\t18736\n", "64\t19828\t130.2\t0\t19828\n", "65\t19368\t130.2\t0\t19368\n", "66\t17498\t130.2\t0\t17498\n", "67\t17618\t130.2\t0\t17618\n", "68\t17173\t130.2\t0\t17173\n", "69\t16890\t130.2\t0\t16890\n", "70\t17665\t130.2\t0\t17665\n", "71\t17246\t130.2\t0\t17246\n", "72\t13619\t130.2\t0\t13619\n", "73\t11916\t130.2\t0\t11916\n", "74\t12049\t130.2\t0\t12049\n", "75\t11099\t130.2\t0\t11099\n", "76\t10056\t130.2\t0\t10056\n", "77\t9524\t130.2\t0\t9524\n", "78\t10361\t130.2\t0\t10361\n", "79\t10067\t130.2\t0\t10067\n", "80\t10028\t130.2\t0\t10028\n", "81\t10163\t130.2\t0\t10163\n", "82\t10034\t130.2\t0\t10034\n", "83\t10391\t130.2\t0\t10391\n", "84\t11587\t130.2\t0\t11587\n", "85\t12206\t130.2\t0\t12206\n", "86\t12211\t130.2\t0\t12211\n", "87\t10488\t130.2\t0\t10488\n", "88\t10761\t130.2\t0\t10761\n", "89\t10151\t130.2\t0\t10151\n", "90\t9630\t130.2\t0\t9630\n", "91\t9225\t130.2\t0\t9225\n", "92\t9081\t130.2\t0\t9081\n", "93\t9288\t130.2\t0\t9288\n", "94\t8170\t130.2\t0\t8170\n", "95\t7043\t130.2\t0\t7043\n", "96\t5081\t130.2\t0\t5081\n", "97\t3216\t130.2\t0\t3216\n", "98\t1924\t130.2\t0\t1924\n", "99\t1534\t130.2\t0\t1534\n", "100\t1020\t130.2\t0\t1020\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 47433 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 50.4%\n", " C: 23.4%\n", " G: 0.0%\n", " T: 26.0%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t20435\t133345.6\t0\t20435\n", "4\t5205\t33336.4\t0\t5205\n", "5\t1921\t8334.1\t0\t1921\n", "6\t660\t2083.5\t0\t660\n", "7\t118\t520.9\t0\t118\n", "8\t100\t130.2\t0\t100\n", "9\t92\t130.2\t0\t92\n", "10\t83\t130.2\t0\t83\n", "11\t81\t130.2\t0\t81\n", "12\t83\t130.2\t0\t83\n", "13\t83\t130.2\t0\t83\n", "14\t81\t130.2\t0\t81\n", "15\t119\t130.2\t0\t119\n", "16\t88\t130.2\t0\t88\n", "17\t94\t130.2\t0\t94\n", "18\t120\t130.2\t0\t120\n", "19\t131\t130.2\t0\t131\n", "20\t187\t130.2\t0\t187\n", "21\t160\t130.2\t0\t160\n", "22\t114\t130.2\t0\t114\n", "23\t115\t130.2\t0\t115\n", "24\t109\t130.2\t0\t109\n", "25\t119\t130.2\t0\t119\n", "26\t167\t130.2\t0\t167\n", "27\t225\t130.2\t0\t225\n", "28\t227\t130.2\t0\t227\n", "29\t307\t130.2\t0\t307\n", "30\t606\t130.2\t0\t606\n", "31\t763\t130.2\t0\t763\n", "32\t1251\t130.2\t0\t1251\n", "33\t1396\t130.2\t0\t1396\n", "34\t1592\t130.2\t0\t1592\n", "35\t2032\t130.2\t0\t2032\n", "36\t2080\t130.2\t0\t2080\n", "37\t1131\t130.2\t0\t1131\n", "38\t157\t130.2\t0\t157\n", "39\t138\t130.2\t0\t138\n", "40\t78\t130.2\t0\t78\n", "41\t76\t130.2\t0\t76\n", "42\t73\t130.2\t0\t73\n", "43\t54\t130.2\t0\t54\n", "44\t67\t130.2\t0\t67\n", "45\t87\t130.2\t0\t87\n", "46\t71\t130.2\t0\t71\n", "47\t49\t130.2\t0\t49\n", "48\t60\t130.2\t0\t60\n", "49\t43\t130.2\t0\t43\n", "50\t64\t130.2\t0\t64\n", "51\t72\t130.2\t0\t72\n", "52\t63\t130.2\t0\t63\n", "53\t59\t130.2\t0\t59\n", "54\t54\t130.2\t0\t54\n", "55\t59\t130.2\t0\t59\n", "56\t43\t130.2\t0\t43\n", "57\t36\t130.2\t0\t36\n", "58\t63\t130.2\t0\t63\n", "59\t43\t130.2\t0\t43\n", "60\t51\t130.2\t0\t51\n", "61\t39\t130.2\t0\t39\n", "62\t38\t130.2\t0\t38\n", "63\t41\t130.2\t0\t41\n", "64\t45\t130.2\t0\t45\n", "65\t36\t130.2\t0\t36\n", "66\t41\t130.2\t0\t41\n", "67\t25\t130.2\t0\t25\n", "68\t36\t130.2\t0\t36\n", "69\t48\t130.2\t0\t48\n", "70\t39\t130.2\t0\t39\n", "71\t44\t130.2\t0\t44\n", "72\t35\t130.2\t0\t35\n", "73\t29\t130.2\t0\t29\n", "74\t27\t130.2\t0\t27\n", "75\t40\t130.2\t0\t40\n", "76\t44\t130.2\t0\t44\n", "77\t39\t130.2\t0\t39\n", "78\t33\t130.2\t0\t33\n", "79\t40\t130.2\t0\t40\n", "80\t29\t130.2\t0\t29\n", "81\t36\t130.2\t0\t36\n", "82\t30\t130.2\t0\t30\n", "83\t49\t130.2\t0\t49\n", "84\t43\t130.2\t0\t43\n", "85\t40\t130.2\t0\t40\n", "86\t53\t130.2\t0\t53\n", "87\t48\t130.2\t0\t48\n", "88\t54\t130.2\t0\t54\n", "89\t62\t130.2\t0\t62\n", "90\t64\t130.2\t0\t64\n", "91\t109\t130.2\t0\t109\n", "92\t126\t130.2\t0\t126\n", "93\t188\t130.2\t0\t188\n", "94\t261\t130.2\t0\t261\n", "95\t311\t130.2\t0\t311\n", "96\t373\t130.2\t0\t373\n", "97\t348\t130.2\t0\t348\n", "98\t259\t130.2\t0\t259\n", "99\t194\t130.2\t0\t194\n", "100\t402\t130.2\t0\t402\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 158155 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.0%\n", " C: 20.9%\n", " G: 17.9%\n", " T: 21.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t119157\t133345.6\t0\t119157\n", "4\t25989\t33336.4\t0\t25989\n", "5\t3717\t8334.1\t0\t3717\n", "6\t357\t2083.5\t0\t357\n", "7\t92\t520.9\t0\t92\n", "8\t105\t520.9\t0\t105\n", "9\t114\t520.9\t0\t114\n", "10\t113\t520.9\t0\t113\n", "11\t84\t520.9\t0\t84\n", "12\t117\t520.9\t0\t117\n", "13\t117\t520.9\t0\t117\n", "14\t100\t520.9\t0\t100\n", "15\t128\t520.9\t0\t128\n", "16\t106\t520.9\t0\t106\n", "17\t103\t520.9\t0\t103\n", "18\t109\t520.9\t0\t109\n", "19\t114\t520.9\t0\t114\n", "20\t99\t520.9\t0\t99\n", "21\t90\t520.9\t0\t90\n", "22\t94\t520.9\t0\t94\n", "23\t85\t520.9\t0\t85\n", "24\t72\t520.9\t0\t72\n", "25\t84\t520.9\t0\t84\n", "26\t95\t520.9\t0\t95\n", "27\t98\t520.9\t0\t98\n", "28\t107\t520.9\t0\t107\n", "29\t109\t520.9\t0\t109\n", "30\t127\t520.9\t0\t127\n", "31\t108\t520.9\t0\t108\n", "32\t136\t520.9\t0\t136\n", "33\t134\t520.9\t0\t134\n", "34\t108\t520.9\t0\t108\n", "35\t124\t520.9\t0\t124\n", "36\t89\t520.9\t0\t89\n", "37\t94\t520.9\t0\t94\n", "38\t75\t520.9\t0\t75\n", "39\t130\t520.9\t0\t130\n", "40\t107\t520.9\t0\t107\n", "41\t81\t520.9\t0\t81\n", "42\t79\t520.9\t0\t79\n", "43\t82\t520.9\t0\t82\n", "44\t113\t520.9\t0\t113\n", "45\t98\t520.9\t0\t98\n", "46\t92\t520.9\t0\t92\n", "47\t132\t520.9\t0\t132\n", "48\t115\t520.9\t0\t115\n", "49\t107\t520.9\t0\t107\n", "50\t111\t520.9\t0\t111\n", "51\t89\t520.9\t0\t89\n", "52\t82\t520.9\t0\t82\n", "53\t84\t520.9\t0\t84\n", "54\t79\t520.9\t0\t79\n", "55\t66\t520.9\t0\t66\n", "56\t80\t520.9\t0\t80\n", "57\t55\t520.9\t0\t55\n", "58\t74\t520.9\t0\t74\n", "59\t73\t520.9\t0\t73\n", "60\t64\t520.9\t0\t64\n", "61\t72\t520.9\t0\t72\n", "62\t77\t520.9\t0\t77\n", "63\t80\t520.9\t0\t80\n", "64\t53\t520.9\t0\t53\n", "65\t87\t520.9\t0\t87\n", "66\t79\t520.9\t0\t79\n", "67\t67\t520.9\t0\t67\n", "68\t83\t520.9\t0\t83\n", "69\t55\t520.9\t0\t55\n", "70\t72\t520.9\t0\t72\n", "71\t62\t520.9\t0\t62\n", "72\t77\t520.9\t0\t77\n", "73\t67\t520.9\t0\t67\n", "74\t95\t520.9\t0\t95\n", "75\t82\t520.9\t0\t82\n", "76\t91\t520.9\t0\t91\n", "77\t75\t520.9\t0\t75\n", "78\t84\t520.9\t0\t84\n", "79\t83\t520.9\t0\t83\n", "80\t83\t520.9\t0\t83\n", "81\t90\t520.9\t0\t90\n", "82\t104\t520.9\t0\t104\n", "83\t112\t520.9\t0\t112\n", "84\t187\t520.9\t0\t187\n", "85\t147\t520.9\t0\t147\n", "86\t110\t520.9\t0\t110\n", "87\t128\t520.9\t0\t128\n", "88\t141\t520.9\t0\t141\n", "89\t111\t520.9\t0\t111\n", "90\t107\t520.9\t0\t107\n", "91\t81\t520.9\t0\t81\n", "92\t48\t520.9\t0\t48\n", "93\t63\t520.9\t0\t63\n", "94\t86\t520.9\t0\t86\n", "95\t62\t520.9\t0\t62\n", "96\t67\t520.9\t0\t67\n", "97\t84\t520.9\t0\t84\n", "98\t95\t520.9\t0\t95\n", "99\t138\t520.9\t0\t138\n", "100\t127\t520.9\t0\t127\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 331_S53_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/331.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 91.09 s (13 us/read; 4.52 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,864,652\n", "Reads with adapters: 4,221,585 (61.5%)\n", "Reads written (passing filters): 6,491,194 (94.6%)\n", "\n", "Total basepairs processed: 686,465,200 bp\n", "Quality-trimmed: 1,808,516 bp (0.3%)\n", "Total written (filtered): 512,994,108 bp (74.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4036078 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.6%\n", " G: 47.7%\n", " T: 22.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t134462\t107260.2\t0\t134462\n", "4\t74539\t26815.0\t0\t74539\n", "5\t57838\t6703.8\t0\t57838\n", "6\t47323\t1675.9\t0\t47323\n", "7\t43759\t419.0\t0\t43759\n", "8\t41367\t104.7\t0\t41367\n", "9\t42497\t104.7\t0\t42497\n", "10\t43957\t104.7\t0\t43957\n", "11\t43563\t104.7\t0\t43563\n", "12\t45313\t104.7\t0\t45313\n", "13\t63358\t104.7\t0\t63358\n", "14\t61977\t104.7\t0\t61977\n", "15\t51433\t104.7\t0\t51433\n", "16\t56291\t104.7\t0\t56291\n", "17\t57516\t104.7\t0\t57516\n", "18\t65893\t104.7\t0\t65893\n", "19\t52865\t104.7\t0\t52865\n", "20\t42503\t104.7\t0\t42503\n", "21\t41172\t104.7\t0\t41172\n", "22\t40058\t104.7\t0\t40058\n", "23\t43207\t104.7\t0\t43207\n", "24\t49550\t104.7\t0\t49550\n", "25\t52021\t104.7\t0\t52021\n", "26\t58519\t104.7\t0\t58519\n", "27\t61592\t104.7\t0\t61592\n", "28\t57582\t104.7\t0\t57582\n", "29\t53688\t104.7\t0\t53688\n", "30\t55183\t104.7\t0\t55183\n", "31\t62591\t104.7\t0\t62591\n", "32\t61959\t104.7\t0\t61959\n", "33\t59226\t104.7\t0\t59226\n", "34\t58330\t104.7\t0\t58330\n", "35\t63132\t104.7\t0\t63132\n", "36\t72730\t104.7\t0\t72730\n", "37\t77036\t104.7\t0\t77036\n", "38\t61476\t104.7\t0\t61476\n", "39\t53595\t104.7\t0\t53595\n", "40\t52948\t104.7\t0\t52948\n", "41\t65197\t104.7\t0\t65197\n", "42\t77483\t104.7\t0\t77483\n", "43\t64375\t104.7\t0\t64375\n", "44\t46324\t104.7\t0\t46324\n", "45\t55550\t104.7\t0\t55550\n", "46\t63628\t104.7\t0\t63628\n", "47\t56503\t104.7\t0\t56503\n", "48\t53080\t104.7\t0\t53080\n", "49\t46498\t104.7\t0\t46498\n", "50\t44838\t104.7\t0\t44838\n", "51\t37034\t104.7\t0\t37034\n", "52\t41671\t104.7\t0\t41671\n", "53\t42499\t104.7\t0\t42499\n", "54\t39655\t104.7\t0\t39655\n", "55\t39210\t104.7\t0\t39210\n", "56\t38994\t104.7\t0\t38994\n", "57\t40052\t104.7\t0\t40052\n", "58\t43358\t104.7\t0\t43358\n", "59\t34388\t104.7\t0\t34388\n", "60\t30683\t104.7\t0\t30683\n", "61\t29245\t104.7\t0\t29245\n", "62\t25219\t104.7\t0\t25219\n", "63\t23635\t104.7\t0\t23635\n", "64\t26612\t104.7\t0\t26612\n", "65\t26891\t104.7\t0\t26891\n", "66\t25625\t104.7\t0\t25625\n", "67\t28180\t104.7\t0\t28180\n", "68\t30620\t104.7\t0\t30620\n", "69\t35411\t104.7\t0\t35411\n", "70\t43930\t104.7\t0\t43930\n", "71\t46572\t104.7\t0\t46572\n", "72\t31229\t104.7\t0\t31229\n", "73\t27037\t104.7\t0\t27037\n", "74\t27893\t104.7\t0\t27893\n", "75\t24709\t104.7\t0\t24709\n", "76\t20671\t104.7\t0\t20671\n", "77\t19919\t104.7\t0\t19919\n", "78\t22137\t104.7\t0\t22137\n", "79\t21501\t104.7\t0\t21501\n", "80\t21144\t104.7\t0\t21144\n", "81\t20173\t104.7\t0\t20173\n", "82\t17943\t104.7\t0\t17943\n", "83\t18578\t104.7\t0\t18578\n", "84\t22448\t104.7\t0\t22448\n", "85\t26266\t104.7\t0\t26266\n", "86\t25682\t104.7\t0\t25682\n", "87\t17940\t104.7\t0\t17940\n", "88\t16961\t104.7\t0\t16961\n", "89\t17664\t104.7\t0\t17664\n", "90\t18984\t104.7\t0\t18984\n", "91\t21138\t104.7\t0\t21138\n", "92\t24072\t104.7\t0\t24072\n", "93\t24990\t104.7\t0\t24990\n", "94\t24887\t104.7\t0\t24887\n", "95\t20524\t104.7\t0\t20524\n", "96\t14571\t104.7\t0\t14571\n", "97\t9605\t104.7\t0\t9605\n", "98\t4950\t104.7\t0\t4950\n", "99\t4671\t104.7\t0\t4671\n", "100\t2782\t104.7\t0\t2782\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 100211 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 69.6%\n", " C: 18.0%\n", " G: 0.0%\n", " T: 12.3%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t20251\t107260.2\t0\t20251\n", "4\t4819\t26815.0\t0\t4819\n", "5\t2852\t6703.8\t0\t2852\n", "6\t1912\t1675.9\t0\t1912\n", "7\t126\t419.0\t0\t126\n", "8\t120\t104.7\t0\t120\n", "9\t133\t104.7\t0\t133\n", "10\t118\t104.7\t0\t118\n", "11\t132\t104.7\t0\t132\n", "12\t129\t104.7\t0\t129\n", "13\t119\t104.7\t0\t119\n", "14\t142\t104.7\t0\t142\n", "15\t139\t104.7\t0\t139\n", "16\t175\t104.7\t0\t175\n", "17\t181\t104.7\t0\t181\n", "18\t312\t104.7\t0\t312\n", "19\t472\t104.7\t0\t472\n", "20\t796\t104.7\t0\t796\n", "21\t563\t104.7\t0\t563\n", "22\t427\t104.7\t0\t427\n", "23\t325\t104.7\t0\t325\n", "24\t347\t104.7\t0\t347\n", "25\t425\t104.7\t0\t425\n", "26\t767\t104.7\t0\t767\n", "27\t882\t104.7\t0\t882\n", "28\t1142\t104.7\t0\t1142\n", "29\t1766\t104.7\t0\t1766\n", "30\t3497\t104.7\t0\t3497\n", "31\t4364\t104.7\t0\t4364\n", "32\t6665\t104.7\t0\t6665\n", "33\t7537\t104.7\t0\t7537\n", "34\t8516\t104.7\t0\t8516\n", "35\t10666\t104.7\t0\t10666\n", "36\t10989\t104.7\t0\t10989\n", "37\t5290\t104.7\t0\t5290\n", "38\t257\t104.7\t0\t257\n", "39\t158\t104.7\t0\t158\n", "40\t40\t104.7\t0\t40\n", "41\t40\t104.7\t0\t40\n", "42\t28\t104.7\t0\t28\n", "43\t34\t104.7\t0\t34\n", "44\t42\t104.7\t0\t42\n", "45\t61\t104.7\t0\t61\n", "46\t50\t104.7\t0\t50\n", "47\t37\t104.7\t0\t37\n", "48\t22\t104.7\t0\t22\n", "49\t22\t104.7\t0\t22\n", "50\t30\t104.7\t0\t30\n", "51\t42\t104.7\t0\t42\n", "52\t37\t104.7\t0\t37\n", "53\t36\t104.7\t0\t36\n", "54\t26\t104.7\t0\t26\n", "55\t31\t104.7\t0\t31\n", "56\t26\t104.7\t0\t26\n", "57\t24\t104.7\t0\t24\n", "58\t26\t104.7\t0\t26\n", "59\t25\t104.7\t0\t25\n", "60\t21\t104.7\t0\t21\n", "61\t36\t104.7\t0\t36\n", "62\t32\t104.7\t0\t32\n", "63\t28\t104.7\t0\t28\n", "64\t30\t104.7\t0\t30\n", "65\t21\t104.7\t0\t21\n", "66\t29\t104.7\t0\t29\n", "67\t21\t104.7\t0\t21\n", "68\t27\t104.7\t0\t27\n", "69\t13\t104.7\t0\t13\n", "70\t15\t104.7\t0\t15\n", "71\t16\t104.7\t0\t16\n", "72\t29\t104.7\t0\t29\n", "73\t14\t104.7\t0\t14\n", "74\t13\t104.7\t0\t13\n", "75\t11\t104.7\t0\t11\n", "76\t10\t104.7\t0\t10\n", "77\t9\t104.7\t0\t9\n", "78\t18\t104.7\t0\t18\n", "79\t11\t104.7\t0\t11\n", "80\t16\t104.7\t0\t16\n", "81\t17\t104.7\t0\t17\n", "82\t11\t104.7\t0\t11\n", "83\t14\t104.7\t0\t14\n", "84\t18\t104.7\t0\t18\n", "85\t28\t104.7\t0\t28\n", "86\t15\t104.7\t0\t15\n", "87\t23\t104.7\t0\t23\n", "88\t23\t104.7\t0\t23\n", "89\t22\t104.7\t0\t22\n", "90\t21\t104.7\t0\t21\n", "91\t47\t104.7\t0\t47\n", "92\t57\t104.7\t0\t57\n", "93\t98\t104.7\t0\t98\n", "94\t155\t104.7\t0\t155\n", "95\t168\t104.7\t0\t168\n", "96\t202\t104.7\t0\t202\n", "97\t220\t104.7\t0\t220\n", "98\t150\t104.7\t0\t150\n", "99\t104\t104.7\t0\t104\n", "100\t208\t104.7\t0\t208\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 85296 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.3%\n", " C: 18.9%\n", " G: 19.2%\n", " T: 22.5%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t61889\t107260.2\t0\t61889\n", "4\t13264\t26815.0\t0\t13264\n", "5\t1812\t6703.8\t0\t1812\n", "6\t239\t1675.9\t0\t239\n", "7\t88\t419.0\t0\t88\n", "8\t109\t419.0\t0\t109\n", "9\t88\t419.0\t0\t88\n", "10\t81\t419.0\t0\t81\n", "11\t105\t419.0\t0\t105\n", "12\t118\t419.0\t0\t118\n", "13\t131\t419.0\t0\t131\n", "14\t138\t419.0\t0\t138\n", "15\t143\t419.0\t0\t143\n", "16\t132\t419.0\t0\t132\n", "17\t200\t419.0\t0\t200\n", "18\t191\t419.0\t0\t191\n", "19\t154\t419.0\t0\t154\n", "20\t166\t419.0\t0\t166\n", "21\t133\t419.0\t0\t133\n", "22\t122\t419.0\t0\t122\n", "23\t89\t419.0\t0\t89\n", "24\t92\t419.0\t0\t92\n", "25\t103\t419.0\t0\t103\n", "26\t106\t419.0\t0\t106\n", "27\t137\t419.0\t0\t137\n", "28\t126\t419.0\t0\t126\n", "29\t122\t419.0\t0\t122\n", "30\t120\t419.0\t0\t120\n", "31\t95\t419.0\t0\t95\n", "32\t119\t419.0\t0\t119\n", "33\t86\t419.0\t0\t86\n", "34\t112\t419.0\t0\t112\n", "35\t83\t419.0\t0\t83\n", "36\t89\t419.0\t0\t89\n", "37\t54\t419.0\t0\t54\n", "38\t61\t419.0\t0\t61\n", "39\t97\t419.0\t0\t97\n", "40\t74\t419.0\t0\t74\n", "41\t64\t419.0\t0\t64\n", "42\t61\t419.0\t0\t61\n", "43\t77\t419.0\t0\t77\n", "44\t34\t419.0\t0\t34\n", "45\t44\t419.0\t0\t44\n", "46\t65\t419.0\t0\t65\n", "47\t55\t419.0\t0\t55\n", "48\t65\t419.0\t0\t65\n", "49\t53\t419.0\t0\t53\n", "50\t60\t419.0\t0\t60\n", "51\t64\t419.0\t0\t64\n", "52\t73\t419.0\t0\t73\n", "53\t95\t419.0\t0\t95\n", "54\t121\t419.0\t0\t121\n", "55\t82\t419.0\t0\t82\n", "56\t75\t419.0\t0\t75\n", "57\t117\t419.0\t0\t117\n", "58\t133\t419.0\t0\t133\n", "59\t98\t419.0\t0\t98\n", "60\t96\t419.0\t0\t96\n", "61\t105\t419.0\t0\t105\n", "62\t94\t419.0\t0\t94\n", "63\t66\t419.0\t0\t66\n", "64\t81\t419.0\t0\t81\n", "65\t83\t419.0\t0\t83\n", "66\t60\t419.0\t0\t60\n", "67\t73\t419.0\t0\t73\n", "68\t74\t419.0\t0\t74\n", "69\t59\t419.0\t0\t59\n", "70\t52\t419.0\t0\t52\n", "71\t55\t419.0\t0\t55\n", "72\t64\t419.0\t0\t64\n", "73\t56\t419.0\t0\t56\n", "74\t91\t419.0\t0\t91\n", "75\t64\t419.0\t0\t64\n", "76\t74\t419.0\t0\t74\n", "77\t76\t419.0\t0\t76\n", "78\t47\t419.0\t0\t47\n", "79\t63\t419.0\t0\t63\n", "80\t46\t419.0\t0\t46\n", "81\t67\t419.0\t0\t67\n", "82\t47\t419.0\t0\t47\n", "83\t74\t419.0\t0\t74\n", "84\t76\t419.0\t0\t76\n", "85\t81\t419.0\t0\t81\n", "86\t105\t419.0\t0\t105\n", "87\t81\t419.0\t0\t81\n", "88\t106\t419.0\t0\t106\n", "89\t79\t419.0\t0\t79\n", "90\t48\t419.0\t0\t48\n", "91\t56\t419.0\t0\t56\n", "92\t33\t419.0\t0\t33\n", "93\t27\t419.0\t0\t27\n", "94\t53\t419.0\t0\t53\n", "95\t27\t419.0\t0\t27\n", "96\t43\t419.0\t0\t43\n", "97\t48\t419.0\t0\t48\n", "98\t70\t419.0\t0\t70\n", "99\t87\t419.0\t0\t87\n", "100\t105\t419.0\t0\t105\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 332_S48_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/332.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 74.22 s (13 us/read; 4.52 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,594,209\n", "Reads with adapters: 3,526,966 (63.0%)\n", "Reads written (passing filters): 5,401,456 (96.6%)\n", "\n", "Total basepairs processed: 559,420,900 bp\n", "Quality-trimmed: 1,541,131 bp (0.3%)\n", "Total written (filtered): 422,082,877 bp (75.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3406672 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.3%\n", " G: 40.6%\n", " T: 30.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t110289\t87409.5\t0\t110289\n", "4\t58762\t21852.4\t0\t58762\n", "5\t45359\t5463.1\t0\t45359\n", "6\t38297\t1365.8\t0\t38297\n", "7\t34527\t341.4\t0\t34527\n", "8\t34392\t85.4\t0\t34392\n", "9\t34091\t85.4\t0\t34091\n", "10\t34699\t85.4\t0\t34699\n", "11\t36119\t85.4\t0\t36119\n", "12\t36528\t85.4\t0\t36528\n", "13\t41875\t85.4\t0\t41875\n", "14\t41966\t85.4\t0\t41966\n", "15\t40697\t85.4\t0\t40697\n", "16\t43726\t85.4\t0\t43726\n", "17\t47287\t85.4\t0\t47287\n", "18\t53365\t85.4\t0\t53365\n", "19\t44450\t85.4\t0\t44450\n", "20\t37157\t85.4\t0\t37157\n", "21\t36295\t85.4\t0\t36295\n", "22\t36019\t85.4\t0\t36019\n", "23\t41043\t85.4\t0\t41043\n", "24\t48078\t85.4\t0\t48078\n", "25\t49279\t85.4\t0\t49279\n", "26\t55635\t85.4\t0\t55635\n", "27\t60529\t85.4\t0\t60529\n", "28\t55757\t85.4\t0\t55757\n", "29\t52891\t85.4\t0\t52891\n", "30\t53721\t85.4\t0\t53721\n", "31\t58953\t85.4\t0\t58953\n", "32\t60951\t85.4\t0\t60951\n", "33\t54620\t85.4\t0\t54620\n", "34\t53219\t85.4\t0\t53219\n", "35\t60215\t85.4\t0\t60215\n", "36\t71747\t85.4\t0\t71747\n", "37\t78749\t85.4\t0\t78749\n", "38\t64268\t85.4\t0\t64268\n", "39\t46986\t85.4\t0\t46986\n", "40\t46581\t85.4\t0\t46581\n", "41\t53319\t85.4\t0\t53319\n", "42\t58758\t85.4\t0\t58758\n", "43\t52531\t85.4\t0\t52531\n", "44\t41819\t85.4\t0\t41819\n", "45\t52917\t85.4\t0\t52917\n", "46\t63127\t85.4\t0\t63127\n", "47\t58551\t85.4\t0\t58551\n", "48\t53691\t85.4\t0\t53691\n", "49\t43223\t85.4\t0\t43223\n", "50\t41204\t85.4\t0\t41204\n", "51\t42781\t85.4\t0\t42781\n", "52\t45486\t85.4\t0\t45486\n", "53\t38352\t85.4\t0\t38352\n", "54\t42798\t85.4\t0\t42798\n", "55\t45738\t85.4\t0\t45738\n", "56\t41005\t85.4\t0\t41005\n", "57\t41461\t85.4\t0\t41461\n", "58\t44863\t85.4\t0\t44863\n", "59\t34471\t85.4\t0\t34471\n", "60\t28367\t85.4\t0\t28367\n", "61\t27576\t85.4\t0\t27576\n", "62\t22754\t85.4\t0\t22754\n", "63\t22079\t85.4\t0\t22079\n", "64\t25826\t85.4\t0\t25826\n", "65\t24945\t85.4\t0\t24945\n", "66\t21243\t85.4\t0\t21243\n", "67\t22348\t85.4\t0\t22348\n", "68\t22609\t85.4\t0\t22609\n", "69\t23768\t85.4\t0\t23768\n", "70\t26566\t85.4\t0\t26566\n", "71\t27015\t85.4\t0\t27015\n", "72\t19491\t85.4\t0\t19491\n", "73\t17776\t85.4\t0\t17776\n", "74\t18180\t85.4\t0\t18180\n", "75\t16074\t85.4\t0\t16074\n", "76\t13465\t85.4\t0\t13465\n", "77\t12763\t85.4\t0\t12763\n", "78\t14297\t85.4\t0\t14297\n", "79\t13107\t85.4\t0\t13107\n", "80\t12762\t85.4\t0\t12762\n", "81\t12106\t85.4\t0\t12106\n", "82\t11352\t85.4\t0\t11352\n", "83\t11435\t85.4\t0\t11435\n", "84\t12740\t85.4\t0\t12740\n", "85\t14125\t85.4\t0\t14125\n", "86\t13572\t85.4\t0\t13572\n", "87\t9898\t85.4\t0\t9898\n", "88\t9329\t85.4\t0\t9329\n", "89\t9215\t85.4\t0\t9215\n", "90\t9497\t85.4\t0\t9497\n", "91\t9415\t85.4\t0\t9415\n", "92\t9388\t85.4\t0\t9388\n", "93\t9283\t85.4\t0\t9283\n", "94\t8787\t85.4\t0\t8787\n", "95\t7318\t85.4\t0\t7318\n", "96\t5538\t85.4\t0\t5538\n", "97\t4172\t85.4\t0\t4172\n", "98\t3141\t85.4\t0\t3141\n", "99\t4382\t85.4\t0\t4382\n", "100\t3751\t85.4\t0\t3751\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 25127 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 49.9%\n", " C: 25.8%\n", " G: 0.0%\n", " T: 24.0%\n", " none/other: 0.3%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9524\t87409.5\t0\t9524\n", "4\t2386\t21852.4\t0\t2386\n", "5\t1166\t5463.1\t0\t1166\n", "6\t724\t1365.8\t0\t724\n", "7\t101\t341.4\t0\t101\n", "8\t88\t85.4\t0\t88\n", "9\t76\t85.4\t0\t76\n", "10\t78\t85.4\t0\t78\n", "11\t48\t85.4\t0\t48\n", "12\t84\t85.4\t0\t84\n", "13\t92\t85.4\t0\t92\n", "14\t75\t85.4\t0\t75\n", "15\t78\t85.4\t0\t78\n", "16\t85\t85.4\t0\t85\n", "17\t91\t85.4\t0\t91\n", "18\t168\t85.4\t0\t168\n", "19\t210\t85.4\t0\t210\n", "20\t424\t85.4\t0\t424\n", "21\t262\t85.4\t0\t262\n", "22\t190\t85.4\t0\t190\n", "23\t124\t85.4\t0\t124\n", "24\t133\t85.4\t0\t133\n", "25\t122\t85.4\t0\t122\n", "26\t134\t85.4\t0\t134\n", "27\t136\t85.4\t0\t136\n", "28\t162\t85.4\t0\t162\n", "29\t224\t85.4\t0\t224\n", "30\t372\t85.4\t0\t372\n", "31\t476\t85.4\t0\t476\n", "32\t608\t85.4\t0\t608\n", "33\t639\t85.4\t0\t639\n", "34\t630\t85.4\t0\t630\n", "35\t874\t85.4\t0\t874\n", "36\t878\t85.4\t0\t878\n", "37\t372\t85.4\t0\t372\n", "38\t70\t85.4\t0\t70\n", "39\t61\t85.4\t0\t61\n", "40\t52\t85.4\t0\t52\n", "41\t53\t85.4\t0\t53\n", "42\t54\t85.4\t0\t54\n", "43\t45\t85.4\t0\t45\n", "44\t43\t85.4\t0\t43\n", "45\t47\t85.4\t0\t47\n", "46\t42\t85.4\t0\t42\n", "47\t33\t85.4\t0\t33\n", "48\t57\t85.4\t0\t57\n", "49\t49\t85.4\t0\t49\n", "50\t47\t85.4\t0\t47\n", "51\t53\t85.4\t0\t53\n", "52\t50\t85.4\t0\t50\n", "53\t41\t85.4\t0\t41\n", "54\t40\t85.4\t0\t40\n", "55\t34\t85.4\t0\t34\n", "56\t35\t85.4\t0\t35\n", "57\t45\t85.4\t0\t45\n", "58\t36\t85.4\t0\t36\n", "59\t40\t85.4\t0\t40\n", "60\t32\t85.4\t0\t32\n", "61\t41\t85.4\t0\t41\n", "62\t38\t85.4\t0\t38\n", "63\t27\t85.4\t0\t27\n", "64\t21\t85.4\t0\t21\n", "65\t39\t85.4\t0\t39\n", "66\t27\t85.4\t0\t27\n", "67\t24\t85.4\t0\t24\n", "68\t26\t85.4\t0\t26\n", "69\t27\t85.4\t0\t27\n", "70\t27\t85.4\t0\t27\n", "71\t22\t85.4\t0\t22\n", "72\t16\t85.4\t0\t16\n", "73\t10\t85.4\t0\t10\n", "74\t21\t85.4\t0\t21\n", "75\t17\t85.4\t0\t17\n", "76\t20\t85.4\t0\t20\n", "77\t13\t85.4\t0\t13\n", "78\t19\t85.4\t0\t19\n", "79\t13\t85.4\t0\t13\n", "80\t17\t85.4\t0\t17\n", "81\t17\t85.4\t0\t17\n", "82\t20\t85.4\t0\t20\n", "83\t18\t85.4\t0\t18\n", "84\t41\t85.4\t0\t41\n", "85\t30\t85.4\t0\t30\n", "86\t41\t85.4\t0\t41\n", "87\t29\t85.4\t0\t29\n", "88\t33\t85.4\t0\t33\n", "89\t38\t85.4\t0\t38\n", "90\t54\t85.4\t0\t54\n", "91\t54\t85.4\t0\t54\n", "92\t93\t85.4\t0\t93\n", "93\t123\t85.4\t0\t123\n", "94\t147\t85.4\t0\t147\n", "95\t197\t85.4\t0\t197\n", "96\t209\t85.4\t0\t209\n", "97\t234\t85.4\t0\t234\n", "98\t135\t85.4\t0\t135\n", "99\t86\t85.4\t0\t86\n", "100\t170\t85.4\t0\t170\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 95167 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 36.0%\n", " C: 17.2%\n", " G: 15.0%\n", " T: 31.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t65683\t87409.5\t0\t65683\n", "4\t18687\t21852.4\t0\t18687\n", "5\t1728\t5463.1\t0\t1728\n", "6\t220\t1365.8\t0\t220\n", "7\t87\t341.4\t0\t87\n", "8\t90\t341.4\t0\t90\n", "9\t89\t341.4\t0\t89\n", "10\t92\t341.4\t0\t92\n", "11\t75\t341.4\t0\t75\n", "12\t99\t341.4\t0\t99\n", "13\t89\t341.4\t0\t89\n", "14\t90\t341.4\t0\t90\n", "15\t106\t341.4\t0\t106\n", "16\t97\t341.4\t0\t97\n", "17\t106\t341.4\t0\t106\n", "18\t100\t341.4\t0\t100\n", "19\t110\t341.4\t0\t110\n", "20\t91\t341.4\t0\t91\n", "21\t111\t341.4\t0\t111\n", "22\t118\t341.4\t0\t118\n", "23\t102\t341.4\t0\t102\n", "24\t82\t341.4\t0\t82\n", "25\t79\t341.4\t0\t79\n", "26\t99\t341.4\t0\t99\n", "27\t89\t341.4\t0\t89\n", "28\t122\t341.4\t0\t122\n", "29\t124\t341.4\t0\t124\n", "30\t125\t341.4\t0\t125\n", "31\t101\t341.4\t0\t101\n", "32\t108\t341.4\t0\t108\n", "33\t142\t341.4\t0\t142\n", "34\t129\t341.4\t0\t129\n", "35\t120\t341.4\t0\t120\n", "36\t119\t341.4\t0\t119\n", "37\t113\t341.4\t0\t113\n", "38\t112\t341.4\t0\t112\n", "39\t108\t341.4\t0\t108\n", "40\t87\t341.4\t0\t87\n", "41\t92\t341.4\t0\t92\n", "42\t74\t341.4\t0\t74\n", "43\t120\t341.4\t0\t120\n", "44\t58\t341.4\t0\t58\n", "45\t80\t341.4\t0\t80\n", "46\t74\t341.4\t0\t74\n", "47\t77\t341.4\t0\t77\n", "48\t59\t341.4\t0\t59\n", "49\t64\t341.4\t0\t64\n", "50\t85\t341.4\t0\t85\n", "51\t81\t341.4\t0\t81\n", "52\t86\t341.4\t0\t86\n", "53\t77\t341.4\t0\t77\n", "54\t80\t341.4\t0\t80\n", "55\t74\t341.4\t0\t74\n", "56\t111\t341.4\t0\t111\n", "57\t136\t341.4\t0\t136\n", "58\t237\t341.4\t0\t237\n", "59\t134\t341.4\t0\t134\n", "60\t225\t341.4\t0\t225\n", "61\t261\t341.4\t0\t261\n", "62\t200\t341.4\t0\t200\n", "63\t136\t341.4\t0\t136\n", "64\t261\t341.4\t0\t261\n", "65\t155\t341.4\t0\t155\n", "66\t132\t341.4\t0\t132\n", "67\t117\t341.4\t0\t117\n", "68\t93\t341.4\t0\t93\n", "69\t58\t341.4\t0\t58\n", "70\t60\t341.4\t0\t60\n", "71\t58\t341.4\t0\t58\n", "72\t60\t341.4\t0\t60\n", "73\t52\t341.4\t0\t52\n", "74\t47\t341.4\t0\t47\n", "75\t47\t341.4\t0\t47\n", "76\t64\t341.4\t0\t64\n", "77\t47\t341.4\t0\t47\n", "78\t63\t341.4\t0\t63\n", "79\t67\t341.4\t0\t67\n", "80\t51\t341.4\t0\t51\n", "81\t43\t341.4\t0\t43\n", "82\t72\t341.4\t0\t72\n", "83\t52\t341.4\t0\t52\n", "84\t58\t341.4\t0\t58\n", "85\t60\t341.4\t0\t60\n", "86\t55\t341.4\t0\t55\n", "87\t84\t341.4\t0\t84\n", "88\t132\t341.4\t0\t132\n", "89\t86\t341.4\t0\t86\n", "90\t75\t341.4\t0\t75\n", "91\t38\t341.4\t0\t38\n", "92\t24\t341.4\t0\t24\n", "93\t30\t341.4\t0\t30\n", "94\t52\t341.4\t0\t52\n", "95\t41\t341.4\t0\t41\n", "96\t29\t341.4\t0\t29\n", "97\t60\t341.4\t0\t60\n", "98\t65\t341.4\t0\t65\n", "99\t123\t341.4\t0\t123\n", "100\t106\t341.4\t0\t106\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 333_S30_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/333.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 69.40 s (13 us/read; 4.66 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,388,994\n", "Reads with adapters: 3,156,004 (58.6%)\n", "Reads written (passing filters): 5,178,798 (96.1%)\n", "\n", "Total basepairs processed: 538,899,400 bp\n", "Quality-trimmed: 1,295,616 bp (0.2%)\n", "Total written (filtered): 422,583,583 bp (78.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3032525 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.0%\n", " G: 36.8%\n", " T: 32.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t119286\t84203.0\t0\t119286\n", "4\t70336\t21050.8\t0\t70336\n", "5\t52703\t5262.7\t0\t52703\n", "6\t44022\t1315.7\t0\t44022\n", "7\t39668\t328.9\t0\t39668\n", "8\t39037\t82.2\t0\t39037\n", "9\t39545\t82.2\t0\t39545\n", "10\t38590\t82.2\t0\t38590\n", "11\t38890\t82.2\t0\t38890\n", "12\t39747\t82.2\t0\t39747\n", "13\t43634\t82.2\t0\t43634\n", "14\t44593\t82.2\t0\t44593\n", "15\t41385\t82.2\t0\t41385\n", "16\t42786\t82.2\t0\t42786\n", "17\t47811\t82.2\t0\t47811\n", "18\t53973\t82.2\t0\t53973\n", "19\t48234\t82.2\t0\t48234\n", "20\t40962\t82.2\t0\t40962\n", "21\t39104\t82.2\t0\t39104\n", "22\t35494\t82.2\t0\t35494\n", "23\t39100\t82.2\t0\t39100\n", "24\t45518\t82.2\t0\t45518\n", "25\t46988\t82.2\t0\t46988\n", "26\t52321\t82.2\t0\t52321\n", "27\t55746\t82.2\t0\t55746\n", "28\t50315\t82.2\t0\t50315\n", "29\t47487\t82.2\t0\t47487\n", "30\t46546\t82.2\t0\t46546\n", "31\t50182\t82.2\t0\t50182\n", "32\t50001\t82.2\t0\t50001\n", "33\t47155\t82.2\t0\t47155\n", "34\t45755\t82.2\t0\t45755\n", "35\t50707\t82.2\t0\t50707\n", "36\t56008\t82.2\t0\t56008\n", "37\t59080\t82.2\t0\t59080\n", "38\t48618\t82.2\t0\t48618\n", "39\t42815\t82.2\t0\t42815\n", "40\t40383\t82.2\t0\t40383\n", "41\t44495\t82.2\t0\t44495\n", "42\t47480\t82.2\t0\t47480\n", "43\t41922\t82.2\t0\t41922\n", "44\t34399\t82.2\t0\t34399\n", "45\t41345\t82.2\t0\t41345\n", "46\t48529\t82.2\t0\t48529\n", "47\t43799\t82.2\t0\t43799\n", "48\t43059\t82.2\t0\t43059\n", "49\t36787\t82.2\t0\t36787\n", "50\t35562\t82.2\t0\t35562\n", "51\t30414\t82.2\t0\t30414\n", "52\t29140\t82.2\t0\t29140\n", "53\t28474\t82.2\t0\t28474\n", "54\t28748\t82.2\t0\t28748\n", "55\t31428\t82.2\t0\t31428\n", "56\t29743\t82.2\t0\t29743\n", "57\t28640\t82.2\t0\t28640\n", "58\t32514\t82.2\t0\t32514\n", "59\t28803\t82.2\t0\t28803\n", "60\t24694\t82.2\t0\t24694\n", "61\t21705\t82.2\t0\t21705\n", "62\t17888\t82.2\t0\t17888\n", "63\t16994\t82.2\t0\t16994\n", "64\t18393\t82.2\t0\t18393\n", "65\t18186\t82.2\t0\t18186\n", "66\t16093\t82.2\t0\t16093\n", "67\t16122\t82.2\t0\t16122\n", "68\t15924\t82.2\t0\t15924\n", "69\t16603\t82.2\t0\t16603\n", "70\t17352\t82.2\t0\t17352\n", "71\t17044\t82.2\t0\t17044\n", "72\t13219\t82.2\t0\t13219\n", "73\t12219\t82.2\t0\t12219\n", "74\t12121\t82.2\t0\t12121\n", "75\t11401\t82.2\t0\t11401\n", "76\t9816\t82.2\t0\t9816\n", "77\t9133\t82.2\t0\t9133\n", "78\t10169\t82.2\t0\t10169\n", "79\t9991\t82.2\t0\t9991\n", "80\t9673\t82.2\t0\t9673\n", "81\t9611\t82.2\t0\t9611\n", "82\t9472\t82.2\t0\t9472\n", "83\t10653\t82.2\t0\t10653\n", "84\t12927\t82.2\t0\t12927\n", "85\t14693\t82.2\t0\t14693\n", "86\t14557\t82.2\t0\t14557\n", "87\t10798\t82.2\t0\t10798\n", "88\t10038\t82.2\t0\t10038\n", "89\t10568\t82.2\t0\t10568\n", "90\t11419\t82.2\t0\t11419\n", "91\t12088\t82.2\t0\t12088\n", "92\t12248\t82.2\t0\t12248\n", "93\t13352\t82.2\t0\t13352\n", "94\t13079\t82.2\t0\t13079\n", "95\t11436\t82.2\t0\t11436\n", "96\t8430\t82.2\t0\t8430\n", "97\t5484\t82.2\t0\t5484\n", "98\t3092\t82.2\t0\t3092\n", "99\t2133\t82.2\t0\t2133\n", "100\t1901\t82.2\t0\t1901\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 35083 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 66.3%\n", " C: 14.9%\n", " G: 0.0%\n", " T: 18.7%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9922\t84203.0\t0\t9922\n", "4\t2405\t21050.8\t0\t2405\n", "5\t1044\t5262.7\t0\t1044\n", "6\t710\t1315.7\t0\t710\n", "7\t202\t328.9\t0\t202\n", "8\t185\t82.2\t0\t185\n", "9\t173\t82.2\t0\t173\n", "10\t166\t82.2\t0\t166\n", "11\t153\t82.2\t0\t153\n", "12\t138\t82.2\t0\t138\n", "13\t146\t82.2\t0\t146\n", "14\t175\t82.2\t0\t175\n", "15\t139\t82.2\t0\t139\n", "16\t160\t82.2\t0\t160\n", "17\t182\t82.2\t0\t182\n", "18\t242\t82.2\t0\t242\n", "19\t348\t82.2\t0\t348\n", "20\t582\t82.2\t0\t582\n", "21\t439\t82.2\t0\t439\n", "22\t261\t82.2\t0\t261\n", "23\t207\t82.2\t0\t207\n", "24\t200\t82.2\t0\t200\n", "25\t222\t82.2\t0\t222\n", "26\t456\t82.2\t0\t456\n", "27\t405\t82.2\t0\t405\n", "28\t407\t82.2\t0\t407\n", "29\t541\t82.2\t0\t541\n", "30\t994\t82.2\t0\t994\n", "31\t1239\t82.2\t0\t1239\n", "32\t1927\t82.2\t0\t1927\n", "33\t1700\t82.2\t0\t1700\n", "34\t1763\t82.2\t0\t1763\n", "35\t2271\t82.2\t0\t2271\n", "36\t2150\t82.2\t0\t2150\n", "37\t865\t82.2\t0\t865\n", "38\t56\t82.2\t0\t56\n", "39\t38\t82.2\t0\t38\n", "40\t32\t82.2\t0\t32\n", "41\t27\t82.2\t0\t27\n", "42\t31\t82.2\t0\t31\n", "43\t25\t82.2\t0\t25\n", "44\t28\t82.2\t0\t28\n", "45\t26\t82.2\t0\t26\n", "46\t23\t82.2\t0\t23\n", "47\t34\t82.2\t0\t34\n", "48\t30\t82.2\t0\t30\n", "49\t30\t82.2\t0\t30\n", "50\t26\t82.2\t0\t26\n", "51\t35\t82.2\t0\t35\n", "52\t27\t82.2\t0\t27\n", "53\t20\t82.2\t0\t20\n", "54\t28\t82.2\t0\t28\n", "55\t24\t82.2\t0\t24\n", "56\t21\t82.2\t0\t21\n", "57\t25\t82.2\t0\t25\n", "58\t22\t82.2\t0\t22\n", "59\t19\t82.2\t0\t19\n", "60\t20\t82.2\t0\t20\n", "61\t22\t82.2\t0\t22\n", "62\t20\t82.2\t0\t20\n", "63\t15\t82.2\t0\t15\n", "64\t16\t82.2\t0\t16\n", "65\t15\t82.2\t0\t15\n", "66\t17\t82.2\t0\t17\n", "67\t10\t82.2\t0\t10\n", "68\t13\t82.2\t0\t13\n", "69\t18\t82.2\t0\t18\n", "70\t8\t82.2\t0\t8\n", "71\t8\t82.2\t0\t8\n", "72\t9\t82.2\t0\t9\n", "73\t8\t82.2\t0\t8\n", "74\t16\t82.2\t0\t16\n", "75\t12\t82.2\t0\t12\n", "76\t11\t82.2\t0\t11\n", "77\t11\t82.2\t0\t11\n", "78\t12\t82.2\t0\t12\n", "79\t11\t82.2\t0\t11\n", "80\t20\t82.2\t0\t20\n", "81\t9\t82.2\t0\t9\n", "82\t14\t82.2\t0\t14\n", "83\t16\t82.2\t0\t16\n", "84\t21\t82.2\t0\t21\n", "85\t30\t82.2\t0\t30\n", "86\t20\t82.2\t0\t20\n", "87\t16\t82.2\t0\t16\n", "88\t25\t82.2\t0\t25\n", "89\t25\t82.2\t0\t25\n", "90\t20\t82.2\t0\t20\n", "91\t26\t82.2\t0\t26\n", "92\t45\t82.2\t0\t45\n", "93\t74\t82.2\t0\t74\n", "94\t96\t82.2\t0\t96\n", "95\t110\t82.2\t0\t110\n", "96\t112\t82.2\t0\t112\n", "97\t107\t82.2\t0\t107\n", "98\t93\t82.2\t0\t93\n", "99\t58\t82.2\t0\t58\n", "100\t128\t82.2\t0\t128\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 88396 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.9%\n", " C: 21.3%\n", " G: 17.2%\n", " T: 17.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t64503\t84203.0\t0\t64503\n", "4\t13592\t21050.8\t0\t13592\n", "5\t2834\t5262.7\t0\t2834\n", "6\t261\t1315.7\t0\t261\n", "7\t98\t328.9\t0\t98\n", "8\t122\t328.9\t0\t122\n", "9\t132\t328.9\t0\t132\n", "10\t111\t328.9\t0\t111\n", "11\t123\t328.9\t0\t123\n", "12\t145\t328.9\t0\t145\n", "13\t125\t328.9\t0\t125\n", "14\t126\t328.9\t0\t126\n", "15\t132\t328.9\t0\t132\n", "16\t133\t328.9\t0\t133\n", "17\t139\t328.9\t0\t139\n", "18\t118\t328.9\t0\t118\n", "19\t131\t328.9\t0\t131\n", "20\t113\t328.9\t0\t113\n", "21\t111\t328.9\t0\t111\n", "22\t101\t328.9\t0\t101\n", "23\t82\t328.9\t0\t82\n", "24\t93\t328.9\t0\t93\n", "25\t86\t328.9\t0\t86\n", "26\t121\t328.9\t0\t121\n", "27\t125\t328.9\t0\t125\n", "28\t116\t328.9\t0\t116\n", "29\t132\t328.9\t0\t132\n", "30\t115\t328.9\t0\t115\n", "31\t98\t328.9\t0\t98\n", "32\t105\t328.9\t0\t105\n", "33\t81\t328.9\t0\t81\n", "34\t92\t328.9\t0\t92\n", "35\t86\t328.9\t0\t86\n", "36\t87\t328.9\t0\t87\n", "37\t76\t328.9\t0\t76\n", "38\t84\t328.9\t0\t84\n", "39\t96\t328.9\t0\t96\n", "40\t91\t328.9\t0\t91\n", "41\t62\t328.9\t0\t62\n", "42\t72\t328.9\t0\t72\n", "43\t97\t328.9\t0\t97\n", "44\t56\t328.9\t0\t56\n", "45\t57\t328.9\t0\t57\n", "46\t55\t328.9\t0\t55\n", "47\t62\t328.9\t0\t62\n", "48\t59\t328.9\t0\t59\n", "49\t62\t328.9\t0\t62\n", "50\t44\t328.9\t0\t44\n", "51\t83\t328.9\t0\t83\n", "52\t46\t328.9\t0\t46\n", "53\t68\t328.9\t0\t68\n", "54\t50\t328.9\t0\t50\n", "55\t52\t328.9\t0\t52\n", "56\t64\t328.9\t0\t64\n", "57\t49\t328.9\t0\t49\n", "58\t63\t328.9\t0\t63\n", "59\t55\t328.9\t0\t55\n", "60\t45\t328.9\t0\t45\n", "61\t61\t328.9\t0\t61\n", "62\t33\t328.9\t0\t33\n", "63\t39\t328.9\t0\t39\n", "64\t47\t328.9\t0\t47\n", "65\t55\t328.9\t0\t55\n", "66\t51\t328.9\t0\t51\n", "67\t47\t328.9\t0\t47\n", "68\t51\t328.9\t0\t51\n", "69\t36\t328.9\t0\t36\n", "70\t56\t328.9\t0\t56\n", "71\t50\t328.9\t0\t50\n", "72\t61\t328.9\t0\t61\n", "73\t43\t328.9\t0\t43\n", "74\t67\t328.9\t0\t67\n", "75\t51\t328.9\t0\t51\n", "76\t42\t328.9\t0\t42\n", "77\t52\t328.9\t0\t52\n", "78\t62\t328.9\t0\t62\n", "79\t65\t328.9\t0\t65\n", "80\t77\t328.9\t0\t77\n", "81\t73\t328.9\t0\t73\n", "82\t113\t328.9\t0\t113\n", "83\t65\t328.9\t0\t65\n", "84\t62\t328.9\t0\t62\n", "85\t68\t328.9\t0\t68\n", "86\t68\t328.9\t0\t68\n", "87\t69\t328.9\t0\t69\n", "88\t91\t328.9\t0\t91\n", "89\t63\t328.9\t0\t63\n", "90\t63\t328.9\t0\t63\n", "91\t45\t328.9\t0\t45\n", "92\t42\t328.9\t0\t42\n", "93\t44\t328.9\t0\t44\n", "94\t55\t328.9\t0\t55\n", "95\t34\t328.9\t0\t34\n", "96\t32\t328.9\t0\t32\n", "97\t45\t328.9\t0\t45\n", "98\t57\t328.9\t0\t57\n", "99\t68\t328.9\t0\t68\n", "100\t76\t328.9\t0\t76\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 334_S50_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/334.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 72.62 s (12 us/read; 4.82 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,839,941\n", "Reads with adapters: 2,698,795 (46.2%)\n", "Reads written (passing filters): 5,704,064 (97.7%)\n", "\n", "Total basepairs processed: 583,994,100 bp\n", "Quality-trimmed: 1,162,497 bp (0.2%)\n", "Total written (filtered): 493,119,303 bp (84.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2563495 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.6%\n", " G: 41.9%\n", " T: 29.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t134729\t91249.1\t0\t134729\n", "4\t71149\t22812.3\t0\t71149\n", "5\t51158\t5703.1\t0\t51158\n", "6\t43429\t1425.8\t0\t43429\n", "7\t36953\t356.4\t0\t36953\n", "8\t34437\t89.1\t0\t34437\n", "9\t35564\t89.1\t0\t35564\n", "10\t35658\t89.1\t0\t35658\n", "11\t36866\t89.1\t0\t36866\n", "12\t37622\t89.1\t0\t37622\n", "13\t46913\t89.1\t0\t46913\n", "14\t46071\t89.1\t0\t46071\n", "15\t40398\t89.1\t0\t40398\n", "16\t42249\t89.1\t0\t42249\n", "17\t44327\t89.1\t0\t44327\n", "18\t49715\t89.1\t0\t49715\n", "19\t40649\t89.1\t0\t40649\n", "20\t32732\t89.1\t0\t32732\n", "21\t31581\t89.1\t0\t31581\n", "22\t31013\t89.1\t0\t31013\n", "23\t33234\t89.1\t0\t33234\n", "24\t37426\t89.1\t0\t37426\n", "25\t38880\t89.1\t0\t38880\n", "26\t43840\t89.1\t0\t43840\n", "27\t46653\t89.1\t0\t46653\n", "28\t42917\t89.1\t0\t42917\n", "29\t39414\t89.1\t0\t39414\n", "30\t40811\t89.1\t0\t40811\n", "31\t45891\t89.1\t0\t45891\n", "32\t43911\t89.1\t0\t43911\n", "33\t40139\t89.1\t0\t40139\n", "34\t38634\t89.1\t0\t38634\n", "35\t42813\t89.1\t0\t42813\n", "36\t50312\t89.1\t0\t50312\n", "37\t55116\t89.1\t0\t55116\n", "38\t42624\t89.1\t0\t42624\n", "39\t35132\t89.1\t0\t35132\n", "40\t33487\t89.1\t0\t33487\n", "41\t40200\t89.1\t0\t40200\n", "42\t46131\t89.1\t0\t46131\n", "43\t39457\t89.1\t0\t39457\n", "44\t29160\t89.1\t0\t29160\n", "45\t33899\t89.1\t0\t33899\n", "46\t38642\t89.1\t0\t38642\n", "47\t33221\t89.1\t0\t33221\n", "48\t31832\t89.1\t0\t31832\n", "49\t26195\t89.1\t0\t26195\n", "50\t25324\t89.1\t0\t25324\n", "51\t20467\t89.1\t0\t20467\n", "52\t20877\t89.1\t0\t20877\n", "53\t20825\t89.1\t0\t20825\n", "54\t23693\t89.1\t0\t23693\n", "55\t21368\t89.1\t0\t21368\n", "56\t19329\t89.1\t0\t19329\n", "57\t17906\t89.1\t0\t17906\n", "58\t20517\t89.1\t0\t20517\n", "59\t17236\t89.1\t0\t17236\n", "60\t14381\t89.1\t0\t14381\n", "61\t13777\t89.1\t0\t13777\n", "62\t11853\t89.1\t0\t11853\n", "63\t11900\t89.1\t0\t11900\n", "64\t13012\t89.1\t0\t13012\n", "65\t12490\t89.1\t0\t12490\n", "66\t11352\t89.1\t0\t11352\n", "67\t12241\t89.1\t0\t12241\n", "68\t12532\t89.1\t0\t12532\n", "69\t13722\t89.1\t0\t13722\n", "70\t16364\t89.1\t0\t16364\n", "71\t16455\t89.1\t0\t16455\n", "72\t11322\t89.1\t0\t11322\n", "73\t9768\t89.1\t0\t9768\n", "74\t9816\t89.1\t0\t9816\n", "75\t8855\t89.1\t0\t8855\n", "76\t7533\t89.1\t0\t7533\n", "77\t7440\t89.1\t0\t7440\n", "78\t8404\t89.1\t0\t8404\n", "79\t7773\t89.1\t0\t7773\n", "80\t7603\t89.1\t0\t7603\n", "81\t7398\t89.1\t0\t7398\n", "82\t6996\t89.1\t0\t6996\n", "83\t7101\t89.1\t0\t7101\n", "84\t7971\t89.1\t0\t7971\n", "85\t9184\t89.1\t0\t9184\n", "86\t8995\t89.1\t0\t8995\n", "87\t7219\t89.1\t0\t7219\n", "88\t6908\t89.1\t0\t6908\n", "89\t6465\t89.1\t0\t6465\n", "90\t6836\t89.1\t0\t6836\n", "91\t7004\t89.1\t0\t7004\n", "92\t7476\t89.1\t0\t7476\n", "93\t8026\t89.1\t0\t8026\n", "94\t7605\t89.1\t0\t7605\n", "95\t6626\t89.1\t0\t6626\n", "96\t4779\t89.1\t0\t4779\n", "97\t3126\t89.1\t0\t3126\n", "98\t1843\t89.1\t0\t1843\n", "99\t1498\t89.1\t0\t1498\n", "100\t1120\t89.1\t0\t1120\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 38421 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.8%\n", " C: 35.1%\n", " G: 0.0%\n", " T: 22.5%\n", " none/other: 0.6%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t16393\t91249.1\t0\t16393\n", "4\t4094\t22812.3\t0\t4094\n", "5\t2270\t5703.1\t0\t2270\n", "6\t1301\t1425.8\t0\t1301\n", "7\t98\t356.4\t0\t98\n", "8\t63\t89.1\t0\t63\n", "9\t56\t89.1\t0\t56\n", "10\t62\t89.1\t0\t62\n", "11\t67\t89.1\t0\t67\n", "12\t60\t89.1\t0\t60\n", "13\t79\t89.1\t0\t79\n", "14\t64\t89.1\t0\t64\n", "15\t75\t89.1\t0\t75\n", "16\t86\t89.1\t0\t86\n", "17\t112\t89.1\t0\t112\n", "18\t125\t89.1\t0\t125\n", "19\t128\t89.1\t0\t128\n", "20\t220\t89.1\t0\t220\n", "21\t161\t89.1\t0\t161\n", "22\t125\t89.1\t0\t125\n", "23\t133\t89.1\t0\t133\n", "24\t103\t89.1\t0\t103\n", "25\t137\t89.1\t0\t137\n", "26\t157\t89.1\t0\t157\n", "27\t209\t89.1\t0\t209\n", "28\t234\t89.1\t0\t234\n", "29\t311\t89.1\t0\t311\n", "30\t544\t89.1\t0\t544\n", "31\t648\t89.1\t0\t648\n", "32\t923\t89.1\t0\t923\n", "33\t981\t89.1\t0\t981\n", "34\t1093\t89.1\t0\t1093\n", "35\t1308\t89.1\t0\t1308\n", "36\t1221\t89.1\t0\t1221\n", "37\t588\t89.1\t0\t588\n", "38\t93\t89.1\t0\t93\n", "39\t89\t89.1\t0\t89\n", "40\t56\t89.1\t0\t56\n", "41\t38\t89.1\t0\t38\n", "42\t44\t89.1\t0\t44\n", "43\t41\t89.1\t0\t41\n", "44\t50\t89.1\t0\t50\n", "45\t36\t89.1\t0\t36\n", "46\t47\t89.1\t0\t47\n", "47\t47\t89.1\t0\t47\n", "48\t61\t89.1\t0\t61\n", "49\t49\t89.1\t0\t49\n", "50\t49\t89.1\t0\t49\n", "51\t48\t89.1\t0\t48\n", "52\t47\t89.1\t0\t47\n", "53\t58\t89.1\t0\t58\n", "54\t31\t89.1\t0\t31\n", "55\t42\t89.1\t0\t42\n", "56\t39\t89.1\t0\t39\n", "57\t41\t89.1\t0\t41\n", "58\t39\t89.1\t0\t39\n", "59\t34\t89.1\t0\t34\n", "60\t34\t89.1\t0\t34\n", "61\t28\t89.1\t0\t28\n", "62\t31\t89.1\t0\t31\n", "63\t32\t89.1\t0\t32\n", "64\t30\t89.1\t0\t30\n", "65\t37\t89.1\t0\t37\n", "66\t23\t89.1\t0\t23\n", "67\t32\t89.1\t0\t32\n", "68\t42\t89.1\t0\t42\n", "69\t40\t89.1\t0\t40\n", "70\t39\t89.1\t0\t39\n", "71\t31\t89.1\t0\t31\n", "72\t34\t89.1\t0\t34\n", "73\t29\t89.1\t0\t29\n", "74\t32\t89.1\t0\t32\n", "75\t32\t89.1\t0\t32\n", "76\t36\t89.1\t0\t36\n", "77\t22\t89.1\t0\t22\n", "78\t34\t89.1\t0\t34\n", "79\t39\t89.1\t0\t39\n", "80\t25\t89.1\t0\t25\n", "81\t28\t89.1\t0\t28\n", "82\t41\t89.1\t0\t41\n", "83\t38\t89.1\t0\t38\n", "84\t44\t89.1\t0\t44\n", "85\t48\t89.1\t0\t48\n", "86\t54\t89.1\t0\t54\n", "87\t28\t89.1\t0\t28\n", "88\t48\t89.1\t0\t48\n", "89\t43\t89.1\t0\t43\n", "90\t44\t89.1\t0\t44\n", "91\t66\t89.1\t0\t66\n", "92\t92\t89.1\t0\t92\n", "93\t137\t89.1\t0\t137\n", "94\t178\t89.1\t0\t178\n", "95\t226\t89.1\t0\t226\n", "96\t334\t89.1\t0\t334\n", "97\t310\t89.1\t0\t310\n", "98\t218\t89.1\t0\t218\n", "99\t120\t89.1\t0\t120\n", "100\t334\t89.1\t0\t334\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 96879 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.6%\n", " C: 22.0%\n", " G: 16.0%\n", " T: 22.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t73814\t91249.1\t0\t73814\n", "4\t15318\t22812.3\t0\t15318\n", "5\t1963\t5703.1\t0\t1963\n", "6\t230\t1425.8\t0\t230\n", "7\t70\t356.4\t0\t70\n", "8\t58\t356.4\t0\t58\n", "9\t68\t356.4\t0\t68\n", "10\t81\t356.4\t0\t81\n", "11\t84\t356.4\t0\t84\n", "12\t80\t356.4\t0\t80\n", "13\t95\t356.4\t0\t95\n", "14\t88\t356.4\t0\t88\n", "15\t98\t356.4\t0\t98\n", "16\t83\t356.4\t0\t83\n", "17\t104\t356.4\t0\t104\n", "18\t106\t356.4\t0\t106\n", "19\t113\t356.4\t0\t113\n", "20\t117\t356.4\t0\t117\n", "21\t78\t356.4\t0\t78\n", "22\t72\t356.4\t0\t72\n", "23\t59\t356.4\t0\t59\n", "24\t73\t356.4\t0\t73\n", "25\t60\t356.4\t0\t60\n", "26\t75\t356.4\t0\t75\n", "27\t81\t356.4\t0\t81\n", "28\t69\t356.4\t0\t69\n", "29\t68\t356.4\t0\t68\n", "30\t74\t356.4\t0\t74\n", "31\t50\t356.4\t0\t50\n", "32\t58\t356.4\t0\t58\n", "33\t43\t356.4\t0\t43\n", "34\t34\t356.4\t0\t34\n", "35\t53\t356.4\t0\t53\n", "36\t36\t356.4\t0\t36\n", "37\t34\t356.4\t0\t34\n", "38\t60\t356.4\t0\t60\n", "39\t35\t356.4\t0\t35\n", "40\t36\t356.4\t0\t36\n", "41\t36\t356.4\t0\t36\n", "42\t42\t356.4\t0\t42\n", "43\t45\t356.4\t0\t45\n", "44\t46\t356.4\t0\t46\n", "45\t56\t356.4\t0\t56\n", "46\t73\t356.4\t0\t73\n", "47\t60\t356.4\t0\t60\n", "48\t56\t356.4\t0\t56\n", "49\t45\t356.4\t0\t45\n", "50\t60\t356.4\t0\t60\n", "51\t53\t356.4\t0\t53\n", "52\t56\t356.4\t0\t56\n", "53\t60\t356.4\t0\t60\n", "54\t49\t356.4\t0\t49\n", "55\t48\t356.4\t0\t48\n", "56\t31\t356.4\t0\t31\n", "57\t49\t356.4\t0\t49\n", "58\t55\t356.4\t0\t55\n", "59\t52\t356.4\t0\t52\n", "60\t34\t356.4\t0\t34\n", "61\t43\t356.4\t0\t43\n", "62\t65\t356.4\t0\t65\n", "63\t52\t356.4\t0\t52\n", "64\t51\t356.4\t0\t51\n", "65\t66\t356.4\t0\t66\n", "66\t61\t356.4\t0\t61\n", "67\t41\t356.4\t0\t41\n", "68\t52\t356.4\t0\t52\n", "69\t37\t356.4\t0\t37\n", "70\t60\t356.4\t0\t60\n", "71\t47\t356.4\t0\t47\n", "72\t39\t356.4\t0\t39\n", "73\t47\t356.4\t0\t47\n", "74\t58\t356.4\t0\t58\n", "75\t60\t356.4\t0\t60\n", "76\t45\t356.4\t0\t45\n", "77\t52\t356.4\t0\t52\n", "78\t55\t356.4\t0\t55\n", "79\t62\t356.4\t0\t62\n", "80\t36\t356.4\t0\t36\n", "81\t45\t356.4\t0\t45\n", "82\t63\t356.4\t0\t63\n", "83\t55\t356.4\t0\t55\n", "84\t82\t356.4\t0\t82\n", "85\t80\t356.4\t0\t80\n", "86\t59\t356.4\t0\t59\n", "87\t73\t356.4\t0\t73\n", "88\t56\t356.4\t0\t56\n", "89\t37\t356.4\t0\t37\n", "90\t34\t356.4\t0\t34\n", "91\t25\t356.4\t0\t25\n", "92\t30\t356.4\t0\t30\n", "93\t29\t356.4\t0\t29\n", "94\t47\t356.4\t0\t47\n", "95\t39\t356.4\t0\t39\n", "96\t47\t356.4\t0\t47\n", "97\t51\t356.4\t0\t51\n", "98\t61\t356.4\t0\t61\n", "99\t113\t356.4\t0\t113\n", "100\t100\t356.4\t0\t100\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 335_S31_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/335.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 68.85 s (13 us/read; 4.70 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,396,716\n", "Reads with adapters: 3,405,322 (63.1%)\n", "Reads written (passing filters): 5,117,435 (94.8%)\n", "\n", "Total basepairs processed: 539,671,600 bp\n", "Quality-trimmed: 1,380,945 bp (0.3%)\n", "Total written (filtered): 400,910,229 bp (74.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3290261 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.9%\n", " G: 39.0%\n", " T: 29.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t109601\t84323.7\t0\t109601\n", "4\t64417\t21080.9\t0\t64417\n", "5\t47130\t5270.2\t0\t47130\n", "6\t40502\t1317.6\t0\t40502\n", "7\t36925\t329.4\t0\t36925\n", "8\t37525\t82.3\t0\t37525\n", "9\t36973\t82.3\t0\t36973\n", "10\t36713\t82.3\t0\t36713\n", "11\t36664\t82.3\t0\t36664\n", "12\t37721\t82.3\t0\t37721\n", "13\t41569\t82.3\t0\t41569\n", "14\t42148\t82.3\t0\t42148\n", "15\t39831\t82.3\t0\t39831\n", "16\t42058\t82.3\t0\t42058\n", "17\t45702\t82.3\t0\t45702\n", "18\t51175\t82.3\t0\t51175\n", "19\t45628\t82.3\t0\t45628\n", "20\t39181\t82.3\t0\t39181\n", "21\t36729\t82.3\t0\t36729\n", "22\t34319\t82.3\t0\t34319\n", "23\t37056\t82.3\t0\t37056\n", "24\t42348\t82.3\t0\t42348\n", "25\t43060\t82.3\t0\t43060\n", "26\t48576\t82.3\t0\t48576\n", "27\t53492\t82.3\t0\t53492\n", "28\t48926\t82.3\t0\t48926\n", "29\t45546\t82.3\t0\t45546\n", "30\t46343\t82.3\t0\t46343\n", "31\t51033\t82.3\t0\t51033\n", "32\t48228\t82.3\t0\t48228\n", "33\t46987\t82.3\t0\t46987\n", "34\t44723\t82.3\t0\t44723\n", "35\t50382\t82.3\t0\t50382\n", "36\t56139\t82.3\t0\t56139\n", "37\t56320\t82.3\t0\t56320\n", "38\t48765\t82.3\t0\t48765\n", "39\t43305\t82.3\t0\t43305\n", "40\t41925\t82.3\t0\t41925\n", "41\t47103\t82.3\t0\t47103\n", "42\t51622\t82.3\t0\t51622\n", "43\t45436\t82.3\t0\t45436\n", "44\t37768\t82.3\t0\t37768\n", "45\t44652\t82.3\t0\t44652\n", "46\t51542\t82.3\t0\t51542\n", "47\t48270\t82.3\t0\t48270\n", "48\t47748\t82.3\t0\t47748\n", "49\t40273\t82.3\t0\t40273\n", "50\t39127\t82.3\t0\t39127\n", "51\t34580\t82.3\t0\t34580\n", "52\t38019\t82.3\t0\t38019\n", "53\t41589\t82.3\t0\t41589\n", "54\t37341\t82.3\t0\t37341\n", "55\t39744\t82.3\t0\t39744\n", "56\t41002\t82.3\t0\t41002\n", "57\t37538\t82.3\t0\t37538\n", "58\t41265\t82.3\t0\t41265\n", "59\t36671\t82.3\t0\t36671\n", "60\t30879\t82.3\t0\t30879\n", "61\t29679\t82.3\t0\t29679\n", "62\t25330\t82.3\t0\t25330\n", "63\t23662\t82.3\t0\t23662\n", "64\t26681\t82.3\t0\t26681\n", "65\t26895\t82.3\t0\t26895\n", "66\t24415\t82.3\t0\t24415\n", "67\t24696\t82.3\t0\t24696\n", "68\t23820\t82.3\t0\t23820\n", "69\t25347\t82.3\t0\t25347\n", "70\t26265\t82.3\t0\t26265\n", "71\t25363\t82.3\t0\t25363\n", "72\t20532\t82.3\t0\t20532\n", "73\t19206\t82.3\t0\t19206\n", "74\t19374\t82.3\t0\t19374\n", "75\t17103\t82.3\t0\t17103\n", "76\t15137\t82.3\t0\t15137\n", "77\t14065\t82.3\t0\t14065\n", "78\t15638\t82.3\t0\t15638\n", "79\t15776\t82.3\t0\t15776\n", "80\t15670\t82.3\t0\t15670\n", "81\t14912\t82.3\t0\t14912\n", "82\t14413\t82.3\t0\t14413\n", "83\t15619\t82.3\t0\t15619\n", "84\t18030\t82.3\t0\t18030\n", "85\t20080\t82.3\t0\t20080\n", "86\t19341\t82.3\t0\t19341\n", "87\t13664\t82.3\t0\t13664\n", "88\t12849\t82.3\t0\t12849\n", "89\t13667\t82.3\t0\t13667\n", "90\t14460\t82.3\t0\t14460\n", "91\t15336\t82.3\t0\t15336\n", "92\t15867\t82.3\t0\t15867\n", "93\t17377\t82.3\t0\t17377\n", "94\t16358\t82.3\t0\t16358\n", "95\t14260\t82.3\t0\t14260\n", "96\t10910\t82.3\t0\t10910\n", "97\t7205\t82.3\t0\t7205\n", "98\t4404\t82.3\t0\t4404\n", "99\t5626\t82.3\t0\t5626\n", "100\t3395\t82.3\t0\t3395\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 35857 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 69.4%\n", " C: 13.9%\n", " G: 0.0%\n", " T: 16.7%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9013\t84323.7\t0\t9013\n", "4\t2141\t21080.9\t0\t2141\n", "5\t797\t5270.2\t0\t797\n", "6\t512\t1317.6\t0\t512\n", "7\t102\t329.4\t0\t102\n", "8\t122\t82.3\t0\t122\n", "9\t111\t82.3\t0\t111\n", "10\t122\t82.3\t0\t122\n", "11\t101\t82.3\t0\t101\n", "12\t99\t82.3\t0\t99\n", "13\t103\t82.3\t0\t103\n", "14\t120\t82.3\t0\t120\n", "15\t104\t82.3\t0\t104\n", "16\t121\t82.3\t0\t121\n", "17\t132\t82.3\t0\t132\n", "18\t236\t82.3\t0\t236\n", "19\t360\t82.3\t0\t360\n", "20\t577\t82.3\t0\t577\n", "21\t382\t82.3\t0\t382\n", "22\t294\t82.3\t0\t294\n", "23\t194\t82.3\t0\t194\n", "24\t185\t82.3\t0\t185\n", "25\t221\t82.3\t0\t221\n", "26\t396\t82.3\t0\t396\n", "27\t456\t82.3\t0\t456\n", "28\t511\t82.3\t0\t511\n", "29\t746\t82.3\t0\t746\n", "30\t1283\t82.3\t0\t1283\n", "31\t1562\t82.3\t0\t1562\n", "32\t2477\t82.3\t0\t2477\n", "33\t2174\t82.3\t0\t2174\n", "34\t2214\t82.3\t0\t2214\n", "35\t2671\t82.3\t0\t2671\n", "36\t2657\t82.3\t0\t2657\n", "37\t1023\t82.3\t0\t1023\n", "38\t66\t82.3\t0\t66\n", "39\t43\t82.3\t0\t43\n", "40\t32\t82.3\t0\t32\n", "41\t34\t82.3\t0\t34\n", "42\t36\t82.3\t0\t36\n", "43\t24\t82.3\t0\t24\n", "44\t26\t82.3\t0\t26\n", "45\t41\t82.3\t0\t41\n", "46\t22\t82.3\t0\t22\n", "47\t20\t82.3\t0\t20\n", "48\t24\t82.3\t0\t24\n", "49\t39\t82.3\t0\t39\n", "50\t38\t82.3\t0\t38\n", "51\t26\t82.3\t0\t26\n", "52\t37\t82.3\t0\t37\n", "53\t28\t82.3\t0\t28\n", "54\t38\t82.3\t0\t38\n", "55\t25\t82.3\t0\t25\n", "56\t19\t82.3\t0\t19\n", "57\t21\t82.3\t0\t21\n", "58\t15\t82.3\t0\t15\n", "59\t19\t82.3\t0\t19\n", "60\t25\t82.3\t0\t25\n", "61\t25\t82.3\t0\t25\n", "62\t19\t82.3\t0\t19\n", "63\t16\t82.3\t0\t16\n", "64\t30\t82.3\t0\t30\n", "65\t17\t82.3\t0\t17\n", "66\t13\t82.3\t0\t13\n", "67\t11\t82.3\t0\t11\n", "68\t15\t82.3\t0\t15\n", "69\t11\t82.3\t0\t11\n", "70\t9\t82.3\t0\t9\n", "71\t7\t82.3\t0\t7\n", "72\t15\t82.3\t0\t15\n", "73\t8\t82.3\t0\t8\n", "74\t6\t82.3\t0\t6\n", "75\t3\t82.3\t0\t3\n", "76\t10\t82.3\t0\t10\n", "77\t8\t82.3\t0\t8\n", "78\t9\t82.3\t0\t9\n", "79\t5\t82.3\t0\t5\n", "80\t4\t82.3\t0\t4\n", "81\t7\t82.3\t0\t7\n", "82\t5\t82.3\t0\t5\n", "83\t4\t82.3\t0\t4\n", "84\t12\t82.3\t0\t12\n", "85\t9\t82.3\t0\t9\n", "86\t10\t82.3\t0\t10\n", "87\t4\t82.3\t0\t4\n", "88\t6\t82.3\t0\t6\n", "89\t8\t82.3\t0\t8\n", "90\t10\t82.3\t0\t10\n", "91\t18\t82.3\t0\t18\n", "92\t25\t82.3\t0\t25\n", "93\t31\t82.3\t0\t31\n", "94\t62\t82.3\t0\t62\n", "95\t75\t82.3\t0\t75\n", "96\t64\t82.3\t0\t64\n", "97\t62\t82.3\t0\t62\n", "98\t55\t82.3\t0\t55\n", "99\t49\t82.3\t0\t49\n", "100\t83\t82.3\t0\t83\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 79204 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.4%\n", " C: 19.4%\n", " G: 17.4%\n", " T: 19.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t58060\t84323.7\t0\t58060\n", "4\t12850\t21080.9\t0\t12850\n", "5\t1990\t5270.2\t0\t1990\n", "6\t214\t1317.6\t0\t214\n", "7\t63\t329.4\t0\t63\n", "8\t55\t329.4\t0\t55\n", "9\t70\t329.4\t0\t70\n", "10\t77\t329.4\t0\t77\n", "11\t60\t329.4\t0\t60\n", "12\t82\t329.4\t0\t82\n", "13\t74\t329.4\t0\t74\n", "14\t83\t329.4\t0\t83\n", "15\t76\t329.4\t0\t76\n", "16\t82\t329.4\t0\t82\n", "17\t107\t329.4\t0\t107\n", "18\t98\t329.4\t0\t98\n", "19\t69\t329.4\t0\t69\n", "20\t87\t329.4\t0\t87\n", "21\t74\t329.4\t0\t74\n", "22\t57\t329.4\t0\t57\n", "23\t68\t329.4\t0\t68\n", "24\t66\t329.4\t0\t66\n", "25\t60\t329.4\t0\t60\n", "26\t77\t329.4\t0\t77\n", "27\t82\t329.4\t0\t82\n", "28\t76\t329.4\t0\t76\n", "29\t74\t329.4\t0\t74\n", "30\t67\t329.4\t0\t67\n", "31\t92\t329.4\t0\t92\n", "32\t83\t329.4\t0\t83\n", "33\t68\t329.4\t0\t68\n", "34\t75\t329.4\t0\t75\n", "35\t83\t329.4\t0\t83\n", "36\t59\t329.4\t0\t59\n", "37\t72\t329.4\t0\t72\n", "38\t77\t329.4\t0\t77\n", "39\t83\t329.4\t0\t83\n", "40\t88\t329.4\t0\t88\n", "41\t78\t329.4\t0\t78\n", "42\t48\t329.4\t0\t48\n", "43\t100\t329.4\t0\t100\n", "44\t40\t329.4\t0\t40\n", "45\t59\t329.4\t0\t59\n", "46\t91\t329.4\t0\t91\n", "47\t50\t329.4\t0\t50\n", "48\t78\t329.4\t0\t78\n", "49\t60\t329.4\t0\t60\n", "50\t73\t329.4\t0\t73\n", "51\t57\t329.4\t0\t57\n", "52\t40\t329.4\t0\t40\n", "53\t60\t329.4\t0\t60\n", "54\t55\t329.4\t0\t55\n", "55\t51\t329.4\t0\t51\n", "56\t53\t329.4\t0\t53\n", "57\t45\t329.4\t0\t45\n", "58\t51\t329.4\t0\t51\n", "59\t41\t329.4\t0\t41\n", "60\t60\t329.4\t0\t60\n", "61\t55\t329.4\t0\t55\n", "62\t45\t329.4\t0\t45\n", "63\t66\t329.4\t0\t66\n", "64\t43\t329.4\t0\t43\n", "65\t54\t329.4\t0\t54\n", "66\t50\t329.4\t0\t50\n", "67\t51\t329.4\t0\t51\n", "68\t59\t329.4\t0\t59\n", "69\t37\t329.4\t0\t37\n", "70\t42\t329.4\t0\t42\n", "71\t57\t329.4\t0\t57\n", "72\t67\t329.4\t0\t67\n", "73\t55\t329.4\t0\t55\n", "74\t73\t329.4\t0\t73\n", "75\t56\t329.4\t0\t56\n", "76\t58\t329.4\t0\t58\n", "77\t77\t329.4\t0\t77\n", "78\t56\t329.4\t0\t56\n", "79\t52\t329.4\t0\t52\n", "80\t86\t329.4\t0\t86\n", "81\t57\t329.4\t0\t57\n", "82\t82\t329.4\t0\t82\n", "83\t73\t329.4\t0\t73\n", "84\t82\t329.4\t0\t82\n", "85\t51\t329.4\t0\t51\n", "86\t72\t329.4\t0\t72\n", "87\t66\t329.4\t0\t66\n", "88\t91\t329.4\t0\t91\n", "89\t66\t329.4\t0\t66\n", "90\t53\t329.4\t0\t53\n", "91\t41\t329.4\t0\t41\n", "92\t33\t329.4\t0\t33\n", "93\t34\t329.4\t0\t34\n", "94\t35\t329.4\t0\t35\n", "95\t42\t329.4\t0\t42\n", "96\t44\t329.4\t0\t44\n", "97\t81\t329.4\t0\t81\n", "98\t43\t329.4\t0\t43\n", "99\t82\t329.4\t0\t82\n", "100\t69\t329.4\t0\t69\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 336_S51_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/336.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 99.95 s (13 us/read; 4.71 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,847,255\n", "Reads with adapters: 4,065,968 (51.8%)\n", "Reads written (passing filters): 7,615,302 (97.0%)\n", "\n", "Total basepairs processed: 784,725,500 bp\n", "Quality-trimmed: 2,198,701 bp (0.3%)\n", "Total written (filtered): 631,505,218 bp (80.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3842144 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.9%\n", " G: 38.2%\n", " T: 32.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t167872\t122613.4\t0\t167872\n", "4\t84763\t30653.3\t0\t84763\n", "5\t58623\t7663.3\t0\t58623\n", "6\t48502\t1915.8\t0\t48502\n", "7\t40100\t479.0\t0\t40100\n", "8\t40100\t119.7\t0\t40100\n", "9\t39651\t119.7\t0\t39651\n", "10\t38425\t119.7\t0\t38425\n", "11\t40867\t119.7\t0\t40867\n", "12\t40141\t119.7\t0\t40141\n", "13\t42681\t119.7\t0\t42681\n", "14\t44090\t119.7\t0\t44090\n", "15\t43366\t119.7\t0\t43366\n", "16\t46645\t119.7\t0\t46645\n", "17\t50130\t119.7\t0\t50130\n", "18\t55330\t119.7\t0\t55330\n", "19\t49601\t119.7\t0\t49601\n", "20\t42635\t119.7\t0\t42635\n", "21\t41058\t119.7\t0\t41058\n", "22\t41192\t119.7\t0\t41192\n", "23\t47026\t119.7\t0\t47026\n", "24\t53893\t119.7\t0\t53893\n", "25\t54115\t119.7\t0\t54115\n", "26\t60327\t119.7\t0\t60327\n", "27\t68107\t119.7\t0\t68107\n", "28\t62477\t119.7\t0\t62477\n", "29\t59250\t119.7\t0\t59250\n", "30\t62773\t119.7\t0\t62773\n", "31\t67854\t119.7\t0\t67854\n", "32\t65547\t119.7\t0\t65547\n", "33\t59120\t119.7\t0\t59120\n", "34\t55637\t119.7\t0\t55637\n", "35\t63215\t119.7\t0\t63215\n", "36\t73958\t119.7\t0\t73958\n", "37\t80387\t119.7\t0\t80387\n", "38\t71280\t119.7\t0\t71280\n", "39\t57479\t119.7\t0\t57479\n", "40\t53326\t119.7\t0\t53326\n", "41\t59468\t119.7\t0\t59468\n", "42\t67920\t119.7\t0\t67920\n", "43\t60634\t119.7\t0\t60634\n", "44\t51320\t119.7\t0\t51320\n", "45\t64343\t119.7\t0\t64343\n", "46\t76999\t119.7\t0\t76999\n", "47\t65853\t119.7\t0\t65853\n", "48\t61839\t119.7\t0\t61839\n", "49\t51712\t119.7\t0\t51712\n", "50\t48257\t119.7\t0\t48257\n", "51\t42920\t119.7\t0\t42920\n", "52\t46434\t119.7\t0\t46434\n", "53\t44024\t119.7\t0\t44024\n", "54\t48436\t119.7\t0\t48436\n", "55\t54235\t119.7\t0\t54235\n", "56\t44864\t119.7\t0\t44864\n", "57\t38806\t119.7\t0\t38806\n", "58\t41125\t119.7\t0\t41125\n", "59\t38397\t119.7\t0\t38397\n", "60\t33154\t119.7\t0\t33154\n", "61\t30224\t119.7\t0\t30224\n", "62\t26187\t119.7\t0\t26187\n", "63\t25919\t119.7\t0\t25919\n", "64\t29151\t119.7\t0\t29151\n", "65\t26817\t119.7\t0\t26817\n", "66\t22860\t119.7\t0\t22860\n", "67\t23766\t119.7\t0\t23766\n", "68\t23958\t119.7\t0\t23958\n", "69\t24873\t119.7\t0\t24873\n", "70\t26527\t119.7\t0\t26527\n", "71\t25207\t119.7\t0\t25207\n", "72\t19690\t119.7\t0\t19690\n", "73\t16963\t119.7\t0\t16963\n", "74\t16918\t119.7\t0\t16918\n", "75\t15690\t119.7\t0\t15690\n", "76\t13243\t119.7\t0\t13243\n", "77\t13452\t119.7\t0\t13452\n", "78\t15980\t119.7\t0\t15980\n", "79\t14450\t119.7\t0\t14450\n", "80\t13795\t119.7\t0\t13795\n", "81\t13680\t119.7\t0\t13680\n", "82\t12843\t119.7\t0\t12843\n", "83\t12644\t119.7\t0\t12644\n", "84\t14037\t119.7\t0\t14037\n", "85\t15500\t119.7\t0\t15500\n", "86\t15217\t119.7\t0\t15217\n", "87\t12321\t119.7\t0\t12321\n", "88\t11512\t119.7\t0\t11512\n", "89\t10866\t119.7\t0\t10866\n", "90\t10573\t119.7\t0\t10573\n", "91\t10130\t119.7\t0\t10130\n", "92\t9389\t119.7\t0\t9389\n", "93\t9061\t119.7\t0\t9061\n", "94\t8201\t119.7\t0\t8201\n", "95\t7185\t119.7\t0\t7185\n", "96\t6033\t119.7\t0\t6033\n", "97\t5164\t119.7\t0\t5164\n", "98\t5448\t119.7\t0\t5448\n", "99\t7277\t119.7\t0\t7277\n", "100\t7110\t119.7\t0\t7110\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 54589 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 58.8%\n", " C: 20.3%\n", " G: 0.0%\n", " T: 20.8%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t17468\t122613.4\t0\t17468\n", "4\t4816\t30653.3\t0\t4816\n", "5\t1972\t7663.3\t0\t1972\n", "6\t543\t1915.8\t0\t543\n", "7\t143\t479.0\t0\t143\n", "8\t128\t119.7\t0\t128\n", "9\t122\t119.7\t0\t122\n", "10\t135\t119.7\t0\t135\n", "11\t99\t119.7\t0\t99\n", "12\t132\t119.7\t0\t132\n", "13\t123\t119.7\t0\t123\n", "14\t132\t119.7\t0\t132\n", "15\t130\t119.7\t0\t130\n", "16\t162\t119.7\t0\t162\n", "17\t185\t119.7\t0\t185\n", "18\t402\t119.7\t0\t402\n", "19\t688\t119.7\t0\t688\n", "20\t1145\t119.7\t0\t1145\n", "21\t669\t119.7\t0\t669\n", "22\t500\t119.7\t0\t500\n", "23\t302\t119.7\t0\t302\n", "24\t267\t119.7\t0\t267\n", "25\t266\t119.7\t0\t266\n", "26\t276\t119.7\t0\t276\n", "27\t285\t119.7\t0\t285\n", "28\t413\t119.7\t0\t413\n", "29\t715\t119.7\t0\t715\n", "30\t1227\t119.7\t0\t1227\n", "31\t1592\t119.7\t0\t1592\n", "32\t2149\t119.7\t0\t2149\n", "33\t2550\t119.7\t0\t2550\n", "34\t2972\t119.7\t0\t2972\n", "35\t3518\t119.7\t0\t3518\n", "36\t3372\t119.7\t0\t3372\n", "37\t1674\t119.7\t0\t1674\n", "38\t172\t119.7\t0\t172\n", "39\t128\t119.7\t0\t128\n", "40\t75\t119.7\t0\t75\n", "41\t68\t119.7\t0\t68\n", "42\t66\t119.7\t0\t66\n", "43\t58\t119.7\t0\t58\n", "44\t66\t119.7\t0\t66\n", "45\t56\t119.7\t0\t56\n", "46\t72\t119.7\t0\t72\n", "47\t47\t119.7\t0\t47\n", "48\t59\t119.7\t0\t59\n", "49\t61\t119.7\t0\t61\n", "50\t61\t119.7\t0\t61\n", "51\t47\t119.7\t0\t47\n", "52\t50\t119.7\t0\t50\n", "53\t57\t119.7\t0\t57\n", "54\t49\t119.7\t0\t49\n", "55\t36\t119.7\t0\t36\n", "56\t52\t119.7\t0\t52\n", "57\t45\t119.7\t0\t45\n", "58\t42\t119.7\t0\t42\n", "59\t34\t119.7\t0\t34\n", "60\t46\t119.7\t0\t46\n", "61\t37\t119.7\t0\t37\n", "62\t42\t119.7\t0\t42\n", "63\t43\t119.7\t0\t43\n", "64\t44\t119.7\t0\t44\n", "65\t33\t119.7\t0\t33\n", "66\t25\t119.7\t0\t25\n", "67\t45\t119.7\t0\t45\n", "68\t32\t119.7\t0\t32\n", "69\t30\t119.7\t0\t30\n", "70\t46\t119.7\t0\t46\n", "71\t36\t119.7\t0\t36\n", "72\t33\t119.7\t0\t33\n", "73\t23\t119.7\t0\t23\n", "74\t39\t119.7\t0\t39\n", "75\t25\t119.7\t0\t25\n", "76\t34\t119.7\t0\t34\n", "77\t33\t119.7\t0\t33\n", "78\t37\t119.7\t0\t37\n", "79\t38\t119.7\t0\t38\n", "80\t28\t119.7\t0\t28\n", "81\t14\t119.7\t0\t14\n", "82\t17\t119.7\t0\t17\n", "83\t19\t119.7\t0\t19\n", "84\t17\t119.7\t0\t17\n", "85\t28\t119.7\t0\t28\n", "86\t18\t119.7\t0\t18\n", "87\t33\t119.7\t0\t33\n", "88\t22\t119.7\t0\t22\n", "89\t28\t119.7\t0\t28\n", "90\t37\t119.7\t0\t37\n", "91\t27\t119.7\t0\t27\n", "92\t39\t119.7\t0\t39\n", "93\t39\t119.7\t0\t39\n", "94\t82\t119.7\t0\t82\n", "95\t91\t119.7\t0\t91\n", "96\t112\t119.7\t0\t112\n", "97\t165\t119.7\t0\t165\n", "98\t142\t119.7\t0\t142\n", "99\t67\t119.7\t0\t67\n", "100\t170\t119.7\t0\t170\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 169235 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 33.9%\n", " C: 18.2%\n", " G: 15.4%\n", " T: 32.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t118101\t122613.4\t0\t118101\n", "4\t32480\t30653.3\t0\t32480\n", "5\t3227\t7663.3\t0\t3227\n", "6\t379\t1915.8\t0\t379\n", "7\t94\t479.0\t0\t94\n", "8\t120\t479.0\t0\t120\n", "9\t105\t479.0\t0\t105\n", "10\t142\t479.0\t0\t142\n", "11\t122\t479.0\t0\t122\n", "12\t141\t479.0\t0\t141\n", "13\t148\t479.0\t0\t148\n", "14\t109\t479.0\t0\t109\n", "15\t143\t479.0\t0\t143\n", "16\t109\t479.0\t0\t109\n", "17\t108\t479.0\t0\t108\n", "18\t135\t479.0\t0\t135\n", "19\t155\t479.0\t0\t155\n", "20\t127\t479.0\t0\t127\n", "21\t121\t479.0\t0\t121\n", "22\t141\t479.0\t0\t141\n", "23\t125\t479.0\t0\t125\n", "24\t106\t479.0\t0\t106\n", "25\t115\t479.0\t0\t115\n", "26\t132\t479.0\t0\t132\n", "27\t169\t479.0\t0\t169\n", "28\t192\t479.0\t0\t192\n", "29\t169\t479.0\t0\t169\n", "30\t230\t479.0\t0\t230\n", "31\t170\t479.0\t0\t170\n", "32\t227\t479.0\t0\t227\n", "33\t198\t479.0\t0\t198\n", "34\t213\t479.0\t0\t213\n", "35\t227\t479.0\t0\t227\n", "36\t240\t479.0\t0\t240\n", "37\t213\t479.0\t0\t213\n", "38\t158\t479.0\t0\t158\n", "39\t194\t479.0\t0\t194\n", "40\t200\t479.0\t0\t200\n", "41\t166\t479.0\t0\t166\n", "42\t153\t479.0\t0\t153\n", "43\t189\t479.0\t0\t189\n", "44\t87\t479.0\t0\t87\n", "45\t141\t479.0\t0\t141\n", "46\t168\t479.0\t0\t168\n", "47\t135\t479.0\t0\t135\n", "48\t120\t479.0\t0\t120\n", "49\t153\t479.0\t0\t153\n", "50\t171\t479.0\t0\t171\n", "51\t131\t479.0\t0\t131\n", "52\t151\t479.0\t0\t151\n", "53\t187\t479.0\t0\t187\n", "54\t81\t479.0\t0\t81\n", "55\t165\t479.0\t0\t165\n", "56\t154\t479.0\t0\t154\n", "57\t330\t479.0\t0\t330\n", "58\t377\t479.0\t0\t377\n", "59\t193\t479.0\t0\t193\n", "60\t690\t479.0\t0\t690\n", "61\t497\t479.0\t0\t497\n", "62\t267\t479.0\t0\t267\n", "63\t269\t479.0\t0\t269\n", "64\t685\t479.0\t0\t685\n", "65\t144\t479.0\t0\t144\n", "66\t241\t479.0\t0\t241\n", "67\t182\t479.0\t0\t182\n", "68\t167\t479.0\t0\t167\n", "69\t80\t479.0\t0\t80\n", "70\t101\t479.0\t0\t101\n", "71\t129\t479.0\t0\t129\n", "72\t104\t479.0\t0\t104\n", "73\t114\t479.0\t0\t114\n", "74\t139\t479.0\t0\t139\n", "75\t86\t479.0\t0\t86\n", "76\t118\t479.0\t0\t118\n", "77\t78\t479.0\t0\t78\n", "78\t80\t479.0\t0\t80\n", "79\t72\t479.0\t0\t72\n", "80\t69\t479.0\t0\t69\n", "81\t72\t479.0\t0\t72\n", "82\t95\t479.0\t0\t95\n", "83\t82\t479.0\t0\t82\n", "84\t81\t479.0\t0\t81\n", "85\t97\t479.0\t0\t97\n", "86\t89\t479.0\t0\t89\n", "87\t177\t479.0\t0\t177\n", "88\t312\t479.0\t0\t312\n", "89\t201\t479.0\t0\t201\n", "90\t179\t479.0\t0\t179\n", "91\t98\t479.0\t0\t98\n", "92\t51\t479.0\t0\t51\n", "93\t51\t479.0\t0\t51\n", "94\t78\t479.0\t0\t78\n", "95\t59\t479.0\t0\t59\n", "96\t50\t479.0\t0\t50\n", "97\t56\t479.0\t0\t56\n", "98\t110\t479.0\t0\t110\n", "99\t127\t479.0\t0\t127\n", "100\t121\t479.0\t0\t121\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 337_S35_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/337.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 145.75 s (13 us/read; 4.45 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 10,801,907\n", "Reads with adapters: 7,483,583 (69.3%)\n", "Reads written (passing filters): 10,460,927 (96.8%)\n", "\n", "Total basepairs processed: 1,080,190,700 bp\n", "Quality-trimmed: 2,803,440 bp (0.3%)\n", "Total written (filtered): 802,492,193 bp (74.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 7306934 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.7%\n", " G: 37.0%\n", " T: 31.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t209722\t168779.8\t0\t209722\n", "4\t133654\t42194.9\t0\t133654\n", "5\t108879\t10548.7\t0\t108879\n", "6\t93413\t2637.2\t0\t93413\n", "7\t89870\t659.3\t0\t89870\n", "8\t91627\t164.8\t0\t91627\n", "9\t91467\t164.8\t0\t91467\n", "10\t89317\t164.8\t0\t89317\n", "11\t90379\t164.8\t0\t90379\n", "12\t91300\t164.8\t0\t91300\n", "13\t92268\t164.8\t0\t92268\n", "14\t96618\t164.8\t0\t96618\n", "15\t95343\t164.8\t0\t95343\n", "16\t100216\t164.8\t0\t100216\n", "17\t112821\t164.8\t0\t112821\n", "18\t127192\t164.8\t0\t127192\n", "19\t115861\t164.8\t0\t115861\n", "20\t97331\t164.8\t0\t97331\n", "21\t95786\t164.8\t0\t95786\n", "22\t86350\t164.8\t0\t86350\n", "23\t95641\t164.8\t0\t95641\n", "24\t111683\t164.8\t0\t111683\n", "25\t114870\t164.8\t0\t114870\n", "26\t130407\t164.8\t0\t130407\n", "27\t137185\t164.8\t0\t137185\n", "28\t124687\t164.8\t0\t124687\n", "29\t118612\t164.8\t0\t118612\n", "30\t120018\t164.8\t0\t120018\n", "31\t132139\t164.8\t0\t132139\n", "32\t130097\t164.8\t0\t130097\n", "33\t120230\t164.8\t0\t120230\n", "34\t116456\t164.8\t0\t116456\n", "35\t136882\t164.8\t0\t136882\n", "36\t156311\t164.8\t0\t156311\n", "37\t159239\t164.8\t0\t159239\n", "38\t134228\t164.8\t0\t134228\n", "39\t118305\t164.8\t0\t118305\n", "40\t106266\t164.8\t0\t106266\n", "41\t113645\t164.8\t0\t113645\n", "42\t122224\t164.8\t0\t122224\n", "43\t107573\t164.8\t0\t107573\n", "44\t84910\t164.8\t0\t84910\n", "45\t105826\t164.8\t0\t105826\n", "46\t123183\t164.8\t0\t123183\n", "47\t113810\t164.8\t0\t113810\n", "48\t117590\t164.8\t0\t117590\n", "49\t98163\t164.8\t0\t98163\n", "50\t95426\t164.8\t0\t95426\n", "51\t81407\t164.8\t0\t81407\n", "52\t88060\t164.8\t0\t88060\n", "53\t84399\t164.8\t0\t84399\n", "54\t79157\t164.8\t0\t79157\n", "55\t87487\t164.8\t0\t87487\n", "56\t86049\t164.8\t0\t86049\n", "57\t78732\t164.8\t0\t78732\n", "58\t86034\t164.8\t0\t86034\n", "59\t71599\t164.8\t0\t71599\n", "60\t62409\t164.8\t0\t62409\n", "61\t57809\t164.8\t0\t57809\n", "62\t46254\t164.8\t0\t46254\n", "63\t43025\t164.8\t0\t43025\n", "64\t49817\t164.8\t0\t49817\n", "65\t50320\t164.8\t0\t50320\n", "66\t42926\t164.8\t0\t42926\n", "67\t42806\t164.8\t0\t42806\n", "68\t40664\t164.8\t0\t40664\n", "69\t41550\t164.8\t0\t41550\n", "70\t42581\t164.8\t0\t42581\n", "71\t40273\t164.8\t0\t40273\n", "72\t31915\t164.8\t0\t31915\n", "73\t29550\t164.8\t0\t29550\n", "74\t29624\t164.8\t0\t29624\n", "75\t25767\t164.8\t0\t25767\n", "76\t21690\t164.8\t0\t21690\n", "77\t19537\t164.8\t0\t19537\n", "78\t22354\t164.8\t0\t22354\n", "79\t21153\t164.8\t0\t21153\n", "80\t21021\t164.8\t0\t21021\n", "81\t19157\t164.8\t0\t19157\n", "82\t18326\t164.8\t0\t18326\n", "83\t19768\t164.8\t0\t19768\n", "84\t22949\t164.8\t0\t22949\n", "85\t25787\t164.8\t0\t25787\n", "86\t24152\t164.8\t0\t24152\n", "87\t15686\t164.8\t0\t15686\n", "88\t13326\t164.8\t0\t13326\n", "89\t15163\t164.8\t0\t15163\n", "90\t16625\t164.8\t0\t16625\n", "91\t18051\t164.8\t0\t18051\n", "92\t19170\t164.8\t0\t19170\n", "93\t22703\t164.8\t0\t22703\n", "94\t20806\t164.8\t0\t20806\n", "95\t17985\t164.8\t0\t17985\n", "96\t13389\t164.8\t0\t13389\n", "97\t8695\t164.8\t0\t8695\n", "98\t4950\t164.8\t0\t4950\n", "99\t6482\t164.8\t0\t6482\n", "100\t2775\t164.8\t0\t2775\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 40506 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 59.7%\n", " C: 20.1%\n", " G: 0.0%\n", " T: 20.1%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t14484\t168779.8\t0\t14484\n", "4\t3629\t42194.9\t0\t3629\n", "5\t1036\t10548.7\t0\t1036\n", "6\t626\t2637.2\t0\t626\n", "7\t180\t659.3\t0\t180\n", "8\t127\t164.8\t0\t127\n", "9\t127\t164.8\t0\t127\n", "10\t109\t164.8\t0\t109\n", "11\t119\t164.8\t0\t119\n", "12\t81\t164.8\t0\t81\n", "13\t118\t164.8\t0\t118\n", "14\t102\t164.8\t0\t102\n", "15\t139\t164.8\t0\t139\n", "16\t132\t164.8\t0\t132\n", "17\t118\t164.8\t0\t118\n", "18\t197\t164.8\t0\t197\n", "19\t222\t164.8\t0\t222\n", "20\t445\t164.8\t0\t445\n", "21\t332\t164.8\t0\t332\n", "22\t255\t164.8\t0\t255\n", "23\t179\t164.8\t0\t179\n", "24\t218\t164.8\t0\t218\n", "25\t246\t164.8\t0\t246\n", "26\t448\t164.8\t0\t448\n", "27\t436\t164.8\t0\t436\n", "28\t469\t164.8\t0\t469\n", "29\t614\t164.8\t0\t614\n", "30\t972\t164.8\t0\t972\n", "31\t1229\t164.8\t0\t1229\n", "32\t1896\t164.8\t0\t1896\n", "33\t1862\t164.8\t0\t1862\n", "34\t1788\t164.8\t0\t1788\n", "35\t2337\t164.8\t0\t2337\n", "36\t2209\t164.8\t0\t2209\n", "37\t827\t164.8\t0\t827\n", "38\t78\t164.8\t0\t78\n", "39\t48\t164.8\t0\t48\n", "40\t64\t164.8\t0\t64\n", "41\t60\t164.8\t0\t60\n", "42\t55\t164.8\t0\t55\n", "43\t65\t164.8\t0\t65\n", "44\t58\t164.8\t0\t58\n", "45\t64\t164.8\t0\t64\n", "46\t52\t164.8\t0\t52\n", "47\t41\t164.8\t0\t41\n", "48\t65\t164.8\t0\t65\n", "49\t56\t164.8\t0\t56\n", "50\t62\t164.8\t0\t62\n", "51\t55\t164.8\t0\t55\n", "52\t36\t164.8\t0\t36\n", "53\t37\t164.8\t0\t37\n", "54\t31\t164.8\t0\t31\n", "55\t30\t164.8\t0\t30\n", "56\t37\t164.8\t0\t37\n", "57\t29\t164.8\t0\t29\n", "58\t45\t164.8\t0\t45\n", "59\t24\t164.8\t0\t24\n", "60\t34\t164.8\t0\t34\n", "61\t39\t164.8\t0\t39\n", "62\t37\t164.8\t0\t37\n", "63\t33\t164.8\t0\t33\n", "64\t26\t164.8\t0\t26\n", "65\t22\t164.8\t0\t22\n", "66\t23\t164.8\t0\t23\n", "67\t21\t164.8\t0\t21\n", "68\t18\t164.8\t0\t18\n", "69\t22\t164.8\t0\t22\n", "70\t19\t164.8\t0\t19\n", "71\t16\t164.8\t0\t16\n", "72\t11\t164.8\t0\t11\n", "73\t10\t164.8\t0\t10\n", "74\t13\t164.8\t0\t13\n", "75\t12\t164.8\t0\t12\n", "76\t5\t164.8\t0\t5\n", "77\t10\t164.8\t0\t10\n", "78\t18\t164.8\t0\t18\n", "79\t7\t164.8\t0\t7\n", "80\t10\t164.8\t0\t10\n", "81\t12\t164.8\t0\t12\n", "82\t8\t164.8\t0\t8\n", "83\t9\t164.8\t0\t9\n", "84\t8\t164.8\t0\t8\n", "85\t16\t164.8\t0\t16\n", "86\t8\t164.8\t0\t8\n", "87\t13\t164.8\t0\t13\n", "88\t7\t164.8\t0\t7\n", "89\t10\t164.8\t0\t10\n", "90\t22\t164.8\t0\t22\n", "91\t20\t164.8\t0\t20\n", "92\t33\t164.8\t0\t33\n", "93\t53\t164.8\t0\t53\n", "94\t70\t164.8\t0\t70\n", "95\t65\t164.8\t0\t65\n", "96\t86\t164.8\t0\t86\n", "97\t69\t164.8\t0\t69\n", "98\t61\t164.8\t0\t61\n", "99\t35\t164.8\t0\t35\n", "100\t95\t164.8\t0\t95\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 136143 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.7%\n", " C: 17.4%\n", " G: 16.0%\n", " T: 20.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t94419\t168779.8\t0\t94419\n", "4\t23743\t42194.9\t0\t23743\n", "5\t4518\t10548.7\t0\t4518\n", "6\t380\t2637.2\t0\t380\n", "7\t168\t659.3\t0\t168\n", "8\t190\t659.3\t0\t190\n", "9\t154\t659.3\t0\t154\n", "10\t188\t659.3\t0\t188\n", "11\t200\t659.3\t0\t200\n", "12\t200\t659.3\t0\t200\n", "13\t204\t659.3\t0\t204\n", "14\t221\t659.3\t0\t221\n", "15\t232\t659.3\t0\t232\n", "16\t215\t659.3\t0\t215\n", "17\t216\t659.3\t0\t216\n", "18\t182\t659.3\t0\t182\n", "19\t179\t659.3\t0\t179\n", "20\t187\t659.3\t0\t187\n", "21\t192\t659.3\t0\t192\n", "22\t183\t659.3\t0\t183\n", "23\t149\t659.3\t0\t149\n", "24\t156\t659.3\t0\t156\n", "25\t197\t659.3\t0\t197\n", "26\t132\t659.3\t0\t132\n", "27\t197\t659.3\t0\t197\n", "28\t189\t659.3\t0\t189\n", "29\t161\t659.3\t0\t161\n", "30\t200\t659.3\t0\t200\n", "31\t197\t659.3\t0\t197\n", "32\t223\t659.3\t0\t223\n", "33\t153\t659.3\t0\t153\n", "34\t199\t659.3\t0\t199\n", "35\t164\t659.3\t0\t164\n", "36\t190\t659.3\t0\t190\n", "37\t147\t659.3\t0\t147\n", "38\t150\t659.3\t0\t150\n", "39\t212\t659.3\t0\t212\n", "40\t203\t659.3\t0\t203\n", "41\t166\t659.3\t0\t166\n", "42\t132\t659.3\t0\t132\n", "43\t178\t659.3\t0\t178\n", "44\t91\t659.3\t0\t91\n", "45\t142\t659.3\t0\t142\n", "46\t164\t659.3\t0\t164\n", "47\t108\t659.3\t0\t108\n", "48\t120\t659.3\t0\t120\n", "49\t129\t659.3\t0\t129\n", "50\t92\t659.3\t0\t92\n", "51\t108\t659.3\t0\t108\n", "52\t114\t659.3\t0\t114\n", "53\t100\t659.3\t0\t100\n", "54\t96\t659.3\t0\t96\n", "55\t94\t659.3\t0\t94\n", "56\t91\t659.3\t0\t91\n", "57\t99\t659.3\t0\t99\n", "58\t99\t659.3\t0\t99\n", "59\t106\t659.3\t0\t106\n", "60\t102\t659.3\t0\t102\n", "61\t88\t659.3\t0\t88\n", "62\t77\t659.3\t0\t77\n", "63\t78\t659.3\t0\t78\n", "64\t81\t659.3\t0\t81\n", "65\t101\t659.3\t0\t101\n", "66\t88\t659.3\t0\t88\n", "67\t87\t659.3\t0\t87\n", "68\t82\t659.3\t0\t82\n", "69\t75\t659.3\t0\t75\n", "70\t63\t659.3\t0\t63\n", "71\t75\t659.3\t0\t75\n", "72\t113\t659.3\t0\t113\n", "73\t110\t659.3\t0\t110\n", "74\t137\t659.3\t0\t137\n", "75\t120\t659.3\t0\t120\n", "76\t121\t659.3\t0\t121\n", "77\t154\t659.3\t0\t154\n", "78\t148\t659.3\t0\t148\n", "79\t143\t659.3\t0\t143\n", "80\t144\t659.3\t0\t144\n", "81\t172\t659.3\t0\t172\n", "82\t189\t659.3\t0\t189\n", "83\t162\t659.3\t0\t162\n", "84\t155\t659.3\t0\t155\n", "85\t147\t659.3\t0\t147\n", "86\t116\t659.3\t0\t116\n", "87\t116\t659.3\t0\t116\n", "88\t132\t659.3\t0\t132\n", "89\t108\t659.3\t0\t108\n", "90\t127\t659.3\t0\t127\n", "91\t68\t659.3\t0\t68\n", "92\t72\t659.3\t0\t72\n", "93\t74\t659.3\t0\t74\n", "94\t71\t659.3\t0\t71\n", "95\t67\t659.3\t0\t67\n", "96\t71\t659.3\t0\t71\n", "97\t100\t659.3\t0\t100\n", "98\t123\t659.3\t0\t123\n", "99\t124\t659.3\t0\t124\n", "100\t143\t659.3\t0\t143\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 338_S4_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/338.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 85.40 s (13 us/read; 4.55 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,474,350\n", "Reads with adapters: 3,769,009 (58.2%)\n", "Reads written (passing filters): 6,309,501 (97.5%)\n", "\n", "Total basepairs processed: 647,435,000 bp\n", "Quality-trimmed: 1,497,859 bp (0.2%)\n", "Total written (filtered): 512,493,423 bp (79.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3615132 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 32.0%\n", " G: 39.0%\n", " T: 29.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t130876\t101161.7\t0\t130876\n", "4\t76347\t25290.4\t0\t76347\n", "5\t56729\t6322.6\t0\t56729\n", "6\t49028\t1580.7\t0\t49028\n", "7\t45118\t395.2\t0\t45118\n", "8\t45871\t98.8\t0\t45871\n", "9\t44995\t98.8\t0\t44995\n", "10\t44696\t98.8\t0\t44696\n", "11\t45488\t98.8\t0\t45488\n", "12\t45986\t98.8\t0\t45986\n", "13\t50161\t98.8\t0\t50161\n", "14\t51318\t98.8\t0\t51318\n", "15\t49187\t98.8\t0\t49187\n", "16\t51369\t98.8\t0\t51369\n", "17\t55959\t98.8\t0\t55959\n", "18\t63166\t98.8\t0\t63166\n", "19\t57940\t98.8\t0\t57940\n", "20\t50008\t98.8\t0\t50008\n", "21\t47761\t98.8\t0\t47761\n", "22\t44450\t98.8\t0\t44450\n", "23\t48797\t98.8\t0\t48797\n", "24\t55781\t98.8\t0\t55781\n", "25\t58913\t98.8\t0\t58913\n", "26\t65221\t98.8\t0\t65221\n", "27\t68251\t98.8\t0\t68251\n", "28\t63545\t98.8\t0\t63545\n", "29\t60105\t98.8\t0\t60105\n", "30\t61332\t98.8\t0\t61332\n", "31\t65451\t98.8\t0\t65451\n", "32\t61375\t98.8\t0\t61375\n", "33\t57812\t98.8\t0\t57812\n", "34\t57213\t98.8\t0\t57213\n", "35\t63088\t98.8\t0\t63088\n", "36\t70772\t98.8\t0\t70772\n", "37\t75315\t98.8\t0\t75315\n", "38\t62115\t98.8\t0\t62115\n", "39\t54727\t98.8\t0\t54727\n", "40\t52548\t98.8\t0\t52548\n", "41\t58236\t98.8\t0\t58236\n", "42\t64055\t98.8\t0\t64055\n", "43\t55978\t98.8\t0\t55978\n", "44\t44433\t98.8\t0\t44433\n", "45\t52326\t98.8\t0\t52326\n", "46\t60209\t98.8\t0\t60209\n", "47\t57750\t98.8\t0\t57750\n", "48\t55788\t98.8\t0\t55788\n", "49\t46205\t98.8\t0\t46205\n", "50\t43705\t98.8\t0\t43705\n", "51\t39190\t98.8\t0\t39190\n", "52\t38581\t98.8\t0\t38581\n", "53\t35548\t98.8\t0\t35548\n", "54\t37674\t98.8\t0\t37674\n", "55\t40357\t98.8\t0\t40357\n", "56\t37258\t98.8\t0\t37258\n", "57\t35913\t98.8\t0\t35913\n", "58\t41097\t98.8\t0\t41097\n", "59\t35708\t98.8\t0\t35708\n", "60\t30920\t98.8\t0\t30920\n", "61\t27312\t98.8\t0\t27312\n", "62\t22196\t98.8\t0\t22196\n", "63\t21127\t98.8\t0\t21127\n", "64\t22955\t98.8\t0\t22955\n", "65\t22525\t98.8\t0\t22525\n", "66\t19825\t98.8\t0\t19825\n", "67\t19637\t98.8\t0\t19637\n", "68\t18761\t98.8\t0\t18761\n", "69\t18628\t98.8\t0\t18628\n", "70\t19758\t98.8\t0\t19758\n", "71\t19049\t98.8\t0\t19049\n", "72\t15219\t98.8\t0\t15219\n", "73\t13842\t98.8\t0\t13842\n", "74\t13626\t98.8\t0\t13626\n", "75\t12374\t98.8\t0\t12374\n", "76\t10578\t98.8\t0\t10578\n", "77\t10082\t98.8\t0\t10082\n", "78\t11004\t98.8\t0\t11004\n", "79\t11083\t98.8\t0\t11083\n", "80\t10874\t98.8\t0\t10874\n", "81\t10362\t98.8\t0\t10362\n", "82\t9622\t98.8\t0\t9622\n", "83\t9992\t98.8\t0\t9992\n", "84\t10785\t98.8\t0\t10785\n", "85\t11975\t98.8\t0\t11975\n", "86\t11579\t98.8\t0\t11579\n", "87\t9023\t98.8\t0\t9023\n", "88\t8364\t98.8\t0\t8364\n", "89\t8433\t98.8\t0\t8433\n", "90\t8362\t98.8\t0\t8362\n", "91\t8225\t98.8\t0\t8225\n", "92\t8046\t98.8\t0\t8046\n", "93\t8715\t98.8\t0\t8715\n", "94\t8515\t98.8\t0\t8515\n", "95\t7412\t98.8\t0\t7412\n", "96\t5526\t98.8\t0\t5526\n", "97\t3569\t98.8\t0\t3569\n", "98\t2216\t98.8\t0\t2216\n", "99\t2791\t98.8\t0\t2791\n", "100\t1420\t98.8\t0\t1420\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 39473 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 56.4%\n", " C: 22.4%\n", " G: 0.0%\n", " T: 21.1%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13347\t101161.7\t0\t13347\n", "4\t3911\t25290.4\t0\t3911\n", "5\t2238\t6322.6\t0\t2238\n", "6\t1696\t1580.7\t0\t1696\n", "7\t677\t395.2\t0\t677\n", "8\t545\t98.8\t0\t545\n", "9\t474\t98.8\t0\t474\n", "10\t477\t98.8\t0\t477\n", "11\t426\t98.8\t0\t426\n", "12\t421\t98.8\t0\t421\n", "13\t385\t98.8\t0\t385\n", "14\t363\t98.8\t0\t363\n", "15\t285\t98.8\t0\t285\n", "16\t337\t98.8\t0\t337\n", "17\t329\t98.8\t0\t329\n", "18\t388\t98.8\t0\t388\n", "19\t441\t98.8\t0\t441\n", "20\t447\t98.8\t0\t447\n", "21\t356\t98.8\t0\t356\n", "22\t317\t98.8\t0\t317\n", "23\t303\t98.8\t0\t303\n", "24\t321\t98.8\t0\t321\n", "25\t370\t98.8\t0\t370\n", "26\t636\t98.8\t0\t636\n", "27\t549\t98.8\t0\t549\n", "28\t479\t98.8\t0\t479\n", "29\t502\t98.8\t0\t502\n", "30\t759\t98.8\t0\t759\n", "31\t713\t98.8\t0\t713\n", "32\t905\t98.8\t0\t905\n", "33\t856\t98.8\t0\t856\n", "34\t865\t98.8\t0\t865\n", "35\t1034\t98.8\t0\t1034\n", "36\t1027\t98.8\t0\t1027\n", "37\t386\t98.8\t0\t386\n", "38\t66\t98.8\t0\t66\n", "39\t39\t98.8\t0\t39\n", "40\t42\t98.8\t0\t42\n", "41\t38\t98.8\t0\t38\n", "42\t47\t98.8\t0\t47\n", "43\t33\t98.8\t0\t33\n", "44\t42\t98.8\t0\t42\n", "45\t48\t98.8\t0\t48\n", "46\t38\t98.8\t0\t38\n", "47\t36\t98.8\t0\t36\n", "48\t38\t98.8\t0\t38\n", "49\t36\t98.8\t0\t36\n", "50\t38\t98.8\t0\t38\n", "51\t39\t98.8\t0\t39\n", "52\t44\t98.8\t0\t44\n", "53\t38\t98.8\t0\t38\n", "54\t40\t98.8\t0\t40\n", "55\t23\t98.8\t0\t23\n", "56\t38\t98.8\t0\t38\n", "57\t32\t98.8\t0\t32\n", "58\t33\t98.8\t0\t33\n", "59\t30\t98.8\t0\t30\n", "60\t32\t98.8\t0\t32\n", "61\t24\t98.8\t0\t24\n", "62\t34\t98.8\t0\t34\n", "63\t26\t98.8\t0\t26\n", "64\t37\t98.8\t0\t37\n", "65\t18\t98.8\t0\t18\n", "66\t26\t98.8\t0\t26\n", "67\t25\t98.8\t0\t25\n", "68\t16\t98.8\t0\t16\n", "69\t21\t98.8\t0\t21\n", "70\t14\t98.8\t0\t14\n", "71\t17\t98.8\t0\t17\n", "72\t1\t98.8\t0\t1\n", "73\t13\t98.8\t0\t13\n", "74\t12\t98.8\t0\t12\n", "75\t4\t98.8\t0\t4\n", "76\t10\t98.8\t0\t10\n", "77\t9\t98.8\t0\t9\n", "78\t9\t98.8\t0\t9\n", "79\t13\t98.8\t0\t13\n", "80\t9\t98.8\t0\t9\n", "81\t10\t98.8\t0\t10\n", "82\t6\t98.8\t0\t6\n", "83\t15\t98.8\t0\t15\n", "84\t16\t98.8\t0\t16\n", "85\t13\t98.8\t0\t13\n", "86\t5\t98.8\t0\t5\n", "87\t13\t98.8\t0\t13\n", "88\t11\t98.8\t0\t11\n", "89\t16\t98.8\t0\t16\n", "90\t11\t98.8\t0\t11\n", "91\t10\t98.8\t0\t10\n", "92\t20\t98.8\t0\t20\n", "93\t38\t98.8\t0\t38\n", "94\t53\t98.8\t0\t53\n", "95\t73\t98.8\t0\t73\n", "96\t79\t98.8\t0\t79\n", "97\t75\t98.8\t0\t75\n", "98\t46\t98.8\t0\t46\n", "99\t74\t98.8\t0\t74\n", "100\t96\t98.8\t0\t96\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 114404 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.7%\n", " C: 20.3%\n", " G: 16.8%\n", " T: 19.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t73923\t101161.7\t0\t73923\n", "4\t14786\t25290.4\t0\t14786\n", "5\t2948\t6322.6\t0\t2948\n", "6\t847\t1580.7\t0\t847\n", "7\t674\t395.2\t0\t674\n", "8\t656\t395.2\t0\t656\n", "9\t554\t395.2\t0\t554\n", "10\t665\t395.2\t0\t665\n", "11\t635\t395.2\t0\t635\n", "12\t639\t395.2\t0\t639\n", "13\t556\t395.2\t0\t556\n", "14\t601\t395.2\t0\t601\n", "15\t602\t395.2\t0\t602\n", "16\t653\t395.2\t0\t653\n", "17\t581\t395.2\t0\t581\n", "18\t561\t395.2\t0\t561\n", "19\t523\t395.2\t0\t523\n", "20\t567\t395.2\t0\t567\n", "21\t535\t395.2\t0\t535\n", "22\t455\t395.2\t0\t455\n", "23\t520\t395.2\t0\t520\n", "24\t455\t395.2\t0\t455\n", "25\t442\t395.2\t0\t442\n", "26\t419\t395.2\t0\t419\n", "27\t406\t395.2\t0\t406\n", "28\t423\t395.2\t0\t423\n", "29\t355\t395.2\t0\t355\n", "30\t397\t395.2\t0\t397\n", "31\t337\t395.2\t0\t337\n", "32\t349\t395.2\t0\t349\n", "33\t307\t395.2\t0\t307\n", "34\t339\t395.2\t0\t339\n", "35\t272\t395.2\t0\t272\n", "36\t307\t395.2\t0\t307\n", "37\t257\t395.2\t0\t257\n", "38\t238\t395.2\t0\t238\n", "39\t275\t395.2\t0\t275\n", "40\t231\t395.2\t0\t231\n", "41\t215\t395.2\t0\t215\n", "42\t208\t395.2\t0\t208\n", "43\t329\t395.2\t0\t329\n", "44\t89\t395.2\t0\t89\n", "45\t177\t395.2\t0\t177\n", "46\t163\t395.2\t0\t163\n", "47\t179\t395.2\t0\t179\n", "48\t168\t395.2\t0\t168\n", "49\t153\t395.2\t0\t153\n", "50\t157\t395.2\t0\t157\n", "51\t156\t395.2\t0\t156\n", "52\t171\t395.2\t0\t171\n", "53\t150\t395.2\t0\t150\n", "54\t126\t395.2\t0\t126\n", "55\t150\t395.2\t0\t150\n", "56\t130\t395.2\t0\t130\n", "57\t104\t395.2\t0\t104\n", "58\t132\t395.2\t0\t132\n", "59\t81\t395.2\t0\t81\n", "60\t102\t395.2\t0\t102\n", "61\t105\t395.2\t0\t105\n", "62\t89\t395.2\t0\t89\n", "63\t65\t395.2\t0\t65\n", "64\t102\t395.2\t0\t102\n", "65\t97\t395.2\t0\t97\n", "66\t85\t395.2\t0\t85\n", "67\t80\t395.2\t0\t80\n", "68\t122\t395.2\t0\t122\n", "69\t64\t395.2\t0\t64\n", "70\t68\t395.2\t0\t68\n", "71\t74\t395.2\t0\t74\n", "72\t81\t395.2\t0\t81\n", "73\t89\t395.2\t0\t89\n", "74\t82\t395.2\t0\t82\n", "75\t70\t395.2\t0\t70\n", "76\t71\t395.2\t0\t71\n", "77\t66\t395.2\t0\t66\n", "78\t54\t395.2\t0\t54\n", "79\t63\t395.2\t0\t63\n", "80\t72\t395.2\t0\t72\n", "81\t72\t395.2\t0\t72\n", "82\t78\t395.2\t0\t78\n", "83\t76\t395.2\t0\t76\n", "84\t92\t395.2\t0\t92\n", "85\t73\t395.2\t0\t73\n", "86\t56\t395.2\t0\t56\n", "87\t70\t395.2\t0\t70\n", "88\t110\t395.2\t0\t110\n", "89\t59\t395.2\t0\t59\n", "90\t69\t395.2\t0\t69\n", "91\t59\t395.2\t0\t59\n", "92\t46\t395.2\t0\t46\n", "93\t41\t395.2\t0\t41\n", "94\t50\t395.2\t0\t50\n", "95\t50\t395.2\t0\t50\n", "96\t42\t395.2\t0\t42\n", "97\t77\t395.2\t0\t77\n", "98\t63\t395.2\t0\t63\n", "99\t95\t395.2\t0\t95\n", "100\t97\t395.2\t0\t97\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 339_S10_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/339.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 97.69 s (13 us/read; 4.55 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,409,330\n", "Reads with adapters: 4,993,613 (67.4%)\n", "Reads written (passing filters): 7,152,967 (96.5%)\n", "\n", "Total basepairs processed: 740,933,000 bp\n", "Quality-trimmed: 2,037,301 bp (0.3%)\n", "Total written (filtered): 542,118,811 bp (73.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4828788 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.4%\n", " G: 39.0%\n", " T: 27.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t128173\t115770.8\t0\t128173\n", "4\t76018\t28942.7\t0\t76018\n", "5\t58999\t7235.7\t0\t58999\n", "6\t51108\t1808.9\t0\t51108\n", "7\t47736\t452.2\t0\t47736\n", "8\t48533\t113.1\t0\t48533\n", "9\t47998\t113.1\t0\t47998\n", "10\t47893\t113.1\t0\t47893\n", "11\t48457\t113.1\t0\t48457\n", "12\t48431\t113.1\t0\t48431\n", "13\t53222\t113.1\t0\t53222\n", "14\t54362\t113.1\t0\t54362\n", "15\t53882\t113.1\t0\t53882\n", "16\t56525\t113.1\t0\t56525\n", "17\t62927\t113.1\t0\t62927\n", "18\t71535\t113.1\t0\t71535\n", "19\t64958\t113.1\t0\t64958\n", "20\t55360\t113.1\t0\t55360\n", "21\t53506\t113.1\t0\t53506\n", "22\t50424\t113.1\t0\t50424\n", "23\t55615\t113.1\t0\t55615\n", "24\t64334\t113.1\t0\t64334\n", "25\t68370\t113.1\t0\t68370\n", "26\t76583\t113.1\t0\t76583\n", "27\t81847\t113.1\t0\t81847\n", "28\t75420\t113.1\t0\t75420\n", "29\t71306\t113.1\t0\t71306\n", "30\t74218\t113.1\t0\t74218\n", "31\t82123\t113.1\t0\t82123\n", "32\t77232\t113.1\t0\t77232\n", "33\t73638\t113.1\t0\t73638\n", "34\t74487\t113.1\t0\t74487\n", "35\t86079\t113.1\t0\t86079\n", "36\t98513\t113.1\t0\t98513\n", "37\t102438\t113.1\t0\t102438\n", "38\t87183\t113.1\t0\t87183\n", "39\t78840\t113.1\t0\t78840\n", "40\t74981\t113.1\t0\t74981\n", "41\t81618\t113.1\t0\t81618\n", "42\t90140\t113.1\t0\t90140\n", "43\t79122\t113.1\t0\t79122\n", "44\t62856\t113.1\t0\t62856\n", "45\t75091\t113.1\t0\t75091\n", "46\t88729\t113.1\t0\t88729\n", "47\t86678\t113.1\t0\t86678\n", "48\t83516\t113.1\t0\t83516\n", "49\t70901\t113.1\t0\t70901\n", "50\t66503\t113.1\t0\t66503\n", "51\t56229\t113.1\t0\t56229\n", "52\t61327\t113.1\t0\t61327\n", "53\t68929\t113.1\t0\t68929\n", "54\t75166\t113.1\t0\t75166\n", "55\t68706\t113.1\t0\t68706\n", "56\t66959\t113.1\t0\t66959\n", "57\t62928\t113.1\t0\t62928\n", "58\t61646\t113.1\t0\t61646\n", "59\t51794\t113.1\t0\t51794\n", "60\t47075\t113.1\t0\t47075\n", "61\t44679\t113.1\t0\t44679\n", "62\t36662\t113.1\t0\t36662\n", "63\t34727\t113.1\t0\t34727\n", "64\t39733\t113.1\t0\t39733\n", "65\t39749\t113.1\t0\t39749\n", "66\t34427\t113.1\t0\t34427\n", "67\t34551\t113.1\t0\t34551\n", "68\t33753\t113.1\t0\t33753\n", "69\t34721\t113.1\t0\t34721\n", "70\t35921\t113.1\t0\t35921\n", "71\t35063\t113.1\t0\t35063\n", "72\t27666\t113.1\t0\t27666\n", "73\t25576\t113.1\t0\t25576\n", "74\t24896\t113.1\t0\t24896\n", "75\t22461\t113.1\t0\t22461\n", "76\t18790\t113.1\t0\t18790\n", "77\t17325\t113.1\t0\t17325\n", "78\t19562\t113.1\t0\t19562\n", "79\t18517\t113.1\t0\t18517\n", "80\t18098\t113.1\t0\t18098\n", "81\t16315\t113.1\t0\t16315\n", "82\t15264\t113.1\t0\t15264\n", "83\t16050\t113.1\t0\t16050\n", "84\t17896\t113.1\t0\t17896\n", "85\t19461\t113.1\t0\t19461\n", "86\t17750\t113.1\t0\t17750\n", "87\t12838\t113.1\t0\t12838\n", "88\t11324\t113.1\t0\t11324\n", "89\t11723\t113.1\t0\t11723\n", "90\t12276\t113.1\t0\t12276\n", "91\t12327\t113.1\t0\t12327\n", "92\t12921\t113.1\t0\t12921\n", "93\t14245\t113.1\t0\t14245\n", "94\t13959\t113.1\t0\t13959\n", "95\t12141\t113.1\t0\t12141\n", "96\t9189\t113.1\t0\t9189\n", "97\t6087\t113.1\t0\t6087\n", "98\t3514\t113.1\t0\t3514\n", "99\t5082\t113.1\t0\t5082\n", "100\t2382\t113.1\t0\t2382\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 65433 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 70.9%\n", " C: 15.4%\n", " G: 0.0%\n", " T: 13.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13891\t115770.8\t0\t13891\n", "4\t3347\t28942.7\t0\t3347\n", "5\t1319\t7235.7\t0\t1319\n", "6\t1108\t1808.9\t0\t1108\n", "7\t207\t452.2\t0\t207\n", "8\t164\t113.1\t0\t164\n", "9\t135\t113.1\t0\t135\n", "10\t163\t113.1\t0\t163\n", "11\t147\t113.1\t0\t147\n", "12\t182\t113.1\t0\t182\n", "13\t151\t113.1\t0\t151\n", "14\t165\t113.1\t0\t165\n", "15\t173\t113.1\t0\t173\n", "16\t221\t113.1\t0\t221\n", "17\t392\t113.1\t0\t392\n", "18\t836\t113.1\t0\t836\n", "19\t1242\t113.1\t0\t1242\n", "20\t2514\t113.1\t0\t2514\n", "21\t1435\t113.1\t0\t1435\n", "22\t691\t113.1\t0\t691\n", "23\t407\t113.1\t0\t407\n", "24\t352\t113.1\t0\t352\n", "25\t390\t113.1\t0\t390\n", "26\t661\t113.1\t0\t661\n", "27\t674\t113.1\t0\t674\n", "28\t844\t113.1\t0\t844\n", "29\t1097\t113.1\t0\t1097\n", "30\t1865\t113.1\t0\t1865\n", "31\t2230\t113.1\t0\t2230\n", "32\t3240\t113.1\t0\t3240\n", "33\t3543\t113.1\t0\t3543\n", "34\t4222\t113.1\t0\t4222\n", "35\t5812\t113.1\t0\t5812\n", "36\t6573\t113.1\t0\t6573\n", "37\t2979\t113.1\t0\t2979\n", "38\t117\t113.1\t0\t117\n", "39\t61\t113.1\t0\t61\n", "40\t39\t113.1\t0\t39\n", "41\t44\t113.1\t0\t44\n", "42\t41\t113.1\t0\t41\n", "43\t41\t113.1\t0\t41\n", "44\t51\t113.1\t0\t51\n", "45\t49\t113.1\t0\t49\n", "46\t43\t113.1\t0\t43\n", "47\t43\t113.1\t0\t43\n", "48\t34\t113.1\t0\t34\n", "49\t45\t113.1\t0\t45\n", "50\t62\t113.1\t0\t62\n", "51\t45\t113.1\t0\t45\n", "52\t38\t113.1\t0\t38\n", "53\t40\t113.1\t0\t40\n", "54\t31\t113.1\t0\t31\n", "55\t34\t113.1\t0\t34\n", "56\t33\t113.1\t0\t33\n", "57\t39\t113.1\t0\t39\n", "58\t29\t113.1\t0\t29\n", "59\t28\t113.1\t0\t28\n", "60\t32\t113.1\t0\t32\n", "61\t31\t113.1\t0\t31\n", "62\t26\t113.1\t0\t26\n", "63\t28\t113.1\t0\t28\n", "64\t30\t113.1\t0\t30\n", "65\t42\t113.1\t0\t42\n", "66\t25\t113.1\t0\t25\n", "67\t23\t113.1\t0\t23\n", "68\t24\t113.1\t0\t24\n", "69\t14\t113.1\t0\t14\n", "70\t19\t113.1\t0\t19\n", "71\t13\t113.1\t0\t13\n", "72\t16\t113.1\t0\t16\n", "73\t6\t113.1\t0\t6\n", "74\t10\t113.1\t0\t10\n", "75\t10\t113.1\t0\t10\n", "76\t11\t113.1\t0\t11\n", "77\t13\t113.1\t0\t13\n", "78\t10\t113.1\t0\t10\n", "79\t13\t113.1\t0\t13\n", "80\t8\t113.1\t0\t8\n", "81\t6\t113.1\t0\t6\n", "82\t12\t113.1\t0\t12\n", "83\t5\t113.1\t0\t5\n", "84\t15\t113.1\t0\t15\n", "85\t6\t113.1\t0\t6\n", "86\t10\t113.1\t0\t10\n", "87\t8\t113.1\t0\t8\n", "88\t6\t113.1\t0\t6\n", "89\t12\t113.1\t0\t12\n", "90\t7\t113.1\t0\t7\n", "91\t18\t113.1\t0\t18\n", "92\t24\t113.1\t0\t24\n", "93\t42\t113.1\t0\t42\n", "94\t51\t113.1\t0\t51\n", "95\t82\t113.1\t0\t82\n", "96\t76\t113.1\t0\t76\n", "97\t73\t113.1\t0\t73\n", "98\t67\t113.1\t0\t67\n", "99\t49\t113.1\t0\t49\n", "100\t101\t113.1\t0\t101\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 99392 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.5%\n", " C: 20.8%\n", " G: 17.0%\n", " T: 20.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t70499\t115770.8\t0\t70499\n", "4\t15614\t28942.7\t0\t15614\n", "5\t3221\t7235.7\t0\t3221\n", "6\t315\t1808.9\t0\t315\n", "7\t161\t452.2\t0\t161\n", "8\t220\t452.2\t0\t220\n", "9\t157\t452.2\t0\t157\n", "10\t162\t452.2\t0\t162\n", "11\t150\t452.2\t0\t150\n", "12\t166\t452.2\t0\t166\n", "13\t159\t452.2\t0\t159\n", "14\t171\t452.2\t0\t171\n", "15\t180\t452.2\t0\t180\n", "16\t174\t452.2\t0\t174\n", "17\t149\t452.2\t0\t149\n", "18\t172\t452.2\t0\t172\n", "19\t153\t452.2\t0\t153\n", "20\t157\t452.2\t0\t157\n", "21\t134\t452.2\t0\t134\n", "22\t151\t452.2\t0\t151\n", "23\t116\t452.2\t0\t116\n", "24\t126\t452.2\t0\t126\n", "25\t159\t452.2\t0\t159\n", "26\t135\t452.2\t0\t135\n", "27\t158\t452.2\t0\t158\n", "28\t180\t452.2\t0\t180\n", "29\t172\t452.2\t0\t172\n", "30\t139\t452.2\t0\t139\n", "31\t139\t452.2\t0\t139\n", "32\t150\t452.2\t0\t150\n", "33\t146\t452.2\t0\t146\n", "34\t158\t452.2\t0\t158\n", "35\t136\t452.2\t0\t136\n", "36\t126\t452.2\t0\t126\n", "37\t151\t452.2\t0\t151\n", "38\t94\t452.2\t0\t94\n", "39\t143\t452.2\t0\t143\n", "40\t137\t452.2\t0\t137\n", "41\t133\t452.2\t0\t133\n", "42\t102\t452.2\t0\t102\n", "43\t146\t452.2\t0\t146\n", "44\t55\t452.2\t0\t55\n", "45\t102\t452.2\t0\t102\n", "46\t88\t452.2\t0\t88\n", "47\t109\t452.2\t0\t109\n", "48\t97\t452.2\t0\t97\n", "49\t70\t452.2\t0\t70\n", "50\t83\t452.2\t0\t83\n", "51\t103\t452.2\t0\t103\n", "52\t78\t452.2\t0\t78\n", "53\t90\t452.2\t0\t90\n", "54\t70\t452.2\t0\t70\n", "55\t101\t452.2\t0\t101\n", "56\t76\t452.2\t0\t76\n", "57\t67\t452.2\t0\t67\n", "58\t100\t452.2\t0\t100\n", "59\t67\t452.2\t0\t67\n", "60\t91\t452.2\t0\t91\n", "61\t86\t452.2\t0\t86\n", "62\t71\t452.2\t0\t71\n", "63\t60\t452.2\t0\t60\n", "64\t62\t452.2\t0\t62\n", "65\t76\t452.2\t0\t76\n", "66\t55\t452.2\t0\t55\n", "67\t64\t452.2\t0\t64\n", "68\t79\t452.2\t0\t79\n", "69\t44\t452.2\t0\t44\n", "70\t48\t452.2\t0\t48\n", "71\t71\t452.2\t0\t71\n", "72\t43\t452.2\t0\t43\n", "73\t64\t452.2\t0\t64\n", "74\t78\t452.2\t0\t78\n", "75\t70\t452.2\t0\t70\n", "76\t66\t452.2\t0\t66\n", "77\t80\t452.2\t0\t80\n", "78\t64\t452.2\t0\t64\n", "79\t83\t452.2\t0\t83\n", "80\t88\t452.2\t0\t88\n", "81\t69\t452.2\t0\t69\n", "82\t91\t452.2\t0\t91\n", "83\t114\t452.2\t0\t114\n", "84\t85\t452.2\t0\t85\n", "85\t77\t452.2\t0\t77\n", "86\t60\t452.2\t0\t60\n", "87\t77\t452.2\t0\t77\n", "88\t110\t452.2\t0\t110\n", "89\t83\t452.2\t0\t83\n", "90\t71\t452.2\t0\t71\n", "91\t46\t452.2\t0\t46\n", "92\t51\t452.2\t0\t51\n", "93\t46\t452.2\t0\t46\n", "94\t49\t452.2\t0\t49\n", "95\t44\t452.2\t0\t44\n", "96\t38\t452.2\t0\t38\n", "97\t42\t452.2\t0\t42\n", "98\t57\t452.2\t0\t57\n", "99\t67\t452.2\t0\t67\n", "100\t105\t452.2\t0\t105\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 341_S19_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/341.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 79.15 s (14 us/read; 4.34 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,721,131\n", "Reads with adapters: 3,924,201 (68.6%)\n", "Reads written (passing filters): 5,451,087 (95.3%)\n", "\n", "Total basepairs processed: 572,113,100 bp\n", "Quality-trimmed: 1,510,229 bp (0.3%)\n", "Total written (filtered): 409,143,110 bp (71.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3726236 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.6%\n", " G: 39.2%\n", " T: 27.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t96895\t89392.7\t0\t96895\n", "4\t58719\t22348.2\t0\t58719\n", "5\t46094\t5587.0\t0\t46094\n", "6\t39082\t1396.8\t0\t39082\n", "7\t36950\t349.2\t0\t36950\n", "8\t37754\t87.3\t0\t37754\n", "9\t37596\t87.3\t0\t37596\n", "10\t36697\t87.3\t0\t36697\n", "11\t36894\t87.3\t0\t36894\n", "12\t37113\t87.3\t0\t37113\n", "13\t38993\t87.3\t0\t38993\n", "14\t40410\t87.3\t0\t40410\n", "15\t39864\t87.3\t0\t39864\n", "16\t42517\t87.3\t0\t42517\n", "17\t46723\t87.3\t0\t46723\n", "18\t54193\t87.3\t0\t54193\n", "19\t48536\t87.3\t0\t48536\n", "20\t41436\t87.3\t0\t41436\n", "21\t40504\t87.3\t0\t40504\n", "22\t36831\t87.3\t0\t36831\n", "23\t40973\t87.3\t0\t40973\n", "24\t47622\t87.3\t0\t47622\n", "25\t49409\t87.3\t0\t49409\n", "26\t55880\t87.3\t0\t55880\n", "27\t60577\t87.3\t0\t60577\n", "28\t53907\t87.3\t0\t53907\n", "29\t51366\t87.3\t0\t51366\n", "30\t51603\t87.3\t0\t51603\n", "31\t57370\t87.3\t0\t57370\n", "32\t57740\t87.3\t0\t57740\n", "33\t54493\t87.3\t0\t54493\n", "34\t52384\t87.3\t0\t52384\n", "35\t59654\t87.3\t0\t59654\n", "36\t66648\t87.3\t0\t66648\n", "37\t66747\t87.3\t0\t66747\n", "38\t58723\t87.3\t0\t58723\n", "39\t53543\t87.3\t0\t53543\n", "40\t50496\t87.3\t0\t50496\n", "41\t57580\t87.3\t0\t57580\n", "42\t65640\t87.3\t0\t65640\n", "43\t58108\t87.3\t0\t58108\n", "44\t44876\t87.3\t0\t44876\n", "45\t57801\t87.3\t0\t57801\n", "46\t69647\t87.3\t0\t69647\n", "47\t65017\t87.3\t0\t65017\n", "48\t63496\t87.3\t0\t63496\n", "49\t52582\t87.3\t0\t52582\n", "50\t51255\t87.3\t0\t51255\n", "51\t43082\t87.3\t0\t43082\n", "52\t46219\t87.3\t0\t46219\n", "53\t49673\t87.3\t0\t49673\n", "54\t54097\t87.3\t0\t54097\n", "55\t44833\t87.3\t0\t44833\n", "56\t48782\t87.3\t0\t48782\n", "57\t52165\t87.3\t0\t52165\n", "58\t53646\t87.3\t0\t53646\n", "59\t44776\t87.3\t0\t44776\n", "60\t38041\t87.3\t0\t38041\n", "61\t36806\t87.3\t0\t36806\n", "62\t30390\t87.3\t0\t30390\n", "63\t28736\t87.3\t0\t28736\n", "64\t33396\t87.3\t0\t33396\n", "65\t34192\t87.3\t0\t34192\n", "66\t29589\t87.3\t0\t29589\n", "67\t29780\t87.3\t0\t29780\n", "68\t29381\t87.3\t0\t29381\n", "69\t30654\t87.3\t0\t30654\n", "70\t31842\t87.3\t0\t31842\n", "71\t30755\t87.3\t0\t30755\n", "72\t23975\t87.3\t0\t23975\n", "73\t22710\t87.3\t0\t22710\n", "74\t23509\t87.3\t0\t23509\n", "75\t20992\t87.3\t0\t20992\n", "76\t17918\t87.3\t0\t17918\n", "77\t15645\t87.3\t0\t15645\n", "78\t18616\t87.3\t0\t18616\n", "79\t17424\t87.3\t0\t17424\n", "80\t17243\t87.3\t0\t17243\n", "81\t15878\t87.3\t0\t15878\n", "82\t14459\t87.3\t0\t14459\n", "83\t15095\t87.3\t0\t15095\n", "84\t17266\t87.3\t0\t17266\n", "85\t19774\t87.3\t0\t19774\n", "86\t18599\t87.3\t0\t18599\n", "87\t12360\t87.3\t0\t12360\n", "88\t10649\t87.3\t0\t10649\n", "89\t11752\t87.3\t0\t11752\n", "90\t12602\t87.3\t0\t12602\n", "91\t13234\t87.3\t0\t13234\n", "92\t14081\t87.3\t0\t14081\n", "93\t16384\t87.3\t0\t16384\n", "94\t16273\t87.3\t0\t16273\n", "95\t14585\t87.3\t0\t14585\n", "96\t11679\t87.3\t0\t11679\n", "97\t7487\t87.3\t0\t7487\n", "98\t4326\t87.3\t0\t4326\n", "99\t8409\t87.3\t0\t8409\n", "100\t3539\t87.3\t0\t3539\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 125614 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 83.9%\n", " C: 7.3%\n", " G: 0.0%\n", " T: 8.8%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9940\t89392.7\t0\t9940\n", "4\t2605\t22348.2\t0\t2605\n", "5\t811\t5587.0\t0\t811\n", "6\t498\t1396.8\t0\t498\n", "7\t109\t349.2\t0\t109\n", "8\t79\t87.3\t0\t79\n", "9\t102\t87.3\t0\t102\n", "10\t107\t87.3\t0\t107\n", "11\t100\t87.3\t0\t100\n", "12\t99\t87.3\t0\t99\n", "13\t111\t87.3\t0\t111\n", "14\t143\t87.3\t0\t143\n", "15\t173\t87.3\t0\t173\n", "16\t279\t87.3\t0\t279\n", "17\t516\t87.3\t0\t516\n", "18\t1022\t87.3\t0\t1022\n", "19\t1577\t87.3\t0\t1577\n", "20\t3016\t87.3\t0\t3016\n", "21\t1800\t87.3\t0\t1800\n", "22\t1002\t87.3\t0\t1002\n", "23\t552\t87.3\t0\t552\n", "24\t660\t87.3\t0\t660\n", "25\t812\t87.3\t0\t812\n", "26\t1770\t87.3\t0\t1770\n", "27\t1939\t87.3\t0\t1939\n", "28\t2731\t87.3\t0\t2731\n", "29\t3582\t87.3\t0\t3582\n", "30\t6692\t87.3\t0\t6692\n", "31\t7519\t87.3\t0\t7519\n", "32\t10341\t87.3\t0\t10341\n", "33\t11525\t87.3\t0\t11525\n", "34\t12251\t87.3\t0\t12251\n", "35\t15692\t87.3\t0\t15692\n", "36\t17057\t87.3\t0\t17057\n", "37\t6755\t87.3\t0\t6755\n", "38\t218\t87.3\t0\t218\n", "39\t76\t87.3\t0\t76\n", "40\t42\t87.3\t0\t42\n", "41\t34\t87.3\t0\t34\n", "42\t28\t87.3\t0\t28\n", "43\t30\t87.3\t0\t30\n", "44\t31\t87.3\t0\t31\n", "45\t34\t87.3\t0\t34\n", "46\t26\t87.3\t0\t26\n", "47\t43\t87.3\t0\t43\n", "48\t40\t87.3\t0\t40\n", "49\t24\t87.3\t0\t24\n", "50\t38\t87.3\t0\t38\n", "51\t33\t87.3\t0\t33\n", "52\t31\t87.3\t0\t31\n", "53\t24\t87.3\t0\t24\n", "54\t16\t87.3\t0\t16\n", "55\t23\t87.3\t0\t23\n", "56\t22\t87.3\t0\t22\n", "57\t25\t87.3\t0\t25\n", "58\t15\t87.3\t0\t15\n", "59\t27\t87.3\t0\t27\n", "60\t14\t87.3\t0\t14\n", "61\t31\t87.3\t0\t31\n", "62\t17\t87.3\t0\t17\n", "63\t20\t87.3\t0\t20\n", "64\t24\t87.3\t0\t24\n", "65\t20\t87.3\t0\t20\n", "66\t20\t87.3\t0\t20\n", "67\t11\t87.3\t0\t11\n", "68\t12\t87.3\t0\t12\n", "69\t20\t87.3\t0\t20\n", "70\t10\t87.3\t0\t10\n", "71\t15\t87.3\t0\t15\n", "72\t12\t87.3\t0\t12\n", "73\t5\t87.3\t0\t5\n", "74\t5\t87.3\t0\t5\n", "75\t9\t87.3\t0\t9\n", "76\t5\t87.3\t0\t5\n", "77\t3\t87.3\t0\t3\n", "78\t12\t87.3\t0\t12\n", "79\t8\t87.3\t0\t8\n", "80\t7\t87.3\t0\t7\n", "81\t7\t87.3\t0\t7\n", "82\t16\t87.3\t0\t16\n", "83\t9\t87.3\t0\t9\n", "84\t8\t87.3\t0\t8\n", "85\t14\t87.3\t0\t14\n", "86\t11\t87.3\t0\t11\n", "87\t8\t87.3\t0\t8\n", "88\t13\t87.3\t0\t13\n", "89\t13\t87.3\t0\t13\n", "90\t19\t87.3\t0\t19\n", "91\t11\t87.3\t0\t11\n", "92\t20\t87.3\t0\t20\n", "93\t30\t87.3\t0\t30\n", "94\t41\t87.3\t0\t41\n", "95\t41\t87.3\t0\t41\n", "96\t56\t87.3\t0\t56\n", "97\t47\t87.3\t0\t47\n", "98\t43\t87.3\t0\t43\n", "99\t28\t87.3\t0\t28\n", "100\t52\t87.3\t0\t52\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 72351 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.8%\n", " C: 20.4%\n", " G: 16.9%\n", " T: 21.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t51279\t89392.7\t0\t51279\n", "4\t11953\t22348.2\t0\t11953\n", "5\t2047\t5587.0\t0\t2047\n", "6\t207\t1396.8\t0\t207\n", "7\t87\t349.2\t0\t87\n", "8\t88\t349.2\t0\t88\n", "9\t65\t349.2\t0\t65\n", "10\t68\t349.2\t0\t68\n", "11\t70\t349.2\t0\t70\n", "12\t101\t349.2\t0\t101\n", "13\t109\t349.2\t0\t109\n", "14\t90\t349.2\t0\t90\n", "15\t84\t349.2\t0\t84\n", "16\t90\t349.2\t0\t90\n", "17\t75\t349.2\t0\t75\n", "18\t114\t349.2\t0\t114\n", "19\t87\t349.2\t0\t87\n", "20\t98\t349.2\t0\t98\n", "21\t86\t349.2\t0\t86\n", "22\t91\t349.2\t0\t91\n", "23\t85\t349.2\t0\t85\n", "24\t78\t349.2\t0\t78\n", "25\t91\t349.2\t0\t91\n", "26\t78\t349.2\t0\t78\n", "27\t124\t349.2\t0\t124\n", "28\t99\t349.2\t0\t99\n", "29\t95\t349.2\t0\t95\n", "30\t89\t349.2\t0\t89\n", "31\t95\t349.2\t0\t95\n", "32\t106\t349.2\t0\t106\n", "33\t96\t349.2\t0\t96\n", "34\t109\t349.2\t0\t109\n", "35\t109\t349.2\t0\t109\n", "36\t108\t349.2\t0\t108\n", "37\t86\t349.2\t0\t86\n", "38\t96\t349.2\t0\t96\n", "39\t78\t349.2\t0\t78\n", "40\t115\t349.2\t0\t115\n", "41\t88\t349.2\t0\t88\n", "42\t77\t349.2\t0\t77\n", "43\t112\t349.2\t0\t112\n", "44\t62\t349.2\t0\t62\n", "45\t64\t349.2\t0\t64\n", "46\t74\t349.2\t0\t74\n", "47\t94\t349.2\t0\t94\n", "48\t79\t349.2\t0\t79\n", "49\t77\t349.2\t0\t77\n", "50\t78\t349.2\t0\t78\n", "51\t79\t349.2\t0\t79\n", "52\t53\t349.2\t0\t53\n", "53\t73\t349.2\t0\t73\n", "54\t60\t349.2\t0\t60\n", "55\t79\t349.2\t0\t79\n", "56\t62\t349.2\t0\t62\n", "57\t63\t349.2\t0\t63\n", "58\t82\t349.2\t0\t82\n", "59\t69\t349.2\t0\t69\n", "60\t64\t349.2\t0\t64\n", "61\t85\t349.2\t0\t85\n", "62\t98\t349.2\t0\t98\n", "63\t54\t349.2\t0\t54\n", "64\t57\t349.2\t0\t57\n", "65\t74\t349.2\t0\t74\n", "66\t69\t349.2\t0\t69\n", "67\t65\t349.2\t0\t65\n", "68\t46\t349.2\t0\t46\n", "69\t41\t349.2\t0\t41\n", "70\t46\t349.2\t0\t46\n", "71\t48\t349.2\t0\t48\n", "72\t45\t349.2\t0\t45\n", "73\t53\t349.2\t0\t53\n", "74\t44\t349.2\t0\t44\n", "75\t59\t349.2\t0\t59\n", "76\t48\t349.2\t0\t48\n", "77\t54\t349.2\t0\t54\n", "78\t53\t349.2\t0\t53\n", "79\t63\t349.2\t0\t63\n", "80\t51\t349.2\t0\t51\n", "81\t59\t349.2\t0\t59\n", "82\t83\t349.2\t0\t83\n", "83\t61\t349.2\t0\t61\n", "84\t71\t349.2\t0\t71\n", "85\t61\t349.2\t0\t61\n", "86\t48\t349.2\t0\t48\n", "87\t83\t349.2\t0\t83\n", "88\t91\t349.2\t0\t91\n", "89\t68\t349.2\t0\t68\n", "90\t55\t349.2\t0\t55\n", "91\t35\t349.2\t0\t35\n", "92\t35\t349.2\t0\t35\n", "93\t36\t349.2\t0\t36\n", "94\t36\t349.2\t0\t36\n", "95\t34\t349.2\t0\t34\n", "96\t21\t349.2\t0\t21\n", "97\t31\t349.2\t0\t31\n", "98\t41\t349.2\t0\t41\n", "99\t60\t349.2\t0\t60\n", "100\t74\t349.2\t0\t74\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 342_S23_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/342.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 127.03 s (14 us/read; 4.18 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,852,593\n", "Reads with adapters: 6,265,430 (70.8%)\n", "Reads written (passing filters): 8,496,317 (96.0%)\n", "\n", "Total basepairs processed: 885,259,300 bp\n", "Quality-trimmed: 2,360,044 bp (0.3%)\n", "Total written (filtered): 649,409,359 bp (73.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 6114645 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.6%\n", " G: 38.5%\n", " T: 27.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t173718\t138321.8\t0\t173718\n", "4\t112574\t34580.4\t0\t112574\n", "5\t95429\t8645.1\t0\t95429\n", "6\t83619\t2161.3\t0\t83619\n", "7\t81530\t540.3\t0\t81530\n", "8\t82480\t135.1\t0\t82480\n", "9\t82050\t135.1\t0\t82050\n", "10\t80875\t135.1\t0\t80875\n", "11\t79753\t135.1\t0\t79753\n", "12\t81454\t135.1\t0\t81454\n", "13\t88843\t135.1\t0\t88843\n", "14\t89959\t135.1\t0\t89959\n", "15\t85380\t135.1\t0\t85380\n", "16\t89463\t135.1\t0\t89463\n", "17\t99585\t135.1\t0\t99585\n", "18\t113835\t135.1\t0\t113835\n", "19\t102111\t135.1\t0\t102111\n", "20\t85317\t135.1\t0\t85317\n", "21\t81238\t135.1\t0\t81238\n", "22\t74466\t135.1\t0\t74466\n", "23\t80333\t135.1\t0\t80333\n", "24\t92159\t135.1\t0\t92159\n", "25\t94827\t135.1\t0\t94827\n", "26\t106011\t135.1\t0\t106011\n", "27\t113426\t135.1\t0\t113426\n", "28\t101764\t135.1\t0\t101764\n", "29\t92495\t135.1\t0\t92495\n", "30\t94789\t135.1\t0\t94789\n", "31\t105422\t135.1\t0\t105422\n", "32\t96827\t135.1\t0\t96827\n", "33\t93761\t135.1\t0\t93761\n", "34\t89611\t135.1\t0\t89611\n", "35\t101054\t135.1\t0\t101054\n", "36\t114280\t135.1\t0\t114280\n", "37\t113670\t135.1\t0\t113670\n", "38\t96309\t135.1\t0\t96309\n", "39\t83533\t135.1\t0\t83533\n", "40\t80604\t135.1\t0\t80604\n", "41\t89594\t135.1\t0\t89594\n", "42\t98405\t135.1\t0\t98405\n", "43\t86862\t135.1\t0\t86862\n", "44\t69498\t135.1\t0\t69498\n", "45\t85706\t135.1\t0\t85706\n", "46\t100018\t135.1\t0\t100018\n", "47\t87198\t135.1\t0\t87198\n", "48\t86094\t135.1\t0\t86094\n", "49\t72139\t135.1\t0\t72139\n", "50\t69426\t135.1\t0\t69426\n", "51\t64587\t135.1\t0\t64587\n", "52\t62299\t135.1\t0\t62299\n", "53\t65789\t135.1\t0\t65789\n", "54\t70248\t135.1\t0\t70248\n", "55\t74069\t135.1\t0\t74069\n", "56\t60266\t135.1\t0\t60266\n", "57\t67295\t135.1\t0\t67295\n", "58\t80644\t135.1\t0\t80644\n", "59\t63837\t135.1\t0\t63837\n", "60\t50150\t135.1\t0\t50150\n", "61\t48537\t135.1\t0\t48537\n", "62\t41772\t135.1\t0\t41772\n", "63\t40247\t135.1\t0\t40247\n", "64\t45941\t135.1\t0\t45941\n", "65\t43334\t135.1\t0\t43334\n", "66\t36609\t135.1\t0\t36609\n", "67\t36855\t135.1\t0\t36855\n", "68\t36265\t135.1\t0\t36265\n", "69\t38107\t135.1\t0\t38107\n", "70\t41902\t135.1\t0\t41902\n", "71\t39959\t135.1\t0\t39959\n", "72\t29806\t135.1\t0\t29806\n", "73\t26771\t135.1\t0\t26771\n", "74\t26524\t135.1\t0\t26524\n", "75\t23421\t135.1\t0\t23421\n", "76\t19237\t135.1\t0\t19237\n", "77\t18462\t135.1\t0\t18462\n", "78\t22669\t135.1\t0\t22669\n", "79\t20897\t135.1\t0\t20897\n", "80\t20003\t135.1\t0\t20003\n", "81\t19065\t135.1\t0\t19065\n", "82\t17934\t135.1\t0\t17934\n", "83\t19054\t135.1\t0\t19054\n", "84\t22948\t135.1\t0\t22948\n", "85\t27246\t135.1\t0\t27246\n", "86\t25914\t135.1\t0\t25914\n", "87\t17249\t135.1\t0\t17249\n", "88\t14502\t135.1\t0\t14502\n", "89\t16459\t135.1\t0\t16459\n", "90\t18324\t135.1\t0\t18324\n", "91\t19478\t135.1\t0\t19478\n", "92\t20432\t135.1\t0\t20432\n", "93\t22853\t135.1\t0\t22853\n", "94\t22274\t135.1\t0\t22274\n", "95\t19084\t135.1\t0\t19084\n", "96\t13864\t135.1\t0\t13864\n", "97\t8916\t135.1\t0\t8916\n", "98\t5057\t135.1\t0\t5057\n", "99\t4650\t135.1\t0\t4650\n", "100\t3346\t135.1\t0\t3346\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 42597 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 65.0%\n", " C: 16.5%\n", " G: 0.0%\n", " T: 18.4%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13182\t138321.8\t0\t13182\n", "4\t3054\t34580.4\t0\t3054\n", "5\t1051\t8645.1\t0\t1051\n", "6\t658\t2161.3\t0\t658\n", "7\t129\t540.3\t0\t129\n", "8\t93\t135.1\t0\t93\n", "9\t85\t135.1\t0\t85\n", "10\t95\t135.1\t0\t95\n", "11\t96\t135.1\t0\t96\n", "12\t104\t135.1\t0\t104\n", "13\t91\t135.1\t0\t91\n", "14\t126\t135.1\t0\t126\n", "15\t117\t135.1\t0\t117\n", "16\t141\t135.1\t0\t141\n", "17\t155\t135.1\t0\t155\n", "18\t316\t135.1\t0\t316\n", "19\t382\t135.1\t0\t382\n", "20\t677\t135.1\t0\t677\n", "21\t509\t135.1\t0\t509\n", "22\t385\t135.1\t0\t385\n", "23\t223\t135.1\t0\t223\n", "24\t229\t135.1\t0\t229\n", "25\t270\t135.1\t0\t270\n", "26\t518\t135.1\t0\t518\n", "27\t509\t135.1\t0\t509\n", "28\t605\t135.1\t0\t605\n", "29\t782\t135.1\t0\t782\n", "30\t1364\t135.1\t0\t1364\n", "31\t1656\t135.1\t0\t1656\n", "32\t2386\t135.1\t0\t2386\n", "33\t2225\t135.1\t0\t2225\n", "34\t2347\t135.1\t0\t2347\n", "35\t2835\t135.1\t0\t2835\n", "36\t2565\t135.1\t0\t2565\n", "37\t845\t135.1\t0\t845\n", "38\t47\t135.1\t0\t47\n", "39\t29\t135.1\t0\t29\n", "40\t41\t135.1\t0\t41\n", "41\t46\t135.1\t0\t46\n", "42\t40\t135.1\t0\t40\n", "43\t41\t135.1\t0\t41\n", "44\t30\t135.1\t0\t30\n", "45\t36\t135.1\t0\t36\n", "46\t36\t135.1\t0\t36\n", "47\t42\t135.1\t0\t42\n", "48\t30\t135.1\t0\t30\n", "49\t39\t135.1\t0\t39\n", "50\t28\t135.1\t0\t28\n", "51\t44\t135.1\t0\t44\n", "52\t31\t135.1\t0\t31\n", "53\t42\t135.1\t0\t42\n", "54\t35\t135.1\t0\t35\n", "55\t25\t135.1\t0\t25\n", "56\t23\t135.1\t0\t23\n", "57\t28\t135.1\t0\t28\n", "58\t19\t135.1\t0\t19\n", "59\t25\t135.1\t0\t25\n", "60\t19\t135.1\t0\t19\n", "61\t25\t135.1\t0\t25\n", "62\t22\t135.1\t0\t22\n", "63\t17\t135.1\t0\t17\n", "64\t18\t135.1\t0\t18\n", "65\t20\t135.1\t0\t20\n", "66\t23\t135.1\t0\t23\n", "67\t14\t135.1\t0\t14\n", "68\t16\t135.1\t0\t16\n", "69\t21\t135.1\t0\t21\n", "70\t13\t135.1\t0\t13\n", "71\t10\t135.1\t0\t10\n", "72\t13\t135.1\t0\t13\n", "73\t13\t135.1\t0\t13\n", "74\t15\t135.1\t0\t15\n", "75\t5\t135.1\t0\t5\n", "76\t4\t135.1\t0\t4\n", "77\t9\t135.1\t0\t9\n", "78\t9\t135.1\t0\t9\n", "79\t8\t135.1\t0\t8\n", "80\t8\t135.1\t0\t8\n", "81\t11\t135.1\t0\t11\n", "82\t12\t135.1\t0\t12\n", "83\t18\t135.1\t0\t18\n", "84\t10\t135.1\t0\t10\n", "85\t14\t135.1\t0\t14\n", "86\t16\t135.1\t0\t16\n", "87\t13\t135.1\t0\t13\n", "88\t10\t135.1\t0\t10\n", "89\t26\t135.1\t0\t26\n", "90\t12\t135.1\t0\t12\n", "91\t19\t135.1\t0\t19\n", "92\t28\t135.1\t0\t28\n", "93\t55\t135.1\t0\t55\n", "94\t73\t135.1\t0\t73\n", "95\t80\t135.1\t0\t80\n", "96\t95\t135.1\t0\t95\n", "97\t67\t135.1\t0\t67\n", "98\t48\t135.1\t0\t48\n", "99\t56\t135.1\t0\t56\n", "100\t70\t135.1\t0\t70\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 108188 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.7%\n", " C: 16.9%\n", " G: 18.7%\n", " T: 19.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t75824\t138321.8\t0\t75824\n", "4\t17372\t34580.4\t0\t17372\n", "5\t3381\t8645.1\t0\t3381\n", "6\t389\t2161.3\t0\t389\n", "7\t142\t540.3\t0\t142\n", "8\t148\t540.3\t0\t148\n", "9\t114\t540.3\t0\t114\n", "10\t155\t540.3\t0\t155\n", "11\t171\t540.3\t0\t171\n", "12\t129\t540.3\t0\t129\n", "13\t151\t540.3\t0\t151\n", "14\t139\t540.3\t0\t139\n", "15\t160\t540.3\t0\t160\n", "16\t150\t540.3\t0\t150\n", "17\t189\t540.3\t0\t189\n", "18\t173\t540.3\t0\t173\n", "19\t190\t540.3\t0\t190\n", "20\t157\t540.3\t0\t157\n", "21\t168\t540.3\t0\t168\n", "22\t128\t540.3\t0\t128\n", "23\t141\t540.3\t0\t141\n", "24\t129\t540.3\t0\t129\n", "25\t117\t540.3\t0\t117\n", "26\t101\t540.3\t0\t101\n", "27\t154\t540.3\t0\t154\n", "28\t140\t540.3\t0\t140\n", "29\t179\t540.3\t0\t179\n", "30\t180\t540.3\t0\t180\n", "31\t134\t540.3\t0\t134\n", "32\t140\t540.3\t0\t140\n", "33\t140\t540.3\t0\t140\n", "34\t146\t540.3\t0\t146\n", "35\t127\t540.3\t0\t127\n", "36\t115\t540.3\t0\t115\n", "37\t126\t540.3\t0\t126\n", "38\t120\t540.3\t0\t120\n", "39\t153\t540.3\t0\t153\n", "40\t161\t540.3\t0\t161\n", "41\t124\t540.3\t0\t124\n", "42\t113\t540.3\t0\t113\n", "43\t164\t540.3\t0\t164\n", "44\t81\t540.3\t0\t81\n", "45\t127\t540.3\t0\t127\n", "46\t128\t540.3\t0\t128\n", "47\t112\t540.3\t0\t112\n", "48\t113\t540.3\t0\t113\n", "49\t124\t540.3\t0\t124\n", "50\t103\t540.3\t0\t103\n", "51\t113\t540.3\t0\t113\n", "52\t77\t540.3\t0\t77\n", "53\t90\t540.3\t0\t90\n", "54\t79\t540.3\t0\t79\n", "55\t88\t540.3\t0\t88\n", "56\t67\t540.3\t0\t67\n", "57\t89\t540.3\t0\t89\n", "58\t79\t540.3\t0\t79\n", "59\t75\t540.3\t0\t75\n", "60\t81\t540.3\t0\t81\n", "61\t81\t540.3\t0\t81\n", "62\t71\t540.3\t0\t71\n", "63\t74\t540.3\t0\t74\n", "64\t75\t540.3\t0\t75\n", "65\t69\t540.3\t0\t69\n", "66\t99\t540.3\t0\t99\n", "67\t67\t540.3\t0\t67\n", "68\t90\t540.3\t0\t90\n", "69\t59\t540.3\t0\t59\n", "70\t70\t540.3\t0\t70\n", "71\t76\t540.3\t0\t76\n", "72\t111\t540.3\t0\t111\n", "73\t112\t540.3\t0\t112\n", "74\t112\t540.3\t0\t112\n", "75\t81\t540.3\t0\t81\n", "76\t107\t540.3\t0\t107\n", "77\t121\t540.3\t0\t121\n", "78\t125\t540.3\t0\t125\n", "79\t143\t540.3\t0\t143\n", "80\t147\t540.3\t0\t147\n", "81\t139\t540.3\t0\t139\n", "82\t209\t540.3\t0\t209\n", "83\t133\t540.3\t0\t133\n", "84\t141\t540.3\t0\t141\n", "85\t156\t540.3\t0\t156\n", "86\t118\t540.3\t0\t118\n", "87\t154\t540.3\t0\t154\n", "88\t150\t540.3\t0\t150\n", "89\t114\t540.3\t0\t114\n", "90\t111\t540.3\t0\t111\n", "91\t91\t540.3\t0\t91\n", "92\t60\t540.3\t0\t60\n", "93\t64\t540.3\t0\t64\n", "94\t81\t540.3\t0\t81\n", "95\t85\t540.3\t0\t85\n", "96\t82\t540.3\t0\t82\n", "97\t116\t540.3\t0\t116\n", "98\t101\t540.3\t0\t101\n", "99\t114\t540.3\t0\t114\n", "100\t119\t540.3\t0\t119\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 343_S14_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/343.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 109.08 s (14 us/read; 4.36 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,922,295\n", "Reads with adapters: 6,510,722 (82.2%)\n", "Reads written (passing filters): 7,400,336 (93.4%)\n", "\n", "Total basepairs processed: 792,229,500 bp\n", "Quality-trimmed: 3,069,556 bp (0.4%)\n", "Total written (filtered): 500,434,935 bp (63.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5937938 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 35.7%\n", " G: 40.7%\n", " T: 23.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t88303\t123785.9\t0\t88303\n", "4\t57026\t30946.5\t0\t57026\n", "5\t48295\t7736.6\t0\t48295\n", "6\t43155\t1934.2\t0\t43155\n", "7\t43110\t483.5\t0\t43110\n", "8\t45335\t120.9\t0\t45335\n", "9\t45301\t120.9\t0\t45301\n", "10\t45242\t120.9\t0\t45242\n", "11\t46359\t120.9\t0\t46359\n", "12\t47297\t120.9\t0\t47297\n", "13\t48812\t120.9\t0\t48812\n", "14\t51100\t120.9\t0\t51100\n", "15\t52252\t120.9\t0\t52252\n", "16\t55807\t120.9\t0\t55807\n", "17\t62537\t120.9\t0\t62537\n", "18\t72943\t120.9\t0\t72943\n", "19\t68330\t120.9\t0\t68330\n", "20\t57670\t120.9\t0\t57670\n", "21\t56276\t120.9\t0\t56276\n", "22\t52727\t120.9\t0\t52727\n", "23\t59099\t120.9\t0\t59099\n", "24\t67877\t120.9\t0\t67877\n", "25\t71326\t120.9\t0\t71326\n", "26\t82130\t120.9\t0\t82130\n", "27\t88869\t120.9\t0\t88869\n", "28\t81118\t120.9\t0\t81118\n", "29\t77411\t120.9\t0\t77411\n", "30\t82006\t120.9\t0\t82006\n", "31\t94009\t120.9\t0\t94009\n", "32\t89965\t120.9\t0\t89965\n", "33\t85937\t120.9\t0\t85937\n", "34\t82691\t120.9\t0\t82691\n", "35\t95428\t120.9\t0\t95428\n", "36\t104411\t120.9\t0\t104411\n", "37\t100545\t120.9\t0\t100545\n", "38\t93456\t120.9\t0\t93456\n", "39\t87665\t120.9\t0\t87665\n", "40\t83328\t120.9\t0\t83328\n", "41\t93822\t120.9\t0\t93822\n", "42\t101263\t120.9\t0\t101263\n", "43\t94342\t120.9\t0\t94342\n", "44\t76253\t120.9\t0\t76253\n", "45\t102218\t120.9\t0\t102218\n", "46\t127677\t120.9\t0\t127677\n", "47\t115292\t120.9\t0\t115292\n", "48\t122275\t120.9\t0\t122275\n", "49\t98715\t120.9\t0\t98715\n", "50\t100613\t120.9\t0\t100613\n", "51\t87649\t120.9\t0\t87649\n", "52\t91382\t120.9\t0\t91382\n", "53\t69650\t120.9\t0\t69650\n", "54\t68868\t120.9\t0\t68868\n", "55\t82365\t120.9\t0\t82365\n", "56\t81342\t120.9\t0\t81342\n", "57\t84305\t120.9\t0\t84305\n", "58\t98404\t120.9\t0\t98404\n", "59\t92234\t120.9\t0\t92234\n", "60\t77854\t120.9\t0\t77854\n", "61\t70459\t120.9\t0\t70459\n", "62\t55881\t120.9\t0\t55881\n", "63\t56570\t120.9\t0\t56570\n", "64\t70297\t120.9\t0\t70297\n", "65\t61780\t120.9\t0\t61780\n", "66\t49169\t120.9\t0\t49169\n", "67\t55291\t120.9\t0\t55291\n", "68\t54763\t120.9\t0\t54763\n", "69\t58485\t120.9\t0\t58485\n", "70\t67980\t120.9\t0\t67980\n", "71\t64848\t120.9\t0\t64848\n", "72\t46420\t120.9\t0\t46420\n", "73\t36252\t120.9\t0\t36252\n", "74\t35474\t120.9\t0\t35474\n", "75\t34141\t120.9\t0\t34141\n", "76\t25310\t120.9\t0\t25310\n", "77\t29718\t120.9\t0\t29718\n", "78\t39561\t120.9\t0\t39561\n", "79\t29768\t120.9\t0\t29768\n", "80\t26623\t120.9\t0\t26623\n", "81\t26754\t120.9\t0\t26754\n", "82\t24976\t120.9\t0\t24976\n", "83\t22966\t120.9\t0\t22966\n", "84\t28880\t120.9\t0\t28880\n", "85\t35314\t120.9\t0\t35314\n", "86\t34414\t120.9\t0\t34414\n", "87\t21571\t120.9\t0\t21571\n", "88\t17335\t120.9\t0\t17335\n", "89\t19504\t120.9\t0\t19504\n", "90\t22335\t120.9\t0\t22335\n", "91\t24735\t120.9\t0\t24735\n", "92\t28654\t120.9\t0\t28654\n", "93\t35519\t120.9\t0\t35519\n", "94\t33424\t120.9\t0\t33424\n", "95\t29998\t120.9\t0\t29998\n", "96\t25076\t120.9\t0\t25076\n", "97\t16260\t120.9\t0\t16260\n", "98\t9872\t120.9\t0\t9872\n", "99\t22793\t120.9\t0\t22793\n", "100\t7097\t120.9\t0\t7097\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 499622 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 89.0%\n", " C: 4.1%\n", " G: 0.0%\n", " T: 6.9%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t7397\t123785.9\t0\t7397\n", "4\t2212\t30946.5\t0\t2212\n", "5\t941\t7736.6\t0\t941\n", "6\t685\t1934.2\t0\t685\n", "7\t416\t483.5\t0\t416\n", "8\t398\t120.9\t0\t398\n", "9\t359\t120.9\t0\t359\n", "10\t442\t120.9\t0\t442\n", "11\t390\t120.9\t0\t390\n", "12\t379\t120.9\t0\t379\n", "13\t425\t120.9\t0\t425\n", "14\t507\t120.9\t0\t507\n", "15\t631\t120.9\t0\t631\n", "16\t908\t120.9\t0\t908\n", "17\t1520\t120.9\t0\t1520\n", "18\t2858\t120.9\t0\t2858\n", "19\t4663\t120.9\t0\t4663\n", "20\t6043\t120.9\t0\t6043\n", "21\t3764\t120.9\t0\t3764\n", "22\t2674\t120.9\t0\t2674\n", "23\t2172\t120.9\t0\t2172\n", "24\t2950\t120.9\t0\t2950\n", "25\t4716\t120.9\t0\t4716\n", "26\t8734\t120.9\t0\t8734\n", "27\t10062\t120.9\t0\t10062\n", "28\t13383\t120.9\t0\t13383\n", "29\t18371\t120.9\t0\t18371\n", "30\t30761\t120.9\t0\t30761\n", "31\t35766\t120.9\t0\t35766\n", "32\t45677\t120.9\t0\t45677\n", "33\t52371\t120.9\t0\t52371\n", "34\t59408\t120.9\t0\t59408\n", "35\t75295\t120.9\t0\t75295\n", "36\t74130\t120.9\t0\t74130\n", "37\t25540\t120.9\t0\t25540\n", "38\t818\t120.9\t0\t818\n", "39\t205\t120.9\t0\t205\n", "40\t92\t120.9\t0\t92\n", "41\t81\t120.9\t0\t81\n", "42\t56\t120.9\t0\t56\n", "43\t61\t120.9\t0\t61\n", "44\t53\t120.9\t0\t53\n", "45\t55\t120.9\t0\t55\n", "46\t63\t120.9\t0\t63\n", "47\t67\t120.9\t0\t67\n", "48\t45\t120.9\t0\t45\n", "49\t59\t120.9\t0\t59\n", "50\t58\t120.9\t0\t58\n", "51\t43\t120.9\t0\t43\n", "52\t53\t120.9\t0\t53\n", "53\t41\t120.9\t0\t41\n", "54\t39\t120.9\t0\t39\n", "55\t39\t120.9\t0\t39\n", "56\t42\t120.9\t0\t42\n", "57\t37\t120.9\t0\t37\n", "58\t30\t120.9\t0\t30\n", "59\t29\t120.9\t0\t29\n", "60\t21\t120.9\t0\t21\n", "61\t24\t120.9\t0\t24\n", "62\t44\t120.9\t0\t44\n", "63\t24\t120.9\t0\t24\n", "64\t22\t120.9\t0\t22\n", "65\t24\t120.9\t0\t24\n", "66\t29\t120.9\t0\t29\n", "67\t20\t120.9\t0\t20\n", "68\t22\t120.9\t0\t22\n", "69\t18\t120.9\t0\t18\n", "70\t9\t120.9\t0\t9\n", "71\t12\t120.9\t0\t12\n", "72\t7\t120.9\t0\t7\n", "73\t8\t120.9\t0\t8\n", "74\t13\t120.9\t0\t13\n", "75\t6\t120.9\t0\t6\n", "76\t8\t120.9\t0\t8\n", "77\t4\t120.9\t0\t4\n", "78\t6\t120.9\t0\t6\n", "79\t2\t120.9\t0\t2\n", "80\t7\t120.9\t0\t7\n", "81\t3\t120.9\t0\t3\n", "82\t11\t120.9\t0\t11\n", "83\t7\t120.9\t0\t7\n", "84\t9\t120.9\t0\t9\n", "85\t10\t120.9\t0\t10\n", "86\t7\t120.9\t0\t7\n", "87\t9\t120.9\t0\t9\n", "88\t6\t120.9\t0\t6\n", "89\t11\t120.9\t0\t11\n", "90\t5\t120.9\t0\t5\n", "91\t9\t120.9\t0\t9\n", "92\t9\t120.9\t0\t9\n", "93\t8\t120.9\t0\t8\n", "94\t22\t120.9\t0\t22\n", "95\t21\t120.9\t0\t21\n", "96\t27\t120.9\t0\t27\n", "97\t31\t120.9\t0\t31\n", "98\t23\t120.9\t0\t23\n", "99\t16\t120.9\t0\t16\n", "100\t34\t120.9\t0\t34\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 73162 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.3%\n", " C: 19.6%\n", " G: 19.3%\n", " T: 19.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t43489\t123785.9\t0\t43489\n", "4\t9939\t30946.5\t0\t9939\n", "5\t1883\t7736.6\t0\t1883\n", "6\t416\t1934.2\t0\t416\n", "7\t310\t483.5\t0\t310\n", "8\t344\t483.5\t0\t344\n", "9\t316\t483.5\t0\t316\n", "10\t344\t483.5\t0\t344\n", "11\t365\t483.5\t0\t365\n", "12\t335\t483.5\t0\t335\n", "13\t327\t483.5\t0\t327\n", "14\t333\t483.5\t0\t333\n", "15\t430\t483.5\t0\t430\n", "16\t368\t483.5\t0\t368\n", "17\t423\t483.5\t0\t423\n", "18\t356\t483.5\t0\t356\n", "19\t311\t483.5\t0\t311\n", "20\t346\t483.5\t0\t346\n", "21\t338\t483.5\t0\t338\n", "22\t328\t483.5\t0\t328\n", "23\t343\t483.5\t0\t343\n", "24\t308\t483.5\t0\t308\n", "25\t300\t483.5\t0\t300\n", "26\t321\t483.5\t0\t321\n", "27\t357\t483.5\t0\t357\n", "28\t303\t483.5\t0\t303\n", "29\t327\t483.5\t0\t327\n", "30\t313\t483.5\t0\t313\n", "31\t294\t483.5\t0\t294\n", "32\t358\t483.5\t0\t358\n", "33\t286\t483.5\t0\t286\n", "34\t301\t483.5\t0\t301\n", "35\t299\t483.5\t0\t299\n", "36\t283\t483.5\t0\t283\n", "37\t335\t483.5\t0\t335\n", "38\t255\t483.5\t0\t255\n", "39\t271\t483.5\t0\t271\n", "40\t301\t483.5\t0\t301\n", "41\t259\t483.5\t0\t259\n", "42\t221\t483.5\t0\t221\n", "43\t353\t483.5\t0\t353\n", "44\t80\t483.5\t0\t80\n", "45\t215\t483.5\t0\t215\n", "46\t279\t483.5\t0\t279\n", "47\t211\t483.5\t0\t211\n", "48\t167\t483.5\t0\t167\n", "49\t209\t483.5\t0\t209\n", "50\t184\t483.5\t0\t184\n", "51\t159\t483.5\t0\t159\n", "52\t182\t483.5\t0\t182\n", "53\t200\t483.5\t0\t200\n", "54\t126\t483.5\t0\t126\n", "55\t179\t483.5\t0\t179\n", "56\t129\t483.5\t0\t129\n", "57\t154\t483.5\t0\t154\n", "58\t139\t483.5\t0\t139\n", "59\t99\t483.5\t0\t99\n", "60\t127\t483.5\t0\t127\n", "61\t159\t483.5\t0\t159\n", "62\t76\t483.5\t0\t76\n", "63\t101\t483.5\t0\t101\n", "64\t142\t483.5\t0\t142\n", "65\t60\t483.5\t0\t60\n", "66\t89\t483.5\t0\t89\n", "67\t90\t483.5\t0\t90\n", "68\t136\t483.5\t0\t136\n", "69\t55\t483.5\t0\t55\n", "70\t37\t483.5\t0\t37\n", "71\t68\t483.5\t0\t68\n", "72\t88\t483.5\t0\t88\n", "73\t72\t483.5\t0\t72\n", "74\t95\t483.5\t0\t95\n", "75\t57\t483.5\t0\t57\n", "76\t64\t483.5\t0\t64\n", "77\t50\t483.5\t0\t50\n", "78\t66\t483.5\t0\t66\n", "79\t44\t483.5\t0\t44\n", "80\t72\t483.5\t0\t72\n", "81\t54\t483.5\t0\t54\n", "82\t78\t483.5\t0\t78\n", "83\t53\t483.5\t0\t53\n", "84\t60\t483.5\t0\t60\n", "85\t76\t483.5\t0\t76\n", "86\t44\t483.5\t0\t44\n", "87\t65\t483.5\t0\t65\n", "88\t95\t483.5\t0\t95\n", "89\t56\t483.5\t0\t56\n", "90\t45\t483.5\t0\t45\n", "91\t38\t483.5\t0\t38\n", "92\t36\t483.5\t0\t36\n", "93\t24\t483.5\t0\t24\n", "94\t45\t483.5\t0\t45\n", "95\t25\t483.5\t0\t25\n", "96\t26\t483.5\t0\t26\n", "97\t32\t483.5\t0\t32\n", "98\t45\t483.5\t0\t45\n", "99\t49\t483.5\t0\t49\n", "100\t67\t483.5\t0\t67\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 344_S27_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/344.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 156.42 s (14 us/read; 4.25 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 11,069,045\n", "Reads with adapters: 9,538,489 (86.2%)\n", "Reads written (passing filters): 10,029,720 (90.6%)\n", "\n", "Total basepairs processed: 1,106,904,500 bp\n", "Quality-trimmed: 4,040,953 bp (0.4%)\n", "Total written (filtered): 630,595,304 bp (57.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 9331485 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 32.6%\n", " G: 46.8%\n", " T: 20.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t80650\t172953.8\t0\t80650\n", "4\t58511\t43238.5\t0\t58511\n", "5\t44529\t10809.6\t0\t44529\n", "6\t42597\t2702.4\t0\t42597\n", "7\t43405\t675.6\t0\t43405\n", "8\t45556\t168.9\t0\t45556\n", "9\t46478\t168.9\t0\t46478\n", "10\t47377\t168.9\t0\t47377\n", "11\t50813\t168.9\t0\t50813\n", "12\t53538\t168.9\t0\t53538\n", "13\t63729\t168.9\t0\t63729\n", "14\t65806\t168.9\t0\t65806\n", "15\t62043\t168.9\t0\t62043\n", "16\t67117\t168.9\t0\t67117\n", "17\t74240\t168.9\t0\t74240\n", "18\t85852\t168.9\t0\t85852\n", "19\t78090\t168.9\t0\t78090\n", "20\t69245\t168.9\t0\t69245\n", "21\t70266\t168.9\t0\t70266\n", "22\t66647\t168.9\t0\t66647\n", "23\t73438\t168.9\t0\t73438\n", "24\t86460\t168.9\t0\t86460\n", "25\t91659\t168.9\t0\t91659\n", "26\t105215\t168.9\t0\t105215\n", "27\t115759\t168.9\t0\t115759\n", "28\t109808\t168.9\t0\t109808\n", "29\t107083\t168.9\t0\t107083\n", "30\t112096\t168.9\t0\t112096\n", "31\t127657\t168.9\t0\t127657\n", "32\t132002\t168.9\t0\t132002\n", "33\t126029\t168.9\t0\t126029\n", "34\t124307\t168.9\t0\t124307\n", "35\t140691\t168.9\t0\t140691\n", "36\t162310\t168.9\t0\t162310\n", "37\t171787\t168.9\t0\t171787\n", "38\t150311\t168.9\t0\t150311\n", "39\t135881\t168.9\t0\t135881\n", "40\t128313\t168.9\t0\t128313\n", "41\t154638\t168.9\t0\t154638\n", "42\t186017\t168.9\t0\t186017\n", "43\t160010\t168.9\t0\t160010\n", "44\t128761\t168.9\t0\t128761\n", "45\t179169\t168.9\t0\t179169\n", "46\t218880\t168.9\t0\t218880\n", "47\t198976\t168.9\t0\t198976\n", "48\t202938\t168.9\t0\t202938\n", "49\t161741\t168.9\t0\t161741\n", "50\t160503\t168.9\t0\t160503\n", "51\t125737\t168.9\t0\t125737\n", "52\t126778\t168.9\t0\t126778\n", "53\t120353\t168.9\t0\t120353\n", "54\t144668\t168.9\t0\t144668\n", "55\t161256\t168.9\t0\t161256\n", "56\t140643\t168.9\t0\t140643\n", "57\t144551\t168.9\t0\t144551\n", "58\t172390\t168.9\t0\t172390\n", "59\t144623\t168.9\t0\t144623\n", "60\t126267\t168.9\t0\t126267\n", "61\t115162\t168.9\t0\t115162\n", "62\t93392\t168.9\t0\t93392\n", "63\t87089\t168.9\t0\t87089\n", "64\t102604\t168.9\t0\t102604\n", "65\t103189\t168.9\t0\t103189\n", "66\t93892\t168.9\t0\t93892\n", "67\t95210\t168.9\t0\t95210\n", "68\t94467\t168.9\t0\t94467\n", "69\t102636\t168.9\t0\t102636\n", "70\t107963\t168.9\t0\t107963\n", "71\t105195\t168.9\t0\t105195\n", "72\t83753\t168.9\t0\t83753\n", "73\t79187\t168.9\t0\t79187\n", "74\t84545\t168.9\t0\t84545\n", "75\t75552\t168.9\t0\t75552\n", "76\t65103\t168.9\t0\t65103\n", "77\t59810\t168.9\t0\t59810\n", "78\t66442\t168.9\t0\t66442\n", "79\t67386\t168.9\t0\t67386\n", "80\t68507\t168.9\t0\t68507\n", "81\t61809\t168.9\t0\t61809\n", "82\t55374\t168.9\t0\t55374\n", "83\t57621\t168.9\t0\t57621\n", "84\t65763\t168.9\t0\t65763\n", "85\t73373\t168.9\t0\t73373\n", "86\t66958\t168.9\t0\t66958\n", "87\t42121\t168.9\t0\t42121\n", "88\t37427\t168.9\t0\t37427\n", "89\t41376\t168.9\t0\t41376\n", "90\t46231\t168.9\t0\t46231\n", "91\t50891\t168.9\t0\t50891\n", "92\t57761\t168.9\t0\t57761\n", "93\t69747\t168.9\t0\t69747\n", "94\t65361\t168.9\t0\t65361\n", "95\t55383\t168.9\t0\t55383\n", "96\t42002\t168.9\t0\t42002\n", "97\t27999\t168.9\t0\t27999\n", "98\t19097\t168.9\t0\t19097\n", "99\t52845\t168.9\t0\t52845\n", "100\t15068\t168.9\t0\t15068\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 114382 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 78.7%\n", " C: 11.6%\n", " G: 0.0%\n", " T: 9.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t12344\t172953.8\t0\t12344\n", "4\t5743\t43238.5\t0\t5743\n", "5\t4606\t10809.6\t0\t4606\n", "6\t3898\t2702.4\t0\t3898\n", "7\t2609\t675.6\t0\t2609\n", "8\t2097\t168.9\t0\t2097\n", "9\t2037\t168.9\t0\t2037\n", "10\t1976\t168.9\t0\t1976\n", "11\t1874\t168.9\t0\t1874\n", "12\t1682\t168.9\t0\t1682\n", "13\t1492\t168.9\t0\t1492\n", "14\t1570\t168.9\t0\t1570\n", "15\t1397\t168.9\t0\t1397\n", "16\t1476\t168.9\t0\t1476\n", "17\t1620\t168.9\t0\t1620\n", "18\t2081\t168.9\t0\t2081\n", "19\t2443\t168.9\t0\t2443\n", "20\t3475\t168.9\t0\t3475\n", "21\t2508\t168.9\t0\t2508\n", "22\t1924\t168.9\t0\t1924\n", "23\t1485\t168.9\t0\t1485\n", "24\t1557\t168.9\t0\t1557\n", "25\t1756\t168.9\t0\t1756\n", "26\t3243\t168.9\t0\t3243\n", "27\t2761\t168.9\t0\t2761\n", "28\t2468\t168.9\t0\t2468\n", "29\t2746\t168.9\t0\t2746\n", "30\t3998\t168.9\t0\t3998\n", "31\t4363\t168.9\t0\t4363\n", "32\t6215\t168.9\t0\t6215\n", "33\t5043\t168.9\t0\t5043\n", "34\t4749\t168.9\t0\t4749\n", "35\t5795\t168.9\t0\t5795\n", "36\t5488\t168.9\t0\t5488\n", "37\t1450\t168.9\t0\t1450\n", "38\t69\t168.9\t0\t69\n", "39\t41\t168.9\t0\t41\n", "40\t41\t168.9\t0\t41\n", "41\t33\t168.9\t0\t33\n", "42\t26\t168.9\t0\t26\n", "43\t35\t168.9\t0\t35\n", "44\t39\t168.9\t0\t39\n", "45\t38\t168.9\t0\t38\n", "46\t42\t168.9\t0\t42\n", "47\t45\t168.9\t0\t45\n", "48\t51\t168.9\t0\t51\n", "49\t31\t168.9\t0\t31\n", "50\t37\t168.9\t0\t37\n", "51\t51\t168.9\t0\t51\n", "52\t43\t168.9\t0\t43\n", "53\t37\t168.9\t0\t37\n", "54\t37\t168.9\t0\t37\n", "55\t54\t168.9\t0\t54\n", "56\t41\t168.9\t0\t41\n", "57\t32\t168.9\t0\t32\n", "58\t33\t168.9\t0\t33\n", "59\t26\t168.9\t0\t26\n", "60\t35\t168.9\t0\t35\n", "61\t20\t168.9\t0\t20\n", "62\t33\t168.9\t0\t33\n", "63\t28\t168.9\t0\t28\n", "64\t26\t168.9\t0\t26\n", "65\t27\t168.9\t0\t27\n", "66\t22\t168.9\t0\t22\n", "67\t27\t168.9\t0\t27\n", "68\t17\t168.9\t0\t17\n", "69\t22\t168.9\t0\t22\n", "70\t21\t168.9\t0\t21\n", "71\t9\t168.9\t0\t9\n", "72\t15\t168.9\t0\t15\n", "73\t10\t168.9\t0\t10\n", "74\t8\t168.9\t0\t8\n", "75\t7\t168.9\t0\t7\n", "76\t14\t168.9\t0\t14\n", "77\t12\t168.9\t0\t12\n", "78\t14\t168.9\t0\t14\n", "79\t13\t168.9\t0\t13\n", "80\t12\t168.9\t0\t12\n", "81\t23\t168.9\t0\t23\n", "82\t27\t168.9\t0\t27\n", "83\t44\t168.9\t0\t44\n", "84\t34\t168.9\t0\t34\n", "85\t54\t168.9\t0\t54\n", "86\t38\t168.9\t0\t38\n", "87\t40\t168.9\t0\t40\n", "88\t42\t168.9\t0\t42\n", "89\t58\t168.9\t0\t58\n", "90\t30\t168.9\t0\t30\n", "91\t30\t168.9\t0\t30\n", "92\t61\t168.9\t0\t61\n", "93\t73\t168.9\t0\t73\n", "94\t77\t168.9\t0\t77\n", "95\t123\t168.9\t0\t123\n", "96\t128\t168.9\t0\t128\n", "97\t108\t168.9\t0\t108\n", "98\t80\t168.9\t0\t80\n", "99\t38\t168.9\t0\t38\n", "100\t31\t168.9\t0\t31\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 92622 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 48.6%\n", " C: 17.9%\n", " G: 18.5%\n", " T: 15.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t40235\t172953.8\t0\t40235\n", "4\t6521\t43238.5\t0\t6521\n", "5\t1628\t10809.6\t0\t1628\n", "6\t817\t2702.4\t0\t817\n", "7\t773\t675.6\t0\t773\n", "8\t670\t675.6\t0\t670\n", "9\t720\t675.6\t0\t720\n", "10\t816\t675.6\t0\t816\n", "11\t848\t675.6\t0\t848\n", "12\t908\t675.6\t0\t908\n", "13\t895\t675.6\t0\t895\n", "14\t886\t675.6\t0\t886\n", "15\t1072\t675.6\t0\t1072\n", "16\t935\t675.6\t0\t935\n", "17\t1035\t675.6\t0\t1035\n", "18\t1043\t675.6\t0\t1043\n", "19\t935\t675.6\t0\t935\n", "20\t1060\t675.6\t0\t1060\n", "21\t1028\t675.6\t0\t1028\n", "22\t997\t675.6\t0\t997\n", "23\t783\t675.6\t0\t783\n", "24\t852\t675.6\t0\t852\n", "25\t862\t675.6\t0\t862\n", "26\t800\t675.6\t0\t800\n", "27\t801\t675.6\t0\t801\n", "28\t816\t675.6\t0\t816\n", "29\t825\t675.6\t0\t825\n", "30\t849\t675.6\t0\t849\n", "31\t769\t675.6\t0\t769\n", "32\t882\t675.6\t0\t882\n", "33\t747\t675.6\t0\t747\n", "34\t825\t675.6\t0\t825\n", "35\t730\t675.6\t0\t730\n", "36\t746\t675.6\t0\t746\n", "37\t642\t675.6\t0\t642\n", "38\t661\t675.6\t0\t661\n", "39\t686\t675.6\t0\t686\n", "40\t671\t675.6\t0\t671\n", "41\t657\t675.6\t0\t657\n", "42\t613\t675.6\t0\t613\n", "43\t999\t675.6\t0\t999\n", "44\t152\t675.6\t0\t152\n", "45\t562\t675.6\t0\t562\n", "46\t530\t675.6\t0\t530\n", "47\t589\t675.6\t0\t589\n", "48\t499\t675.6\t0\t499\n", "49\t609\t675.6\t0\t609\n", "50\t553\t675.6\t0\t553\n", "51\t507\t675.6\t0\t507\n", "52\t475\t675.6\t0\t475\n", "53\t506\t675.6\t0\t506\n", "54\t430\t675.6\t0\t430\n", "55\t517\t675.6\t0\t517\n", "56\t489\t675.6\t0\t489\n", "57\t360\t675.6\t0\t360\n", "58\t431\t675.6\t0\t431\n", "59\t329\t675.6\t0\t329\n", "60\t311\t675.6\t0\t311\n", "61\t348\t675.6\t0\t348\n", "62\t333\t675.6\t0\t333\n", "63\t203\t675.6\t0\t203\n", "64\t266\t675.6\t0\t266\n", "65\t281\t675.6\t0\t281\n", "66\t274\t675.6\t0\t274\n", "67\t280\t675.6\t0\t280\n", "68\t400\t675.6\t0\t400\n", "69\t48\t675.6\t0\t48\n", "70\t77\t675.6\t0\t77\n", "71\t179\t675.6\t0\t179\n", "72\t182\t675.6\t0\t182\n", "73\t158\t675.6\t0\t158\n", "74\t155\t675.6\t0\t155\n", "75\t80\t675.6\t0\t80\n", "76\t76\t675.6\t0\t76\n", "77\t53\t675.6\t0\t53\n", "78\t78\t675.6\t0\t78\n", "79\t57\t675.6\t0\t57\n", "80\t55\t675.6\t0\t55\n", "81\t48\t675.6\t0\t48\n", "82\t55\t675.6\t0\t55\n", "83\t60\t675.6\t0\t60\n", "84\t77\t675.6\t0\t77\n", "85\t63\t675.6\t0\t63\n", "86\t65\t675.6\t0\t65\n", "87\t99\t675.6\t0\t99\n", "88\t114\t675.6\t0\t114\n", "89\t83\t675.6\t0\t83\n", "90\t73\t675.6\t0\t73\n", "91\t63\t675.6\t0\t63\n", "92\t23\t675.6\t0\t23\n", "93\t40\t675.6\t0\t40\n", "94\t39\t675.6\t0\t39\n", "95\t28\t675.6\t0\t28\n", "96\t45\t675.6\t0\t45\n", "97\t37\t675.6\t0\t37\n", "98\t39\t675.6\t0\t39\n", "99\t54\t675.6\t0\t54\n", "100\t47\t675.6\t0\t47\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 345_S16_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/345.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 80.91 s (14 us/read; 4.33 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,841,702\n", "Reads with adapters: 4,804,086 (82.2%)\n", "Reads written (passing filters): 5,460,373 (93.5%)\n", "\n", "Total basepairs processed: 584,170,200 bp\n", "Quality-trimmed: 2,384,997 bp (0.4%)\n", "Total written (filtered): 365,454,712 bp (62.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4739343 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 35.2%\n", " G: 39.3%\n", " T: 25.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t71108\t91276.6\t0\t71108\n", "4\t48466\t22819.1\t0\t48466\n", "5\t40757\t5704.8\t0\t40757\n", "6\t36944\t1426.2\t0\t36944\n", "7\t36694\t356.5\t0\t36694\n", "8\t37341\t89.1\t0\t37341\n", "9\t37544\t89.1\t0\t37544\n", "10\t37419\t89.1\t0\t37419\n", "11\t38050\t89.1\t0\t38050\n", "12\t38928\t89.1\t0\t38928\n", "13\t40514\t89.1\t0\t40514\n", "14\t42658\t89.1\t0\t42658\n", "15\t42338\t89.1\t0\t42338\n", "16\t46136\t89.1\t0\t46136\n", "17\t52511\t89.1\t0\t52511\n", "18\t59976\t89.1\t0\t59976\n", "19\t54812\t89.1\t0\t54812\n", "20\t46751\t89.1\t0\t46751\n", "21\t45402\t89.1\t0\t45402\n", "22\t42217\t89.1\t0\t42217\n", "23\t47221\t89.1\t0\t47221\n", "24\t54693\t89.1\t0\t54693\n", "25\t57633\t89.1\t0\t57633\n", "26\t66667\t89.1\t0\t66667\n", "27\t70637\t89.1\t0\t70637\n", "28\t63999\t89.1\t0\t63999\n", "29\t60550\t89.1\t0\t60550\n", "30\t62208\t89.1\t0\t62208\n", "31\t69814\t89.1\t0\t69814\n", "32\t68626\t89.1\t0\t68626\n", "33\t68373\t89.1\t0\t68373\n", "34\t64754\t89.1\t0\t64754\n", "35\t74013\t89.1\t0\t74013\n", "36\t82211\t89.1\t0\t82211\n", "37\t79180\t89.1\t0\t79180\n", "38\t72079\t89.1\t0\t72079\n", "39\t66497\t89.1\t0\t66497\n", "40\t66278\t89.1\t0\t66278\n", "41\t75644\t89.1\t0\t75644\n", "42\t83336\t89.1\t0\t83336\n", "43\t76069\t89.1\t0\t76069\n", "44\t61861\t89.1\t0\t61861\n", "45\t77058\t89.1\t0\t77058\n", "46\t93785\t89.1\t0\t93785\n", "47\t89428\t89.1\t0\t89428\n", "48\t87798\t89.1\t0\t87798\n", "49\t74707\t89.1\t0\t74707\n", "50\t73655\t89.1\t0\t73655\n", "51\t65583\t89.1\t0\t65583\n", "52\t69167\t89.1\t0\t69167\n", "53\t77777\t89.1\t0\t77777\n", "54\t72906\t89.1\t0\t72906\n", "55\t75860\t89.1\t0\t75860\n", "56\t73445\t89.1\t0\t73445\n", "57\t69996\t89.1\t0\t69996\n", "58\t74739\t89.1\t0\t74739\n", "59\t63352\t89.1\t0\t63352\n", "60\t57252\t89.1\t0\t57252\n", "61\t56419\t89.1\t0\t56419\n", "62\t46008\t89.1\t0\t46008\n", "63\t43467\t89.1\t0\t43467\n", "64\t52544\t89.1\t0\t52544\n", "65\t53220\t89.1\t0\t53220\n", "66\t43831\t89.1\t0\t43831\n", "67\t44775\t89.1\t0\t44775\n", "68\t45108\t89.1\t0\t45108\n", "69\t47216\t89.1\t0\t47216\n", "70\t49943\t89.1\t0\t49943\n", "71\t48329\t89.1\t0\t48329\n", "72\t37815\t89.1\t0\t37815\n", "73\t33657\t89.1\t0\t33657\n", "74\t33578\t89.1\t0\t33578\n", "75\t30124\t89.1\t0\t30124\n", "76\t24116\t89.1\t0\t24116\n", "77\t23257\t89.1\t0\t23257\n", "78\t28234\t89.1\t0\t28234\n", "79\t26002\t89.1\t0\t26002\n", "80\t24393\t89.1\t0\t24393\n", "81\t23095\t89.1\t0\t23095\n", "82\t22217\t89.1\t0\t22217\n", "83\t22290\t89.1\t0\t22290\n", "84\t26247\t89.1\t0\t26247\n", "85\t29918\t89.1\t0\t29918\n", "86\t28067\t89.1\t0\t28067\n", "87\t18591\t89.1\t0\t18591\n", "88\t15806\t89.1\t0\t15806\n", "89\t17092\t89.1\t0\t17092\n", "90\t18682\t89.1\t0\t18682\n", "91\t19623\t89.1\t0\t19623\n", "92\t20849\t89.1\t0\t20849\n", "93\t24255\t89.1\t0\t24255\n", "94\t21978\t89.1\t0\t21978\n", "95\t18104\t89.1\t0\t18104\n", "96\t13528\t89.1\t0\t13528\n", "97\t8143\t89.1\t0\t8143\n", "98\t4540\t89.1\t0\t4540\n", "99\t6315\t89.1\t0\t6315\n", "100\t2550\t89.1\t0\t2550\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 20727 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 67.1%\n", " C: 15.4%\n", " G: 0.0%\n", " T: 17.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t5324\t91276.6\t0\t5324\n", "4\t1257\t22819.1\t0\t1257\n", "5\t423\t5704.8\t0\t423\n", "6\t243\t1426.2\t0\t243\n", "7\t57\t356.5\t0\t57\n", "8\t63\t89.1\t0\t63\n", "9\t55\t89.1\t0\t55\n", "10\t56\t89.1\t0\t56\n", "11\t52\t89.1\t0\t52\n", "12\t54\t89.1\t0\t54\n", "13\t56\t89.1\t0\t56\n", "14\t56\t89.1\t0\t56\n", "15\t58\t89.1\t0\t58\n", "16\t73\t89.1\t0\t73\n", "17\t86\t89.1\t0\t86\n", "18\t119\t89.1\t0\t119\n", "19\t197\t89.1\t0\t197\n", "20\t283\t89.1\t0\t283\n", "21\t197\t89.1\t0\t197\n", "22\t143\t89.1\t0\t143\n", "23\t105\t89.1\t0\t105\n", "24\t128\t89.1\t0\t128\n", "25\t151\t89.1\t0\t151\n", "26\t290\t89.1\t0\t290\n", "27\t271\t89.1\t0\t271\n", "28\t320\t89.1\t0\t320\n", "29\t452\t89.1\t0\t452\n", "30\t757\t89.1\t0\t757\n", "31\t914\t89.1\t0\t914\n", "32\t1343\t89.1\t0\t1343\n", "33\t1252\t89.1\t0\t1252\n", "34\t1276\t89.1\t0\t1276\n", "35\t1481\t89.1\t0\t1481\n", "36\t1479\t89.1\t0\t1479\n", "37\t468\t89.1\t0\t468\n", "38\t28\t89.1\t0\t28\n", "39\t28\t89.1\t0\t28\n", "40\t37\t89.1\t0\t37\n", "41\t33\t89.1\t0\t33\n", "42\t34\t89.1\t0\t34\n", "43\t24\t89.1\t0\t24\n", "44\t33\t89.1\t0\t33\n", "45\t43\t89.1\t0\t43\n", "46\t41\t89.1\t0\t41\n", "47\t43\t89.1\t0\t43\n", "48\t32\t89.1\t0\t32\n", "49\t36\t89.1\t0\t36\n", "50\t38\t89.1\t0\t38\n", "51\t33\t89.1\t0\t33\n", "52\t30\t89.1\t0\t30\n", "53\t21\t89.1\t0\t21\n", "54\t23\t89.1\t0\t23\n", "55\t29\t89.1\t0\t29\n", "56\t22\t89.1\t0\t22\n", "57\t31\t89.1\t0\t31\n", "58\t26\t89.1\t0\t26\n", "59\t19\t89.1\t0\t19\n", "60\t23\t89.1\t0\t23\n", "61\t14\t89.1\t0\t14\n", "62\t20\t89.1\t0\t20\n", "63\t12\t89.1\t0\t12\n", "64\t20\t89.1\t0\t20\n", "65\t25\t89.1\t0\t25\n", "66\t18\t89.1\t0\t18\n", "67\t14\t89.1\t0\t14\n", "68\t12\t89.1\t0\t12\n", "69\t12\t89.1\t0\t12\n", "70\t10\t89.1\t0\t10\n", "71\t6\t89.1\t0\t6\n", "72\t7\t89.1\t0\t7\n", "73\t13\t89.1\t0\t13\n", "74\t9\t89.1\t0\t9\n", "75\t4\t89.1\t0\t4\n", "76\t3\t89.1\t0\t3\n", "77\t4\t89.1\t0\t4\n", "78\t7\t89.1\t0\t7\n", "79\t2\t89.1\t0\t2\n", "80\t3\t89.1\t0\t3\n", "81\t3\t89.1\t0\t3\n", "82\t5\t89.1\t0\t5\n", "83\t8\t89.1\t0\t8\n", "84\t5\t89.1\t0\t5\n", "85\t7\t89.1\t0\t7\n", "86\t10\t89.1\t0\t10\n", "87\t6\t89.1\t0\t6\n", "88\t7\t89.1\t0\t7\n", "89\t6\t89.1\t0\t6\n", "90\t4\t89.1\t0\t4\n", "91\t4\t89.1\t0\t4\n", "92\t11\t89.1\t0\t11\n", "93\t24\t89.1\t0\t24\n", "94\t18\t89.1\t0\t18\n", "95\t35\t89.1\t0\t35\n", "96\t25\t89.1\t0\t25\n", "97\t29\t89.1\t0\t29\n", "98\t20\t89.1\t0\t20\n", "99\t15\t89.1\t0\t15\n", "100\t24\t89.1\t0\t24\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 44016 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.5%\n", " C: 17.6%\n", " G: 19.6%\n", " T: 19.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t30884\t91276.6\t0\t30884\n", "4\t6736\t22819.1\t0\t6736\n", "5\t1200\t5704.8\t0\t1200\n", "6\t160\t1426.2\t0\t160\n", "7\t82\t356.5\t0\t82\n", "8\t72\t356.5\t0\t72\n", "9\t58\t356.5\t0\t58\n", "10\t62\t356.5\t0\t62\n", "11\t76\t356.5\t0\t76\n", "12\t83\t356.5\t0\t83\n", "13\t84\t356.5\t0\t84\n", "14\t84\t356.5\t0\t84\n", "15\t81\t356.5\t0\t81\n", "16\t85\t356.5\t0\t85\n", "17\t78\t356.5\t0\t78\n", "18\t92\t356.5\t0\t92\n", "19\t94\t356.5\t0\t94\n", "20\t78\t356.5\t0\t78\n", "21\t71\t356.5\t0\t71\n", "22\t80\t356.5\t0\t80\n", "23\t60\t356.5\t0\t60\n", "24\t80\t356.5\t0\t80\n", "25\t70\t356.5\t0\t70\n", "26\t76\t356.5\t0\t76\n", "27\t91\t356.5\t0\t91\n", "28\t92\t356.5\t0\t92\n", "29\t76\t356.5\t0\t76\n", "30\t79\t356.5\t0\t79\n", "31\t69\t356.5\t0\t69\n", "32\t79\t356.5\t0\t79\n", "33\t75\t356.5\t0\t75\n", "34\t79\t356.5\t0\t79\n", "35\t77\t356.5\t0\t77\n", "36\t74\t356.5\t0\t74\n", "37\t60\t356.5\t0\t60\n", "38\t53\t356.5\t0\t53\n", "39\t64\t356.5\t0\t64\n", "40\t64\t356.5\t0\t64\n", "41\t66\t356.5\t0\t66\n", "42\t54\t356.5\t0\t54\n", "43\t67\t356.5\t0\t67\n", "44\t38\t356.5\t0\t38\n", "45\t49\t356.5\t0\t49\n", "46\t69\t356.5\t0\t69\n", "47\t52\t356.5\t0\t52\n", "48\t38\t356.5\t0\t38\n", "49\t45\t356.5\t0\t45\n", "50\t43\t356.5\t0\t43\n", "51\t43\t356.5\t0\t43\n", "52\t48\t356.5\t0\t48\n", "53\t56\t356.5\t0\t56\n", "54\t37\t356.5\t0\t37\n", "55\t40\t356.5\t0\t40\n", "56\t52\t356.5\t0\t52\n", "57\t43\t356.5\t0\t43\n", "58\t48\t356.5\t0\t48\n", "59\t36\t356.5\t0\t36\n", "60\t41\t356.5\t0\t41\n", "61\t41\t356.5\t0\t41\n", "62\t31\t356.5\t0\t31\n", "63\t21\t356.5\t0\t21\n", "64\t35\t356.5\t0\t35\n", "65\t38\t356.5\t0\t38\n", "66\t24\t356.5\t0\t24\n", "67\t39\t356.5\t0\t39\n", "68\t38\t356.5\t0\t38\n", "69\t31\t356.5\t0\t31\n", "70\t20\t356.5\t0\t20\n", "71\t34\t356.5\t0\t34\n", "72\t50\t356.5\t0\t50\n", "73\t29\t356.5\t0\t29\n", "74\t40\t356.5\t0\t40\n", "75\t32\t356.5\t0\t32\n", "76\t41\t356.5\t0\t41\n", "77\t39\t356.5\t0\t39\n", "78\t43\t356.5\t0\t43\n", "79\t28\t356.5\t0\t28\n", "80\t53\t356.5\t0\t53\n", "81\t49\t356.5\t0\t49\n", "82\t61\t356.5\t0\t61\n", "83\t67\t356.5\t0\t67\n", "84\t48\t356.5\t0\t48\n", "85\t40\t356.5\t0\t40\n", "86\t32\t356.5\t0\t32\n", "87\t54\t356.5\t0\t54\n", "88\t47\t356.5\t0\t47\n", "89\t44\t356.5\t0\t44\n", "90\t39\t356.5\t0\t39\n", "91\t24\t356.5\t0\t24\n", "92\t22\t356.5\t0\t22\n", "93\t21\t356.5\t0\t21\n", "94\t41\t356.5\t0\t41\n", "95\t19\t356.5\t0\t19\n", "96\t25\t356.5\t0\t25\n", "97\t30\t356.5\t0\t30\n", "98\t43\t356.5\t0\t43\n", "99\t44\t356.5\t0\t44\n", "100\t36\t356.5\t0\t36\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 346_S18_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/346.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 78.83 s (13 us/read; 4.48 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,885,469\n", "Reads with adapters: 4,087,029 (69.4%)\n", "Reads written (passing filters): 5,675,956 (96.4%)\n", "\n", "Total basepairs processed: 588,546,900 bp\n", "Quality-trimmed: 1,660,634 bp (0.3%)\n", "Total written (filtered): 427,335,753 bp (72.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3880606 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 34.9%\n", " G: 39.9%\n", " T: 25.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t97755\t91960.5\t0\t97755\n", "4\t60506\t22990.1\t0\t60506\n", "5\t46732\t5747.5\t0\t46732\n", "6\t41781\t1436.9\t0\t41781\n", "7\t40165\t359.2\t0\t40165\n", "8\t41430\t89.8\t0\t41430\n", "9\t40924\t89.8\t0\t40924\n", "10\t40604\t89.8\t0\t40604\n", "11\t40693\t89.8\t0\t40693\n", "12\t42075\t89.8\t0\t42075\n", "13\t43830\t89.8\t0\t43830\n", "14\t45952\t89.8\t0\t45952\n", "15\t45472\t89.8\t0\t45472\n", "16\t48247\t89.8\t0\t48247\n", "17\t52809\t89.8\t0\t52809\n", "18\t61036\t89.8\t0\t61036\n", "19\t55205\t89.8\t0\t55205\n", "20\t46426\t89.8\t0\t46426\n", "21\t45369\t89.8\t0\t45369\n", "22\t42276\t89.8\t0\t42276\n", "23\t46808\t89.8\t0\t46808\n", "24\t53372\t89.8\t0\t53372\n", "25\t55323\t89.8\t0\t55323\n", "26\t62862\t89.8\t0\t62862\n", "27\t67159\t89.8\t0\t67159\n", "28\t61029\t89.8\t0\t61029\n", "29\t57231\t89.8\t0\t57231\n", "30\t56660\t89.8\t0\t56660\n", "31\t63985\t89.8\t0\t63985\n", "32\t62990\t89.8\t0\t62990\n", "33\t61736\t89.8\t0\t61736\n", "34\t57297\t89.8\t0\t57297\n", "35\t65763\t89.8\t0\t65763\n", "36\t71959\t89.8\t0\t71959\n", "37\t71202\t89.8\t0\t71202\n", "38\t63044\t89.8\t0\t63044\n", "39\t60892\t89.8\t0\t60892\n", "40\t57673\t89.8\t0\t57673\n", "41\t66733\t89.8\t0\t66733\n", "42\t75606\t89.8\t0\t75606\n", "43\t66535\t89.8\t0\t66535\n", "44\t51963\t89.8\t0\t51963\n", "45\t65925\t89.8\t0\t65925\n", "46\t78823\t89.8\t0\t78823\n", "47\t72908\t89.8\t0\t72908\n", "48\t67208\t89.8\t0\t67208\n", "49\t55403\t89.8\t0\t55403\n", "50\t55014\t89.8\t0\t55014\n", "51\t51935\t89.8\t0\t51935\n", "52\t57775\t89.8\t0\t57775\n", "53\t54189\t89.8\t0\t54189\n", "54\t47005\t89.8\t0\t47005\n", "55\t45204\t89.8\t0\t45204\n", "56\t41576\t89.8\t0\t41576\n", "57\t46856\t89.8\t0\t46856\n", "58\t56431\t89.8\t0\t56431\n", "59\t48327\t89.8\t0\t48327\n", "60\t37275\t89.8\t0\t37275\n", "61\t35413\t89.8\t0\t35413\n", "62\t29818\t89.8\t0\t29818\n", "63\t27258\t89.8\t0\t27258\n", "64\t31748\t89.8\t0\t31748\n", "65\t31567\t89.8\t0\t31567\n", "66\t26841\t89.8\t0\t26841\n", "67\t27144\t89.8\t0\t27144\n", "68\t26505\t89.8\t0\t26505\n", "69\t26673\t89.8\t0\t26673\n", "70\t28223\t89.8\t0\t28223\n", "71\t26716\t89.8\t0\t26716\n", "72\t20985\t89.8\t0\t20985\n", "73\t19384\t89.8\t0\t19384\n", "74\t19614\t89.8\t0\t19614\n", "75\t16824\t89.8\t0\t16824\n", "76\t14127\t89.8\t0\t14127\n", "77\t12965\t89.8\t0\t12965\n", "78\t14939\t89.8\t0\t14939\n", "79\t14143\t89.8\t0\t14143\n", "80\t13497\t89.8\t0\t13497\n", "81\t12304\t89.8\t0\t12304\n", "82\t11552\t89.8\t0\t11552\n", "83\t12132\t89.8\t0\t12132\n", "84\t13861\t89.8\t0\t13861\n", "85\t15303\t89.8\t0\t15303\n", "86\t14445\t89.8\t0\t14445\n", "87\t9673\t89.8\t0\t9673\n", "88\t8376\t89.8\t0\t8376\n", "89\t9232\t89.8\t0\t9232\n", "90\t9759\t89.8\t0\t9759\n", "91\t10435\t89.8\t0\t10435\n", "92\t11378\t89.8\t0\t11378\n", "93\t13044\t89.8\t0\t13044\n", "94\t12360\t89.8\t0\t12360\n", "95\t10576\t89.8\t0\t10576\n", "96\t8090\t89.8\t0\t8090\n", "97\t5184\t89.8\t0\t5184\n", "98\t3043\t89.8\t0\t3043\n", "99\t4787\t89.8\t0\t4787\n", "100\t1725\t89.8\t0\t1725\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 119890 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 82.7%\n", " C: 8.0%\n", " G: 0.0%\n", " T: 9.3%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10412\t91960.5\t0\t10412\n", "4\t2882\t22990.1\t0\t2882\n", "5\t1444\t5747.5\t0\t1444\n", "6\t1089\t1436.9\t0\t1089\n", "7\t457\t359.2\t0\t457\n", "8\t378\t89.8\t0\t378\n", "9\t368\t89.8\t0\t368\n", "10\t375\t89.8\t0\t375\n", "11\t347\t89.8\t0\t347\n", "12\t313\t89.8\t0\t313\n", "13\t290\t89.8\t0\t290\n", "14\t347\t89.8\t0\t347\n", "15\t377\t89.8\t0\t377\n", "16\t394\t89.8\t0\t394\n", "17\t636\t89.8\t0\t636\n", "18\t1017\t89.8\t0\t1017\n", "19\t1287\t89.8\t0\t1287\n", "20\t1965\t89.8\t0\t1965\n", "21\t1286\t89.8\t0\t1286\n", "22\t846\t89.8\t0\t846\n", "23\t598\t89.8\t0\t598\n", "24\t648\t89.8\t0\t648\n", "25\t864\t89.8\t0\t864\n", "26\t1826\t89.8\t0\t1826\n", "27\t1977\t89.8\t0\t1977\n", "28\t2376\t89.8\t0\t2376\n", "29\t2869\t89.8\t0\t2869\n", "30\t5072\t89.8\t0\t5072\n", "31\t5943\t89.8\t0\t5943\n", "32\t8088\t89.8\t0\t8088\n", "33\t9621\t89.8\t0\t9621\n", "34\t10831\t89.8\t0\t10831\n", "35\t14309\t89.8\t0\t14309\n", "36\t17679\t89.8\t0\t17679\n", "37\t7094\t89.8\t0\t7094\n", "38\t290\t89.8\t0\t290\n", "39\t112\t89.8\t0\t112\n", "40\t36\t89.8\t0\t36\n", "41\t37\t89.8\t0\t37\n", "42\t54\t89.8\t0\t54\n", "43\t43\t89.8\t0\t43\n", "44\t44\t89.8\t0\t44\n", "45\t46\t89.8\t0\t46\n", "46\t33\t89.8\t0\t33\n", "47\t40\t89.8\t0\t40\n", "48\t37\t89.8\t0\t37\n", "49\t45\t89.8\t0\t45\n", "50\t37\t89.8\t0\t37\n", "51\t33\t89.8\t0\t33\n", "52\t43\t89.8\t0\t43\n", "53\t42\t89.8\t0\t42\n", "54\t52\t89.8\t0\t52\n", "55\t52\t89.8\t0\t52\n", "56\t53\t89.8\t0\t53\n", "57\t47\t89.8\t0\t47\n", "58\t42\t89.8\t0\t42\n", "59\t47\t89.8\t0\t47\n", "60\t38\t89.8\t0\t38\n", "61\t36\t89.8\t0\t36\n", "62\t41\t89.8\t0\t41\n", "63\t31\t89.8\t0\t31\n", "64\t21\t89.8\t0\t21\n", "65\t22\t89.8\t0\t22\n", "66\t26\t89.8\t0\t26\n", "67\t20\t89.8\t0\t20\n", "68\t12\t89.8\t0\t12\n", "69\t22\t89.8\t0\t22\n", "70\t20\t89.8\t0\t20\n", "71\t8\t89.8\t0\t8\n", "72\t12\t89.8\t0\t12\n", "73\t12\t89.8\t0\t12\n", "74\t13\t89.8\t0\t13\n", "75\t10\t89.8\t0\t10\n", "76\t22\t89.8\t0\t22\n", "77\t11\t89.8\t0\t11\n", "78\t32\t89.8\t0\t32\n", "79\t27\t89.8\t0\t27\n", "80\t21\t89.8\t0\t21\n", "81\t44\t89.8\t0\t44\n", "82\t44\t89.8\t0\t44\n", "83\t59\t89.8\t0\t59\n", "84\t90\t89.8\t0\t90\n", "85\t86\t89.8\t0\t86\n", "86\t77\t89.8\t0\t77\n", "87\t73\t89.8\t0\t73\n", "88\t68\t89.8\t0\t68\n", "89\t91\t89.8\t0\t91\n", "90\t59\t89.8\t0\t59\n", "91\t93\t89.8\t0\t93\n", "92\t122\t89.8\t0\t122\n", "93\t144\t89.8\t0\t144\n", "94\t155\t89.8\t0\t155\n", "95\t184\t89.8\t0\t184\n", "96\t179\t89.8\t0\t179\n", "97\t154\t89.8\t0\t154\n", "98\t75\t89.8\t0\t75\n", "99\t26\t89.8\t0\t26\n", "100\t40\t89.8\t0\t40\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 86533 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.5%\n", " C: 20.7%\n", " G: 18.7%\n", " T: 18.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t54527\t91960.5\t0\t54527\n", "4\t11061\t22990.1\t0\t11061\n", "5\t2193\t5747.5\t0\t2193\n", "6\t487\t1436.9\t0\t487\n", "7\t373\t359.2\t0\t373\n", "8\t393\t359.2\t0\t393\n", "9\t413\t359.2\t0\t413\n", "10\t449\t359.2\t0\t449\n", "11\t351\t359.2\t0\t351\n", "12\t400\t359.2\t0\t400\n", "13\t413\t359.2\t0\t413\n", "14\t412\t359.2\t0\t412\n", "15\t438\t359.2\t0\t438\n", "16\t469\t359.2\t0\t469\n", "17\t433\t359.2\t0\t433\n", "18\t450\t359.2\t0\t450\n", "19\t369\t359.2\t0\t369\n", "20\t418\t359.2\t0\t418\n", "21\t417\t359.2\t0\t417\n", "22\t415\t359.2\t0\t415\n", "23\t401\t359.2\t0\t401\n", "24\t357\t359.2\t0\t357\n", "25\t373\t359.2\t0\t373\n", "26\t332\t359.2\t0\t332\n", "27\t383\t359.2\t0\t383\n", "28\t341\t359.2\t0\t341\n", "29\t340\t359.2\t0\t340\n", "30\t362\t359.2\t0\t362\n", "31\t295\t359.2\t0\t295\n", "32\t338\t359.2\t0\t338\n", "33\t315\t359.2\t0\t315\n", "34\t303\t359.2\t0\t303\n", "35\t261\t359.2\t0\t261\n", "36\t290\t359.2\t0\t290\n", "37\t282\t359.2\t0\t282\n", "38\t241\t359.2\t0\t241\n", "39\t259\t359.2\t0\t259\n", "40\t259\t359.2\t0\t259\n", "41\t251\t359.2\t0\t251\n", "42\t196\t359.2\t0\t196\n", "43\t338\t359.2\t0\t338\n", "44\t54\t359.2\t0\t54\n", "45\t191\t359.2\t0\t191\n", "46\t202\t359.2\t0\t202\n", "47\t178\t359.2\t0\t178\n", "48\t161\t359.2\t0\t161\n", "49\t169\t359.2\t0\t169\n", "50\t177\t359.2\t0\t177\n", "51\t150\t359.2\t0\t150\n", "52\t134\t359.2\t0\t134\n", "53\t141\t359.2\t0\t141\n", "54\t149\t359.2\t0\t149\n", "55\t158\t359.2\t0\t158\n", "56\t152\t359.2\t0\t152\n", "57\t108\t359.2\t0\t108\n", "58\t131\t359.2\t0\t131\n", "59\t91\t359.2\t0\t91\n", "60\t107\t359.2\t0\t107\n", "61\t93\t359.2\t0\t93\n", "62\t117\t359.2\t0\t117\n", "63\t84\t359.2\t0\t84\n", "64\t95\t359.2\t0\t95\n", "65\t121\t359.2\t0\t121\n", "66\t101\t359.2\t0\t101\n", "67\t103\t359.2\t0\t103\n", "68\t122\t359.2\t0\t122\n", "69\t45\t359.2\t0\t45\n", "70\t53\t359.2\t0\t53\n", "71\t76\t359.2\t0\t76\n", "72\t75\t359.2\t0\t75\n", "73\t80\t359.2\t0\t80\n", "74\t63\t359.2\t0\t63\n", "75\t86\t359.2\t0\t86\n", "76\t63\t359.2\t0\t63\n", "77\t57\t359.2\t0\t57\n", "78\t50\t359.2\t0\t50\n", "79\t48\t359.2\t0\t48\n", "80\t62\t359.2\t0\t62\n", "81\t61\t359.2\t0\t61\n", "82\t72\t359.2\t0\t72\n", "83\t61\t359.2\t0\t61\n", "84\t84\t359.2\t0\t84\n", "85\t69\t359.2\t0\t69\n", "86\t58\t359.2\t0\t58\n", "87\t65\t359.2\t0\t65\n", "88\t74\t359.2\t0\t74\n", "89\t59\t359.2\t0\t59\n", "90\t57\t359.2\t0\t57\n", "91\t38\t359.2\t0\t38\n", "92\t24\t359.2\t0\t24\n", "93\t32\t359.2\t0\t32\n", "94\t30\t359.2\t0\t30\n", "95\t41\t359.2\t0\t41\n", "96\t36\t359.2\t0\t36\n", "97\t36\t359.2\t0\t36\n", "98\t42\t359.2\t0\t42\n", "99\t64\t359.2\t0\t64\n", "100\t85\t359.2\t0\t85\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 347_S43_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/347.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 82.78 s (12 us/read; 4.88 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,730,240\n", "Reads with adapters: 2,866,006 (42.6%)\n", "Reads written (passing filters): 6,508,706 (96.7%)\n", "\n", "Total basepairs processed: 673,024,000 bp\n", "Quality-trimmed: 1,865,904 bp (0.3%)\n", "Total written (filtered): 570,715,221 bp (84.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2681528 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.5%\n", " G: 32.4%\n", " T: 39.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t171420\t105160.0\t0\t171420\n", "4\t89448\t26290.0\t0\t89448\n", "5\t57883\t6572.5\t0\t57883\n", "6\t44494\t1643.1\t0\t44494\n", "7\t37502\t410.8\t0\t37502\n", "8\t36442\t102.7\t0\t36442\n", "9\t35157\t102.7\t0\t35157\n", "10\t34041\t102.7\t0\t34041\n", "11\t34707\t102.7\t0\t34707\n", "12\t34415\t102.7\t0\t34415\n", "13\t35430\t102.7\t0\t35430\n", "14\t36559\t102.7\t0\t36559\n", "15\t36229\t102.7\t0\t36229\n", "16\t37573\t102.7\t0\t37573\n", "17\t40889\t102.7\t0\t40889\n", "18\t44708\t102.7\t0\t44708\n", "19\t39831\t102.7\t0\t39831\n", "20\t34064\t102.7\t0\t34064\n", "21\t32054\t102.7\t0\t32054\n", "22\t30383\t102.7\t0\t30383\n", "23\t32980\t102.7\t0\t32980\n", "24\t37147\t102.7\t0\t37147\n", "25\t37402\t102.7\t0\t37402\n", "26\t40620\t102.7\t0\t40620\n", "27\t43391\t102.7\t0\t43391\n", "28\t39840\t102.7\t0\t39840\n", "29\t37836\t102.7\t0\t37836\n", "30\t37853\t102.7\t0\t37853\n", "31\t39844\t102.7\t0\t39844\n", "32\t38884\t102.7\t0\t38884\n", "33\t36495\t102.7\t0\t36495\n", "34\t35443\t102.7\t0\t35443\n", "35\t38485\t102.7\t0\t38485\n", "36\t42021\t102.7\t0\t42021\n", "37\t43469\t102.7\t0\t43469\n", "38\t37460\t102.7\t0\t37460\n", "39\t33145\t102.7\t0\t33145\n", "40\t31725\t102.7\t0\t31725\n", "41\t33354\t102.7\t0\t33354\n", "42\t35298\t102.7\t0\t35298\n", "43\t32465\t102.7\t0\t32465\n", "44\t28906\t102.7\t0\t28906\n", "45\t32280\t102.7\t0\t32280\n", "46\t36268\t102.7\t0\t36268\n", "47\t34642\t102.7\t0\t34642\n", "48\t33045\t102.7\t0\t33045\n", "49\t29916\t102.7\t0\t29916\n", "50\t28187\t102.7\t0\t28187\n", "51\t27326\t102.7\t0\t27326\n", "52\t26703\t102.7\t0\t26703\n", "53\t25789\t102.7\t0\t25789\n", "54\t28225\t102.7\t0\t28225\n", "55\t29937\t102.7\t0\t29937\n", "56\t25296\t102.7\t0\t25296\n", "57\t23845\t102.7\t0\t23845\n", "58\t25109\t102.7\t0\t25109\n", "59\t23165\t102.7\t0\t23165\n", "60\t20564\t102.7\t0\t20564\n", "61\t19690\t102.7\t0\t19690\n", "62\t17840\t102.7\t0\t17840\n", "63\t17090\t102.7\t0\t17090\n", "64\t17614\t102.7\t0\t17614\n", "65\t17280\t102.7\t0\t17280\n", "66\t16356\t102.7\t0\t16356\n", "67\t16259\t102.7\t0\t16259\n", "68\t16028\t102.7\t0\t16028\n", "69\t15526\t102.7\t0\t15526\n", "70\t15593\t102.7\t0\t15593\n", "71\t15085\t102.7\t0\t15085\n", "72\t12604\t102.7\t0\t12604\n", "73\t11874\t102.7\t0\t11874\n", "74\t11545\t102.7\t0\t11545\n", "75\t11150\t102.7\t0\t11150\n", "76\t10380\t102.7\t0\t10380\n", "77\t9974\t102.7\t0\t9974\n", "78\t10373\t102.7\t0\t10373\n", "79\t10768\t102.7\t0\t10768\n", "80\t10973\t102.7\t0\t10973\n", "81\t11150\t102.7\t0\t11150\n", "82\t11545\t102.7\t0\t11545\n", "83\t12084\t102.7\t0\t12084\n", "84\t13124\t102.7\t0\t13124\n", "85\t13429\t102.7\t0\t13429\n", "86\t14183\t102.7\t0\t14183\n", "87\t13298\t102.7\t0\t13298\n", "88\t13368\t102.7\t0\t13368\n", "89\t12459\t102.7\t0\t12459\n", "90\t11655\t102.7\t0\t11655\n", "91\t10791\t102.7\t0\t10791\n", "92\t10024\t102.7\t0\t10024\n", "93\t8787\t102.7\t0\t8787\n", "94\t7443\t102.7\t0\t7443\n", "95\t6141\t102.7\t0\t6141\n", "96\t4899\t102.7\t0\t4899\n", "97\t3849\t102.7\t0\t3849\n", "98\t3663\t102.7\t0\t3663\n", "99\t3894\t102.7\t0\t3894\n", "100\t4151\t102.7\t0\t4151\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 35049 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.7%\n", " C: 25.3%\n", " G: 0.0%\n", " T: 31.8%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t18922\t105160.0\t0\t18922\n", "4\t4760\t26290.0\t0\t4760\n", "5\t1801\t6572.5\t0\t1801\n", "6\t483\t1643.1\t0\t483\n", "7\t85\t410.8\t0\t85\n", "8\t80\t102.7\t0\t80\n", "9\t62\t102.7\t0\t62\n", "10\t57\t102.7\t0\t57\n", "11\t60\t102.7\t0\t60\n", "12\t57\t102.7\t0\t57\n", "13\t57\t102.7\t0\t57\n", "14\t68\t102.7\t0\t68\n", "15\t73\t102.7\t0\t73\n", "16\t76\t102.7\t0\t76\n", "17\t96\t102.7\t0\t96\n", "18\t128\t102.7\t0\t128\n", "19\t148\t102.7\t0\t148\n", "20\t256\t102.7\t0\t256\n", "21\t174\t102.7\t0\t174\n", "22\t118\t102.7\t0\t118\n", "23\t93\t102.7\t0\t93\n", "24\t90\t102.7\t0\t90\n", "25\t82\t102.7\t0\t82\n", "26\t96\t102.7\t0\t96\n", "27\t106\t102.7\t0\t106\n", "28\t95\t102.7\t0\t95\n", "29\t151\t102.7\t0\t151\n", "30\t218\t102.7\t0\t218\n", "31\t242\t102.7\t0\t242\n", "32\t351\t102.7\t0\t351\n", "33\t404\t102.7\t0\t404\n", "34\t453\t102.7\t0\t453\n", "35\t580\t102.7\t0\t580\n", "36\t589\t102.7\t0\t589\n", "37\t362\t102.7\t0\t362\n", "38\t77\t102.7\t0\t77\n", "39\t72\t102.7\t0\t72\n", "40\t52\t102.7\t0\t52\n", "41\t46\t102.7\t0\t46\n", "42\t57\t102.7\t0\t57\n", "43\t53\t102.7\t0\t53\n", "44\t60\t102.7\t0\t60\n", "45\t45\t102.7\t0\t45\n", "46\t48\t102.7\t0\t48\n", "47\t57\t102.7\t0\t57\n", "48\t64\t102.7\t0\t64\n", "49\t49\t102.7\t0\t49\n", "50\t50\t102.7\t0\t50\n", "51\t59\t102.7\t0\t59\n", "52\t51\t102.7\t0\t51\n", "53\t57\t102.7\t0\t57\n", "54\t49\t102.7\t0\t49\n", "55\t52\t102.7\t0\t52\n", "56\t43\t102.7\t0\t43\n", "57\t38\t102.7\t0\t38\n", "58\t39\t102.7\t0\t39\n", "59\t38\t102.7\t0\t38\n", "60\t33\t102.7\t0\t33\n", "61\t30\t102.7\t0\t30\n", "62\t38\t102.7\t0\t38\n", "63\t33\t102.7\t0\t33\n", "64\t32\t102.7\t0\t32\n", "65\t30\t102.7\t0\t30\n", "66\t41\t102.7\t0\t41\n", "67\t25\t102.7\t0\t25\n", "68\t26\t102.7\t0\t26\n", "69\t33\t102.7\t0\t33\n", "70\t28\t102.7\t0\t28\n", "71\t15\t102.7\t0\t15\n", "72\t30\t102.7\t0\t30\n", "73\t12\t102.7\t0\t12\n", "74\t18\t102.7\t0\t18\n", "75\t17\t102.7\t0\t17\n", "76\t33\t102.7\t0\t33\n", "77\t27\t102.7\t0\t27\n", "78\t22\t102.7\t0\t22\n", "79\t25\t102.7\t0\t25\n", "80\t23\t102.7\t0\t23\n", "81\t29\t102.7\t0\t29\n", "82\t22\t102.7\t0\t22\n", "83\t27\t102.7\t0\t27\n", "84\t42\t102.7\t0\t42\n", "85\t41\t102.7\t0\t41\n", "86\t37\t102.7\t0\t37\n", "87\t36\t102.7\t0\t36\n", "88\t37\t102.7\t0\t37\n", "89\t38\t102.7\t0\t38\n", "90\t37\t102.7\t0\t37\n", "91\t79\t102.7\t0\t79\n", "92\t59\t102.7\t0\t59\n", "93\t93\t102.7\t0\t93\n", "94\t131\t102.7\t0\t131\n", "95\t150\t102.7\t0\t150\n", "96\t223\t102.7\t0\t223\n", "97\t221\t102.7\t0\t221\n", "98\t204\t102.7\t0\t204\n", "99\t120\t102.7\t0\t120\n", "100\t223\t102.7\t0\t223\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 149429 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 38.6%\n", " C: 20.0%\n", " G: 17.9%\n", " T: 23.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t111813\t105160.0\t0\t111813\n", "4\t25750\t26290.0\t0\t25750\n", "5\t3623\t6572.5\t0\t3623\n", "6\t310\t1643.1\t0\t310\n", "7\t74\t410.8\t0\t74\n", "8\t76\t410.8\t0\t76\n", "9\t76\t410.8\t0\t76\n", "10\t64\t410.8\t0\t64\n", "11\t75\t410.8\t0\t75\n", "12\t68\t410.8\t0\t68\n", "13\t90\t410.8\t0\t90\n", "14\t70\t410.8\t0\t70\n", "15\t86\t410.8\t0\t86\n", "16\t65\t410.8\t0\t65\n", "17\t94\t410.8\t0\t94\n", "18\t73\t410.8\t0\t73\n", "19\t76\t410.8\t0\t76\n", "20\t75\t410.8\t0\t75\n", "21\t67\t410.8\t0\t67\n", "22\t63\t410.8\t0\t63\n", "23\t46\t410.8\t0\t46\n", "24\t59\t410.8\t0\t59\n", "25\t61\t410.8\t0\t61\n", "26\t55\t410.8\t0\t55\n", "27\t88\t410.8\t0\t88\n", "28\t76\t410.8\t0\t76\n", "29\t77\t410.8\t0\t77\n", "30\t100\t410.8\t0\t100\n", "31\t103\t410.8\t0\t103\n", "32\t89\t410.8\t0\t89\n", "33\t103\t410.8\t0\t103\n", "34\t112\t410.8\t0\t112\n", "35\t89\t410.8\t0\t89\n", "36\t91\t410.8\t0\t91\n", "37\t59\t410.8\t0\t59\n", "38\t87\t410.8\t0\t87\n", "39\t106\t410.8\t0\t106\n", "40\t109\t410.8\t0\t109\n", "41\t95\t410.8\t0\t95\n", "42\t83\t410.8\t0\t83\n", "43\t93\t410.8\t0\t93\n", "44\t92\t410.8\t0\t92\n", "45\t109\t410.8\t0\t109\n", "46\t120\t410.8\t0\t120\n", "47\t103\t410.8\t0\t103\n", "48\t91\t410.8\t0\t91\n", "49\t77\t410.8\t0\t77\n", "50\t78\t410.8\t0\t78\n", "51\t81\t410.8\t0\t81\n", "52\t76\t410.8\t0\t76\n", "53\t83\t410.8\t0\t83\n", "54\t79\t410.8\t0\t79\n", "55\t61\t410.8\t0\t61\n", "56\t89\t410.8\t0\t89\n", "57\t69\t410.8\t0\t69\n", "58\t102\t410.8\t0\t102\n", "59\t83\t410.8\t0\t83\n", "60\t118\t410.8\t0\t118\n", "61\t133\t410.8\t0\t133\n", "62\t107\t410.8\t0\t107\n", "63\t80\t410.8\t0\t80\n", "64\t101\t410.8\t0\t101\n", "65\t81\t410.8\t0\t81\n", "66\t84\t410.8\t0\t84\n", "67\t72\t410.8\t0\t72\n", "68\t70\t410.8\t0\t70\n", "69\t52\t410.8\t0\t52\n", "70\t72\t410.8\t0\t72\n", "71\t80\t410.8\t0\t80\n", "72\t61\t410.8\t0\t61\n", "73\t75\t410.8\t0\t75\n", "74\t91\t410.8\t0\t91\n", "75\t67\t410.8\t0\t67\n", "76\t101\t410.8\t0\t101\n", "77\t98\t410.8\t0\t98\n", "78\t82\t410.8\t0\t82\n", "79\t84\t410.8\t0\t84\n", "80\t79\t410.8\t0\t79\n", "81\t91\t410.8\t0\t91\n", "82\t125\t410.8\t0\t125\n", "83\t110\t410.8\t0\t110\n", "84\t93\t410.8\t0\t93\n", "85\t90\t410.8\t0\t90\n", "86\t77\t410.8\t0\t77\n", "87\t99\t410.8\t0\t99\n", "88\t136\t410.8\t0\t136\n", "89\t123\t410.8\t0\t123\n", "90\t102\t410.8\t0\t102\n", "91\t64\t410.8\t0\t64\n", "92\t45\t410.8\t0\t45\n", "93\t37\t410.8\t0\t37\n", "94\t62\t410.8\t0\t62\n", "95\t48\t410.8\t0\t48\n", "96\t61\t410.8\t0\t61\n", "97\t72\t410.8\t0\t72\n", "98\t106\t410.8\t0\t106\n", "99\t113\t410.8\t0\t113\n", "100\t125\t410.8\t0\t125\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 348_S3_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/348.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 95.32 s (13 us/read; 4.62 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,334,816\n", "Reads with adapters: 4,414,649 (60.2%)\n", "Reads written (passing filters): 7,102,992 (96.8%)\n", "\n", "Total basepairs processed: 733,481,600 bp\n", "Quality-trimmed: 1,933,700 bp (0.3%)\n", "Total written (filtered): 570,623,718 bp (77.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4258991 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.8%\n", " G: 39.5%\n", " T: 28.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t154571\t114606.5\t0\t154571\n", "4\t89720\t28651.6\t0\t89720\n", "5\t68170\t7162.9\t0\t68170\n", "6\t58148\t1790.7\t0\t58148\n", "7\t54716\t447.7\t0\t54716\n", "8\t54793\t111.9\t0\t54793\n", "9\t54297\t111.9\t0\t54297\n", "10\t53535\t111.9\t0\t53535\n", "11\t55257\t111.9\t0\t55257\n", "12\t57038\t111.9\t0\t57038\n", "13\t68390\t111.9\t0\t68390\n", "14\t67716\t111.9\t0\t67716\n", "15\t60759\t111.9\t0\t60759\n", "16\t61980\t111.9\t0\t61980\n", "17\t65806\t111.9\t0\t65806\n", "18\t74382\t111.9\t0\t74382\n", "19\t67674\t111.9\t0\t67674\n", "20\t57348\t111.9\t0\t57348\n", "21\t54602\t111.9\t0\t54602\n", "22\t51214\t111.9\t0\t51214\n", "23\t54401\t111.9\t0\t54401\n", "24\t62067\t111.9\t0\t62067\n", "25\t63579\t111.9\t0\t63579\n", "26\t71259\t111.9\t0\t71259\n", "27\t74988\t111.9\t0\t74988\n", "28\t67977\t111.9\t0\t67977\n", "29\t62912\t111.9\t0\t62912\n", "30\t62951\t111.9\t0\t62951\n", "31\t68516\t111.9\t0\t68516\n", "32\t66795\t111.9\t0\t66795\n", "33\t63922\t111.9\t0\t63922\n", "34\t61947\t111.9\t0\t61947\n", "35\t68238\t111.9\t0\t68238\n", "36\t74583\t111.9\t0\t74583\n", "37\t76781\t111.9\t0\t76781\n", "38\t65412\t111.9\t0\t65412\n", "39\t58985\t111.9\t0\t58985\n", "40\t58159\t111.9\t0\t58159\n", "41\t66672\t111.9\t0\t66672\n", "42\t75150\t111.9\t0\t75150\n", "43\t64898\t111.9\t0\t64898\n", "44\t52154\t111.9\t0\t52154\n", "45\t60899\t111.9\t0\t60899\n", "46\t70257\t111.9\t0\t70257\n", "47\t64639\t111.9\t0\t64639\n", "48\t61482\t111.9\t0\t61482\n", "49\t53106\t111.9\t0\t53106\n", "50\t52249\t111.9\t0\t52249\n", "51\t45797\t111.9\t0\t45797\n", "52\t45069\t111.9\t0\t45069\n", "53\t44830\t111.9\t0\t44830\n", "54\t44579\t111.9\t0\t44579\n", "55\t48647\t111.9\t0\t48647\n", "56\t44851\t111.9\t0\t44851\n", "57\t47672\t111.9\t0\t47672\n", "58\t49506\t111.9\t0\t49506\n", "59\t40667\t111.9\t0\t40667\n", "60\t34997\t111.9\t0\t34997\n", "61\t33159\t111.9\t0\t33159\n", "62\t29111\t111.9\t0\t29111\n", "63\t27971\t111.9\t0\t27971\n", "64\t30971\t111.9\t0\t30971\n", "65\t29824\t111.9\t0\t29824\n", "66\t24892\t111.9\t0\t24892\n", "67\t26009\t111.9\t0\t26009\n", "68\t26672\t111.9\t0\t26672\n", "69\t27361\t111.9\t0\t27361\n", "70\t29820\t111.9\t0\t29820\n", "71\t28979\t111.9\t0\t28979\n", "72\t21891\t111.9\t0\t21891\n", "73\t18745\t111.9\t0\t18745\n", "74\t17914\t111.9\t0\t17914\n", "75\t16469\t111.9\t0\t16469\n", "76\t13649\t111.9\t0\t13649\n", "77\t13888\t111.9\t0\t13888\n", "78\t16539\t111.9\t0\t16539\n", "79\t15456\t111.9\t0\t15456\n", "80\t14404\t111.9\t0\t14404\n", "81\t14173\t111.9\t0\t14173\n", "82\t13207\t111.9\t0\t13207\n", "83\t13198\t111.9\t0\t13198\n", "84\t14821\t111.9\t0\t14821\n", "85\t16953\t111.9\t0\t16953\n", "86\t16680\t111.9\t0\t16680\n", "87\t12280\t111.9\t0\t12280\n", "88\t11108\t111.9\t0\t11108\n", "89\t10791\t111.9\t0\t10791\n", "90\t11103\t111.9\t0\t11103\n", "91\t11027\t111.9\t0\t11027\n", "92\t10987\t111.9\t0\t10987\n", "93\t11917\t111.9\t0\t11917\n", "94\t11805\t111.9\t0\t11805\n", "95\t10356\t111.9\t0\t10356\n", "96\t7945\t111.9\t0\t7945\n", "97\t5136\t111.9\t0\t5136\n", "98\t3160\t111.9\t0\t3160\n", "99\t4783\t111.9\t0\t4783\n", "100\t2128\t111.9\t0\t2128\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 42586 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 56.8%\n", " C: 21.6%\n", " G: 0.0%\n", " T: 21.4%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t15030\t114606.5\t0\t15030\n", "4\t3914\t28651.6\t0\t3914\n", "5\t1986\t7162.9\t0\t1986\n", "6\t1375\t1790.7\t0\t1375\n", "7\t378\t447.7\t0\t378\n", "8\t287\t111.9\t0\t287\n", "9\t260\t111.9\t0\t260\n", "10\t297\t111.9\t0\t297\n", "11\t223\t111.9\t0\t223\n", "12\t212\t111.9\t0\t212\n", "13\t193\t111.9\t0\t193\n", "14\t225\t111.9\t0\t225\n", "15\t213\t111.9\t0\t213\n", "16\t235\t111.9\t0\t235\n", "17\t245\t111.9\t0\t245\n", "18\t335\t111.9\t0\t335\n", "19\t401\t111.9\t0\t401\n", "20\t541\t111.9\t0\t541\n", "21\t375\t111.9\t0\t375\n", "22\t267\t111.9\t0\t267\n", "23\t218\t111.9\t0\t218\n", "24\t271\t111.9\t0\t271\n", "25\t314\t111.9\t0\t314\n", "26\t472\t111.9\t0\t472\n", "27\t436\t111.9\t0\t436\n", "28\t416\t111.9\t0\t416\n", "29\t595\t111.9\t0\t595\n", "30\t928\t111.9\t0\t928\n", "31\t1094\t111.9\t0\t1094\n", "32\t1584\t111.9\t0\t1584\n", "33\t1446\t111.9\t0\t1446\n", "34\t1443\t111.9\t0\t1443\n", "35\t1749\t111.9\t0\t1749\n", "36\t1693\t111.9\t0\t1693\n", "37\t594\t111.9\t0\t594\n", "38\t67\t111.9\t0\t67\n", "39\t53\t111.9\t0\t53\n", "40\t36\t111.9\t0\t36\n", "41\t44\t111.9\t0\t44\n", "42\t48\t111.9\t0\t48\n", "43\t52\t111.9\t0\t52\n", "44\t50\t111.9\t0\t50\n", "45\t48\t111.9\t0\t48\n", "46\t42\t111.9\t0\t42\n", "47\t43\t111.9\t0\t43\n", "48\t46\t111.9\t0\t46\n", "49\t50\t111.9\t0\t50\n", "50\t46\t111.9\t0\t46\n", "51\t45\t111.9\t0\t45\n", "52\t51\t111.9\t0\t51\n", "53\t38\t111.9\t0\t38\n", "54\t41\t111.9\t0\t41\n", "55\t28\t111.9\t0\t28\n", "56\t34\t111.9\t0\t34\n", "57\t34\t111.9\t0\t34\n", "58\t32\t111.9\t0\t32\n", "59\t33\t111.9\t0\t33\n", "60\t29\t111.9\t0\t29\n", "61\t27\t111.9\t0\t27\n", "62\t24\t111.9\t0\t24\n", "63\t24\t111.9\t0\t24\n", "64\t19\t111.9\t0\t19\n", "65\t25\t111.9\t0\t25\n", "66\t25\t111.9\t0\t25\n", "67\t16\t111.9\t0\t16\n", "68\t23\t111.9\t0\t23\n", "69\t16\t111.9\t0\t16\n", "70\t28\t111.9\t0\t28\n", "71\t19\t111.9\t0\t19\n", "72\t20\t111.9\t0\t20\n", "73\t6\t111.9\t0\t6\n", "74\t15\t111.9\t0\t15\n", "75\t13\t111.9\t0\t13\n", "76\t17\t111.9\t0\t17\n", "77\t12\t111.9\t0\t12\n", "78\t13\t111.9\t0\t13\n", "79\t18\t111.9\t0\t18\n", "80\t20\t111.9\t0\t20\n", "81\t21\t111.9\t0\t21\n", "82\t11\t111.9\t0\t11\n", "83\t16\t111.9\t0\t16\n", "84\t13\t111.9\t0\t13\n", "85\t15\t111.9\t0\t15\n", "86\t14\t111.9\t0\t14\n", "87\t17\t111.9\t0\t17\n", "88\t17\t111.9\t0\t17\n", "89\t14\t111.9\t0\t14\n", "90\t26\t111.9\t0\t26\n", "91\t16\t111.9\t0\t16\n", "92\t28\t111.9\t0\t28\n", "93\t43\t111.9\t0\t43\n", "94\t80\t111.9\t0\t80\n", "95\t104\t111.9\t0\t104\n", "96\t127\t111.9\t0\t127\n", "97\t119\t111.9\t0\t119\n", "98\t95\t111.9\t0\t95\n", "99\t66\t111.9\t0\t66\n", "100\t129\t111.9\t0\t129\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 113072 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.9%\n", " C: 20.2%\n", " G: 17.7%\n", " T: 20.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t79357\t114606.5\t0\t79357\n", "4\t16683\t28651.6\t0\t16683\n", "5\t3014\t7162.9\t0\t3014\n", "6\t414\t1790.7\t0\t414\n", "7\t240\t447.7\t0\t240\n", "8\t289\t447.7\t0\t289\n", "9\t256\t447.7\t0\t256\n", "10\t288\t447.7\t0\t288\n", "11\t240\t447.7\t0\t240\n", "12\t289\t447.7\t0\t289\n", "13\t237\t447.7\t0\t237\n", "14\t267\t447.7\t0\t267\n", "15\t237\t447.7\t0\t237\n", "16\t293\t447.7\t0\t293\n", "17\t264\t447.7\t0\t264\n", "18\t258\t447.7\t0\t258\n", "19\t235\t447.7\t0\t235\n", "20\t283\t447.7\t0\t283\n", "21\t268\t447.7\t0\t268\n", "22\t273\t447.7\t0\t273\n", "23\t235\t447.7\t0\t235\n", "24\t240\t447.7\t0\t240\n", "25\t227\t447.7\t0\t227\n", "26\t241\t447.7\t0\t241\n", "27\t223\t447.7\t0\t223\n", "28\t197\t447.7\t0\t197\n", "29\t214\t447.7\t0\t214\n", "30\t229\t447.7\t0\t229\n", "31\t206\t447.7\t0\t206\n", "32\t215\t447.7\t0\t215\n", "33\t180\t447.7\t0\t180\n", "34\t194\t447.7\t0\t194\n", "35\t178\t447.7\t0\t178\n", "36\t165\t447.7\t0\t165\n", "37\t174\t447.7\t0\t174\n", "38\t184\t447.7\t0\t184\n", "39\t204\t447.7\t0\t204\n", "40\t199\t447.7\t0\t199\n", "41\t156\t447.7\t0\t156\n", "42\t137\t447.7\t0\t137\n", "43\t201\t447.7\t0\t201\n", "44\t94\t447.7\t0\t94\n", "45\t143\t447.7\t0\t143\n", "46\t142\t447.7\t0\t142\n", "47\t126\t447.7\t0\t126\n", "48\t116\t447.7\t0\t116\n", "49\t122\t447.7\t0\t122\n", "50\t142\t447.7\t0\t142\n", "51\t90\t447.7\t0\t90\n", "52\t118\t447.7\t0\t118\n", "53\t140\t447.7\t0\t140\n", "54\t83\t447.7\t0\t83\n", "55\t95\t447.7\t0\t95\n", "56\t109\t447.7\t0\t109\n", "57\t101\t447.7\t0\t101\n", "58\t102\t447.7\t0\t102\n", "59\t76\t447.7\t0\t76\n", "60\t104\t447.7\t0\t104\n", "61\t127\t447.7\t0\t127\n", "62\t88\t447.7\t0\t88\n", "63\t67\t447.7\t0\t67\n", "64\t77\t447.7\t0\t77\n", "65\t72\t447.7\t0\t72\n", "66\t58\t447.7\t0\t58\n", "67\t73\t447.7\t0\t73\n", "68\t112\t447.7\t0\t112\n", "69\t63\t447.7\t0\t63\n", "70\t74\t447.7\t0\t74\n", "71\t82\t447.7\t0\t82\n", "72\t75\t447.7\t0\t75\n", "73\t96\t447.7\t0\t96\n", "74\t82\t447.7\t0\t82\n", "75\t62\t447.7\t0\t62\n", "76\t95\t447.7\t0\t95\n", "77\t95\t447.7\t0\t95\n", "78\t74\t447.7\t0\t74\n", "79\t92\t447.7\t0\t92\n", "80\t74\t447.7\t0\t74\n", "81\t97\t447.7\t0\t97\n", "82\t69\t447.7\t0\t69\n", "83\t123\t447.7\t0\t123\n", "84\t116\t447.7\t0\t116\n", "85\t86\t447.7\t0\t86\n", "86\t82\t447.7\t0\t82\n", "87\t80\t447.7\t0\t80\n", "88\t113\t447.7\t0\t113\n", "89\t85\t447.7\t0\t85\n", "90\t64\t447.7\t0\t64\n", "91\t55\t447.7\t0\t55\n", "92\t59\t447.7\t0\t59\n", "93\t49\t447.7\t0\t49\n", "94\t63\t447.7\t0\t63\n", "95\t55\t447.7\t0\t55\n", "96\t64\t447.7\t0\t64\n", "97\t86\t447.7\t0\t86\n", "98\t92\t447.7\t0\t92\n", "99\t104\t447.7\t0\t104\n", "100\t105\t447.7\t0\t105\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 349_S34_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/349.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 84.20 s (14 us/read; 4.22 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,924,537\n", "Reads with adapters: 4,857,550 (82.0%)\n", "Reads written (passing filters): 5,518,471 (93.1%)\n", "\n", "Total basepairs processed: 592,453,700 bp\n", "Quality-trimmed: 2,120,908 bp (0.4%)\n", "Total written (filtered): 374,849,639 bp (63.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4753404 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 36.1%\n", " G: 41.0%\n", " T: 22.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t67793\t92570.9\t0\t67793\n", "4\t46842\t23142.7\t0\t46842\n", "5\t39521\t5785.7\t0\t39521\n", "6\t37303\t1446.4\t0\t37303\n", "7\t38133\t361.6\t0\t38133\n", "8\t39145\t90.4\t0\t39145\n", "9\t40120\t90.4\t0\t40120\n", "10\t40157\t90.4\t0\t40157\n", "11\t41635\t90.4\t0\t41635\n", "12\t43559\t90.4\t0\t43559\n", "13\t46125\t90.4\t0\t46125\n", "14\t48349\t90.4\t0\t48349\n", "15\t47355\t90.4\t0\t47355\n", "16\t51023\t90.4\t0\t51023\n", "17\t57517\t90.4\t0\t57517\n", "18\t64662\t90.4\t0\t64662\n", "19\t58537\t90.4\t0\t58537\n", "20\t50623\t90.4\t0\t50623\n", "21\t49301\t90.4\t0\t49301\n", "22\t46009\t90.4\t0\t46009\n", "23\t50941\t90.4\t0\t50941\n", "24\t58312\t90.4\t0\t58312\n", "25\t62994\t90.4\t0\t62994\n", "26\t70109\t90.4\t0\t70109\n", "27\t74730\t90.4\t0\t74730\n", "28\t67729\t90.4\t0\t67729\n", "29\t64028\t90.4\t0\t64028\n", "30\t65034\t90.4\t0\t65034\n", "31\t72934\t90.4\t0\t72934\n", "32\t71443\t90.4\t0\t71443\n", "33\t69182\t90.4\t0\t69182\n", "34\t66972\t90.4\t0\t66972\n", "35\t76374\t90.4\t0\t76374\n", "36\t83768\t90.4\t0\t83768\n", "37\t84536\t90.4\t0\t84536\n", "38\t74472\t90.4\t0\t74472\n", "39\t68733\t90.4\t0\t68733\n", "40\t67642\t90.4\t0\t67642\n", "41\t77050\t90.4\t0\t77050\n", "42\t83834\t90.4\t0\t83834\n", "43\t74640\t90.4\t0\t74640\n", "44\t60576\t90.4\t0\t60576\n", "45\t75422\t90.4\t0\t75422\n", "46\t90360\t90.4\t0\t90360\n", "47\t82107\t90.4\t0\t82107\n", "48\t80105\t90.4\t0\t80105\n", "49\t66944\t90.4\t0\t66944\n", "50\t65983\t90.4\t0\t65983\n", "51\t56519\t90.4\t0\t56519\n", "52\t62850\t90.4\t0\t62850\n", "53\t67324\t90.4\t0\t67324\n", "54\t72735\t90.4\t0\t72735\n", "55\t78064\t90.4\t0\t78064\n", "56\t77181\t90.4\t0\t77181\n", "57\t64562\t90.4\t0\t64562\n", "58\t65422\t90.4\t0\t65422\n", "59\t57592\t90.4\t0\t57592\n", "60\t51820\t90.4\t0\t51820\n", "61\t50217\t90.4\t0\t50217\n", "62\t41909\t90.4\t0\t41909\n", "63\t40526\t90.4\t0\t40526\n", "64\t47519\t90.4\t0\t47519\n", "65\t47039\t90.4\t0\t47039\n", "66\t40963\t90.4\t0\t40963\n", "67\t41881\t90.4\t0\t41881\n", "68\t40967\t90.4\t0\t40967\n", "69\t43622\t90.4\t0\t43622\n", "70\t46304\t90.4\t0\t46304\n", "71\t45357\t90.4\t0\t45357\n", "72\t35871\t90.4\t0\t35871\n", "73\t33555\t90.4\t0\t33555\n", "74\t33972\t90.4\t0\t33972\n", "75\t30122\t90.4\t0\t30122\n", "76\t25377\t90.4\t0\t25377\n", "77\t23880\t90.4\t0\t23880\n", "78\t28161\t90.4\t0\t28161\n", "79\t26598\t90.4\t0\t26598\n", "80\t25849\t90.4\t0\t25849\n", "81\t23678\t90.4\t0\t23678\n", "82\t22721\t90.4\t0\t22721\n", "83\t24015\t90.4\t0\t24015\n", "84\t28527\t90.4\t0\t28527\n", "85\t32141\t90.4\t0\t32141\n", "86\t29307\t90.4\t0\t29307\n", "87\t18494\t90.4\t0\t18494\n", "88\t16549\t90.4\t0\t16549\n", "89\t18357\t90.4\t0\t18357\n", "90\t19872\t90.4\t0\t19872\n", "91\t20665\t90.4\t0\t20665\n", "92\t22374\t90.4\t0\t22374\n", "93\t25547\t90.4\t0\t25547\n", "94\t25196\t90.4\t0\t25196\n", "95\t21049\t90.4\t0\t21049\n", "96\t15375\t90.4\t0\t15375\n", "97\t9390\t90.4\t0\t9390\n", "98\t5566\t90.4\t0\t5566\n", "99\t7357\t90.4\t0\t7357\n", "100\t2803\t90.4\t0\t2803\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 41597 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 69.8%\n", " C: 17.5%\n", " G: 0.0%\n", " T: 12.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t8323\t92570.9\t0\t8323\n", "4\t2653\t23142.7\t0\t2653\n", "5\t1405\t5785.7\t0\t1405\n", "6\t1218\t1446.4\t0\t1218\n", "7\t667\t361.6\t0\t667\n", "8\t542\t90.4\t0\t542\n", "9\t489\t90.4\t0\t489\n", "10\t578\t90.4\t0\t578\n", "11\t489\t90.4\t0\t489\n", "12\t415\t90.4\t0\t415\n", "13\t394\t90.4\t0\t394\n", "14\t389\t90.4\t0\t389\n", "15\t349\t90.4\t0\t349\n", "16\t380\t90.4\t0\t380\n", "17\t377\t90.4\t0\t377\n", "18\t448\t90.4\t0\t448\n", "19\t578\t90.4\t0\t578\n", "20\t663\t90.4\t0\t663\n", "21\t557\t90.4\t0\t557\n", "22\t481\t90.4\t0\t481\n", "23\t372\t90.4\t0\t372\n", "24\t387\t90.4\t0\t387\n", "25\t480\t90.4\t0\t480\n", "26\t929\t90.4\t0\t929\n", "27\t882\t90.4\t0\t882\n", "28\t766\t90.4\t0\t766\n", "29\t973\t90.4\t0\t973\n", "30\t1392\t90.4\t0\t1392\n", "31\t1461\t90.4\t0\t1461\n", "32\t2182\t90.4\t0\t2182\n", "33\t1875\t90.4\t0\t1875\n", "34\t1748\t90.4\t0\t1748\n", "35\t2106\t90.4\t0\t2106\n", "36\t1921\t90.4\t0\t1921\n", "37\t593\t90.4\t0\t593\n", "38\t50\t90.4\t0\t50\n", "39\t36\t90.4\t0\t36\n", "40\t43\t90.4\t0\t43\n", "41\t24\t90.4\t0\t24\n", "42\t31\t90.4\t0\t31\n", "43\t42\t90.4\t0\t42\n", "44\t28\t90.4\t0\t28\n", "45\t36\t90.4\t0\t36\n", "46\t26\t90.4\t0\t26\n", "47\t21\t90.4\t0\t21\n", "48\t36\t90.4\t0\t36\n", "49\t38\t90.4\t0\t38\n", "50\t38\t90.4\t0\t38\n", "51\t45\t90.4\t0\t45\n", "52\t33\t90.4\t0\t33\n", "53\t33\t90.4\t0\t33\n", "54\t24\t90.4\t0\t24\n", "55\t25\t90.4\t0\t25\n", "56\t26\t90.4\t0\t26\n", "57\t23\t90.4\t0\t23\n", "58\t36\t90.4\t0\t36\n", "59\t30\t90.4\t0\t30\n", "60\t17\t90.4\t0\t17\n", "61\t18\t90.4\t0\t18\n", "62\t19\t90.4\t0\t19\n", "63\t18\t90.4\t0\t18\n", "64\t20\t90.4\t0\t20\n", "65\t21\t90.4\t0\t21\n", "66\t17\t90.4\t0\t17\n", "67\t19\t90.4\t0\t19\n", "68\t10\t90.4\t0\t10\n", "69\t8\t90.4\t0\t8\n", "70\t6\t90.4\t0\t6\n", "71\t3\t90.4\t0\t3\n", "72\t8\t90.4\t0\t8\n", "73\t2\t90.4\t0\t2\n", "74\t1\t90.4\t0\t1\n", "75\t4\t90.4\t0\t4\n", "76\t8\t90.4\t0\t8\n", "77\t8\t90.4\t0\t8\n", "78\t4\t90.4\t0\t4\n", "79\t26\t90.4\t0\t26\n", "80\t14\t90.4\t0\t14\n", "81\t23\t90.4\t0\t23\n", "82\t22\t90.4\t0\t22\n", "83\t48\t90.4\t0\t48\n", "84\t43\t90.4\t0\t43\n", "85\t59\t90.4\t0\t59\n", "86\t32\t90.4\t0\t32\n", "87\t36\t90.4\t0\t36\n", "88\t25\t90.4\t0\t25\n", "89\t49\t90.4\t0\t49\n", "90\t42\t90.4\t0\t42\n", "91\t43\t90.4\t0\t43\n", "92\t62\t90.4\t0\t62\n", "93\t92\t90.4\t0\t92\n", "94\t98\t90.4\t0\t98\n", "95\t126\t90.4\t0\t126\n", "96\t126\t90.4\t0\t126\n", "97\t109\t90.4\t0\t109\n", "98\t80\t90.4\t0\t80\n", "99\t23\t90.4\t0\t23\n", "100\t22\t90.4\t0\t22\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 62549 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.3%\n", " C: 25.8%\n", " G: 19.9%\n", " T: 14.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t32924\t92570.9\t0\t32924\n", "4\t6985\t23142.7\t0\t6985\n", "5\t3480\t5785.7\t0\t3480\n", "6\t499\t1446.4\t0\t499\n", "7\t344\t361.6\t0\t344\n", "8\t413\t361.6\t0\t413\n", "9\t370\t361.6\t0\t370\n", "10\t395\t361.6\t0\t395\n", "11\t335\t361.6\t0\t335\n", "12\t339\t361.6\t0\t339\n", "13\t371\t361.6\t0\t371\n", "14\t385\t361.6\t0\t385\n", "15\t415\t361.6\t0\t415\n", "16\t393\t361.6\t0\t393\n", "17\t396\t361.6\t0\t396\n", "18\t417\t361.6\t0\t417\n", "19\t357\t361.6\t0\t357\n", "20\t375\t361.6\t0\t375\n", "21\t345\t361.6\t0\t345\n", "22\t325\t361.6\t0\t325\n", "23\t367\t361.6\t0\t367\n", "24\t303\t361.6\t0\t303\n", "25\t363\t361.6\t0\t363\n", "26\t327\t361.6\t0\t327\n", "27\t351\t361.6\t0\t351\n", "28\t346\t361.6\t0\t346\n", "29\t304\t361.6\t0\t304\n", "30\t310\t361.6\t0\t310\n", "31\t302\t361.6\t0\t302\n", "32\t347\t361.6\t0\t347\n", "33\t342\t361.6\t0\t342\n", "34\t323\t361.6\t0\t323\n", "35\t316\t361.6\t0\t316\n", "36\t290\t361.6\t0\t290\n", "37\t308\t361.6\t0\t308\n", "38\t329\t361.6\t0\t329\n", "39\t288\t361.6\t0\t288\n", "40\t291\t361.6\t0\t291\n", "41\t322\t361.6\t0\t322\n", "42\t229\t361.6\t0\t229\n", "43\t366\t361.6\t0\t366\n", "44\t74\t361.6\t0\t74\n", "45\t222\t361.6\t0\t222\n", "46\t208\t361.6\t0\t208\n", "47\t209\t361.6\t0\t209\n", "48\t207\t361.6\t0\t207\n", "49\t176\t361.6\t0\t176\n", "50\t199\t361.6\t0\t199\n", "51\t182\t361.6\t0\t182\n", "52\t201\t361.6\t0\t201\n", "53\t189\t361.6\t0\t189\n", "54\t180\t361.6\t0\t180\n", "55\t156\t361.6\t0\t156\n", "56\t192\t361.6\t0\t192\n", "57\t144\t361.6\t0\t144\n", "58\t168\t361.6\t0\t168\n", "59\t129\t361.6\t0\t129\n", "60\t153\t361.6\t0\t153\n", "61\t164\t361.6\t0\t164\n", "62\t184\t361.6\t0\t184\n", "63\t179\t361.6\t0\t179\n", "64\t113\t361.6\t0\t113\n", "65\t111\t361.6\t0\t111\n", "66\t112\t361.6\t0\t112\n", "67\t124\t361.6\t0\t124\n", "68\t181\t361.6\t0\t181\n", "69\t35\t361.6\t0\t35\n", "70\t47\t361.6\t0\t47\n", "71\t85\t361.6\t0\t85\n", "72\t93\t361.6\t0\t93\n", "73\t84\t361.6\t0\t84\n", "74\t91\t361.6\t0\t91\n", "75\t64\t361.6\t0\t64\n", "76\t61\t361.6\t0\t61\n", "77\t71\t361.6\t0\t71\n", "78\t58\t361.6\t0\t58\n", "79\t57\t361.6\t0\t57\n", "80\t74\t361.6\t0\t74\n", "81\t60\t361.6\t0\t60\n", "82\t66\t361.6\t0\t66\n", "83\t81\t361.6\t0\t81\n", "84\t45\t361.6\t0\t45\n", "85\t61\t361.6\t0\t61\n", "86\t47\t361.6\t0\t47\n", "87\t61\t361.6\t0\t61\n", "88\t72\t361.6\t0\t72\n", "89\t47\t361.6\t0\t47\n", "90\t35\t361.6\t0\t35\n", "91\t45\t361.6\t0\t45\n", "92\t27\t361.6\t0\t27\n", "93\t44\t361.6\t0\t44\n", "94\t42\t361.6\t0\t42\n", "95\t51\t361.6\t0\t51\n", "96\t37\t361.6\t0\t37\n", "97\t29\t361.6\t0\t29\n", "98\t44\t361.6\t0\t44\n", "99\t49\t361.6\t0\t49\n", "100\t42\t361.6\t0\t42\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: Undetermined_S0_L001_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/Undetermined.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 138.63 s (13 us/read; 4.78 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 11,043,082\n", "Reads with adapters: 4,296,025 (38.9%)\n", "Reads written (passing filters): 10,587,637 (95.9%)\n", "\n", "Total basepairs processed: 1,104,308,200 bp\n", "Quality-trimmed: 4,001,301 bp (0.4%)\n", "Total written (filtered): 922,516,792 bp (83.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4029424 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 33.6%\n", " G: 31.8%\n", " T: 34.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t209260\t172548.2\t0\t209260\n", "4\t99887\t43137.0\t0\t99887\n", "5\t60999\t10784.3\t0\t60999\n", "6\t41730\t2696.1\t0\t41730\n", "7\t36117\t674.0\t0\t36117\n", "8\t34201\t168.5\t0\t34201\n", "9\t34150\t168.5\t0\t34150\n", "10\t33446\t168.5\t0\t33446\n", "11\t34954\t168.5\t0\t34954\n", "12\t35801\t168.5\t0\t35801\n", "13\t38355\t168.5\t0\t38355\n", "14\t39512\t168.5\t0\t39512\n", "15\t38675\t168.5\t0\t38675\n", "16\t40809\t168.5\t0\t40809\n", "17\t43913\t168.5\t0\t43913\n", "18\t49085\t168.5\t0\t49085\n", "19\t45699\t168.5\t0\t45699\n", "20\t40663\t168.5\t0\t40663\n", "21\t40889\t168.5\t0\t40889\n", "22\t38734\t168.5\t0\t38734\n", "23\t40371\t168.5\t0\t40371\n", "24\t44777\t168.5\t0\t44777\n", "25\t46420\t168.5\t0\t46420\n", "26\t52662\t168.5\t0\t52662\n", "27\t57228\t168.5\t0\t57228\n", "28\t53500\t168.5\t0\t53500\n", "29\t53277\t168.5\t0\t53277\n", "30\t52632\t168.5\t0\t52632\n", "31\t55841\t168.5\t0\t55841\n", "32\t56247\t168.5\t0\t56247\n", "33\t53559\t168.5\t0\t53559\n", "34\t54125\t168.5\t0\t54125\n", "35\t59171\t168.5\t0\t59171\n", "36\t63047\t168.5\t0\t63047\n", "37\t64994\t168.5\t0\t64994\n", "38\t57253\t168.5\t0\t57253\n", "39\t51573\t168.5\t0\t51573\n", "40\t50135\t168.5\t0\t50135\n", "41\t56449\t168.5\t0\t56449\n", "42\t61442\t168.5\t0\t61442\n", "43\t54888\t168.5\t0\t54888\n", "44\t48051\t168.5\t0\t48051\n", "45\t55142\t168.5\t0\t55142\n", "46\t61117\t168.5\t0\t61117\n", "47\t59936\t168.5\t0\t59936\n", "48\t57959\t168.5\t0\t57959\n", "49\t52357\t168.5\t0\t52357\n", "50\t50438\t168.5\t0\t50438\n", "51\t49193\t168.5\t0\t49193\n", "52\t48300\t168.5\t0\t48300\n", "53\t47483\t168.5\t0\t47483\n", "54\t48468\t168.5\t0\t48468\n", "55\t50399\t168.5\t0\t50399\n", "56\t48041\t168.5\t0\t48041\n", "57\t46681\t168.5\t0\t46681\n", "58\t47954\t168.5\t0\t47954\n", "59\t42579\t168.5\t0\t42579\n", "60\t39416\t168.5\t0\t39416\n", "61\t35697\t168.5\t0\t35697\n", "62\t33827\t168.5\t0\t33827\n", "63\t34488\t168.5\t0\t34488\n", "64\t33935\t168.5\t0\t33935\n", "65\t32679\t168.5\t0\t32679\n", "66\t32981\t168.5\t0\t32981\n", "67\t32213\t168.5\t0\t32213\n", "68\t31719\t168.5\t0\t31719\n", "69\t32183\t168.5\t0\t32183\n", "70\t32039\t168.5\t0\t32039\n", "71\t28687\t168.5\t0\t28687\n", "72\t26085\t168.5\t0\t26085\n", "73\t25009\t168.5\t0\t25009\n", "74\t23973\t168.5\t0\t23973\n", "75\t22582\t168.5\t0\t22582\n", "76\t21814\t168.5\t0\t21814\n", "77\t22073\t168.5\t0\t22073\n", "78\t22034\t168.5\t0\t22034\n", "79\t21920\t168.5\t0\t21920\n", "80\t21914\t168.5\t0\t21914\n", "81\t22101\t168.5\t0\t22101\n", "82\t22195\t168.5\t0\t22195\n", "83\t23560\t168.5\t0\t23560\n", "84\t24836\t168.5\t0\t24836\n", "85\t26174\t168.5\t0\t26174\n", "86\t26593\t168.5\t0\t26593\n", "87\t26647\t168.5\t0\t26647\n", "88\t28066\t168.5\t0\t28066\n", "89\t26383\t168.5\t0\t26383\n", "90\t25063\t168.5\t0\t25063\n", "91\t24177\t168.5\t0\t24177\n", "92\t24267\t168.5\t0\t24267\n", "93\t23893\t168.5\t0\t23893\n", "94\t22153\t168.5\t0\t22153\n", "95\t18973\t168.5\t0\t18973\n", "96\t15935\t168.5\t0\t15935\n", "97\t12800\t168.5\t0\t12800\n", "98\t10690\t168.5\t0\t10690\n", "99\t12179\t168.5\t0\t12179\n", "100\t14903\t168.5\t0\t14903\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 72163 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 53.7%\n", " C: 19.9%\n", " G: 0.0%\n", " T: 26.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t34240\t172548.2\t0\t34240\n", "4\t7634\t43137.0\t0\t7634\n", "5\t1441\t10784.3\t0\t1441\n", "6\t657\t2696.1\t0\t657\n", "7\t364\t674.0\t0\t364\n", "8\t325\t168.5\t0\t325\n", "9\t268\t168.5\t0\t268\n", "10\t233\t168.5\t0\t233\n", "11\t251\t168.5\t0\t251\n", "12\t244\t168.5\t0\t244\n", "13\t272\t168.5\t0\t272\n", "14\t218\t168.5\t0\t218\n", "15\t254\t168.5\t0\t254\n", "16\t273\t168.5\t0\t273\n", "17\t293\t168.5\t0\t293\n", "18\t281\t168.5\t0\t281\n", "19\t393\t168.5\t0\t393\n", "20\t443\t168.5\t0\t443\n", "21\t458\t168.5\t0\t458\n", "22\t403\t168.5\t0\t403\n", "23\t321\t168.5\t0\t321\n", "24\t348\t168.5\t0\t348\n", "25\t378\t168.5\t0\t378\n", "26\t450\t168.5\t0\t450\n", "27\t595\t168.5\t0\t595\n", "28\t596\t168.5\t0\t596\n", "29\t693\t168.5\t0\t693\n", "30\t976\t168.5\t0\t976\n", "31\t1218\t168.5\t0\t1218\n", "32\t1425\t168.5\t0\t1425\n", "33\t1762\t168.5\t0\t1762\n", "34\t1981\t168.5\t0\t1981\n", "35\t2437\t168.5\t0\t2437\n", "36\t2002\t168.5\t0\t2002\n", "37\t1566\t168.5\t0\t1566\n", "38\t758\t168.5\t0\t758\n", "39\t332\t168.5\t0\t332\n", "40\t256\t168.5\t0\t256\n", "41\t216\t168.5\t0\t216\n", "42\t208\t168.5\t0\t208\n", "43\t239\t168.5\t0\t239\n", "44\t210\t168.5\t0\t210\n", "45\t198\t168.5\t0\t198\n", "46\t204\t168.5\t0\t204\n", "47\t200\t168.5\t0\t200\n", "48\t193\t168.5\t0\t193\n", "49\t181\t168.5\t0\t181\n", "50\t162\t168.5\t0\t162\n", "51\t168\t168.5\t0\t168\n", "52\t168\t168.5\t0\t168\n", "53\t135\t168.5\t0\t135\n", "54\t139\t168.5\t0\t139\n", "55\t125\t168.5\t0\t125\n", "56\t125\t168.5\t0\t125\n", "57\t148\t168.5\t0\t148\n", "58\t108\t168.5\t0\t108\n", "59\t114\t168.5\t0\t114\n", "60\t127\t168.5\t0\t127\n", "61\t82\t168.5\t0\t82\n", "62\t84\t168.5\t0\t84\n", "63\t87\t168.5\t0\t87\n", "64\t80\t168.5\t0\t80\n", "65\t87\t168.5\t0\t87\n", "66\t86\t168.5\t0\t86\n", "67\t94\t168.5\t0\t94\n", "68\t73\t168.5\t0\t73\n", "69\t78\t168.5\t0\t78\n", "70\t94\t168.5\t0\t94\n", "71\t81\t168.5\t0\t81\n", "72\t48\t168.5\t0\t48\n", "73\t5\t168.5\t0\t5\n", "74\t7\t168.5\t0\t7\n", "75\t7\t168.5\t0\t7\n", "76\t8\t168.5\t0\t8\n", "77\t13\t168.5\t0\t13\n", "78\t5\t168.5\t0\t5\n", "79\t14\t168.5\t0\t14\n", "80\t7\t168.5\t0\t7\n", "81\t8\t168.5\t0\t8\n", "82\t11\t168.5\t0\t11\n", "83\t11\t168.5\t0\t11\n", "84\t10\t168.5\t0\t10\n", "85\t17\t168.5\t0\t17\n", "86\t16\t168.5\t0\t16\n", "87\t16\t168.5\t0\t16\n", "88\t11\t168.5\t0\t11\n", "89\t20\t168.5\t0\t20\n", "90\t23\t168.5\t0\t23\n", "91\t28\t168.5\t0\t28\n", "92\t41\t168.5\t0\t41\n", "93\t42\t168.5\t0\t42\n", "94\t44\t168.5\t0\t44\n", "95\t71\t168.5\t0\t71\n", "96\t88\t168.5\t0\t88\n", "97\t81\t168.5\t0\t81\n", "98\t54\t168.5\t0\t54\n", "99\t51\t168.5\t0\t51\n", "100\t73\t168.5\t0\t73\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 194438 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 35.6%\n", " C: 26.0%\n", " G: 21.0%\n", " T: 17.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t147485\t172548.2\t0\t147485\n", "4\t29597\t43137.0\t0\t29597\n", "5\t2176\t10784.3\t0\t2176\n", "6\t579\t2696.1\t0\t579\n", "7\t403\t674.0\t0\t403\n", "8\t512\t674.0\t0\t512\n", "9\t316\t674.0\t0\t316\n", "10\t403\t674.0\t0\t403\n", "11\t397\t674.0\t0\t397\n", "12\t361\t674.0\t0\t361\n", "13\t392\t674.0\t0\t392\n", "14\t362\t674.0\t0\t362\n", "15\t358\t674.0\t0\t358\n", "16\t340\t674.0\t0\t340\n", "17\t340\t674.0\t0\t340\n", "18\t322\t674.0\t0\t322\n", "19\t318\t674.0\t0\t318\n", "20\t316\t674.0\t0\t316\n", "21\t314\t674.0\t0\t314\n", "22\t270\t674.0\t0\t270\n", "23\t290\t674.0\t0\t290\n", "24\t244\t674.0\t0\t244\n", "25\t272\t674.0\t0\t272\n", "26\t262\t674.0\t0\t262\n", "27\t269\t674.0\t0\t269\n", "28\t244\t674.0\t0\t244\n", "29\t243\t674.0\t0\t243\n", "30\t259\t674.0\t0\t259\n", "31\t256\t674.0\t0\t256\n", "32\t229\t674.0\t0\t229\n", "33\t244\t674.0\t0\t244\n", "34\t227\t674.0\t0\t227\n", "35\t210\t674.0\t0\t210\n", "36\t229\t674.0\t0\t229\n", "37\t204\t674.0\t0\t204\n", "38\t209\t674.0\t0\t209\n", "39\t236\t674.0\t0\t236\n", "40\t260\t674.0\t0\t260\n", "41\t122\t674.0\t0\t122\n", "42\t162\t674.0\t0\t162\n", "43\t142\t674.0\t0\t142\n", "44\t155\t674.0\t0\t155\n", "45\t137\t674.0\t0\t137\n", "46\t139\t674.0\t0\t139\n", "47\t109\t674.0\t0\t109\n", "48\t116\t674.0\t0\t116\n", "49\t109\t674.0\t0\t109\n", "50\t138\t674.0\t0\t138\n", "51\t98\t674.0\t0\t98\n", "52\t130\t674.0\t0\t130\n", "53\t147\t674.0\t0\t147\n", "54\t92\t674.0\t0\t92\n", "55\t128\t674.0\t0\t128\n", "56\t73\t674.0\t0\t73\n", "57\t120\t674.0\t0\t120\n", "58\t97\t674.0\t0\t97\n", "59\t72\t674.0\t0\t72\n", "60\t92\t674.0\t0\t92\n", "61\t91\t674.0\t0\t91\n", "62\t72\t674.0\t0\t72\n", "63\t82\t674.0\t0\t82\n", "64\t81\t674.0\t0\t81\n", "65\t74\t674.0\t0\t74\n", "66\t56\t674.0\t0\t56\n", "67\t50\t674.0\t0\t50\n", "68\t54\t674.0\t0\t54\n", "69\t47\t674.0\t0\t47\n", "70\t92\t674.0\t0\t92\n", "71\t61\t674.0\t0\t61\n", "72\t44\t674.0\t0\t44\n", "73\t52\t674.0\t0\t52\n", "74\t38\t674.0\t0\t38\n", "75\t43\t674.0\t0\t43\n", "76\t48\t674.0\t0\t48\n", "77\t51\t674.0\t0\t51\n", "78\t41\t674.0\t0\t41\n", "79\t45\t674.0\t0\t45\n", "80\t38\t674.0\t0\t38\n", "81\t39\t674.0\t0\t39\n", "82\t63\t674.0\t0\t63\n", "83\t64\t674.0\t0\t64\n", "84\t52\t674.0\t0\t52\n", "85\t52\t674.0\t0\t52\n", "86\t49\t674.0\t0\t49\n", "87\t55\t674.0\t0\t55\n", "88\t62\t674.0\t0\t62\n", "89\t45\t674.0\t0\t45\n", "90\t41\t674.0\t0\t41\n", "91\t23\t674.0\t0\t23\n", "92\t24\t674.0\t0\t24\n", "93\t38\t674.0\t0\t38\n", "94\t35\t674.0\t0\t35\n", "95\t32\t674.0\t0\t32\n", "96\t32\t674.0\t0\t32\n", "97\t51\t674.0\t0\t51\n", "98\t49\t674.0\t0\t49\n", "99\t76\t674.0\t0\t76\n", "100\t70\t674.0\t0\t70\n" ] } ], "source": [ "%%bash\n", "\n", "# create output file names (with location in relative path)\n", "for file in *_L001_R1_001.fastq\n", "do\n", "sample=\"$(basename -a $file | cut -d \"_\" -f 1)\"\n", "trimmed_file=\"$sample.trim.fastq\"\n", "\n", "# run cutadapt on each file\n", "/Users/laura/.local/bin/cutadapt $file -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 \\\n", "-o ../../qc-processing/cutadapt/$trimmed_file\n", "done" ] }, { "cell_type": "code", "execution_count": 63, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Bumblebee/O.lurida_QuantSeq-2020/raw-data/Batch2_77plex_lane2_done\n" ] } ], "source": [ "# Move to other batch to trim \n", "cd {workingdir}raw-data/Batch2_77plex_lane2_done/" ] }, { "cell_type": "code", "execution_count": 64, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 34_S68_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/34.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 99.96 s (14 us/read; 4.16 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,927,864\n", "Reads with adapters: 3,573,565 (51.6%)\n", "Reads written (passing filters): 6,737,872 (97.3%)\n", "\n", "Total basepairs processed: 692,786,400 bp\n", "Quality-trimmed: 2,062,788 bp (0.3%)\n", "Total written (filtered): 558,817,666 bp (80.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3265197 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.2%\n", " G: 38.9%\n", " T: 33.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t142043\t108247.9\t0\t142043\n", "4\t69859\t27062.0\t0\t69859\n", "5\t49516\t6765.5\t0\t49516\n", "6\t42256\t1691.4\t0\t42256\n", "7\t36205\t422.8\t0\t36205\n", "8\t37867\t105.7\t0\t37867\n", "9\t38484\t105.7\t0\t38484\n", "10\t37351\t105.7\t0\t37351\n", "11\t35726\t105.7\t0\t35726\n", "12\t36328\t105.7\t0\t36328\n", "13\t40630\t105.7\t0\t40630\n", "14\t41903\t105.7\t0\t41903\n", "15\t41224\t105.7\t0\t41224\n", "16\t43853\t105.7\t0\t43853\n", "17\t46782\t105.7\t0\t46782\n", "18\t52880\t105.7\t0\t52880\n", "19\t48659\t105.7\t0\t48659\n", "20\t40729\t105.7\t0\t40729\n", "21\t38864\t105.7\t0\t38864\n", "22\t35544\t105.7\t0\t35544\n", "23\t38409\t105.7\t0\t38409\n", "24\t43615\t105.7\t0\t43615\n", "25\t44938\t105.7\t0\t44938\n", "26\t49559\t105.7\t0\t49559\n", "27\t55649\t105.7\t0\t55649\n", "28\t52284\t105.7\t0\t52284\n", "29\t50336\t105.7\t0\t50336\n", "30\t52602\t105.7\t0\t52602\n", "31\t54029\t105.7\t0\t54029\n", "32\t49416\t105.7\t0\t49416\n", "33\t47076\t105.7\t0\t47076\n", "34\t45226\t105.7\t0\t45226\n", "35\t52424\t105.7\t0\t52424\n", "36\t59181\t105.7\t0\t59181\n", "37\t59540\t105.7\t0\t59540\n", "38\t51783\t105.7\t0\t51783\n", "39\t46632\t105.7\t0\t46632\n", "40\t44273\t105.7\t0\t44273\n", "41\t44371\t105.7\t0\t44371\n", "42\t46308\t105.7\t0\t46308\n", "43\t41791\t105.7\t0\t41791\n", "44\t36695\t105.7\t0\t36695\n", "45\t44269\t105.7\t0\t44269\n", "46\t50677\t105.7\t0\t50677\n", "47\t46661\t105.7\t0\t46661\n", "48\t45357\t105.7\t0\t45357\n", "49\t37829\t105.7\t0\t37829\n", "50\t36337\t105.7\t0\t36337\n", "51\t37940\t105.7\t0\t37940\n", "52\t39855\t105.7\t0\t39855\n", "53\t37574\t105.7\t0\t37574\n", "54\t39788\t105.7\t0\t39788\n", "55\t43153\t105.7\t0\t43153\n", "56\t42886\t105.7\t0\t42886\n", "57\t37424\t105.7\t0\t37424\n", "58\t40185\t105.7\t0\t40185\n", "59\t36191\t105.7\t0\t36191\n", "60\t31519\t105.7\t0\t31519\n", "61\t29046\t105.7\t0\t29046\n", "62\t25044\t105.7\t0\t25044\n", "63\t25326\t105.7\t0\t25326\n", "64\t29048\t105.7\t0\t29048\n", "65\t27063\t105.7\t0\t27063\n", "66\t24917\t105.7\t0\t24917\n", "67\t25190\t105.7\t0\t25190\n", "68\t24736\t105.7\t0\t24736\n", "69\t26343\t105.7\t0\t26343\n", "70\t27694\t105.7\t0\t27694\n", "71\t26192\t105.7\t0\t26192\n", "72\t20405\t105.7\t0\t20405\n", "73\t17715\t105.7\t0\t17715\n", "74\t17371\t105.7\t0\t17371\n", "75\t15267\t105.7\t0\t15267\n", "76\t12975\t105.7\t0\t12975\n", "77\t12674\t105.7\t0\t12674\n", "78\t14239\t105.7\t0\t14239\n", "79\t13085\t105.7\t0\t13085\n", "80\t12762\t105.7\t0\t12762\n", "81\t11911\t105.7\t0\t11911\n", "82\t11556\t105.7\t0\t11556\n", "83\t11313\t105.7\t0\t11313\n", "84\t12895\t105.7\t0\t12895\n", "85\t13580\t105.7\t0\t13580\n", "86\t12154\t105.7\t0\t12154\n", "87\t9208\t105.7\t0\t9208\n", "88\t8391\t105.7\t0\t8391\n", "89\t8148\t105.7\t0\t8148\n", "90\t8409\t105.7\t0\t8409\n", "91\t8197\t105.7\t0\t8197\n", "92\t8230\t105.7\t0\t8230\n", "93\t8339\t105.7\t0\t8339\n", "94\t8108\t105.7\t0\t8108\n", "95\t7197\t105.7\t0\t7197\n", "96\t5985\t105.7\t0\t5985\n", "97\t4490\t105.7\t0\t4490\n", "98\t3444\t105.7\t0\t3444\n", "99\t3472\t105.7\t0\t3472\n", "100\t2593\t105.7\t0\t2593\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 179904 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 74.3%\n", " C: 17.2%\n", " G: 0.0%\n", " T: 8.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t19949\t108247.9\t0\t19949\n", "4\t10358\t27062.0\t0\t10358\n", "5\t10745\t6765.5\t0\t10745\n", "6\t4241\t1691.4\t0\t4241\n", "7\t2173\t422.8\t0\t2173\n", "8\t1989\t105.7\t0\t1989\n", "9\t1852\t105.7\t0\t1852\n", "10\t1908\t105.7\t0\t1908\n", "11\t2373\t105.7\t0\t2373\n", "12\t1707\t105.7\t0\t1707\n", "13\t1629\t105.7\t0\t1629\n", "14\t1575\t105.7\t0\t1575\n", "15\t1489\t105.7\t0\t1489\n", "16\t1495\t105.7\t0\t1495\n", "17\t1453\t105.7\t0\t1453\n", "18\t2049\t105.7\t0\t2049\n", "19\t2080\t105.7\t0\t2080\n", "20\t2555\t105.7\t0\t2555\n", "21\t1881\t105.7\t0\t1881\n", "22\t1532\t105.7\t0\t1532\n", "23\t1124\t105.7\t0\t1124\n", "24\t1247\t105.7\t0\t1247\n", "25\t1331\t105.7\t0\t1331\n", "26\t2150\t105.7\t0\t2150\n", "27\t2205\t105.7\t0\t2205\n", "28\t2286\t105.7\t0\t2286\n", "29\t2704\t105.7\t0\t2704\n", "30\t4940\t105.7\t0\t4940\n", "31\t5856\t105.7\t0\t5856\n", "32\t9868\t105.7\t0\t9868\n", "33\t11321\t105.7\t0\t11321\n", "34\t13074\t105.7\t0\t13074\n", "35\t17734\t105.7\t0\t17734\n", "36\t16951\t105.7\t0\t16951\n", "37\t8529\t105.7\t0\t8529\n", "38\t589\t105.7\t0\t589\n", "39\t362\t105.7\t0\t362\n", "40\t84\t105.7\t0\t84\n", "41\t40\t105.7\t0\t40\n", "42\t58\t105.7\t0\t58\n", "43\t50\t105.7\t0\t50\n", "44\t60\t105.7\t0\t60\n", "45\t45\t105.7\t0\t45\n", "46\t73\t105.7\t0\t73\n", "47\t46\t105.7\t0\t46\n", "48\t41\t105.7\t0\t41\n", "49\t42\t105.7\t0\t42\n", "50\t50\t105.7\t0\t50\n", "51\t87\t105.7\t0\t87\n", "52\t68\t105.7\t0\t68\n", "53\t66\t105.7\t0\t66\n", "54\t59\t105.7\t0\t59\n", "55\t45\t105.7\t0\t45\n", "56\t30\t105.7\t0\t30\n", "57\t48\t105.7\t0\t48\n", "58\t64\t105.7\t0\t64\n", "59\t33\t105.7\t0\t33\n", "60\t35\t105.7\t0\t35\n", "61\t40\t105.7\t0\t40\n", "62\t40\t105.7\t0\t40\n", "63\t32\t105.7\t0\t32\n", "64\t36\t105.7\t0\t36\n", "65\t35\t105.7\t0\t35\n", "66\t27\t105.7\t0\t27\n", "67\t19\t105.7\t0\t19\n", "68\t22\t105.7\t0\t22\n", "69\t19\t105.7\t0\t19\n", "70\t17\t105.7\t0\t17\n", "71\t12\t105.7\t0\t12\n", "72\t11\t105.7\t0\t11\n", "73\t15\t105.7\t0\t15\n", "74\t8\t105.7\t0\t8\n", "75\t24\t105.7\t0\t24\n", "76\t23\t105.7\t0\t23\n", "77\t16\t105.7\t0\t16\n", "78\t13\t105.7\t0\t13\n", "79\t7\t105.7\t0\t7\n", "80\t6\t105.7\t0\t6\n", "81\t6\t105.7\t0\t6\n", "82\t8\t105.7\t0\t8\n", "83\t11\t105.7\t0\t11\n", "84\t10\t105.7\t0\t10\n", "85\t5\t105.7\t0\t5\n", "86\t8\t105.7\t0\t8\n", "87\t5\t105.7\t0\t5\n", "88\t13\t105.7\t0\t13\n", "89\t28\t105.7\t0\t28\n", "90\t16\t105.7\t0\t16\n", "91\t25\t105.7\t0\t25\n", "92\t23\t105.7\t0\t23\n", "93\t30\t105.7\t0\t30\n", "94\t46\t105.7\t0\t46\n", "95\t189\t105.7\t0\t189\n", "96\t139\t105.7\t0\t139\n", "97\t166\t105.7\t0\t166\n", "98\t170\t105.7\t0\t170\n", "99\t93\t105.7\t0\t93\n", "100\t63\t105.7\t0\t63\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 128464 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 47.4%\n", " C: 25.1%\n", " G: 8.7%\n", " T: 18.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t84657\t108247.9\t0\t84657\n", "4\t20310\t27062.0\t0\t20310\n", "5\t2582\t6765.5\t0\t2582\n", "6\t384\t1691.4\t0\t384\n", "7\t305\t422.8\t0\t305\n", "8\t337\t422.8\t0\t337\n", "9\t282\t422.8\t0\t282\n", "10\t211\t422.8\t0\t211\n", "11\t365\t422.8\t0\t365\n", "12\t638\t422.8\t0\t638\n", "13\t848\t422.8\t0\t848\n", "14\t873\t422.8\t0\t873\n", "15\t782\t422.8\t0\t782\n", "16\t600\t422.8\t0\t600\n", "17\t648\t422.8\t0\t648\n", "18\t528\t422.8\t0\t528\n", "19\t591\t422.8\t0\t591\n", "20\t548\t422.8\t0\t548\n", "21\t435\t422.8\t0\t435\n", "22\t428\t422.8\t0\t428\n", "23\t275\t422.8\t0\t275\n", "24\t236\t422.8\t0\t236\n", "25\t260\t422.8\t0\t260\n", "26\t252\t422.8\t0\t252\n", "27\t299\t422.8\t0\t299\n", "28\t274\t422.8\t0\t274\n", "29\t237\t422.8\t0\t237\n", "30\t208\t422.8\t0\t208\n", "31\t214\t422.8\t0\t214\n", "32\t209\t422.8\t0\t209\n", "33\t210\t422.8\t0\t210\n", "34\t200\t422.8\t0\t200\n", "35\t184\t422.8\t0\t184\n", "36\t187\t422.8\t0\t187\n", "37\t216\t422.8\t0\t216\n", "38\t210\t422.8\t0\t210\n", "39\t218\t422.8\t0\t218\n", "40\t211\t422.8\t0\t211\n", "41\t213\t422.8\t0\t213\n", "42\t175\t422.8\t0\t175\n", "43\t296\t422.8\t0\t296\n", "44\t52\t422.8\t0\t52\n", "45\t158\t422.8\t0\t158\n", "46\t217\t422.8\t0\t217\n", "47\t182\t422.8\t0\t182\n", "48\t159\t422.8\t0\t159\n", "49\t183\t422.8\t0\t183\n", "50\t202\t422.8\t0\t202\n", "51\t226\t422.8\t0\t226\n", "52\t235\t422.8\t0\t235\n", "53\t340\t422.8\t0\t340\n", "54\t385\t422.8\t0\t385\n", "55\t411\t422.8\t0\t411\n", "56\t372\t422.8\t0\t372\n", "57\t338\t422.8\t0\t338\n", "58\t302\t422.8\t0\t302\n", "59\t181\t422.8\t0\t181\n", "60\t296\t422.8\t0\t296\n", "61\t204\t422.8\t0\t204\n", "62\t162\t422.8\t0\t162\n", "63\t153\t422.8\t0\t153\n", "64\t194\t422.8\t0\t194\n", "65\t136\t422.8\t0\t136\n", "66\t137\t422.8\t0\t137\n", "67\t134\t422.8\t0\t134\n", "68\t198\t422.8\t0\t198\n", "69\t28\t422.8\t0\t28\n", "70\t45\t422.8\t0\t45\n", "71\t74\t422.8\t0\t74\n", "72\t92\t422.8\t0\t92\n", "73\t128\t422.8\t0\t128\n", "74\t134\t422.8\t0\t134\n", "75\t78\t422.8\t0\t78\n", "76\t58\t422.8\t0\t58\n", "77\t59\t422.8\t0\t59\n", "78\t43\t422.8\t0\t43\n", "79\t13\t422.8\t0\t13\n", "80\t43\t422.8\t0\t43\n", "81\t24\t422.8\t0\t24\n", "82\t36\t422.8\t0\t36\n", "83\t29\t422.8\t0\t29\n", "84\t20\t422.8\t0\t20\n", "85\t34\t422.8\t0\t34\n", "86\t34\t422.8\t0\t34\n", "87\t57\t422.8\t0\t57\n", "88\t71\t422.8\t0\t71\n", "89\t66\t422.8\t0\t66\n", "90\t55\t422.8\t0\t55\n", "91\t33\t422.8\t0\t33\n", "92\t31\t422.8\t0\t31\n", "93\t34\t422.8\t0\t34\n", "94\t22\t422.8\t0\t22\n", "95\t24\t422.8\t0\t24\n", "96\t19\t422.8\t0\t19\n", "97\t64\t422.8\t0\t64\n", "98\t88\t422.8\t0\t88\n", "99\t107\t422.8\t0\t107\n", "100\t128\t422.8\t0\t128\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 35_S72_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/35.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 36.23 s (13 us/read; 4.52 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 2,727,730\n", "Reads with adapters: 2,326,314 (85.3%)\n", "Reads written (passing filters): 2,162,122 (79.3%)\n", "\n", "Total basepairs processed: 272,773,000 bp\n", "Quality-trimmed: 854,146 bp (0.3%)\n", "Total written (filtered): 145,502,788 bp (53.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1539298 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 41.5%\n", " G: 34.4%\n", " T: 24.0%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t18114\t42620.8\t0\t18114\n", "4\t18194\t10655.2\t0\t18194\n", "5\t4147\t2663.8\t0\t4147\n", "6\t3710\t665.9\t0\t3710\n", "7\t3936\t166.5\t0\t3936\n", "8\t4109\t41.6\t0\t4109\n", "9\t4331\t41.6\t0\t4331\n", "10\t4076\t41.6\t0\t4076\n", "11\t3913\t41.6\t0\t3913\n", "12\t4009\t41.6\t0\t4009\n", "13\t4866\t41.6\t0\t4866\n", "14\t5232\t41.6\t0\t5232\n", "15\t5396\t41.6\t0\t5396\n", "16\t6103\t41.6\t0\t6103\n", "17\t6348\t41.6\t0\t6348\n", "18\t7246\t41.6\t0\t7246\n", "19\t7104\t41.6\t0\t7104\n", "20\t6258\t41.6\t0\t6258\n", "21\t6374\t41.6\t0\t6374\n", "22\t5965\t41.6\t0\t5965\n", "23\t6263\t41.6\t0\t6263\n", "24\t7381\t41.6\t0\t7381\n", "25\t7516\t41.6\t0\t7516\n", "26\t8723\t41.6\t0\t8723\n", "27\t10105\t41.6\t0\t10105\n", "28\t9863\t41.6\t0\t9863\n", "29\t9415\t41.6\t0\t9415\n", "30\t9690\t41.6\t0\t9690\n", "31\t11467\t41.6\t0\t11467\n", "32\t10808\t41.6\t0\t10808\n", "33\t10657\t41.6\t0\t10657\n", "34\t11440\t41.6\t0\t11440\n", "35\t12681\t41.6\t0\t12681\n", "36\t13617\t41.6\t0\t13617\n", "37\t13313\t41.6\t0\t13313\n", "38\t12050\t41.6\t0\t12050\n", "39\t10772\t41.6\t0\t10772\n", "40\t10985\t41.6\t0\t10985\n", "41\t11946\t41.6\t0\t11946\n", "42\t12371\t41.6\t0\t12371\n", "43\t11417\t41.6\t0\t11417\n", "44\t10315\t41.6\t0\t10315\n", "45\t12655\t41.6\t0\t12655\n", "46\t14146\t41.6\t0\t14146\n", "47\t14208\t41.6\t0\t14208\n", "48\t13858\t41.6\t0\t13858\n", "49\t12433\t41.6\t0\t12433\n", "50\t12086\t41.6\t0\t12086\n", "51\t12081\t41.6\t0\t12081\n", "52\t14442\t41.6\t0\t14442\n", "53\t17173\t41.6\t0\t17173\n", "54\t17240\t41.6\t0\t17240\n", "55\t17136\t41.6\t0\t17136\n", "56\t17128\t41.6\t0\t17128\n", "57\t16965\t41.6\t0\t16965\n", "58\t18954\t41.6\t0\t18954\n", "59\t17193\t41.6\t0\t17193\n", "60\t15041\t41.6\t0\t15041\n", "61\t14763\t41.6\t0\t14763\n", "62\t13735\t41.6\t0\t13735\n", "63\t14571\t41.6\t0\t14571\n", "64\t15722\t41.6\t0\t15722\n", "65\t15762\t41.6\t0\t15762\n", "66\t16208\t41.6\t0\t16208\n", "67\t17540\t41.6\t0\t17540\n", "68\t20323\t41.6\t0\t20323\n", "69\t23845\t41.6\t0\t23845\n", "70\t25967\t41.6\t0\t25967\n", "71\t23913\t41.6\t0\t23913\n", "72\t21640\t41.6\t0\t21640\n", "73\t20925\t41.6\t0\t20925\n", "74\t21740\t41.6\t0\t21740\n", "75\t20679\t41.6\t0\t20679\n", "76\t19411\t41.6\t0\t19411\n", "77\t19308\t41.6\t0\t19308\n", "78\t20408\t41.6\t0\t20408\n", "79\t20570\t41.6\t0\t20570\n", "80\t20415\t41.6\t0\t20415\n", "81\t19537\t41.6\t0\t19537\n", "82\t19493\t41.6\t0\t19493\n", "83\t20765\t41.6\t0\t20765\n", "84\t23195\t41.6\t0\t23195\n", "85\t25134\t41.6\t0\t25134\n", "86\t23015\t41.6\t0\t23015\n", "87\t16874\t41.6\t0\t16874\n", "88\t15976\t41.6\t0\t15976\n", "89\t16053\t41.6\t0\t16053\n", "90\t17197\t41.6\t0\t17197\n", "91\t18997\t41.6\t0\t18997\n", "92\t28280\t41.6\t0\t28280\n", "93\t51232\t41.6\t0\t51232\n", "94\t52530\t41.6\t0\t52530\n", "95\t45978\t41.6\t0\t45978\n", "96\t36055\t41.6\t0\t36055\n", "97\t26666\t41.6\t0\t26666\n", "98\t22086\t41.6\t0\t22086\n", "99\t38522\t41.6\t0\t38522\n", "100\t29303\t41.6\t0\t29303\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 703207 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 89.6%\n", " C: 4.8%\n", " G: 0.0%\n", " T: 5.6%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t11190\t42620.8\t0\t11190\n", "4\t10939\t10655.2\t0\t10939\n", "5\t14805\t2663.8\t0\t14805\n", "6\t12629\t665.9\t0\t12629\n", "7\t9914\t166.5\t0\t9914\n", "8\t8368\t41.6\t0\t8368\n", "9\t7126\t41.6\t0\t7126\n", "10\t7007\t41.6\t0\t7007\n", "11\t8178\t41.6\t0\t8178\n", "12\t6264\t41.6\t0\t6264\n", "13\t6438\t41.6\t0\t6438\n", "14\t6531\t41.6\t0\t6531\n", "15\t5954\t41.6\t0\t5954\n", "16\t6788\t41.6\t0\t6788\n", "17\t8688\t41.6\t0\t8688\n", "18\t18517\t41.6\t0\t18517\n", "19\t32286\t41.6\t0\t32286\n", "20\t65733\t41.6\t0\t65733\n", "21\t38195\t41.6\t0\t38195\n", "22\t19369\t41.6\t0\t19369\n", "23\t9203\t41.6\t0\t9203\n", "24\t6644\t41.6\t0\t6644\n", "25\t6338\t41.6\t0\t6338\n", "26\t7386\t41.6\t0\t7386\n", "27\t7723\t41.6\t0\t7723\n", "28\t8424\t41.6\t0\t8424\n", "29\t11531\t41.6\t0\t11531\n", "30\t22655\t41.6\t0\t22655\n", "31\t26965\t41.6\t0\t26965\n", "32\t44898\t41.6\t0\t44898\n", "33\t46145\t41.6\t0\t46145\n", "34\t47628\t41.6\t0\t47628\n", "35\t62149\t41.6\t0\t62149\n", "36\t71503\t41.6\t0\t71503\n", "37\t17157\t41.6\t0\t17157\n", "38\t331\t41.6\t0\t331\n", "39\t50\t41.6\t0\t50\n", "40\t18\t41.6\t0\t18\n", "41\t28\t41.6\t0\t28\n", "42\t36\t41.6\t0\t36\n", "43\t34\t41.6\t0\t34\n", "44\t18\t41.6\t0\t18\n", "45\t23\t41.6\t0\t23\n", "46\t28\t41.6\t0\t28\n", "47\t25\t41.6\t0\t25\n", "48\t29\t41.6\t0\t29\n", "49\t26\t41.6\t0\t26\n", "50\t22\t41.6\t0\t22\n", "51\t16\t41.6\t0\t16\n", "52\t19\t41.6\t0\t19\n", "53\t17\t41.6\t0\t17\n", "54\t24\t41.6\t0\t24\n", "55\t27\t41.6\t0\t27\n", "56\t27\t41.6\t0\t27\n", "57\t30\t41.6\t0\t30\n", "58\t35\t41.6\t0\t35\n", "59\t19\t41.6\t0\t19\n", "60\t19\t41.6\t0\t19\n", "61\t15\t41.6\t0\t15\n", "62\t29\t41.6\t0\t29\n", "63\t21\t41.6\t0\t21\n", "64\t20\t41.6\t0\t20\n", "65\t8\t41.6\t0\t8\n", "66\t11\t41.6\t0\t11\n", "67\t15\t41.6\t0\t15\n", "68\t14\t41.6\t0\t14\n", "69\t26\t41.6\t0\t26\n", "70\t35\t41.6\t0\t35\n", "71\t12\t41.6\t0\t12\n", "72\t9\t41.6\t0\t9\n", "73\t30\t41.6\t0\t30\n", "74\t3\t41.6\t0\t3\n", "75\t4\t41.6\t0\t4\n", "76\t3\t41.6\t0\t3\n", "78\t4\t41.6\t0\t4\n", "80\t2\t41.6\t0\t2\n", "81\t1\t41.6\t0\t1\n", "82\t21\t41.6\t0\t21\n", "83\t1\t41.6\t0\t1\n", "84\t3\t41.6\t0\t3\n", "85\t2\t41.6\t0\t2\n", "86\t1\t41.6\t0\t1\n", "87\t3\t41.6\t0\t3\n", "88\t6\t41.6\t0\t6\n", "89\t11\t41.6\t0\t11\n", "90\t21\t41.6\t0\t21\n", "91\t5\t41.6\t0\t5\n", "92\t1\t41.6\t0\t1\n", "93\t5\t41.6\t0\t5\n", "94\t20\t41.6\t0\t20\n", "95\t197\t41.6\t0\t197\n", "96\t83\t41.6\t0\t83\n", "97\t130\t41.6\t0\t130\n", "98\t197\t41.6\t0\t197\n", "99\t41\t41.6\t0\t41\n", "100\t28\t41.6\t0\t28\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 83809 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.0%\n", " C: 16.3%\n", " G: 26.0%\n", " T: 18.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t5813\t42620.8\t0\t5813\n", "4\t1350\t10655.2\t0\t1350\n", "5\t266\t2663.8\t0\t266\n", "6\t244\t665.9\t0\t244\n", "7\t345\t166.5\t0\t345\n", "8\t198\t166.5\t0\t198\n", "9\t207\t166.5\t0\t207\n", "10\t189\t166.5\t0\t189\n", "11\t312\t166.5\t0\t312\n", "12\t298\t166.5\t0\t298\n", "13\t355\t166.5\t0\t355\n", "14\t452\t166.5\t0\t452\n", "15\t321\t166.5\t0\t321\n", "16\t455\t166.5\t0\t455\n", "17\t391\t166.5\t0\t391\n", "18\t432\t166.5\t0\t432\n", "19\t529\t166.5\t0\t529\n", "20\t672\t166.5\t0\t672\n", "21\t755\t166.5\t0\t755\n", "22\t786\t166.5\t0\t786\n", "23\t604\t166.5\t0\t604\n", "24\t570\t166.5\t0\t570\n", "25\t589\t166.5\t0\t589\n", "26\t678\t166.5\t0\t678\n", "27\t577\t166.5\t0\t577\n", "28\t776\t166.5\t0\t776\n", "29\t608\t166.5\t0\t608\n", "30\t822\t166.5\t0\t822\n", "31\t553\t166.5\t0\t553\n", "32\t716\t166.5\t0\t716\n", "33\t1046\t166.5\t0\t1046\n", "34\t839\t166.5\t0\t839\n", "35\t1061\t166.5\t0\t1061\n", "36\t899\t166.5\t0\t899\n", "37\t951\t166.5\t0\t951\n", "38\t901\t166.5\t0\t901\n", "39\t806\t166.5\t0\t806\n", "40\t961\t166.5\t0\t961\n", "41\t1082\t166.5\t0\t1082\n", "42\t818\t166.5\t0\t818\n", "43\t1558\t166.5\t0\t1558\n", "44\t194\t166.5\t0\t194\n", "45\t889\t166.5\t0\t889\n", "46\t903\t166.5\t0\t903\n", "47\t756\t166.5\t0\t756\n", "48\t933\t166.5\t0\t933\n", "49\t844\t166.5\t0\t844\n", "50\t1029\t166.5\t0\t1029\n", "51\t810\t166.5\t0\t810\n", "52\t1073\t166.5\t0\t1073\n", "53\t974\t166.5\t0\t974\n", "54\t1078\t166.5\t0\t1078\n", "55\t1181\t166.5\t0\t1181\n", "56\t1729\t166.5\t0\t1729\n", "57\t2508\t166.5\t0\t2508\n", "58\t4663\t166.5\t0\t4663\n", "59\t2105\t166.5\t0\t2105\n", "60\t3985\t166.5\t0\t3985\n", "61\t3579\t166.5\t0\t3579\n", "62\t2877\t166.5\t0\t2877\n", "63\t1584\t166.5\t0\t1584\n", "64\t3344\t166.5\t0\t3344\n", "65\t2108\t166.5\t0\t2108\n", "66\t1885\t166.5\t0\t1885\n", "67\t1617\t166.5\t0\t1617\n", "68\t1855\t166.5\t0\t1855\n", "69\t178\t166.5\t0\t178\n", "70\t313\t166.5\t0\t313\n", "71\t885\t166.5\t0\t885\n", "72\t883\t166.5\t0\t883\n", "73\t595\t166.5\t0\t595\n", "74\t640\t166.5\t0\t640\n", "75\t195\t166.5\t0\t195\n", "76\t155\t166.5\t0\t155\n", "77\t30\t166.5\t0\t30\n", "78\t32\t166.5\t0\t32\n", "79\t19\t166.5\t0\t19\n", "80\t14\t166.5\t0\t14\n", "81\t7\t166.5\t0\t7\n", "82\t9\t166.5\t0\t9\n", "83\t18\t166.5\t0\t18\n", "84\t70\t166.5\t0\t70\n", "85\t88\t166.5\t0\t88\n", "86\t270\t166.5\t0\t270\n", "87\t473\t166.5\t0\t473\n", "88\t1250\t166.5\t0\t1250\n", "89\t685\t166.5\t0\t685\n", "90\t338\t166.5\t0\t338\n", "91\t133\t166.5\t0\t133\n", "92\t88\t166.5\t0\t88\n", "93\t22\t166.5\t0\t22\n", "94\t53\t166.5\t0\t53\n", "95\t8\t166.5\t0\t8\n", "96\t16\t166.5\t0\t16\n", "97\t9\t166.5\t0\t9\n", "98\t9\t166.5\t0\t9\n", "99\t24\t166.5\t0\t24\n", "100\t12\t166.5\t0\t12\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 37_S70_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/37.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 100.07 s (13 us/read; 4.56 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,605,760\n", "Reads with adapters: 4,040,702 (53.1%)\n", "Reads written (passing filters): 7,420,499 (97.6%)\n", "\n", "Total basepairs processed: 760,576,000 bp\n", "Quality-trimmed: 1,887,375 bp (0.2%)\n", "Total written (filtered): 604,676,308 bp (79.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3606932 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 25.4%\n", " G: 41.8%\n", " T: 32.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t161827\t118840.0\t0\t161827\n", "4\t61248\t29710.0\t0\t61248\n", "5\t42939\t7427.5\t0\t42939\n", "6\t32648\t1856.9\t0\t32648\n", "7\t30289\t464.2\t0\t30289\n", "8\t33452\t116.1\t0\t33452\n", "9\t34473\t116.1\t0\t34473\n", "10\t31672\t116.1\t0\t31672\n", "11\t31869\t116.1\t0\t31869\n", "12\t30922\t116.1\t0\t30922\n", "13\t35300\t116.1\t0\t35300\n", "14\t38083\t116.1\t0\t38083\n", "15\t36547\t116.1\t0\t36547\n", "16\t39951\t116.1\t0\t39951\n", "17\t42510\t116.1\t0\t42510\n", "18\t49429\t116.1\t0\t49429\n", "19\t44990\t116.1\t0\t44990\n", "20\t39065\t116.1\t0\t39065\n", "21\t37489\t116.1\t0\t37489\n", "22\t34151\t116.1\t0\t34151\n", "23\t37492\t116.1\t0\t37492\n", "24\t43739\t116.1\t0\t43739\n", "25\t46564\t116.1\t0\t46564\n", "26\t52544\t116.1\t0\t52544\n", "27\t63557\t116.1\t0\t63557\n", "28\t65334\t116.1\t0\t65334\n", "29\t65447\t116.1\t0\t65447\n", "30\t68691\t116.1\t0\t68691\n", "31\t68258\t116.1\t0\t68258\n", "32\t64750\t116.1\t0\t64750\n", "33\t55155\t116.1\t0\t55155\n", "34\t56611\t116.1\t0\t56611\n", "35\t64422\t116.1\t0\t64422\n", "36\t83344\t116.1\t0\t83344\n", "37\t105164\t116.1\t0\t105164\n", "38\t75488\t116.1\t0\t75488\n", "39\t58273\t116.1\t0\t58273\n", "40\t53021\t116.1\t0\t53021\n", "41\t49009\t116.1\t0\t49009\n", "42\t50763\t116.1\t0\t50763\n", "43\t45074\t116.1\t0\t45074\n", "44\t40288\t116.1\t0\t40288\n", "45\t49155\t116.1\t0\t49155\n", "46\t58188\t116.1\t0\t58188\n", "47\t55183\t116.1\t0\t55183\n", "48\t53875\t116.1\t0\t53875\n", "49\t43393\t116.1\t0\t43393\n", "50\t41152\t116.1\t0\t41152\n", "51\t38997\t116.1\t0\t38997\n", "52\t39766\t116.1\t0\t39766\n", "53\t41239\t116.1\t0\t41239\n", "54\t46494\t116.1\t0\t46494\n", "55\t49960\t116.1\t0\t49960\n", "56\t51510\t116.1\t0\t51510\n", "57\t49708\t116.1\t0\t49708\n", "58\t54089\t116.1\t0\t54089\n", "59\t41156\t116.1\t0\t41156\n", "60\t35190\t116.1\t0\t35190\n", "61\t33487\t116.1\t0\t33487\n", "62\t28574\t116.1\t0\t28574\n", "63\t29231\t116.1\t0\t29231\n", "64\t33410\t116.1\t0\t33410\n", "65\t31598\t116.1\t0\t31598\n", "66\t29539\t116.1\t0\t29539\n", "67\t29936\t116.1\t0\t29936\n", "68\t27965\t116.1\t0\t27965\n", "69\t28091\t116.1\t0\t28091\n", "70\t29999\t116.1\t0\t29999\n", "71\t29128\t116.1\t0\t29128\n", "72\t23740\t116.1\t0\t23740\n", "73\t20668\t116.1\t0\t20668\n", "74\t20710\t116.1\t0\t20710\n", "75\t17503\t116.1\t0\t17503\n", "76\t14660\t116.1\t0\t14660\n", "77\t14193\t116.1\t0\t14193\n", "78\t15576\t116.1\t0\t15576\n", "79\t14261\t116.1\t0\t14261\n", "80\t14174\t116.1\t0\t14174\n", "81\t12701\t116.1\t0\t12701\n", "82\t11538\t116.1\t0\t11538\n", "83\t11839\t116.1\t0\t11839\n", "84\t12337\t116.1\t0\t12337\n", "85\t13455\t116.1\t0\t13455\n", "86\t12410\t116.1\t0\t12410\n", "87\t7950\t116.1\t0\t7950\n", "88\t6529\t116.1\t0\t6529\n", "89\t6889\t116.1\t0\t6889\n", "90\t7197\t116.1\t0\t7197\n", "91\t7248\t116.1\t0\t7248\n", "92\t7646\t116.1\t0\t7646\n", "93\t8776\t116.1\t0\t8776\n", "94\t9160\t116.1\t0\t9160\n", "95\t8548\t116.1\t0\t8548\n", "96\t7429\t116.1\t0\t7429\n", "97\t5694\t116.1\t0\t5694\n", "98\t4644\t116.1\t0\t4644\n", "99\t4785\t116.1\t0\t4785\n", "100\t2817\t116.1\t0\t2817\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 273588 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 86.8%\n", " C: 6.9%\n", " G: 0.0%\n", " T: 6.3%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t11860\t118840.0\t0\t11860\n", "4\t4534\t29710.0\t0\t4534\n", "5\t3513\t7427.5\t0\t3513\n", "6\t1728\t1856.9\t0\t1728\n", "7\t991\t464.2\t0\t991\n", "8\t870\t116.1\t0\t870\n", "9\t873\t116.1\t0\t873\n", "10\t862\t116.1\t0\t862\n", "11\t949\t116.1\t0\t949\n", "12\t828\t116.1\t0\t828\n", "13\t722\t116.1\t0\t722\n", "14\t800\t116.1\t0\t800\n", "15\t749\t116.1\t0\t749\n", "16\t821\t116.1\t0\t821\n", "17\t920\t116.1\t0\t920\n", "18\t1404\t116.1\t0\t1404\n", "19\t1666\t116.1\t0\t1666\n", "20\t2298\t116.1\t0\t2298\n", "21\t1728\t116.1\t0\t1728\n", "22\t1441\t116.1\t0\t1441\n", "23\t1099\t116.1\t0\t1099\n", "24\t1198\t116.1\t0\t1198\n", "25\t1543\t116.1\t0\t1543\n", "26\t2570\t116.1\t0\t2570\n", "27\t2727\t116.1\t0\t2727\n", "28\t3400\t116.1\t0\t3400\n", "29\t5026\t116.1\t0\t5026\n", "30\t10900\t116.1\t0\t10900\n", "31\t12861\t116.1\t0\t12861\n", "32\t22388\t116.1\t0\t22388\n", "33\t26068\t116.1\t0\t26068\n", "34\t31687\t116.1\t0\t31687\n", "35\t42588\t116.1\t0\t42588\n", "36\t41768\t116.1\t0\t41768\n", "37\t22690\t116.1\t0\t22690\n", "38\t1410\t116.1\t0\t1410\n", "39\t1228\t116.1\t0\t1228\n", "40\t108\t116.1\t0\t108\n", "41\t77\t116.1\t0\t77\n", "42\t92\t116.1\t0\t92\n", "43\t71\t116.1\t0\t71\n", "44\t57\t116.1\t0\t57\n", "45\t72\t116.1\t0\t72\n", "46\t99\t116.1\t0\t99\n", "47\t74\t116.1\t0\t74\n", "48\t63\t116.1\t0\t63\n", "49\t75\t116.1\t0\t75\n", "50\t95\t116.1\t0\t95\n", "51\t137\t116.1\t0\t137\n", "52\t121\t116.1\t0\t121\n", "53\t86\t116.1\t0\t86\n", "54\t72\t116.1\t0\t72\n", "55\t77\t116.1\t0\t77\n", "56\t66\t116.1\t0\t66\n", "57\t70\t116.1\t0\t70\n", "58\t79\t116.1\t0\t79\n", "59\t64\t116.1\t0\t64\n", "60\t61\t116.1\t0\t61\n", "61\t87\t116.1\t0\t87\n", "62\t56\t116.1\t0\t56\n", "63\t56\t116.1\t0\t56\n", "64\t50\t116.1\t0\t50\n", "65\t39\t116.1\t0\t39\n", "66\t44\t116.1\t0\t44\n", "67\t37\t116.1\t0\t37\n", "68\t37\t116.1\t0\t37\n", "69\t30\t116.1\t0\t30\n", "70\t18\t116.1\t0\t18\n", "71\t24\t116.1\t0\t24\n", "72\t21\t116.1\t0\t21\n", "73\t15\t116.1\t0\t15\n", "74\t20\t116.1\t0\t20\n", "75\t9\t116.1\t0\t9\n", "76\t6\t116.1\t0\t6\n", "77\t3\t116.1\t0\t3\n", "78\t14\t116.1\t0\t14\n", "79\t4\t116.1\t0\t4\n", "80\t7\t116.1\t0\t7\n", "81\t13\t116.1\t0\t13\n", "82\t2\t116.1\t0\t2\n", "83\t22\t116.1\t0\t22\n", "84\t6\t116.1\t0\t6\n", "85\t16\t116.1\t0\t16\n", "86\t6\t116.1\t0\t6\n", "87\t8\t116.1\t0\t8\n", "88\t1\t116.1\t0\t1\n", "89\t11\t116.1\t0\t11\n", "90\t14\t116.1\t0\t14\n", "91\t25\t116.1\t0\t25\n", "92\t5\t116.1\t0\t5\n", "93\t28\t116.1\t0\t28\n", "94\t29\t116.1\t0\t29\n", "95\t111\t116.1\t0\t111\n", "96\t57\t116.1\t0\t57\n", "97\t101\t116.1\t0\t101\n", "98\t85\t116.1\t0\t85\n", "99\t32\t116.1\t0\t32\n", "100\t15\t116.1\t0\t15\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 160182 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 49.3%\n", " C: 15.1%\n", " G: 9.0%\n", " T: 26.6%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t90790\t118840.0\t0\t90790\n", "4\t27239\t29710.0\t0\t27239\n", "5\t2427\t7427.5\t0\t2427\n", "6\t593\t1856.9\t0\t593\n", "7\t521\t464.2\t0\t521\n", "8\t508\t464.2\t0\t508\n", "9\t450\t464.2\t0\t450\n", "10\t549\t464.2\t0\t549\n", "11\t518\t464.2\t0\t518\n", "12\t966\t464.2\t0\t966\n", "13\t1826\t464.2\t0\t1826\n", "14\t1769\t464.2\t0\t1769\n", "15\t1517\t464.2\t0\t1517\n", "16\t1102\t464.2\t0\t1102\n", "17\t1290\t464.2\t0\t1290\n", "18\t1114\t464.2\t0\t1114\n", "19\t901\t464.2\t0\t901\n", "20\t1024\t464.2\t0\t1024\n", "21\t723\t464.2\t0\t723\n", "22\t775\t464.2\t0\t775\n", "23\t621\t464.2\t0\t621\n", "24\t606\t464.2\t0\t606\n", "25\t679\t464.2\t0\t679\n", "26\t659\t464.2\t0\t659\n", "27\t601\t464.2\t0\t601\n", "28\t676\t464.2\t0\t676\n", "29\t519\t464.2\t0\t519\n", "30\t559\t464.2\t0\t559\n", "31\t422\t464.2\t0\t422\n", "32\t453\t464.2\t0\t453\n", "33\t475\t464.2\t0\t475\n", "34\t442\t464.2\t0\t442\n", "35\t401\t464.2\t0\t401\n", "36\t448\t464.2\t0\t448\n", "37\t513\t464.2\t0\t513\n", "38\t525\t464.2\t0\t525\n", "39\t506\t464.2\t0\t506\n", "40\t385\t464.2\t0\t385\n", "41\t400\t464.2\t0\t400\n", "42\t305\t464.2\t0\t305\n", "43\t676\t464.2\t0\t676\n", "44\t102\t464.2\t0\t102\n", "45\t441\t464.2\t0\t441\n", "46\t394\t464.2\t0\t394\n", "47\t355\t464.2\t0\t355\n", "48\t268\t464.2\t0\t268\n", "49\t400\t464.2\t0\t400\n", "50\t418\t464.2\t0\t418\n", "51\t391\t464.2\t0\t391\n", "52\t345\t464.2\t0\t345\n", "53\t405\t464.2\t0\t405\n", "54\t379\t464.2\t0\t379\n", "55\t457\t464.2\t0\t457\n", "56\t433\t464.2\t0\t433\n", "57\t396\t464.2\t0\t396\n", "58\t506\t464.2\t0\t506\n", "59\t262\t464.2\t0\t262\n", "60\t503\t464.2\t0\t503\n", "61\t562\t464.2\t0\t562\n", "62\t357\t464.2\t0\t357\n", "63\t298\t464.2\t0\t298\n", "64\t470\t464.2\t0\t470\n", "65\t282\t464.2\t0\t282\n", "66\t366\t464.2\t0\t366\n", "67\t281\t464.2\t0\t281\n", "68\t388\t464.2\t0\t388\n", "69\t40\t464.2\t0\t40\n", "70\t59\t464.2\t0\t59\n", "71\t189\t464.2\t0\t189\n", "72\t182\t464.2\t0\t182\n", "73\t153\t464.2\t0\t153\n", "74\t216\t464.2\t0\t216\n", "75\t121\t464.2\t0\t121\n", "76\t85\t464.2\t0\t85\n", "77\t88\t464.2\t0\t88\n", "78\t30\t464.2\t0\t30\n", "79\t38\t464.2\t0\t38\n", "80\t41\t464.2\t0\t41\n", "81\t35\t464.2\t0\t35\n", "82\t40\t464.2\t0\t40\n", "83\t44\t464.2\t0\t44\n", "84\t62\t464.2\t0\t62\n", "85\t74\t464.2\t0\t74\n", "86\t33\t464.2\t0\t33\n", "87\t66\t464.2\t0\t66\n", "88\t242\t464.2\t0\t242\n", "89\t152\t464.2\t0\t152\n", "90\t89\t464.2\t0\t89\n", "91\t78\t464.2\t0\t78\n", "92\t67\t464.2\t0\t67\n", "93\t66\t464.2\t0\t66\n", "94\t68\t464.2\t0\t68\n", "95\t36\t464.2\t0\t36\n", "96\t63\t464.2\t0\t63\n", "97\t173\t464.2\t0\t173\n", "98\t157\t464.2\t0\t157\n", "99\t245\t464.2\t0\t245\n", "100\t218\t464.2\t0\t218\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 39_S52_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/39.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 80.05 s (13 us/read; 4.49 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,993,536\n", "Reads with adapters: 3,542,728 (59.1%)\n", "Reads written (passing filters): 5,800,354 (96.8%)\n", "\n", "Total basepairs processed: 599,353,600 bp\n", "Quality-trimmed: 1,639,426 bp (0.3%)\n", "Total written (filtered): 464,735,231 bp (77.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3398604 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.8%\n", " G: 39.7%\n", " T: 30.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t118864\t93649.0\t0\t118864\n", "4\t64704\t23412.2\t0\t64704\n", "5\t49280\t5853.1\t0\t49280\n", "6\t41008\t1463.3\t0\t41008\n", "7\t36246\t365.8\t0\t36246\n", "8\t36676\t91.5\t0\t36676\n", "9\t36167\t91.5\t0\t36167\n", "10\t34956\t91.5\t0\t34956\n", "11\t34380\t91.5\t0\t34380\n", "12\t35478\t91.5\t0\t35478\n", "13\t38308\t91.5\t0\t38308\n", "14\t39357\t91.5\t0\t39357\n", "15\t39598\t91.5\t0\t39598\n", "16\t41094\t91.5\t0\t41094\n", "17\t45162\t91.5\t0\t45162\n", "18\t52618\t91.5\t0\t52618\n", "19\t48184\t91.5\t0\t48184\n", "20\t41544\t91.5\t0\t41544\n", "21\t40376\t91.5\t0\t40376\n", "22\t37251\t91.5\t0\t37251\n", "23\t40015\t91.5\t0\t40015\n", "24\t47446\t91.5\t0\t47446\n", "25\t49370\t91.5\t0\t49370\n", "26\t56937\t91.5\t0\t56937\n", "27\t63790\t91.5\t0\t63790\n", "28\t59401\t91.5\t0\t59401\n", "29\t56160\t91.5\t0\t56160\n", "30\t57338\t91.5\t0\t57338\n", "31\t62300\t91.5\t0\t62300\n", "32\t60855\t91.5\t0\t60855\n", "33\t55776\t91.5\t0\t55776\n", "34\t55375\t91.5\t0\t55375\n", "35\t62901\t91.5\t0\t62901\n", "36\t75692\t91.5\t0\t75692\n", "37\t83883\t91.5\t0\t83883\n", "38\t64380\t91.5\t0\t64380\n", "39\t51448\t91.5\t0\t51448\n", "40\t48274\t91.5\t0\t48274\n", "41\t51969\t91.5\t0\t51969\n", "42\t55936\t91.5\t0\t55936\n", "43\t49015\t91.5\t0\t49015\n", "44\t39774\t91.5\t0\t39774\n", "45\t48845\t91.5\t0\t48845\n", "46\t58285\t91.5\t0\t58285\n", "47\t54367\t91.5\t0\t54367\n", "48\t54773\t91.5\t0\t54773\n", "49\t45229\t91.5\t0\t45229\n", "50\t42456\t91.5\t0\t42456\n", "51\t38023\t91.5\t0\t38023\n", "52\t38028\t91.5\t0\t38028\n", "53\t42209\t91.5\t0\t42209\n", "54\t43022\t91.5\t0\t43022\n", "55\t44824\t91.5\t0\t44824\n", "56\t36589\t91.5\t0\t36589\n", "57\t38888\t91.5\t0\t38888\n", "58\t47098\t91.5\t0\t47098\n", "59\t36959\t91.5\t0\t36959\n", "60\t29037\t91.5\t0\t29037\n", "61\t26835\t91.5\t0\t26835\n", "62\t22643\t91.5\t0\t22643\n", "63\t21707\t91.5\t0\t21707\n", "64\t23820\t91.5\t0\t23820\n", "65\t23596\t91.5\t0\t23596\n", "66\t20984\t91.5\t0\t20984\n", "67\t20506\t91.5\t0\t20506\n", "68\t19889\t91.5\t0\t19889\n", "69\t20962\t91.5\t0\t20962\n", "70\t22095\t91.5\t0\t22095\n", "71\t20942\t91.5\t0\t20942\n", "72\t16858\t91.5\t0\t16858\n", "73\t14918\t91.5\t0\t14918\n", "74\t14851\t91.5\t0\t14851\n", "75\t12837\t91.5\t0\t12837\n", "76\t11083\t91.5\t0\t11083\n", "77\t10214\t91.5\t0\t10214\n", "78\t11746\t91.5\t0\t11746\n", "79\t11172\t91.5\t0\t11172\n", "80\t11289\t91.5\t0\t11289\n", "81\t10748\t91.5\t0\t10748\n", "82\t10214\t91.5\t0\t10214\n", "83\t10978\t91.5\t0\t10978\n", "84\t12353\t91.5\t0\t12353\n", "85\t13974\t91.5\t0\t13974\n", "86\t13518\t91.5\t0\t13518\n", "87\t9774\t91.5\t0\t9774\n", "88\t9055\t91.5\t0\t9055\n", "89\t9675\t91.5\t0\t9675\n", "90\t10401\t91.5\t0\t10401\n", "91\t10586\t91.5\t0\t10586\n", "92\t10720\t91.5\t0\t10720\n", "93\t11624\t91.5\t0\t11624\n", "94\t10790\t91.5\t0\t10790\n", "95\t9082\t91.5\t0\t9082\n", "96\t6610\t91.5\t0\t6610\n", "97\t4491\t91.5\t0\t4491\n", "98\t2663\t91.5\t0\t2663\n", "99\t2726\t91.5\t0\t2726\n", "100\t1757\t91.5\t0\t1757\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 40385 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 51.7%\n", " C: 24.4%\n", " G: 0.0%\n", " T: 23.8%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t15079\t93649.0\t0\t15079\n", "4\t5000\t23412.2\t0\t5000\n", "5\t2672\t5853.1\t0\t2672\n", "6\t1849\t1463.3\t0\t1849\n", "7\t553\t365.8\t0\t553\n", "8\t406\t91.5\t0\t406\n", "9\t355\t91.5\t0\t355\n", "10\t287\t91.5\t0\t287\n", "11\t317\t91.5\t0\t317\n", "12\t287\t91.5\t0\t287\n", "13\t227\t91.5\t0\t227\n", "14\t266\t91.5\t0\t266\n", "15\t230\t91.5\t0\t230\n", "16\t231\t91.5\t0\t231\n", "17\t272\t91.5\t0\t272\n", "18\t298\t91.5\t0\t298\n", "19\t337\t91.5\t0\t337\n", "20\t373\t91.5\t0\t373\n", "21\t278\t91.5\t0\t278\n", "22\t248\t91.5\t0\t248\n", "23\t215\t91.5\t0\t215\n", "24\t236\t91.5\t0\t236\n", "25\t283\t91.5\t0\t283\n", "26\t532\t91.5\t0\t532\n", "27\t535\t91.5\t0\t535\n", "28\t426\t91.5\t0\t426\n", "29\t472\t91.5\t0\t472\n", "30\t714\t91.5\t0\t714\n", "31\t789\t91.5\t0\t789\n", "32\t1100\t91.5\t0\t1100\n", "33\t932\t91.5\t0\t932\n", "34\t944\t91.5\t0\t944\n", "35\t1126\t91.5\t0\t1126\n", "36\t978\t91.5\t0\t978\n", "37\t336\t91.5\t0\t336\n", "38\t34\t91.5\t0\t34\n", "39\t26\t91.5\t0\t26\n", "40\t30\t91.5\t0\t30\n", "41\t29\t91.5\t0\t29\n", "42\t25\t91.5\t0\t25\n", "43\t22\t91.5\t0\t22\n", "44\t32\t91.5\t0\t32\n", "45\t34\t91.5\t0\t34\n", "46\t23\t91.5\t0\t23\n", "47\t35\t91.5\t0\t35\n", "48\t29\t91.5\t0\t29\n", "49\t27\t91.5\t0\t27\n", "50\t31\t91.5\t0\t31\n", "51\t22\t91.5\t0\t22\n", "52\t33\t91.5\t0\t33\n", "53\t31\t91.5\t0\t31\n", "54\t14\t91.5\t0\t14\n", "55\t24\t91.5\t0\t24\n", "56\t18\t91.5\t0\t18\n", "57\t19\t91.5\t0\t19\n", "58\t18\t91.5\t0\t18\n", "59\t11\t91.5\t0\t11\n", "60\t19\t91.5\t0\t19\n", "61\t18\t91.5\t0\t18\n", "62\t30\t91.5\t0\t30\n", "63\t12\t91.5\t0\t12\n", "64\t15\t91.5\t0\t15\n", "65\t20\t91.5\t0\t20\n", "66\t15\t91.5\t0\t15\n", "67\t15\t91.5\t0\t15\n", "68\t12\t91.5\t0\t12\n", "69\t11\t91.5\t0\t11\n", "70\t15\t91.5\t0\t15\n", "71\t8\t91.5\t0\t8\n", "72\t7\t91.5\t0\t7\n", "73\t6\t91.5\t0\t6\n", "74\t12\t91.5\t0\t12\n", "75\t9\t91.5\t0\t9\n", "76\t4\t91.5\t0\t4\n", "77\t5\t91.5\t0\t5\n", "78\t3\t91.5\t0\t3\n", "79\t4\t91.5\t0\t4\n", "80\t9\t91.5\t0\t9\n", "81\t9\t91.5\t0\t9\n", "82\t4\t91.5\t0\t4\n", "83\t4\t91.5\t0\t4\n", "84\t6\t91.5\t0\t6\n", "85\t5\t91.5\t0\t5\n", "86\t2\t91.5\t0\t2\n", "87\t1\t91.5\t0\t1\n", "88\t1\t91.5\t0\t1\n", "89\t4\t91.5\t0\t4\n", "90\t2\t91.5\t0\t2\n", "91\t11\t91.5\t0\t11\n", "92\t8\t91.5\t0\t8\n", "93\t39\t91.5\t0\t39\n", "94\t42\t91.5\t0\t42\n", "95\t41\t91.5\t0\t41\n", "96\t45\t91.5\t0\t45\n", "97\t36\t91.5\t0\t36\n", "98\t44\t91.5\t0\t44\n", "99\t31\t91.5\t0\t31\n", "100\t51\t91.5\t0\t51\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 103739 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.3%\n", " C: 23.0%\n", " G: 14.4%\n", " T: 22.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t74509\t93649.0\t0\t74509\n", "4\t14496\t23412.2\t0\t14496\n", "5\t2191\t5853.1\t0\t2191\n", "6\t376\t1463.3\t0\t376\n", "7\t231\t365.8\t0\t231\n", "8\t269\t365.8\t0\t269\n", "9\t242\t365.8\t0\t242\n", "10\t240\t365.8\t0\t240\n", "11\t236\t365.8\t0\t236\n", "12\t286\t365.8\t0\t286\n", "13\t303\t365.8\t0\t303\n", "14\t281\t365.8\t0\t281\n", "15\t338\t365.8\t0\t338\n", "16\t304\t365.8\t0\t304\n", "17\t284\t365.8\t0\t284\n", "18\t279\t365.8\t0\t279\n", "19\t261\t365.8\t0\t261\n", "20\t254\t365.8\t0\t254\n", "21\t263\t365.8\t0\t263\n", "22\t227\t365.8\t0\t227\n", "23\t212\t365.8\t0\t212\n", "24\t215\t365.8\t0\t215\n", "25\t188\t365.8\t0\t188\n", "26\t163\t365.8\t0\t163\n", "27\t180\t365.8\t0\t180\n", "28\t172\t365.8\t0\t172\n", "29\t195\t365.8\t0\t195\n", "30\t191\t365.8\t0\t191\n", "31\t156\t365.8\t0\t156\n", "32\t188\t365.8\t0\t188\n", "33\t149\t365.8\t0\t149\n", "34\t152\t365.8\t0\t152\n", "35\t171\t365.8\t0\t171\n", "36\t132\t365.8\t0\t132\n", "37\t133\t365.8\t0\t133\n", "38\t149\t365.8\t0\t149\n", "39\t198\t365.8\t0\t198\n", "40\t145\t365.8\t0\t145\n", "41\t144\t365.8\t0\t144\n", "42\t117\t365.8\t0\t117\n", "43\t164\t365.8\t0\t164\n", "44\t70\t365.8\t0\t70\n", "45\t158\t365.8\t0\t158\n", "46\t116\t365.8\t0\t116\n", "47\t147\t365.8\t0\t147\n", "48\t102\t365.8\t0\t102\n", "49\t106\t365.8\t0\t106\n", "50\t80\t365.8\t0\t80\n", "51\t93\t365.8\t0\t93\n", "52\t85\t365.8\t0\t85\n", "53\t111\t365.8\t0\t111\n", "54\t90\t365.8\t0\t90\n", "55\t79\t365.8\t0\t79\n", "56\t75\t365.8\t0\t75\n", "57\t67\t365.8\t0\t67\n", "58\t95\t365.8\t0\t95\n", "59\t58\t365.8\t0\t58\n", "60\t71\t365.8\t0\t71\n", "61\t73\t365.8\t0\t73\n", "62\t76\t365.8\t0\t76\n", "63\t62\t365.8\t0\t62\n", "64\t58\t365.8\t0\t58\n", "65\t68\t365.8\t0\t68\n", "66\t75\t365.8\t0\t75\n", "67\t86\t365.8\t0\t86\n", "68\t81\t365.8\t0\t81\n", "69\t45\t365.8\t0\t45\n", "70\t31\t365.8\t0\t31\n", "71\t68\t365.8\t0\t68\n", "72\t78\t365.8\t0\t78\n", "73\t72\t365.8\t0\t72\n", "74\t91\t365.8\t0\t91\n", "75\t60\t365.8\t0\t60\n", "76\t97\t365.8\t0\t97\n", "77\t81\t365.8\t0\t81\n", "78\t62\t365.8\t0\t62\n", "79\t72\t365.8\t0\t72\n", "80\t94\t365.8\t0\t94\n", "81\t74\t365.8\t0\t74\n", "82\t81\t365.8\t0\t81\n", "83\t88\t365.8\t0\t88\n", "84\t75\t365.8\t0\t75\n", "85\t84\t365.8\t0\t84\n", "86\t56\t365.8\t0\t56\n", "87\t52\t365.8\t0\t52\n", "88\t73\t365.8\t0\t73\n", "89\t54\t365.8\t0\t54\n", "90\t71\t365.8\t0\t71\n", "91\t43\t365.8\t0\t43\n", "92\t45\t365.8\t0\t45\n", "93\t42\t365.8\t0\t42\n", "94\t65\t365.8\t0\t65\n", "95\t37\t365.8\t0\t37\n", "96\t66\t365.8\t0\t66\n", "97\t70\t365.8\t0\t70\n", "98\t77\t365.8\t0\t77\n", "99\t80\t365.8\t0\t80\n", "100\t89\t365.8\t0\t89\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 401_S10_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/401.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 50.01 s (12 us/read; 4.97 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 4,142,817\n", "Reads with adapters: 1,523,085 (36.8%)\n", "Reads written (passing filters): 4,090,721 (98.7%)\n", "\n", "Total basepairs processed: 414,281,700 bp\n", "Quality-trimmed: 633,161 bp (0.2%)\n", "Total written (filtered): 368,985,356 bp (89.1%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1390173 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 25.8%\n", " G: 40.9%\n", " T: 33.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t107479\t64731.5\t0\t107479\n", "4\t53558\t16182.9\t0\t53558\n", "5\t35172\t4045.7\t0\t35172\n", "6\t27933\t1011.4\t0\t27933\n", "7\t21143\t252.9\t0\t21143\n", "8\t18689\t63.2\t0\t18689\n", "9\t18102\t63.2\t0\t18102\n", "10\t18366\t63.2\t0\t18366\n", "11\t18721\t63.2\t0\t18721\n", "12\t20839\t63.2\t0\t20839\n", "13\t32786\t63.2\t0\t32786\n", "14\t30740\t63.2\t0\t30740\n", "15\t22747\t63.2\t0\t22747\n", "16\t22203\t63.2\t0\t22203\n", "17\t22270\t63.2\t0\t22270\n", "18\t25008\t63.2\t0\t25008\n", "19\t20656\t63.2\t0\t20656\n", "20\t17186\t63.2\t0\t17186\n", "21\t16826\t63.2\t0\t16826\n", "22\t15628\t63.2\t0\t15628\n", "23\t16851\t63.2\t0\t16851\n", "24\t19922\t63.2\t0\t19922\n", "25\t20337\t63.2\t0\t20337\n", "26\t22892\t63.2\t0\t22892\n", "27\t25945\t63.2\t0\t25945\n", "28\t23716\t63.2\t0\t23716\n", "29\t21773\t63.2\t0\t21773\n", "30\t21537\t63.2\t0\t21537\n", "31\t22759\t63.2\t0\t22759\n", "32\t22889\t63.2\t0\t22889\n", "33\t21656\t63.2\t0\t21656\n", "34\t21966\t63.2\t0\t21966\n", "35\t23346\t63.2\t0\t23346\n", "36\t28374\t63.2\t0\t28374\n", "37\t33630\t63.2\t0\t33630\n", "38\t24122\t63.2\t0\t24122\n", "39\t18708\t63.2\t0\t18708\n", "40\t17201\t63.2\t0\t17201\n", "41\t17766\t63.2\t0\t17766\n", "42\t19435\t63.2\t0\t19435\n", "43\t16851\t63.2\t0\t16851\n", "44\t13491\t63.2\t0\t13491\n", "45\t15865\t63.2\t0\t15865\n", "46\t18393\t63.2\t0\t18393\n", "47\t17362\t63.2\t0\t17362\n", "48\t15884\t63.2\t0\t15884\n", "49\t13357\t63.2\t0\t13357\n", "50\t11722\t63.2\t0\t11722\n", "51\t10623\t63.2\t0\t10623\n", "52\t10954\t63.2\t0\t10954\n", "53\t11384\t63.2\t0\t11384\n", "54\t12242\t63.2\t0\t12242\n", "55\t12224\t63.2\t0\t12224\n", "56\t11442\t63.2\t0\t11442\n", "57\t11636\t63.2\t0\t11636\n", "58\t13023\t63.2\t0\t13023\n", "59\t9803\t63.2\t0\t9803\n", "60\t8088\t63.2\t0\t8088\n", "61\t7186\t63.2\t0\t7186\n", "62\t6179\t63.2\t0\t6179\n", "63\t5743\t63.2\t0\t5743\n", "64\t5942\t63.2\t0\t5942\n", "65\t5924\t63.2\t0\t5924\n", "66\t5540\t63.2\t0\t5540\n", "67\t5435\t63.2\t0\t5435\n", "68\t5442\t63.2\t0\t5442\n", "69\t5744\t63.2\t0\t5744\n", "70\t6011\t63.2\t0\t6011\n", "71\t5767\t63.2\t0\t5767\n", "72\t4668\t63.2\t0\t4668\n", "73\t4432\t63.2\t0\t4432\n", "74\t4239\t63.2\t0\t4239\n", "75\t3764\t63.2\t0\t3764\n", "76\t3213\t63.2\t0\t3213\n", "77\t3051\t63.2\t0\t3051\n", "78\t3071\t63.2\t0\t3071\n", "79\t3204\t63.2\t0\t3204\n", "80\t3223\t63.2\t0\t3223\n", "81\t2991\t63.2\t0\t2991\n", "82\t2881\t63.2\t0\t2881\n", "83\t2942\t63.2\t0\t2942\n", "84\t3529\t63.2\t0\t3529\n", "85\t3701\t63.2\t0\t3701\n", "86\t3451\t63.2\t0\t3451\n", "87\t2837\t63.2\t0\t2837\n", "88\t2691\t63.2\t0\t2691\n", "89\t2594\t63.2\t0\t2594\n", "90\t2507\t63.2\t0\t2507\n", "91\t2512\t63.2\t0\t2512\n", "92\t2386\t63.2\t0\t2386\n", "93\t2376\t63.2\t0\t2376\n", "94\t2237\t63.2\t0\t2237\n", "95\t2040\t63.2\t0\t2040\n", "96\t1642\t63.2\t0\t1642\n", "97\t1124\t63.2\t0\t1124\n", "98\t903\t63.2\t0\t903\n", "99\t1096\t63.2\t0\t1096\n", "100\t734\t63.2\t0\t734\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 39693 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.4%\n", " C: 35.0%\n", " G: 0.0%\n", " T: 19.4%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t19554\t64731.5\t0\t19554\n", "4\t5072\t16182.9\t0\t5072\n", "5\t3062\t4045.7\t0\t3062\n", "6\t2395\t1011.4\t0\t2395\n", "7\t510\t252.9\t0\t510\n", "8\t325\t63.2\t0\t325\n", "9\t323\t63.2\t0\t323\n", "10\t354\t63.2\t0\t354\n", "11\t403\t63.2\t0\t403\n", "12\t316\t63.2\t0\t316\n", "13\t267\t63.2\t0\t267\n", "14\t255\t63.2\t0\t255\n", "15\t202\t63.2\t0\t202\n", "16\t198\t63.2\t0\t198\n", "17\t220\t63.2\t0\t220\n", "18\t309\t63.2\t0\t309\n", "19\t347\t63.2\t0\t347\n", "20\t439\t63.2\t0\t439\n", "21\t306\t63.2\t0\t306\n", "22\t203\t63.2\t0\t203\n", "23\t150\t63.2\t0\t150\n", "24\t146\t63.2\t0\t146\n", "25\t135\t63.2\t0\t135\n", "26\t195\t63.2\t0\t195\n", "27\t195\t63.2\t0\t195\n", "28\t156\t63.2\t0\t156\n", "29\t128\t63.2\t0\t128\n", "30\t185\t63.2\t0\t185\n", "31\t210\t63.2\t0\t210\n", "32\t305\t63.2\t0\t305\n", "33\t300\t63.2\t0\t300\n", "34\t295\t63.2\t0\t295\n", "35\t427\t63.2\t0\t427\n", "36\t466\t63.2\t0\t466\n", "37\t211\t63.2\t0\t211\n", "38\t24\t63.2\t0\t24\n", "39\t24\t63.2\t0\t24\n", "40\t27\t63.2\t0\t27\n", "41\t16\t63.2\t0\t16\n", "42\t12\t63.2\t0\t12\n", "43\t17\t63.2\t0\t17\n", "44\t6\t63.2\t0\t6\n", "45\t9\t63.2\t0\t9\n", "46\t14\t63.2\t0\t14\n", "47\t12\t63.2\t0\t12\n", "48\t9\t63.2\t0\t9\n", "49\t15\t63.2\t0\t15\n", "50\t13\t63.2\t0\t13\n", "51\t15\t63.2\t0\t15\n", "52\t29\t63.2\t0\t29\n", "53\t6\t63.2\t0\t6\n", "54\t10\t63.2\t0\t10\n", "55\t18\t63.2\t0\t18\n", "56\t14\t63.2\t0\t14\n", "57\t13\t63.2\t0\t13\n", "58\t11\t63.2\t0\t11\n", "59\t9\t63.2\t0\t9\n", "60\t9\t63.2\t0\t9\n", "61\t12\t63.2\t0\t12\n", "62\t1\t63.2\t0\t1\n", "63\t6\t63.2\t0\t6\n", "64\t4\t63.2\t0\t4\n", "65\t10\t63.2\t0\t10\n", "66\t8\t63.2\t0\t8\n", "67\t7\t63.2\t0\t7\n", "68\t6\t63.2\t0\t6\n", "69\t3\t63.2\t0\t3\n", "70\t6\t63.2\t0\t6\n", "71\t4\t63.2\t0\t4\n", "72\t3\t63.2\t0\t3\n", "73\t11\t63.2\t0\t11\n", "74\t2\t63.2\t0\t2\n", "75\t10\t63.2\t0\t10\n", "76\t5\t63.2\t0\t5\n", "77\t2\t63.2\t0\t2\n", "78\t2\t63.2\t0\t2\n", "79\t7\t63.2\t0\t7\n", "80\t4\t63.2\t0\t4\n", "81\t3\t63.2\t0\t3\n", "82\t5\t63.2\t0\t5\n", "83\t2\t63.2\t0\t2\n", "84\t4\t63.2\t0\t4\n", "85\t3\t63.2\t0\t3\n", "86\t3\t63.2\t0\t3\n", "87\t9\t63.2\t0\t9\n", "88\t5\t63.2\t0\t5\n", "89\t9\t63.2\t0\t9\n", "90\t9\t63.2\t0\t9\n", "91\t10\t63.2\t0\t10\n", "92\t23\t63.2\t0\t23\n", "93\t44\t63.2\t0\t44\n", "94\t87\t63.2\t0\t87\n", "95\t87\t63.2\t0\t87\n", "96\t70\t63.2\t0\t70\n", "97\t96\t63.2\t0\t96\n", "98\t69\t63.2\t0\t69\n", "99\t38\t63.2\t0\t38\n", "100\t108\t63.2\t0\t108\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 93219 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 38.8%\n", " C: 24.1%\n", " G: 15.9%\n", " T: 21.1%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t68773\t64731.5\t0\t68773\n", "4\t13669\t16182.9\t0\t13669\n", "5\t1679\t4045.7\t0\t1679\n", "6\t206\t1011.4\t0\t206\n", "7\t150\t252.9\t0\t150\n", "8\t145\t252.9\t0\t145\n", "9\t143\t252.9\t0\t143\n", "10\t161\t252.9\t0\t161\n", "11\t193\t252.9\t0\t193\n", "12\t211\t252.9\t0\t211\n", "13\t239\t252.9\t0\t239\n", "14\t180\t252.9\t0\t180\n", "15\t259\t252.9\t0\t259\n", "16\t232\t252.9\t0\t232\n", "17\t200\t252.9\t0\t200\n", "18\t196\t252.9\t0\t196\n", "19\t247\t252.9\t0\t247\n", "20\t184\t252.9\t0\t184\n", "21\t173\t252.9\t0\t173\n", "22\t143\t252.9\t0\t143\n", "23\t113\t252.9\t0\t113\n", "24\t129\t252.9\t0\t129\n", "25\t135\t252.9\t0\t135\n", "26\t121\t252.9\t0\t121\n", "27\t107\t252.9\t0\t107\n", "28\t112\t252.9\t0\t112\n", "29\t108\t252.9\t0\t108\n", "30\t120\t252.9\t0\t120\n", "31\t80\t252.9\t0\t80\n", "32\t86\t252.9\t0\t86\n", "33\t95\t252.9\t0\t95\n", "34\t112\t252.9\t0\t112\n", "35\t99\t252.9\t0\t99\n", "36\t78\t252.9\t0\t78\n", "37\t80\t252.9\t0\t80\n", "38\t90\t252.9\t0\t90\n", "39\t100\t252.9\t0\t100\n", "40\t102\t252.9\t0\t102\n", "41\t82\t252.9\t0\t82\n", "42\t60\t252.9\t0\t60\n", "43\t113\t252.9\t0\t113\n", "44\t50\t252.9\t0\t50\n", "45\t94\t252.9\t0\t94\n", "46\t73\t252.9\t0\t73\n", "47\t90\t252.9\t0\t90\n", "48\t80\t252.9\t0\t80\n", "49\t64\t252.9\t0\t64\n", "50\t72\t252.9\t0\t72\n", "51\t89\t252.9\t0\t89\n", "52\t79\t252.9\t0\t79\n", "53\t76\t252.9\t0\t76\n", "54\t74\t252.9\t0\t74\n", "55\t72\t252.9\t0\t72\n", "56\t91\t252.9\t0\t91\n", "57\t78\t252.9\t0\t78\n", "58\t90\t252.9\t0\t90\n", "59\t55\t252.9\t0\t55\n", "60\t89\t252.9\t0\t89\n", "61\t67\t252.9\t0\t67\n", "62\t82\t252.9\t0\t82\n", "63\t62\t252.9\t0\t62\n", "64\t62\t252.9\t0\t62\n", "65\t71\t252.9\t0\t71\n", "66\t56\t252.9\t0\t56\n", "67\t75\t252.9\t0\t75\n", "68\t69\t252.9\t0\t69\n", "69\t54\t252.9\t0\t54\n", "70\t38\t252.9\t0\t38\n", "71\t61\t252.9\t0\t61\n", "72\t45\t252.9\t0\t45\n", "73\t57\t252.9\t0\t57\n", "74\t52\t252.9\t0\t52\n", "75\t60\t252.9\t0\t60\n", "76\t79\t252.9\t0\t79\n", "77\t67\t252.9\t0\t67\n", "78\t49\t252.9\t0\t49\n", "79\t53\t252.9\t0\t53\n", "80\t55\t252.9\t0\t55\n", "81\t63\t252.9\t0\t63\n", "82\t62\t252.9\t0\t62\n", "83\t49\t252.9\t0\t49\n", "84\t52\t252.9\t0\t52\n", "85\t57\t252.9\t0\t57\n", "86\t57\t252.9\t0\t57\n", "87\t58\t252.9\t0\t58\n", "88\t84\t252.9\t0\t84\n", "89\t63\t252.9\t0\t63\n", "90\t52\t252.9\t0\t52\n", "91\t52\t252.9\t0\t52\n", "92\t46\t252.9\t0\t46\n", "93\t32\t252.9\t0\t32\n", "94\t26\t252.9\t0\t26\n", "95\t43\t252.9\t0\t43\n", "96\t41\t252.9\t0\t41\n", "97\t51\t252.9\t0\t51\n", "98\t63\t252.9\t0\t63\n", "99\t108\t252.9\t0\t108\n", "100\t125\t252.9\t0\t125\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 402_S5_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/402.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 78.65 s (14 us/read; 4.44 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,817,900\n", "Reads with adapters: 3,779,464 (65.0%)\n", "Reads written (passing filters): 5,669,857 (97.5%)\n", "\n", "Total basepairs processed: 581,790,000 bp\n", "Quality-trimmed: 1,780,961 bp (0.3%)\n", "Total written (filtered): 440,915,494 bp (75.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3661363 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.0%\n", " G: 42.3%\n", " T: 26.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t113271\t90904.7\t0\t113271\n", "4\t64633\t22726.2\t0\t64633\n", "5\t51810\t5681.5\t0\t51810\n", "6\t43649\t1420.4\t0\t43649\n", "7\t40321\t355.1\t0\t40321\n", "8\t40923\t88.8\t0\t40923\n", "9\t40329\t88.8\t0\t40329\n", "10\t40382\t88.8\t0\t40382\n", "11\t39587\t88.8\t0\t39587\n", "12\t39941\t88.8\t0\t39941\n", "13\t43589\t88.8\t0\t43589\n", "14\t45177\t88.8\t0\t45177\n", "15\t44231\t88.8\t0\t44231\n", "16\t46305\t88.8\t0\t46305\n", "17\t49911\t88.8\t0\t49911\n", "18\t57335\t88.8\t0\t57335\n", "19\t54725\t88.8\t0\t54725\n", "20\t46641\t88.8\t0\t46641\n", "21\t44703\t88.8\t0\t44703\n", "22\t41274\t88.8\t0\t41274\n", "23\t44664\t88.8\t0\t44664\n", "24\t53674\t88.8\t0\t53674\n", "25\t57437\t88.8\t0\t57437\n", "26\t63348\t88.8\t0\t63348\n", "27\t66460\t88.8\t0\t66460\n", "28\t62550\t88.8\t0\t62550\n", "29\t60229\t88.8\t0\t60229\n", "30\t63408\t88.8\t0\t63408\n", "31\t68421\t88.8\t0\t68421\n", "32\t66085\t88.8\t0\t66085\n", "33\t60374\t88.8\t0\t60374\n", "34\t60685\t88.8\t0\t60685\n", "35\t67986\t88.8\t0\t67986\n", "36\t80892\t88.8\t0\t80892\n", "37\t87585\t88.8\t0\t87585\n", "38\t69893\t88.8\t0\t69893\n", "39\t58066\t88.8\t0\t58066\n", "40\t55245\t88.8\t0\t55245\n", "41\t60635\t88.8\t0\t60635\n", "42\t67675\t88.8\t0\t67675\n", "43\t57573\t88.8\t0\t57573\n", "44\t46978\t88.8\t0\t46978\n", "45\t57927\t88.8\t0\t57927\n", "46\t68204\t88.8\t0\t68204\n", "47\t61390\t88.8\t0\t61390\n", "48\t62189\t88.8\t0\t62189\n", "49\t51504\t88.8\t0\t51504\n", "50\t50256\t88.8\t0\t50256\n", "51\t44182\t88.8\t0\t44182\n", "52\t46545\t88.8\t0\t46545\n", "53\t49419\t88.8\t0\t49419\n", "54\t48503\t88.8\t0\t48503\n", "55\t50884\t88.8\t0\t50884\n", "56\t49095\t88.8\t0\t49095\n", "57\t41548\t88.8\t0\t41548\n", "58\t42165\t88.8\t0\t42165\n", "59\t32943\t88.8\t0\t32943\n", "60\t29791\t88.8\t0\t29791\n", "61\t27410\t88.8\t0\t27410\n", "62\t22895\t88.8\t0\t22895\n", "63\t22064\t88.8\t0\t22064\n", "64\t24641\t88.8\t0\t24641\n", "65\t24117\t88.8\t0\t24117\n", "66\t21732\t88.8\t0\t21732\n", "67\t21330\t88.8\t0\t21330\n", "68\t20746\t88.8\t0\t20746\n", "69\t21740\t88.8\t0\t21740\n", "70\t22618\t88.8\t0\t22618\n", "71\t21949\t88.8\t0\t21949\n", "72\t17275\t88.8\t0\t17275\n", "73\t15884\t88.8\t0\t15884\n", "74\t15327\t88.8\t0\t15327\n", "75\t13267\t88.8\t0\t13267\n", "76\t11235\t88.8\t0\t11235\n", "77\t10173\t88.8\t0\t10173\n", "78\t11401\t88.8\t0\t11401\n", "79\t10909\t88.8\t0\t10909\n", "80\t10927\t88.8\t0\t10927\n", "81\t10052\t88.8\t0\t10052\n", "82\t9095\t88.8\t0\t9095\n", "83\t9679\t88.8\t0\t9679\n", "84\t10717\t88.8\t0\t10717\n", "85\t11382\t88.8\t0\t11382\n", "86\t10427\t88.8\t0\t10427\n", "87\t7381\t88.8\t0\t7381\n", "88\t6787\t88.8\t0\t6787\n", "89\t7116\t88.8\t0\t7116\n", "90\t7542\t88.8\t0\t7542\n", "91\t7398\t88.8\t0\t7398\n", "92\t7512\t88.8\t0\t7512\n", "93\t7832\t88.8\t0\t7832\n", "94\t7439\t88.8\t0\t7439\n", "95\t6410\t88.8\t0\t6410\n", "96\t4565\t88.8\t0\t4565\n", "97\t2760\t88.8\t0\t2760\n", "98\t1708\t88.8\t0\t1708\n", "99\t1664\t88.8\t0\t1664\n", "100\t1112\t88.8\t0\t1112\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28055 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 48.8%\n", " C: 32.4%\n", " G: 0.0%\n", " T: 18.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t14089\t90904.7\t0\t14089\n", "4\t3449\t22726.2\t0\t3449\n", "5\t1254\t5681.5\t0\t1254\n", "6\t992\t1420.4\t0\t992\n", "7\t159\t355.1\t0\t159\n", "8\t129\t88.8\t0\t129\n", "9\t97\t88.8\t0\t97\n", "10\t108\t88.8\t0\t108\n", "11\t108\t88.8\t0\t108\n", "12\t125\t88.8\t0\t125\n", "13\t84\t88.8\t0\t84\n", "14\t88\t88.8\t0\t88\n", "15\t81\t88.8\t0\t81\n", "16\t100\t88.8\t0\t100\n", "17\t104\t88.8\t0\t104\n", "18\t107\t88.8\t0\t107\n", "19\t167\t88.8\t0\t167\n", "20\t219\t88.8\t0\t219\n", "21\t143\t88.8\t0\t143\n", "22\t109\t88.8\t0\t109\n", "23\t110\t88.8\t0\t110\n", "24\t115\t88.8\t0\t115\n", "25\t106\t88.8\t0\t106\n", "26\t174\t88.8\t0\t174\n", "27\t143\t88.8\t0\t143\n", "28\t159\t88.8\t0\t159\n", "29\t223\t88.8\t0\t223\n", "30\t375\t88.8\t0\t375\n", "31\t412\t88.8\t0\t412\n", "32\t671\t88.8\t0\t671\n", "33\t556\t88.8\t0\t556\n", "34\t506\t88.8\t0\t506\n", "35\t655\t88.8\t0\t655\n", "36\t611\t88.8\t0\t611\n", "37\t211\t88.8\t0\t211\n", "38\t29\t88.8\t0\t29\n", "39\t27\t88.8\t0\t27\n", "40\t26\t88.8\t0\t26\n", "41\t29\t88.8\t0\t29\n", "42\t22\t88.8\t0\t22\n", "43\t35\t88.8\t0\t35\n", "44\t26\t88.8\t0\t26\n", "45\t22\t88.8\t0\t22\n", "46\t26\t88.8\t0\t26\n", "47\t24\t88.8\t0\t24\n", "48\t28\t88.8\t0\t28\n", "49\t38\t88.8\t0\t38\n", "50\t26\t88.8\t0\t26\n", "51\t24\t88.8\t0\t24\n", "52\t22\t88.8\t0\t22\n", "53\t18\t88.8\t0\t18\n", "54\t21\t88.8\t0\t21\n", "55\t30\t88.8\t0\t30\n", "56\t20\t88.8\t0\t20\n", "57\t19\t88.8\t0\t19\n", "58\t14\t88.8\t0\t14\n", "59\t16\t88.8\t0\t16\n", "60\t15\t88.8\t0\t15\n", "61\t15\t88.8\t0\t15\n", "62\t9\t88.8\t0\t9\n", "63\t17\t88.8\t0\t17\n", "64\t8\t88.8\t0\t8\n", "65\t21\t88.8\t0\t21\n", "66\t10\t88.8\t0\t10\n", "67\t17\t88.8\t0\t17\n", "68\t7\t88.8\t0\t7\n", "69\t11\t88.8\t0\t11\n", "70\t16\t88.8\t0\t16\n", "71\t4\t88.8\t0\t4\n", "72\t9\t88.8\t0\t9\n", "73\t7\t88.8\t0\t7\n", "74\t4\t88.8\t0\t4\n", "75\t4\t88.8\t0\t4\n", "76\t7\t88.8\t0\t7\n", "77\t2\t88.8\t0\t2\n", "78\t3\t88.8\t0\t3\n", "79\t9\t88.8\t0\t9\n", "80\t11\t88.8\t0\t11\n", "81\t6\t88.8\t0\t6\n", "82\t10\t88.8\t0\t10\n", "83\t5\t88.8\t0\t5\n", "84\t3\t88.8\t0\t3\n", "85\t10\t88.8\t0\t10\n", "86\t7\t88.8\t0\t7\n", "87\t4\t88.8\t0\t4\n", "88\t9\t88.8\t0\t9\n", "89\t10\t88.8\t0\t10\n", "90\t7\t88.8\t0\t7\n", "91\t13\t88.8\t0\t13\n", "92\t19\t88.8\t0\t19\n", "93\t35\t88.8\t0\t35\n", "94\t56\t88.8\t0\t56\n", "95\t78\t88.8\t0\t78\n", "96\t77\t88.8\t0\t77\n", "97\t61\t88.8\t0\t61\n", "98\t45\t88.8\t0\t45\n", "99\t50\t88.8\t0\t50\n", "100\t63\t88.8\t0\t63\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 90046 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.8%\n", " C: 19.1%\n", " G: 17.1%\n", " T: 21.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t63136\t90904.7\t0\t63136\n", "4\t13964\t22726.2\t0\t13964\n", "5\t2645\t5681.5\t0\t2645\n", "6\t307\t1420.4\t0\t307\n", "7\t164\t355.1\t0\t164\n", "8\t199\t355.1\t0\t199\n", "9\t165\t355.1\t0\t165\n", "10\t188\t355.1\t0\t188\n", "11\t139\t355.1\t0\t139\n", "12\t210\t355.1\t0\t210\n", "13\t210\t355.1\t0\t210\n", "14\t216\t355.1\t0\t216\n", "15\t250\t355.1\t0\t250\n", "16\t195\t355.1\t0\t195\n", "17\t203\t355.1\t0\t203\n", "18\t221\t355.1\t0\t221\n", "19\t263\t355.1\t0\t263\n", "20\t183\t355.1\t0\t183\n", "21\t208\t355.1\t0\t208\n", "22\t192\t355.1\t0\t192\n", "23\t191\t355.1\t0\t191\n", "24\t165\t355.1\t0\t165\n", "25\t155\t355.1\t0\t155\n", "26\t116\t355.1\t0\t116\n", "27\t165\t355.1\t0\t165\n", "28\t154\t355.1\t0\t154\n", "29\t126\t355.1\t0\t126\n", "30\t132\t355.1\t0\t132\n", "31\t124\t355.1\t0\t124\n", "32\t124\t355.1\t0\t124\n", "33\t115\t355.1\t0\t115\n", "34\t102\t355.1\t0\t102\n", "35\t117\t355.1\t0\t117\n", "36\t91\t355.1\t0\t91\n", "37\t107\t355.1\t0\t107\n", "38\t121\t355.1\t0\t121\n", "39\t117\t355.1\t0\t117\n", "40\t135\t355.1\t0\t135\n", "41\t107\t355.1\t0\t107\n", "42\t97\t355.1\t0\t97\n", "43\t142\t355.1\t0\t142\n", "44\t58\t355.1\t0\t58\n", "45\t101\t355.1\t0\t101\n", "46\t110\t355.1\t0\t110\n", "47\t90\t355.1\t0\t90\n", "48\t74\t355.1\t0\t74\n", "49\t75\t355.1\t0\t75\n", "50\t104\t355.1\t0\t104\n", "51\t80\t355.1\t0\t80\n", "52\t73\t355.1\t0\t73\n", "53\t79\t355.1\t0\t79\n", "54\t81\t355.1\t0\t81\n", "55\t82\t355.1\t0\t82\n", "56\t87\t355.1\t0\t87\n", "57\t63\t355.1\t0\t63\n", "58\t74\t355.1\t0\t74\n", "59\t57\t355.1\t0\t57\n", "60\t62\t355.1\t0\t62\n", "61\t59\t355.1\t0\t59\n", "62\t54\t355.1\t0\t54\n", "63\t74\t355.1\t0\t74\n", "64\t49\t355.1\t0\t49\n", "65\t61\t355.1\t0\t61\n", "66\t70\t355.1\t0\t70\n", "67\t63\t355.1\t0\t63\n", "68\t69\t355.1\t0\t69\n", "69\t61\t355.1\t0\t61\n", "70\t49\t355.1\t0\t49\n", "71\t65\t355.1\t0\t65\n", "72\t61\t355.1\t0\t61\n", "73\t64\t355.1\t0\t64\n", "74\t69\t355.1\t0\t69\n", "75\t82\t355.1\t0\t82\n", "76\t69\t355.1\t0\t69\n", "77\t87\t355.1\t0\t87\n", "78\t65\t355.1\t0\t65\n", "79\t61\t355.1\t0\t61\n", "80\t74\t355.1\t0\t74\n", "81\t88\t355.1\t0\t88\n", "82\t108\t355.1\t0\t108\n", "83\t82\t355.1\t0\t82\n", "84\t85\t355.1\t0\t85\n", "85\t93\t355.1\t0\t93\n", "86\t65\t355.1\t0\t65\n", "87\t90\t355.1\t0\t90\n", "88\t89\t355.1\t0\t89\n", "89\t59\t355.1\t0\t59\n", "90\t75\t355.1\t0\t75\n", "91\t37\t355.1\t0\t37\n", "92\t30\t355.1\t0\t30\n", "93\t54\t355.1\t0\t54\n", "94\t61\t355.1\t0\t61\n", "95\t52\t355.1\t0\t52\n", "96\t37\t355.1\t0\t37\n", "97\t54\t355.1\t0\t54\n", "98\t81\t355.1\t0\t81\n", "99\t111\t355.1\t0\t111\n", "100\t78\t355.1\t0\t78\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 403_S30_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/403.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 89.81 s (13 us/read; 4.52 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,761,607\n", "Reads with adapters: 4,038,883 (59.7%)\n", "Reads written (passing filters): 6,633,816 (98.1%)\n", "\n", "Total basepairs processed: 676,160,700 bp\n", "Quality-trimmed: 1,585,034 bp (0.2%)\n", "Total written (filtered): 538,571,994 bp (79.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3880843 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.8%\n", " G: 39.2%\n", " T: 29.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t148652\t105650.1\t0\t148652\n", "4\t90081\t26412.5\t0\t90081\n", "5\t69768\t6603.1\t0\t69768\n", "6\t57520\t1650.8\t0\t57520\n", "7\t51915\t412.7\t0\t51915\n", "8\t51740\t103.2\t0\t51740\n", "9\t50693\t103.2\t0\t50693\n", "10\t49002\t103.2\t0\t49002\n", "11\t49651\t103.2\t0\t49651\n", "12\t50006\t103.2\t0\t50006\n", "13\t51609\t103.2\t0\t51609\n", "14\t53504\t103.2\t0\t53504\n", "15\t52818\t103.2\t0\t52818\n", "16\t54755\t103.2\t0\t54755\n", "17\t61375\t103.2\t0\t61375\n", "18\t72490\t103.2\t0\t72490\n", "19\t66541\t103.2\t0\t66541\n", "20\t55889\t103.2\t0\t55889\n", "21\t55414\t103.2\t0\t55414\n", "22\t49383\t103.2\t0\t49383\n", "23\t54735\t103.2\t0\t54735\n", "24\t63408\t103.2\t0\t63408\n", "25\t64311\t103.2\t0\t64311\n", "26\t73726\t103.2\t0\t73726\n", "27\t81220\t103.2\t0\t81220\n", "28\t72871\t103.2\t0\t72871\n", "29\t68818\t103.2\t0\t68818\n", "30\t70546\t103.2\t0\t70546\n", "31\t77614\t103.2\t0\t77614\n", "32\t72804\t103.2\t0\t72804\n", "33\t66276\t103.2\t0\t66276\n", "34\t63225\t103.2\t0\t63225\n", "35\t72887\t103.2\t0\t72887\n", "36\t84229\t103.2\t0\t84229\n", "37\t84445\t103.2\t0\t84445\n", "38\t69200\t103.2\t0\t69200\n", "39\t58435\t103.2\t0\t58435\n", "40\t53974\t103.2\t0\t53974\n", "41\t58436\t103.2\t0\t58436\n", "42\t64123\t103.2\t0\t64123\n", "43\t56229\t103.2\t0\t56229\n", "44\t43257\t103.2\t0\t43257\n", "45\t55232\t103.2\t0\t55232\n", "46\t67423\t103.2\t0\t67423\n", "47\t63600\t103.2\t0\t63600\n", "48\t61452\t103.2\t0\t61452\n", "49\t49101\t103.2\t0\t49101\n", "50\t45513\t103.2\t0\t45513\n", "51\t38592\t103.2\t0\t38592\n", "52\t41262\t103.2\t0\t41262\n", "53\t46239\t103.2\t0\t46239\n", "54\t45276\t103.2\t0\t45276\n", "55\t46246\t103.2\t0\t46246\n", "56\t39060\t103.2\t0\t39060\n", "57\t40098\t103.2\t0\t40098\n", "58\t47986\t103.2\t0\t47986\n", "59\t33499\t103.2\t0\t33499\n", "60\t26377\t103.2\t0\t26377\n", "61\t24668\t103.2\t0\t24668\n", "62\t20373\t103.2\t0\t20373\n", "63\t19586\t103.2\t0\t19586\n", "64\t22350\t103.2\t0\t22350\n", "65\t21509\t103.2\t0\t21509\n", "66\t18190\t103.2\t0\t18190\n", "67\t17915\t103.2\t0\t17915\n", "68\t16634\t103.2\t0\t16634\n", "69\t17016\t103.2\t0\t17016\n", "70\t17620\t103.2\t0\t17620\n", "71\t16698\t103.2\t0\t16698\n", "72\t12874\t103.2\t0\t12874\n", "73\t11362\t103.2\t0\t11362\n", "74\t11301\t103.2\t0\t11301\n", "75\t9670\t103.2\t0\t9670\n", "76\t7910\t103.2\t0\t7910\n", "77\t7291\t103.2\t0\t7291\n", "78\t8239\t103.2\t0\t8239\n", "79\t7777\t103.2\t0\t7777\n", "80\t7827\t103.2\t0\t7827\n", "81\t7312\t103.2\t0\t7312\n", "82\t6859\t103.2\t0\t6859\n", "83\t7223\t103.2\t0\t7223\n", "84\t8423\t103.2\t0\t8423\n", "85\t9419\t103.2\t0\t9419\n", "86\t8906\t103.2\t0\t8906\n", "87\t6090\t103.2\t0\t6090\n", "88\t5496\t103.2\t0\t5496\n", "89\t6197\t103.2\t0\t6197\n", "90\t6761\t103.2\t0\t6761\n", "91\t6779\t103.2\t0\t6779\n", "92\t7019\t103.2\t0\t7019\n", "93\t7779\t103.2\t0\t7779\n", "94\t7288\t103.2\t0\t7288\n", "95\t6162\t103.2\t0\t6162\n", "96\t4578\t103.2\t0\t4578\n", "97\t2937\t103.2\t0\t2937\n", "98\t1664\t103.2\t0\t1664\n", "99\t1570\t103.2\t0\t1570\n", "100\t1040\t103.2\t0\t1040\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 37344 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 66.3%\n", " C: 13.8%\n", " G: 0.0%\n", " T: 19.7%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t11424\t105650.1\t0\t11424\n", "4\t2741\t26412.5\t0\t2741\n", "5\t983\t6603.1\t0\t983\n", "6\t562\t1650.8\t0\t562\n", "7\t226\t412.7\t0\t226\n", "8\t197\t103.2\t0\t197\n", "9\t166\t103.2\t0\t166\n", "10\t152\t103.2\t0\t152\n", "11\t171\t103.2\t0\t171\n", "12\t141\t103.2\t0\t141\n", "13\t164\t103.2\t0\t164\n", "14\t173\t103.2\t0\t173\n", "15\t132\t103.2\t0\t132\n", "16\t130\t103.2\t0\t130\n", "17\t159\t103.2\t0\t159\n", "18\t172\t103.2\t0\t172\n", "19\t218\t103.2\t0\t218\n", "20\t246\t103.2\t0\t246\n", "21\t193\t103.2\t0\t193\n", "22\t187\t103.2\t0\t187\n", "23\t163\t103.2\t0\t163\n", "24\t190\t103.2\t0\t190\n", "25\t229\t103.2\t0\t229\n", "26\t359\t103.2\t0\t359\n", "27\t414\t103.2\t0\t414\n", "28\t423\t103.2\t0\t423\n", "29\t615\t103.2\t0\t615\n", "30\t1068\t103.2\t0\t1068\n", "31\t1281\t103.2\t0\t1281\n", "32\t1902\t103.2\t0\t1902\n", "33\t1881\t103.2\t0\t1881\n", "34\t2003\t103.2\t0\t2003\n", "35\t2796\t103.2\t0\t2796\n", "36\t2794\t103.2\t0\t2794\n", "37\t1002\t103.2\t0\t1002\n", "38\t61\t103.2\t0\t61\n", "39\t56\t103.2\t0\t56\n", "40\t38\t103.2\t0\t38\n", "41\t30\t103.2\t0\t30\n", "42\t38\t103.2\t0\t38\n", "43\t36\t103.2\t0\t36\n", "44\t16\t103.2\t0\t16\n", "45\t21\t103.2\t0\t21\n", "46\t38\t103.2\t0\t38\n", "47\t27\t103.2\t0\t27\n", "48\t32\t103.2\t0\t32\n", "49\t29\t103.2\t0\t29\n", "50\t28\t103.2\t0\t28\n", "51\t26\t103.2\t0\t26\n", "52\t30\t103.2\t0\t30\n", "53\t26\t103.2\t0\t26\n", "54\t28\t103.2\t0\t28\n", "55\t18\t103.2\t0\t18\n", "56\t31\t103.2\t0\t31\n", "57\t18\t103.2\t0\t18\n", "58\t21\t103.2\t0\t21\n", "59\t17\t103.2\t0\t17\n", "60\t25\t103.2\t0\t25\n", "61\t27\t103.2\t0\t27\n", "62\t21\t103.2\t0\t21\n", "63\t19\t103.2\t0\t19\n", "64\t11\t103.2\t0\t11\n", "65\t23\t103.2\t0\t23\n", "66\t25\t103.2\t0\t25\n", "67\t22\t103.2\t0\t22\n", "68\t22\t103.2\t0\t22\n", "69\t9\t103.2\t0\t9\n", "70\t9\t103.2\t0\t9\n", "71\t14\t103.2\t0\t14\n", "72\t11\t103.2\t0\t11\n", "73\t4\t103.2\t0\t4\n", "74\t3\t103.2\t0\t3\n", "75\t7\t103.2\t0\t7\n", "76\t5\t103.2\t0\t5\n", "77\t6\t103.2\t0\t6\n", "78\t6\t103.2\t0\t6\n", "79\t8\t103.2\t0\t8\n", "80\t4\t103.2\t0\t4\n", "81\t12\t103.2\t0\t12\n", "82\t7\t103.2\t0\t7\n", "83\t7\t103.2\t0\t7\n", "84\t9\t103.2\t0\t9\n", "85\t7\t103.2\t0\t7\n", "86\t7\t103.2\t0\t7\n", "87\t6\t103.2\t0\t6\n", "88\t12\t103.2\t0\t12\n", "89\t13\t103.2\t0\t13\n", "90\t11\t103.2\t0\t11\n", "91\t12\t103.2\t0\t12\n", "92\t35\t103.2\t0\t35\n", "93\t53\t103.2\t0\t53\n", "94\t89\t103.2\t0\t89\n", "95\t87\t103.2\t0\t87\n", "96\t87\t103.2\t0\t87\n", "97\t86\t103.2\t0\t86\n", "98\t51\t103.2\t0\t51\n", "99\t48\t103.2\t0\t48\n", "100\t102\t103.2\t0\t102\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 120696 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.4%\n", " C: 20.4%\n", " G: 16.2%\n", " T: 19.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t82616\t105650.1\t0\t82616\n", "4\t17777\t26412.5\t0\t17777\n", "5\t3551\t6603.1\t0\t3551\n", "6\t564\t1650.8\t0\t564\n", "7\t330\t412.7\t0\t330\n", "8\t361\t412.7\t0\t361\n", "9\t337\t412.7\t0\t337\n", "10\t385\t412.7\t0\t385\n", "11\t347\t412.7\t0\t347\n", "12\t375\t412.7\t0\t375\n", "13\t413\t412.7\t0\t413\n", "14\t350\t412.7\t0\t350\n", "15\t374\t412.7\t0\t374\n", "16\t362\t412.7\t0\t362\n", "17\t347\t412.7\t0\t347\n", "18\t362\t412.7\t0\t362\n", "19\t303\t412.7\t0\t303\n", "20\t323\t412.7\t0\t323\n", "21\t302\t412.7\t0\t302\n", "22\t274\t412.7\t0\t274\n", "23\t311\t412.7\t0\t311\n", "24\t268\t412.7\t0\t268\n", "25\t233\t412.7\t0\t233\n", "26\t256\t412.7\t0\t256\n", "27\t277\t412.7\t0\t277\n", "28\t292\t412.7\t0\t292\n", "29\t268\t412.7\t0\t268\n", "30\t237\t412.7\t0\t237\n", "31\t228\t412.7\t0\t228\n", "32\t261\t412.7\t0\t261\n", "33\t218\t412.7\t0\t218\n", "34\t233\t412.7\t0\t233\n", "35\t247\t412.7\t0\t247\n", "36\t192\t412.7\t0\t192\n", "37\t213\t412.7\t0\t213\n", "38\t159\t412.7\t0\t159\n", "39\t218\t412.7\t0\t218\n", "40\t214\t412.7\t0\t214\n", "41\t198\t412.7\t0\t198\n", "42\t142\t412.7\t0\t142\n", "43\t253\t412.7\t0\t253\n", "44\t107\t412.7\t0\t107\n", "45\t178\t412.7\t0\t178\n", "46\t172\t412.7\t0\t172\n", "47\t164\t412.7\t0\t164\n", "48\t144\t412.7\t0\t144\n", "49\t157\t412.7\t0\t157\n", "50\t110\t412.7\t0\t110\n", "51\t126\t412.7\t0\t126\n", "52\t125\t412.7\t0\t125\n", "53\t114\t412.7\t0\t114\n", "54\t121\t412.7\t0\t121\n", "55\t91\t412.7\t0\t91\n", "56\t77\t412.7\t0\t77\n", "57\t81\t412.7\t0\t81\n", "58\t97\t412.7\t0\t97\n", "59\t83\t412.7\t0\t83\n", "60\t92\t412.7\t0\t92\n", "61\t96\t412.7\t0\t96\n", "62\t91\t412.7\t0\t91\n", "63\t92\t412.7\t0\t92\n", "64\t85\t412.7\t0\t85\n", "65\t67\t412.7\t0\t67\n", "66\t84\t412.7\t0\t84\n", "67\t70\t412.7\t0\t70\n", "68\t85\t412.7\t0\t85\n", "69\t80\t412.7\t0\t80\n", "70\t70\t412.7\t0\t70\n", "71\t79\t412.7\t0\t79\n", "72\t71\t412.7\t0\t71\n", "73\t99\t412.7\t0\t99\n", "74\t100\t412.7\t0\t100\n", "75\t72\t412.7\t0\t72\n", "76\t86\t412.7\t0\t86\n", "77\t112\t412.7\t0\t112\n", "78\t111\t412.7\t0\t111\n", "79\t106\t412.7\t0\t106\n", "80\t129\t412.7\t0\t129\n", "81\t113\t412.7\t0\t113\n", "82\t142\t412.7\t0\t142\n", "83\t128\t412.7\t0\t128\n", "84\t116\t412.7\t0\t116\n", "85\t93\t412.7\t0\t93\n", "86\t86\t412.7\t0\t86\n", "87\t119\t412.7\t0\t119\n", "88\t135\t412.7\t0\t135\n", "89\t89\t412.7\t0\t89\n", "90\t84\t412.7\t0\t84\n", "91\t69\t412.7\t0\t69\n", "92\t67\t412.7\t0\t67\n", "93\t57\t412.7\t0\t57\n", "94\t80\t412.7\t0\t80\n", "95\t50\t412.7\t0\t50\n", "96\t71\t412.7\t0\t71\n", "97\t79\t412.7\t0\t79\n", "98\t95\t412.7\t0\t95\n", "99\t112\t412.7\t0\t112\n", "100\t116\t412.7\t0\t116\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 404_S42_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/404.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 90.91 s (13 us/read; 4.62 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,000,213\n", "Reads with adapters: 3,816,590 (54.5%)\n", "Reads written (passing filters): 6,901,932 (98.6%)\n", "\n", "Total basepairs processed: 700,021,300 bp\n", "Quality-trimmed: 1,462,815 bp (0.2%)\n", "Total written (filtered): 580,811,111 bp (83.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3654895 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.2%\n", " G: 36.6%\n", " T: 36.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t181012\t109378.3\t0\t181012\n", "4\t107632\t27344.6\t0\t107632\n", "5\t80898\t6836.1\t0\t80898\n", "6\t65438\t1709.0\t0\t65438\n", "7\t55063\t427.3\t0\t55063\n", "8\t50011\t106.8\t0\t50011\n", "9\t49443\t106.8\t0\t49443\n", "10\t46929\t106.8\t0\t46929\n", "11\t47660\t106.8\t0\t47660\n", "12\t48526\t106.8\t0\t48526\n", "13\t54808\t106.8\t0\t54808\n", "14\t55079\t106.8\t0\t55079\n", "15\t52999\t106.8\t0\t52999\n", "16\t55226\t106.8\t0\t55226\n", "17\t61072\t106.8\t0\t61072\n", "18\t70000\t106.8\t0\t70000\n", "19\t63882\t106.8\t0\t63882\n", "20\t54324\t106.8\t0\t54324\n", "21\t53533\t106.8\t0\t53533\n", "22\t48896\t106.8\t0\t48896\n", "23\t53520\t106.8\t0\t53520\n", "24\t63984\t106.8\t0\t63984\n", "25\t64893\t106.8\t0\t64893\n", "26\t74724\t106.8\t0\t74724\n", "27\t84894\t106.8\t0\t84894\n", "28\t78432\t106.8\t0\t78432\n", "29\t72578\t106.8\t0\t72578\n", "30\t73542\t106.8\t0\t73542\n", "31\t77801\t106.8\t0\t77801\n", "32\t72717\t106.8\t0\t72717\n", "33\t64929\t106.8\t0\t64929\n", "34\t62919\t106.8\t0\t62919\n", "35\t70359\t106.8\t0\t70359\n", "36\t87612\t106.8\t0\t87612\n", "37\t96123\t106.8\t0\t96123\n", "38\t71930\t106.8\t0\t71930\n", "39\t54672\t106.8\t0\t54672\n", "40\t50638\t106.8\t0\t50638\n", "41\t52360\t106.8\t0\t52360\n", "42\t57604\t106.8\t0\t57604\n", "43\t48204\t106.8\t0\t48204\n", "44\t38755\t106.8\t0\t38755\n", "45\t46970\t106.8\t0\t46970\n", "46\t54855\t106.8\t0\t54855\n", "47\t50050\t106.8\t0\t50050\n", "48\t49417\t106.8\t0\t49417\n", "49\t40228\t106.8\t0\t40228\n", "50\t36121\t106.8\t0\t36121\n", "51\t32256\t106.8\t0\t32256\n", "52\t33591\t106.8\t0\t33591\n", "53\t34740\t106.8\t0\t34740\n", "54\t31536\t106.8\t0\t31536\n", "55\t35450\t106.8\t0\t35450\n", "56\t35299\t106.8\t0\t35299\n", "57\t31095\t106.8\t0\t31095\n", "58\t29696\t106.8\t0\t29696\n", "59\t22645\t106.8\t0\t22645\n", "60\t19065\t106.8\t0\t19065\n", "61\t17582\t106.8\t0\t17582\n", "62\t14773\t106.8\t0\t14773\n", "63\t13832\t106.8\t0\t13832\n", "64\t14642\t106.8\t0\t14642\n", "65\t14246\t106.8\t0\t14246\n", "66\t12772\t106.8\t0\t12772\n", "67\t12104\t106.8\t0\t12104\n", "68\t11433\t106.8\t0\t11433\n", "69\t11476\t106.8\t0\t11476\n", "70\t11810\t106.8\t0\t11810\n", "71\t11218\t106.8\t0\t11218\n", "72\t8851\t106.8\t0\t8851\n", "73\t7996\t106.8\t0\t7996\n", "74\t7956\t106.8\t0\t7956\n", "75\t6774\t106.8\t0\t6774\n", "76\t5784\t106.8\t0\t5784\n", "77\t5241\t106.8\t0\t5241\n", "78\t5692\t106.8\t0\t5692\n", "79\t5364\t106.8\t0\t5364\n", "80\t5704\t106.8\t0\t5704\n", "81\t5306\t106.8\t0\t5306\n", "82\t4975\t106.8\t0\t4975\n", "83\t5460\t106.8\t0\t5460\n", "84\t6297\t106.8\t0\t6297\n", "85\t6937\t106.8\t0\t6937\n", "86\t6714\t106.8\t0\t6714\n", "87\t4921\t106.8\t0\t4921\n", "88\t4493\t106.8\t0\t4493\n", "89\t4745\t106.8\t0\t4745\n", "90\t5030\t106.8\t0\t5030\n", "91\t5094\t106.8\t0\t5094\n", "92\t5323\t106.8\t0\t5323\n", "93\t5537\t106.8\t0\t5537\n", "94\t5351\t106.8\t0\t5351\n", "95\t4739\t106.8\t0\t4739\n", "96\t3666\t106.8\t0\t3666\n", "97\t2594\t106.8\t0\t2594\n", "98\t1611\t106.8\t0\t1611\n", "99\t1247\t106.8\t0\t1247\n", "100\t970\t106.8\t0\t970\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 33767 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 51.1%\n", " C: 27.3%\n", " G: 0.0%\n", " T: 21.5%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t15073\t109378.3\t0\t15073\n", "4\t3756\t27344.6\t0\t3756\n", "5\t1618\t6836.1\t0\t1618\n", "6\t1145\t1709.0\t0\t1145\n", "7\t338\t427.3\t0\t338\n", "8\t268\t106.8\t0\t268\n", "9\t202\t106.8\t0\t202\n", "10\t193\t106.8\t0\t193\n", "11\t205\t106.8\t0\t205\n", "12\t175\t106.8\t0\t175\n", "13\t128\t106.8\t0\t128\n", "14\t173\t106.8\t0\t173\n", "15\t146\t106.8\t0\t146\n", "16\t142\t106.8\t0\t142\n", "17\t138\t106.8\t0\t138\n", "18\t209\t106.8\t0\t209\n", "19\t235\t106.8\t0\t235\n", "20\t245\t106.8\t0\t245\n", "21\t186\t106.8\t0\t186\n", "22\t184\t106.8\t0\t184\n", "23\t162\t106.8\t0\t162\n", "24\t149\t106.8\t0\t149\n", "25\t181\t106.8\t0\t181\n", "26\t273\t106.8\t0\t273\n", "27\t340\t106.8\t0\t340\n", "28\t314\t106.8\t0\t314\n", "29\t301\t106.8\t0\t301\n", "30\t545\t106.8\t0\t545\n", "31\t603\t106.8\t0\t603\n", "32\t872\t106.8\t0\t872\n", "33\t841\t106.8\t0\t841\n", "34\t830\t106.8\t0\t830\n", "35\t1003\t106.8\t0\t1003\n", "36\t865\t106.8\t0\t865\n", "37\t319\t106.8\t0\t319\n", "38\t44\t106.8\t0\t44\n", "39\t24\t106.8\t0\t24\n", "40\t22\t106.8\t0\t22\n", "41\t19\t106.8\t0\t19\n", "42\t14\t106.8\t0\t14\n", "43\t17\t106.8\t0\t17\n", "44\t26\t106.8\t0\t26\n", "45\t17\t106.8\t0\t17\n", "46\t28\t106.8\t0\t28\n", "47\t19\t106.8\t0\t19\n", "48\t21\t106.8\t0\t21\n", "49\t17\t106.8\t0\t17\n", "50\t21\t106.8\t0\t21\n", "51\t20\t106.8\t0\t20\n", "52\t8\t106.8\t0\t8\n", "53\t9\t106.8\t0\t9\n", "54\t20\t106.8\t0\t20\n", "55\t14\t106.8\t0\t14\n", "56\t12\t106.8\t0\t12\n", "57\t9\t106.8\t0\t9\n", "58\t12\t106.8\t0\t12\n", "59\t10\t106.8\t0\t10\n", "60\t8\t106.8\t0\t8\n", "61\t10\t106.8\t0\t10\n", "62\t15\t106.8\t0\t15\n", "63\t11\t106.8\t0\t11\n", "64\t13\t106.8\t0\t13\n", "65\t9\t106.8\t0\t9\n", "66\t7\t106.8\t0\t7\n", "67\t8\t106.8\t0\t8\n", "68\t12\t106.8\t0\t12\n", "69\t12\t106.8\t0\t12\n", "70\t6\t106.8\t0\t6\n", "71\t6\t106.8\t0\t6\n", "72\t8\t106.8\t0\t8\n", "73\t2\t106.8\t0\t2\n", "74\t7\t106.8\t0\t7\n", "75\t2\t106.8\t0\t2\n", "76\t2\t106.8\t0\t2\n", "77\t7\t106.8\t0\t7\n", "78\t10\t106.8\t0\t10\n", "79\t8\t106.8\t0\t8\n", "80\t5\t106.8\t0\t5\n", "81\t3\t106.8\t0\t3\n", "82\t11\t106.8\t0\t11\n", "83\t5\t106.8\t0\t5\n", "84\t1\t106.8\t0\t1\n", "85\t4\t106.8\t0\t4\n", "86\t8\t106.8\t0\t8\n", "87\t3\t106.8\t0\t3\n", "88\t5\t106.8\t0\t5\n", "89\t6\t106.8\t0\t6\n", "90\t8\t106.8\t0\t8\n", "91\t12\t106.8\t0\t12\n", "92\t28\t106.8\t0\t28\n", "93\t87\t106.8\t0\t87\n", "94\t113\t106.8\t0\t113\n", "95\t167\t106.8\t0\t167\n", "96\t83\t106.8\t0\t83\n", "97\t87\t106.8\t0\t87\n", "98\t60\t106.8\t0\t60\n", "99\t46\t106.8\t0\t46\n", "100\t102\t106.8\t0\t102\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 127928 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.8%\n", " C: 19.5%\n", " G: 13.9%\n", " T: 24.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t89271\t109378.3\t0\t89271\n", "4\t20116\t27344.6\t0\t20116\n", "5\t2922\t6836.1\t0\t2922\n", "6\t494\t1709.0\t0\t494\n", "7\t325\t427.3\t0\t325\n", "8\t316\t427.3\t0\t316\n", "9\t365\t427.3\t0\t365\n", "10\t342\t427.3\t0\t342\n", "11\t314\t427.3\t0\t314\n", "12\t309\t427.3\t0\t309\n", "13\t299\t427.3\t0\t299\n", "14\t350\t427.3\t0\t350\n", "15\t292\t427.3\t0\t292\n", "16\t370\t427.3\t0\t370\n", "17\t273\t427.3\t0\t273\n", "18\t285\t427.3\t0\t285\n", "19\t275\t427.3\t0\t275\n", "20\t283\t427.3\t0\t283\n", "21\t262\t427.3\t0\t262\n", "22\t256\t427.3\t0\t256\n", "23\t223\t427.3\t0\t223\n", "24\t236\t427.3\t0\t236\n", "25\t197\t427.3\t0\t197\n", "26\t216\t427.3\t0\t216\n", "27\t213\t427.3\t0\t213\n", "28\t212\t427.3\t0\t212\n", "29\t212\t427.3\t0\t212\n", "30\t222\t427.3\t0\t222\n", "31\t210\t427.3\t0\t210\n", "32\t190\t427.3\t0\t190\n", "33\t181\t427.3\t0\t181\n", "34\t200\t427.3\t0\t200\n", "35\t191\t427.3\t0\t191\n", "36\t166\t427.3\t0\t166\n", "37\t181\t427.3\t0\t181\n", "38\t170\t427.3\t0\t170\n", "39\t176\t427.3\t0\t176\n", "40\t195\t427.3\t0\t195\n", "41\t174\t427.3\t0\t174\n", "42\t130\t427.3\t0\t130\n", "43\t178\t427.3\t0\t178\n", "44\t101\t427.3\t0\t101\n", "45\t139\t427.3\t0\t139\n", "46\t144\t427.3\t0\t144\n", "47\t152\t427.3\t0\t152\n", "48\t126\t427.3\t0\t126\n", "49\t147\t427.3\t0\t147\n", "50\t115\t427.3\t0\t115\n", "51\t144\t427.3\t0\t144\n", "52\t103\t427.3\t0\t103\n", "53\t107\t427.3\t0\t107\n", "54\t93\t427.3\t0\t93\n", "55\t108\t427.3\t0\t108\n", "56\t100\t427.3\t0\t100\n", "57\t80\t427.3\t0\t80\n", "58\t96\t427.3\t0\t96\n", "59\t72\t427.3\t0\t72\n", "60\t111\t427.3\t0\t111\n", "61\t90\t427.3\t0\t90\n", "62\t97\t427.3\t0\t97\n", "63\t80\t427.3\t0\t80\n", "64\t68\t427.3\t0\t68\n", "65\t86\t427.3\t0\t86\n", "66\t91\t427.3\t0\t91\n", "67\t98\t427.3\t0\t98\n", "68\t101\t427.3\t0\t101\n", "69\t56\t427.3\t0\t56\n", "70\t66\t427.3\t0\t66\n", "71\t87\t427.3\t0\t87\n", "72\t102\t427.3\t0\t102\n", "73\t103\t427.3\t0\t103\n", "74\t114\t427.3\t0\t114\n", "75\t109\t427.3\t0\t109\n", "76\t104\t427.3\t0\t104\n", "77\t120\t427.3\t0\t120\n", "78\t108\t427.3\t0\t108\n", "79\t123\t427.3\t0\t123\n", "80\t145\t427.3\t0\t145\n", "81\t141\t427.3\t0\t141\n", "82\t156\t427.3\t0\t156\n", "83\t123\t427.3\t0\t123\n", "84\t121\t427.3\t0\t121\n", "85\t101\t427.3\t0\t101\n", "86\t86\t427.3\t0\t86\n", "87\t109\t427.3\t0\t109\n", "88\t114\t427.3\t0\t114\n", "89\t117\t427.3\t0\t117\n", "90\t96\t427.3\t0\t96\n", "91\t91\t427.3\t0\t91\n", "92\t84\t427.3\t0\t84\n", "93\t64\t427.3\t0\t64\n", "94\t102\t427.3\t0\t102\n", "95\t71\t427.3\t0\t71\n", "96\t69\t427.3\t0\t69\n", "97\t123\t427.3\t0\t123\n", "98\t146\t427.3\t0\t146\n", "99\t165\t427.3\t0\t165\n", "100\t171\t427.3\t0\t171\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 411_S9_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/411.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 88.79 s (13 us/read; 4.49 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,647,774\n", "Reads with adapters: 3,687,764 (55.5%)\n", "Reads written (passing filters): 6,514,655 (98.0%)\n", "\n", "Total basepairs processed: 664,777,400 bp\n", "Quality-trimmed: 1,644,397 bp (0.2%)\n", "Total written (filtered): 537,208,478 bp (80.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3540267 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.9%\n", " G: 40.4%\n", " T: 29.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t148683\t103871.5\t0\t148683\n", "4\t81979\t25967.9\t0\t81979\n", "5\t60358\t6492.0\t0\t60358\n", "6\t49791\t1623.0\t0\t49791\n", "7\t43848\t405.7\t0\t43848\n", "8\t43907\t101.4\t0\t43907\n", "9\t43190\t101.4\t0\t43190\n", "10\t42808\t101.4\t0\t42808\n", "11\t43606\t101.4\t0\t43606\n", "12\t44937\t101.4\t0\t44937\n", "13\t53329\t101.4\t0\t53329\n", "14\t53064\t101.4\t0\t53064\n", "15\t48430\t101.4\t0\t48430\n", "16\t49874\t101.4\t0\t49874\n", "17\t54491\t101.4\t0\t54491\n", "18\t62214\t101.4\t0\t62214\n", "19\t56783\t101.4\t0\t56783\n", "20\t48231\t101.4\t0\t48231\n", "21\t46337\t101.4\t0\t46337\n", "22\t42600\t101.4\t0\t42600\n", "23\t44991\t101.4\t0\t44991\n", "24\t52499\t101.4\t0\t52499\n", "25\t55393\t101.4\t0\t55393\n", "26\t62765\t101.4\t0\t62765\n", "27\t69145\t101.4\t0\t69145\n", "28\t64891\t101.4\t0\t64891\n", "29\t61588\t101.4\t0\t61588\n", "30\t62231\t101.4\t0\t62231\n", "31\t65506\t101.4\t0\t65506\n", "32\t65335\t101.4\t0\t65335\n", "33\t59551\t101.4\t0\t59551\n", "34\t60008\t101.4\t0\t60008\n", "35\t65796\t101.4\t0\t65796\n", "36\t77654\t101.4\t0\t77654\n", "37\t87298\t101.4\t0\t87298\n", "38\t66844\t101.4\t0\t66844\n", "39\t53127\t101.4\t0\t53127\n", "40\t50260\t101.4\t0\t50260\n", "41\t54246\t101.4\t0\t54246\n", "42\t58439\t101.4\t0\t58439\n", "43\t51113\t101.4\t0\t51113\n", "44\t42102\t101.4\t0\t42102\n", "45\t49803\t101.4\t0\t49803\n", "46\t56549\t101.4\t0\t56549\n", "47\t53119\t101.4\t0\t53119\n", "48\t54012\t101.4\t0\t54012\n", "49\t44915\t101.4\t0\t44915\n", "50\t41729\t101.4\t0\t41729\n", "51\t36512\t101.4\t0\t36512\n", "52\t35308\t101.4\t0\t35308\n", "53\t35718\t101.4\t0\t35718\n", "54\t39262\t101.4\t0\t39262\n", "55\t44240\t101.4\t0\t44240\n", "56\t43756\t101.4\t0\t43756\n", "57\t38813\t101.4\t0\t38813\n", "58\t37671\t101.4\t0\t37671\n", "59\t30374\t101.4\t0\t30374\n", "60\t26580\t101.4\t0\t26580\n", "61\t23949\t101.4\t0\t23949\n", "62\t20276\t101.4\t0\t20276\n", "63\t18986\t101.4\t0\t18986\n", "64\t20680\t101.4\t0\t20680\n", "65\t20155\t101.4\t0\t20155\n", "66\t18465\t101.4\t0\t18465\n", "67\t17606\t101.4\t0\t17606\n", "68\t16960\t101.4\t0\t16960\n", "69\t17360\t101.4\t0\t17360\n", "70\t17918\t101.4\t0\t17918\n", "71\t16954\t101.4\t0\t16954\n", "72\t13897\t101.4\t0\t13897\n", "73\t12109\t101.4\t0\t12109\n", "74\t11812\t101.4\t0\t11812\n", "75\t10172\t101.4\t0\t10172\n", "76\t8756\t101.4\t0\t8756\n", "77\t8160\t101.4\t0\t8160\n", "78\t8870\t101.4\t0\t8870\n", "79\t8492\t101.4\t0\t8492\n", "80\t8732\t101.4\t0\t8732\n", "81\t8198\t101.4\t0\t8198\n", "82\t7898\t101.4\t0\t7898\n", "83\t7939\t101.4\t0\t7939\n", "84\t8896\t101.4\t0\t8896\n", "85\t9739\t101.4\t0\t9739\n", "86\t9297\t101.4\t0\t9297\n", "87\t7409\t101.4\t0\t7409\n", "88\t7026\t101.4\t0\t7026\n", "89\t6882\t101.4\t0\t6882\n", "90\t6915\t101.4\t0\t6915\n", "91\t6689\t101.4\t0\t6689\n", "92\t6744\t101.4\t0\t6744\n", "93\t6671\t101.4\t0\t6671\n", "94\t6319\t101.4\t0\t6319\n", "95\t5294\t101.4\t0\t5294\n", "96\t3736\t101.4\t0\t3736\n", "97\t2429\t101.4\t0\t2429\n", "98\t1560\t101.4\t0\t1560\n", "99\t1736\t101.4\t0\t1736\n", "100\t978\t101.4\t0\t978\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27382 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 46.0%\n", " C: 28.0%\n", " G: 0.0%\n", " T: 25.9%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t14736\t103871.5\t0\t14736\n", "4\t3396\t25967.9\t0\t3396\n", "5\t1529\t6492.0\t0\t1529\n", "6\t950\t1623.0\t0\t950\n", "7\t150\t405.7\t0\t150\n", "8\t132\t101.4\t0\t132\n", "9\t109\t101.4\t0\t109\n", "10\t102\t101.4\t0\t102\n", "11\t102\t101.4\t0\t102\n", "12\t84\t101.4\t0\t84\n", "13\t112\t101.4\t0\t112\n", "14\t96\t101.4\t0\t96\n", "15\t82\t101.4\t0\t82\n", "16\t80\t101.4\t0\t80\n", "17\t99\t101.4\t0\t99\n", "18\t92\t101.4\t0\t92\n", "19\t102\t101.4\t0\t102\n", "20\t165\t101.4\t0\t165\n", "21\t114\t101.4\t0\t114\n", "22\t110\t101.4\t0\t110\n", "23\t86\t101.4\t0\t86\n", "24\t102\t101.4\t0\t102\n", "25\t80\t101.4\t0\t80\n", "26\t126\t101.4\t0\t126\n", "27\t148\t101.4\t0\t148\n", "28\t118\t101.4\t0\t118\n", "29\t155\t101.4\t0\t155\n", "30\t236\t101.4\t0\t236\n", "31\t304\t101.4\t0\t304\n", "32\t458\t101.4\t0\t458\n", "33\t375\t101.4\t0\t375\n", "34\t318\t101.4\t0\t318\n", "35\t454\t101.4\t0\t454\n", "36\t436\t101.4\t0\t436\n", "37\t188\t101.4\t0\t188\n", "38\t28\t101.4\t0\t28\n", "39\t16\t101.4\t0\t16\n", "40\t22\t101.4\t0\t22\n", "41\t13\t101.4\t0\t13\n", "42\t31\t101.4\t0\t31\n", "43\t23\t101.4\t0\t23\n", "44\t25\t101.4\t0\t25\n", "45\t28\t101.4\t0\t28\n", "46\t32\t101.4\t0\t32\n", "47\t28\t101.4\t0\t28\n", "48\t31\t101.4\t0\t31\n", "49\t29\t101.4\t0\t29\n", "50\t31\t101.4\t0\t31\n", "51\t23\t101.4\t0\t23\n", "52\t22\t101.4\t0\t22\n", "53\t23\t101.4\t0\t23\n", "54\t27\t101.4\t0\t27\n", "55\t17\t101.4\t0\t17\n", "56\t15\t101.4\t0\t15\n", "57\t25\t101.4\t0\t25\n", "58\t21\t101.4\t0\t21\n", "59\t12\t101.4\t0\t12\n", "60\t16\t101.4\t0\t16\n", "61\t19\t101.4\t0\t19\n", "62\t19\t101.4\t0\t19\n", "63\t18\t101.4\t0\t18\n", "64\t15\t101.4\t0\t15\n", "65\t13\t101.4\t0\t13\n", "66\t22\t101.4\t0\t22\n", "67\t9\t101.4\t0\t9\n", "68\t10\t101.4\t0\t10\n", "69\t8\t101.4\t0\t8\n", "70\t16\t101.4\t0\t16\n", "71\t9\t101.4\t0\t9\n", "72\t6\t101.4\t0\t6\n", "73\t11\t101.4\t0\t11\n", "74\t2\t101.4\t0\t2\n", "75\t6\t101.4\t0\t6\n", "76\t12\t101.4\t0\t12\n", "77\t8\t101.4\t0\t8\n", "78\t5\t101.4\t0\t5\n", "79\t8\t101.4\t0\t8\n", "80\t7\t101.4\t0\t7\n", "81\t7\t101.4\t0\t7\n", "82\t5\t101.4\t0\t5\n", "83\t8\t101.4\t0\t8\n", "84\t16\t101.4\t0\t16\n", "85\t10\t101.4\t0\t10\n", "86\t6\t101.4\t0\t6\n", "87\t12\t101.4\t0\t12\n", "88\t2\t101.4\t0\t2\n", "89\t10\t101.4\t0\t10\n", "90\t13\t101.4\t0\t13\n", "91\t15\t101.4\t0\t15\n", "92\t21\t101.4\t0\t21\n", "93\t43\t101.4\t0\t43\n", "94\t61\t101.4\t0\t61\n", "95\t77\t101.4\t0\t77\n", "96\t95\t101.4\t0\t95\n", "97\t81\t101.4\t0\t81\n", "98\t56\t101.4\t0\t56\n", "99\t66\t101.4\t0\t66\n", "100\t91\t101.4\t0\t91\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 120115 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.6%\n", " C: 21.8%\n", " G: 15.1%\n", " T: 22.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t89452\t103871.5\t0\t89452\n", "4\t17992\t25967.9\t0\t17992\n", "5\t3164\t6492.0\t0\t3164\n", "6\t306\t1623.0\t0\t306\n", "7\t144\t405.7\t0\t144\n", "8\t135\t405.7\t0\t135\n", "9\t153\t405.7\t0\t153\n", "10\t156\t405.7\t0\t156\n", "11\t141\t405.7\t0\t141\n", "12\t161\t405.7\t0\t161\n", "13\t154\t405.7\t0\t154\n", "14\t144\t405.7\t0\t144\n", "15\t197\t405.7\t0\t197\n", "16\t186\t405.7\t0\t186\n", "17\t190\t405.7\t0\t190\n", "18\t150\t405.7\t0\t150\n", "19\t201\t405.7\t0\t201\n", "20\t147\t405.7\t0\t147\n", "21\t124\t405.7\t0\t124\n", "22\t141\t405.7\t0\t141\n", "23\t120\t405.7\t0\t120\n", "24\t127\t405.7\t0\t127\n", "25\t134\t405.7\t0\t134\n", "26\t118\t405.7\t0\t118\n", "27\t128\t405.7\t0\t128\n", "28\t103\t405.7\t0\t103\n", "29\t115\t405.7\t0\t115\n", "30\t122\t405.7\t0\t122\n", "31\t116\t405.7\t0\t116\n", "32\t109\t405.7\t0\t109\n", "33\t109\t405.7\t0\t109\n", "34\t92\t405.7\t0\t92\n", "35\t101\t405.7\t0\t101\n", "36\t108\t405.7\t0\t108\n", "37\t91\t405.7\t0\t91\n", "38\t102\t405.7\t0\t102\n", "39\t125\t405.7\t0\t125\n", "40\t100\t405.7\t0\t100\n", "41\t85\t405.7\t0\t85\n", "42\t83\t405.7\t0\t83\n", "43\t125\t405.7\t0\t125\n", "44\t67\t405.7\t0\t67\n", "45\t85\t405.7\t0\t85\n", "46\t72\t405.7\t0\t72\n", "47\t75\t405.7\t0\t75\n", "48\t76\t405.7\t0\t76\n", "49\t75\t405.7\t0\t75\n", "50\t76\t405.7\t0\t76\n", "51\t83\t405.7\t0\t83\n", "52\t74\t405.7\t0\t74\n", "53\t82\t405.7\t0\t82\n", "54\t64\t405.7\t0\t64\n", "55\t60\t405.7\t0\t60\n", "56\t63\t405.7\t0\t63\n", "57\t65\t405.7\t0\t65\n", "58\t58\t405.7\t0\t58\n", "59\t61\t405.7\t0\t61\n", "60\t79\t405.7\t0\t79\n", "61\t95\t405.7\t0\t95\n", "62\t63\t405.7\t0\t63\n", "63\t65\t405.7\t0\t65\n", "64\t48\t405.7\t0\t48\n", "65\t59\t405.7\t0\t59\n", "66\t57\t405.7\t0\t57\n", "67\t68\t405.7\t0\t68\n", "68\t51\t405.7\t0\t51\n", "69\t40\t405.7\t0\t40\n", "70\t71\t405.7\t0\t71\n", "71\t52\t405.7\t0\t52\n", "72\t74\t405.7\t0\t74\n", "73\t78\t405.7\t0\t78\n", "74\t67\t405.7\t0\t67\n", "75\t53\t405.7\t0\t53\n", "76\t102\t405.7\t0\t102\n", "77\t80\t405.7\t0\t80\n", "78\t87\t405.7\t0\t87\n", "79\t85\t405.7\t0\t85\n", "80\t95\t405.7\t0\t95\n", "81\t120\t405.7\t0\t120\n", "82\t133\t405.7\t0\t133\n", "83\t106\t405.7\t0\t106\n", "84\t97\t405.7\t0\t97\n", "85\t84\t405.7\t0\t84\n", "86\t67\t405.7\t0\t67\n", "87\t122\t405.7\t0\t122\n", "88\t90\t405.7\t0\t90\n", "89\t79\t405.7\t0\t79\n", "90\t79\t405.7\t0\t79\n", "91\t45\t405.7\t0\t45\n", "92\t59\t405.7\t0\t59\n", "93\t49\t405.7\t0\t49\n", "94\t82\t405.7\t0\t82\n", "95\t56\t405.7\t0\t56\n", "96\t61\t405.7\t0\t61\n", "97\t90\t405.7\t0\t90\n", "98\t93\t405.7\t0\t93\n", "99\t129\t405.7\t0\t129\n", "100\t118\t405.7\t0\t118\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 412_S74_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/412.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 91.88 s (13 us/read; 4.61 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,052,231\n", "Reads with adapters: 3,653,804 (51.8%)\n", "Reads written (passing filters): 6,700,690 (95.0%)\n", "\n", "Total basepairs processed: 705,223,100 bp\n", "Quality-trimmed: 1,740,564 bp (0.2%)\n", "Total written (filtered): 561,987,901 bp (79.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2640515 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 24.9%\n", " G: 41.7%\n", " T: 33.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t147558\t110191.1\t0\t147558\n", "4\t61628\t27547.8\t0\t61628\n", "5\t46263\t6886.9\t0\t46263\n", "6\t26909\t1721.7\t0\t26909\n", "7\t25720\t430.4\t0\t25720\n", "8\t22757\t107.6\t0\t22757\n", "9\t25433\t107.6\t0\t25433\n", "10\t21262\t107.6\t0\t21262\n", "11\t21534\t107.6\t0\t21534\n", "12\t18515\t107.6\t0\t18515\n", "13\t20193\t107.6\t0\t20193\n", "14\t21324\t107.6\t0\t21324\n", "15\t21258\t107.6\t0\t21258\n", "16\t23006\t107.6\t0\t23006\n", "17\t26727\t107.6\t0\t26727\n", "18\t31502\t107.6\t0\t31502\n", "19\t30618\t107.6\t0\t30618\n", "20\t26399\t107.6\t0\t26399\n", "21\t27107\t107.6\t0\t27107\n", "22\t24732\t107.6\t0\t24732\n", "23\t30647\t107.6\t0\t30647\n", "24\t38134\t107.6\t0\t38134\n", "25\t40488\t107.6\t0\t40488\n", "26\t42232\t107.6\t0\t42232\n", "27\t51844\t107.6\t0\t51844\n", "28\t49231\t107.6\t0\t49231\n", "29\t50627\t107.6\t0\t50627\n", "30\t52323\t107.6\t0\t52323\n", "31\t55424\t107.6\t0\t55424\n", "32\t50050\t107.6\t0\t50050\n", "33\t40157\t107.6\t0\t40157\n", "34\t38987\t107.6\t0\t38987\n", "35\t47526\t107.6\t0\t47526\n", "36\t68071\t107.6\t0\t68071\n", "37\t93331\t107.6\t0\t93331\n", "38\t65633\t107.6\t0\t65633\n", "39\t38848\t107.6\t0\t38848\n", "40\t30891\t107.6\t0\t30891\n", "41\t25294\t107.6\t0\t25294\n", "42\t25510\t107.6\t0\t25510\n", "43\t21357\t107.6\t0\t21357\n", "44\t18907\t107.6\t0\t18907\n", "45\t28195\t107.6\t0\t28195\n", "46\t36572\t107.6\t0\t36572\n", "47\t38751\t107.6\t0\t38751\n", "48\t43109\t107.6\t0\t43109\n", "49\t36297\t107.6\t0\t36297\n", "50\t26207\t107.6\t0\t26207\n", "51\t22442\t107.6\t0\t22442\n", "52\t18239\t107.6\t0\t18239\n", "53\t19437\t107.6\t0\t19437\n", "54\t23599\t107.6\t0\t23599\n", "55\t30446\t107.6\t0\t30446\n", "56\t29659\t107.6\t0\t29659\n", "57\t22176\t107.6\t0\t22176\n", "58\t29697\t107.6\t0\t29697\n", "59\t18809\t107.6\t0\t18809\n", "60\t15228\t107.6\t0\t15228\n", "61\t14914\t107.6\t0\t14914\n", "62\t13537\t107.6\t0\t13537\n", "63\t17244\t107.6\t0\t17244\n", "64\t19018\t107.6\t0\t19018\n", "65\t13171\t107.6\t0\t13171\n", "66\t12163\t107.6\t0\t12163\n", "67\t12077\t107.6\t0\t12077\n", "68\t10032\t107.6\t0\t10032\n", "69\t10719\t107.6\t0\t10719\n", "70\t14024\t107.6\t0\t14024\n", "71\t13340\t107.6\t0\t13340\n", "72\t10936\t107.6\t0\t10936\n", "73\t8267\t107.6\t0\t8267\n", "74\t7343\t107.6\t0\t7343\n", "75\t6856\t107.6\t0\t6856\n", "76\t6551\t107.6\t0\t6551\n", "77\t7550\t107.6\t0\t7550\n", "78\t8528\t107.6\t0\t8528\n", "79\t7150\t107.6\t0\t7150\n", "80\t7199\t107.6\t0\t7199\n", "81\t6975\t107.6\t0\t6975\n", "82\t6099\t107.6\t0\t6099\n", "83\t6548\t107.6\t0\t6548\n", "84\t7744\t107.6\t0\t7744\n", "85\t9889\t107.6\t0\t9889\n", "86\t9633\t107.6\t0\t9633\n", "87\t6707\t107.6\t0\t6707\n", "88\t5640\t107.6\t0\t5640\n", "89\t6301\t107.6\t0\t6301\n", "90\t7575\t107.6\t0\t7575\n", "91\t10422\t107.6\t0\t10422\n", "92\t16171\t107.6\t0\t16171\n", "93\t26503\t107.6\t0\t26503\n", "94\t34935\t107.6\t0\t34935\n", "95\t37493\t107.6\t0\t37493\n", "96\t32551\t107.6\t0\t32551\n", "97\t27702\t107.6\t0\t27702\n", "98\t21730\t107.6\t0\t21730\n", "99\t31541\t107.6\t0\t31541\n", "100\t22917\t107.6\t0\t22917\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 905613 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 91.6%\n", " C: 2.9%\n", " G: 0.0%\n", " T: 5.5%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t3081\t110191.1\t0\t3081\n", "4\t1408\t27547.8\t0\t1408\n", "5\t341\t6886.9\t0\t341\n", "6\t264\t1721.7\t0\t264\n", "7\t299\t430.4\t0\t299\n", "8\t347\t107.6\t0\t347\n", "9\t335\t107.6\t0\t335\n", "10\t418\t107.6\t0\t418\n", "11\t353\t107.6\t0\t353\n", "12\t386\t107.6\t0\t386\n", "13\t407\t107.6\t0\t407\n", "14\t487\t107.6\t0\t487\n", "15\t618\t107.6\t0\t618\n", "16\t940\t107.6\t0\t940\n", "17\t1614\t107.6\t0\t1614\n", "18\t3669\t107.6\t0\t3669\n", "19\t7206\t107.6\t0\t7206\n", "20\t6947\t107.6\t0\t6947\n", "21\t5062\t107.6\t0\t5062\n", "22\t3583\t107.6\t0\t3583\n", "23\t2659\t107.6\t0\t2659\n", "24\t2834\t107.6\t0\t2834\n", "25\t3879\t107.6\t0\t3879\n", "26\t5631\t107.6\t0\t5631\n", "27\t7980\t107.6\t0\t7980\n", "28\t13430\t107.6\t0\t13430\n", "29\t23568\t107.6\t0\t23568\n", "30\t43108\t107.6\t0\t43108\n", "31\t60960\t107.6\t0\t60960\n", "32\t93268\t107.6\t0\t93268\n", "33\t99037\t107.6\t0\t99037\n", "34\t131717\t107.6\t0\t131717\n", "35\t181154\t107.6\t0\t181154\n", "36\t141739\t107.6\t0\t141739\n", "37\t49407\t107.6\t0\t49407\n", "38\t1871\t107.6\t0\t1871\n", "39\t324\t107.6\t0\t324\n", "40\t86\t107.6\t0\t86\n", "41\t141\t107.6\t0\t141\n", "42\t237\t107.6\t0\t237\n", "43\t316\t107.6\t0\t316\n", "44\t332\t107.6\t0\t332\n", "45\t434\t107.6\t0\t434\n", "46\t775\t107.6\t0\t775\n", "47\t1089\t107.6\t0\t1089\n", "48\t593\t107.6\t0\t593\n", "49\t259\t107.6\t0\t259\n", "50\t207\t107.6\t0\t207\n", "51\t185\t107.6\t0\t185\n", "52\t191\t107.6\t0\t191\n", "53\t96\t107.6\t0\t96\n", "54\t11\t107.6\t0\t11\n", "55\t10\t107.6\t0\t10\n", "56\t8\t107.6\t0\t8\n", "57\t3\t107.6\t0\t3\n", "58\t16\t107.6\t0\t16\n", "59\t7\t107.6\t0\t7\n", "60\t16\t107.6\t0\t16\n", "61\t18\t107.6\t0\t18\n", "62\t78\t107.6\t0\t78\n", "63\t7\t107.6\t0\t7\n", "64\t7\t107.6\t0\t7\n", "65\t2\t107.6\t0\t2\n", "66\t2\t107.6\t0\t2\n", "67\t1\t107.6\t0\t1\n", "68\t4\t107.6\t0\t4\n", "69\t2\t107.6\t0\t2\n", "70\t4\t107.6\t0\t4\n", "72\t1\t107.6\t0\t1\n", "73\t8\t107.6\t0\t8\n", "74\t7\t107.6\t0\t7\n", "75\t9\t107.6\t0\t9\n", "76\t1\t107.6\t0\t1\n", "77\t2\t107.6\t0\t2\n", "79\t4\t107.6\t0\t4\n", "80\t3\t107.6\t0\t3\n", "81\t2\t107.6\t0\t2\n", "82\t7\t107.6\t0\t7\n", "83\t2\t107.6\t0\t2\n", "84\t1\t107.6\t0\t1\n", "85\t6\t107.6\t0\t6\n", "86\t1\t107.6\t0\t1\n", "88\t1\t107.6\t0\t1\n", "89\t1\t107.6\t0\t1\n", "94\t1\t107.6\t0\t1\n", "95\t4\t107.6\t0\t4\n", "97\t1\t107.6\t0\t1\n", "98\t5\t107.6\t0\t5\n", "99\t77\t107.6\t0\t77\n", "100\t1\t107.6\t0\t1\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 107676 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 46.5%\n", " C: 17.5%\n", " G: 7.9%\n", " T: 27.9%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t69819\t110191.1\t0\t69819\n", "4\t17409\t27547.8\t0\t17409\n", "5\t1513\t6886.9\t0\t1513\n", "6\t131\t1721.7\t0\t131\n", "7\t112\t430.4\t0\t112\n", "8\t355\t430.4\t0\t355\n", "9\t165\t430.4\t0\t165\n", "10\t230\t430.4\t0\t230\n", "11\t59\t430.4\t0\t59\n", "12\t358\t430.4\t0\t358\n", "13\t171\t430.4\t0\t171\n", "14\t164\t430.4\t0\t164\n", "15\t231\t430.4\t0\t231\n", "16\t234\t430.4\t0\t234\n", "17\t165\t430.4\t0\t165\n", "18\t267\t430.4\t0\t267\n", "19\t135\t430.4\t0\t135\n", "20\t210\t430.4\t0\t210\n", "21\t186\t430.4\t0\t186\n", "22\t224\t430.4\t0\t224\n", "23\t341\t430.4\t0\t341\n", "24\t271\t430.4\t0\t271\n", "25\t250\t430.4\t0\t250\n", "26\t137\t430.4\t0\t137\n", "27\t233\t430.4\t0\t233\n", "28\t302\t430.4\t0\t302\n", "29\t214\t430.4\t0\t214\n", "30\t437\t430.4\t0\t437\n", "31\t125\t430.4\t0\t125\n", "32\t256\t430.4\t0\t256\n", "33\t278\t430.4\t0\t278\n", "34\t238\t430.4\t0\t238\n", "35\t253\t430.4\t0\t253\n", "36\t390\t430.4\t0\t390\n", "37\t208\t430.4\t0\t208\n", "38\t184\t430.4\t0\t184\n", "39\t222\t430.4\t0\t222\n", "40\t275\t430.4\t0\t275\n", "41\t318\t430.4\t0\t318\n", "42\t225\t430.4\t0\t225\n", "43\t398\t430.4\t0\t398\n", "44\t102\t430.4\t0\t102\n", "45\t267\t430.4\t0\t267\n", "46\t552\t430.4\t0\t552\n", "47\t225\t430.4\t0\t225\n", "48\t89\t430.4\t0\t89\n", "49\t373\t430.4\t0\t373\n", "50\t223\t430.4\t0\t223\n", "51\t265\t430.4\t0\t265\n", "52\t387\t430.4\t0\t387\n", "53\t405\t430.4\t0\t405\n", "54\t141\t430.4\t0\t141\n", "55\t313\t430.4\t0\t313\n", "56\t144\t430.4\t0\t144\n", "57\t437\t430.4\t0\t437\n", "58\t121\t430.4\t0\t121\n", "59\t155\t430.4\t0\t155\n", "60\t921\t430.4\t0\t921\n", "61\t203\t430.4\t0\t203\n", "62\t193\t430.4\t0\t193\n", "63\t289\t430.4\t0\t289\n", "64\t608\t430.4\t0\t608\n", "65\t28\t430.4\t0\t28\n", "66\t152\t430.4\t0\t152\n", "67\t212\t430.4\t0\t212\n", "68\t334\t430.4\t0\t334\n", "69\t27\t430.4\t0\t27\n", "70\t9\t430.4\t0\t9\n", "71\t82\t430.4\t0\t82\n", "72\t218\t430.4\t0\t218\n", "73\t120\t430.4\t0\t120\n", "74\t104\t430.4\t0\t104\n", "75\t99\t430.4\t0\t99\n", "76\t21\t430.4\t0\t21\n", "77\t190\t430.4\t0\t190\n", "78\t28\t430.4\t0\t28\n", "79\t47\t430.4\t0\t47\n", "80\t13\t430.4\t0\t13\n", "81\t34\t430.4\t0\t34\n", "82\t117\t430.4\t0\t117\n", "83\t30\t430.4\t0\t30\n", "84\t25\t430.4\t0\t25\n", "85\t120\t430.4\t0\t120\n", "86\t81\t430.4\t0\t81\n", "87\t66\t430.4\t0\t66\n", "88\t286\t430.4\t0\t286\n", "89\t207\t430.4\t0\t207\n", "90\t19\t430.4\t0\t19\n", "91\t4\t430.4\t0\t4\n", "92\t11\t430.4\t0\t11\n", "93\t2\t430.4\t0\t2\n", "94\t8\t430.4\t0\t8\n", "95\t51\t430.4\t0\t51\n", "96\t73\t430.4\t0\t73\n", "97\t178\t430.4\t0\t178\n", "98\t7\t430.4\t0\t7\n", "99\t115\t430.4\t0\t115\n", "100\t452\t430.4\t0\t452\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 413_S38_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/413.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 81.77 s (13 us/read; 4.71 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,420,294\n", "Reads with adapters: 3,808,429 (59.3%)\n", "Reads written (passing filters): 6,340,392 (98.8%)\n", "\n", "Total basepairs processed: 642,029,400 bp\n", "Quality-trimmed: 1,575,247 bp (0.2%)\n", "Total written (filtered): 515,043,262 bp (80.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3669396 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.5%\n", " G: 36.4%\n", " T: 34.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t151359\t100317.1\t0\t151359\n", "4\t86455\t25079.3\t0\t86455\n", "5\t66481\t6269.8\t0\t66481\n", "6\t52966\t1567.5\t0\t52966\n", "7\t48871\t391.9\t0\t48871\n", "8\t49388\t98.0\t0\t49388\n", "9\t48609\t98.0\t0\t48609\n", "10\t46057\t98.0\t0\t46057\n", "11\t46924\t98.0\t0\t46924\n", "12\t46323\t98.0\t0\t46323\n", "13\t48349\t98.0\t0\t48349\n", "14\t50417\t98.0\t0\t50417\n", "15\t50485\t98.0\t0\t50485\n", "16\t52293\t98.0\t0\t52293\n", "17\t58172\t98.0\t0\t58172\n", "18\t67577\t98.0\t0\t67577\n", "19\t62476\t98.0\t0\t62476\n", "20\t51934\t98.0\t0\t51934\n", "21\t49867\t98.0\t0\t49867\n", "22\t46065\t98.0\t0\t46065\n", "23\t51557\t98.0\t0\t51557\n", "24\t58794\t98.0\t0\t58794\n", "25\t59442\t98.0\t0\t59442\n", "26\t67802\t98.0\t0\t67802\n", "27\t75240\t98.0\t0\t75240\n", "28\t68021\t98.0\t0\t68021\n", "29\t65206\t98.0\t0\t65206\n", "30\t67100\t98.0\t0\t67100\n", "31\t71532\t98.0\t0\t71532\n", "32\t71067\t98.0\t0\t71067\n", "33\t63825\t98.0\t0\t63825\n", "34\t61531\t98.0\t0\t61531\n", "35\t70404\t98.0\t0\t70404\n", "36\t82241\t98.0\t0\t82241\n", "37\t87101\t98.0\t0\t87101\n", "38\t71819\t98.0\t0\t71819\n", "39\t57132\t98.0\t0\t57132\n", "40\t53955\t98.0\t0\t53955\n", "41\t54558\t98.0\t0\t54558\n", "42\t60654\t98.0\t0\t60654\n", "43\t52759\t98.0\t0\t52759\n", "44\t43502\t98.0\t0\t43502\n", "45\t55021\t98.0\t0\t55021\n", "46\t65060\t98.0\t0\t65060\n", "47\t58365\t98.0\t0\t58365\n", "48\t59558\t98.0\t0\t59558\n", "49\t46976\t98.0\t0\t46976\n", "50\t45141\t98.0\t0\t45141\n", "51\t39869\t98.0\t0\t39869\n", "52\t45978\t98.0\t0\t45978\n", "53\t52368\t98.0\t0\t52368\n", "54\t44530\t98.0\t0\t44530\n", "55\t43936\t98.0\t0\t43936\n", "56\t34578\t98.0\t0\t34578\n", "57\t35539\t98.0\t0\t35539\n", "58\t38806\t98.0\t0\t38806\n", "59\t29942\t98.0\t0\t29942\n", "60\t24843\t98.0\t0\t24843\n", "61\t24248\t98.0\t0\t24248\n", "62\t20070\t98.0\t0\t20070\n", "63\t19628\t98.0\t0\t19628\n", "64\t22241\t98.0\t0\t22241\n", "65\t21316\t98.0\t0\t21316\n", "66\t17428\t98.0\t0\t17428\n", "67\t16659\t98.0\t0\t16659\n", "68\t16163\t98.0\t0\t16163\n", "69\t16158\t98.0\t0\t16158\n", "70\t17174\t98.0\t0\t17174\n", "71\t16191\t98.0\t0\t16191\n", "72\t12310\t98.0\t0\t12310\n", "73\t10407\t98.0\t0\t10407\n", "74\t9812\t98.0\t0\t9812\n", "75\t8164\t98.0\t0\t8164\n", "76\t6397\t98.0\t0\t6397\n", "77\t6165\t98.0\t0\t6165\n", "78\t7167\t98.0\t0\t7167\n", "79\t6418\t98.0\t0\t6418\n", "80\t5943\t98.0\t0\t5943\n", "81\t5444\t98.0\t0\t5444\n", "82\t5088\t98.0\t0\t5088\n", "83\t5131\t98.0\t0\t5131\n", "84\t5596\t98.0\t0\t5596\n", "85\t6243\t98.0\t0\t6243\n", "86\t5885\t98.0\t0\t5885\n", "87\t4121\t98.0\t0\t4121\n", "88\t3572\t98.0\t0\t3572\n", "89\t3726\t98.0\t0\t3726\n", "90\t3900\t98.0\t0\t3900\n", "91\t3790\t98.0\t0\t3790\n", "92\t3444\t98.0\t0\t3444\n", "93\t3421\t98.0\t0\t3421\n", "94\t3447\t98.0\t0\t3447\n", "95\t2924\t98.0\t0\t2924\n", "96\t2194\t98.0\t0\t2194\n", "97\t1686\t98.0\t0\t1686\n", "98\t1021\t98.0\t0\t1021\n", "99\t1103\t98.0\t0\t1103\n", "100\t781\t98.0\t0\t781\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 19770 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 52.9%\n", " C: 18.9%\n", " G: 0.0%\n", " T: 28.2%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10009\t100317.1\t0\t10009\n", "4\t2182\t25079.3\t0\t2182\n", "5\t623\t6269.8\t0\t623\n", "6\t365\t1567.5\t0\t365\n", "7\t122\t391.9\t0\t122\n", "8\t95\t98.0\t0\t95\n", "9\t80\t98.0\t0\t80\n", "10\t65\t98.0\t0\t65\n", "11\t82\t98.0\t0\t82\n", "12\t90\t98.0\t0\t90\n", "13\t93\t98.0\t0\t93\n", "14\t74\t98.0\t0\t74\n", "15\t81\t98.0\t0\t81\n", "16\t83\t98.0\t0\t83\n", "17\t96\t98.0\t0\t96\n", "18\t103\t98.0\t0\t103\n", "19\t160\t98.0\t0\t160\n", "20\t255\t98.0\t0\t255\n", "21\t163\t98.0\t0\t163\n", "22\t127\t98.0\t0\t127\n", "23\t98\t98.0\t0\t98\n", "24\t83\t98.0\t0\t83\n", "25\t78\t98.0\t0\t78\n", "26\t98\t98.0\t0\t98\n", "27\t92\t98.0\t0\t92\n", "28\t102\t98.0\t0\t102\n", "29\t110\t98.0\t0\t110\n", "30\t205\t98.0\t0\t205\n", "31\t222\t98.0\t0\t222\n", "32\t318\t98.0\t0\t318\n", "33\t375\t98.0\t0\t375\n", "34\t393\t98.0\t0\t393\n", "35\t544\t98.0\t0\t544\n", "36\t489\t98.0\t0\t489\n", "37\t238\t98.0\t0\t238\n", "38\t73\t98.0\t0\t73\n", "39\t74\t98.0\t0\t74\n", "40\t78\t98.0\t0\t78\n", "41\t102\t98.0\t0\t102\n", "42\t112\t98.0\t0\t112\n", "43\t69\t98.0\t0\t69\n", "44\t26\t98.0\t0\t26\n", "45\t23\t98.0\t0\t23\n", "46\t24\t98.0\t0\t24\n", "47\t28\t98.0\t0\t28\n", "48\t24\t98.0\t0\t24\n", "49\t26\t98.0\t0\t26\n", "50\t26\t98.0\t0\t26\n", "51\t20\t98.0\t0\t20\n", "52\t19\t98.0\t0\t19\n", "53\t25\t98.0\t0\t25\n", "54\t19\t98.0\t0\t19\n", "55\t10\t98.0\t0\t10\n", "56\t21\t98.0\t0\t21\n", "57\t20\t98.0\t0\t20\n", "58\t15\t98.0\t0\t15\n", "59\t15\t98.0\t0\t15\n", "60\t18\t98.0\t0\t18\n", "61\t13\t98.0\t0\t13\n", "62\t20\t98.0\t0\t20\n", "63\t10\t98.0\t0\t10\n", "64\t9\t98.0\t0\t9\n", "65\t9\t98.0\t0\t9\n", "66\t13\t98.0\t0\t13\n", "67\t8\t98.0\t0\t8\n", "68\t10\t98.0\t0\t10\n", "69\t10\t98.0\t0\t10\n", "70\t9\t98.0\t0\t9\n", "71\t5\t98.0\t0\t5\n", "72\t1\t98.0\t0\t1\n", "73\t5\t98.0\t0\t5\n", "74\t1\t98.0\t0\t1\n", "75\t1\t98.0\t0\t1\n", "76\t1\t98.0\t0\t1\n", "77\t4\t98.0\t0\t4\n", "78\t5\t98.0\t0\t5\n", "79\t4\t98.0\t0\t4\n", "80\t3\t98.0\t0\t3\n", "81\t4\t98.0\t0\t4\n", "82\t3\t98.0\t0\t3\n", "83\t4\t98.0\t0\t4\n", "84\t2\t98.0\t0\t2\n", "85\t7\t98.0\t0\t7\n", "86\t3\t98.0\t0\t3\n", "87\t6\t98.0\t0\t6\n", "88\t5\t98.0\t0\t5\n", "89\t6\t98.0\t0\t6\n", "91\t7\t98.0\t0\t7\n", "92\t10\t98.0\t0\t10\n", "93\t16\t98.0\t0\t16\n", "94\t35\t98.0\t0\t35\n", "95\t55\t98.0\t0\t55\n", "96\t35\t98.0\t0\t35\n", "97\t47\t98.0\t0\t47\n", "98\t24\t98.0\t0\t24\n", "99\t38\t98.0\t0\t38\n", "100\t62\t98.0\t0\t62\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 119263 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.9%\n", " C: 17.8%\n", " G: 13.9%\n", " T: 26.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t81639\t100317.1\t0\t81639\n", "4\t21218\t25079.3\t0\t21218\n", "5\t3643\t6269.8\t0\t3643\n", "6\t383\t1567.5\t0\t383\n", "7\t161\t391.9\t0\t161\n", "8\t219\t391.9\t0\t219\n", "9\t233\t391.9\t0\t233\n", "10\t180\t391.9\t0\t180\n", "11\t199\t391.9\t0\t199\n", "12\t207\t391.9\t0\t207\n", "13\t211\t391.9\t0\t211\n", "14\t192\t391.9\t0\t192\n", "15\t189\t391.9\t0\t189\n", "16\t176\t391.9\t0\t176\n", "17\t192\t391.9\t0\t192\n", "18\t207\t391.9\t0\t207\n", "19\t160\t391.9\t0\t160\n", "20\t168\t391.9\t0\t168\n", "21\t160\t391.9\t0\t160\n", "22\t164\t391.9\t0\t164\n", "23\t177\t391.9\t0\t177\n", "24\t150\t391.9\t0\t150\n", "25\t168\t391.9\t0\t168\n", "26\t156\t391.9\t0\t156\n", "27\t181\t391.9\t0\t181\n", "28\t171\t391.9\t0\t171\n", "29\t156\t391.9\t0\t156\n", "30\t157\t391.9\t0\t157\n", "31\t145\t391.9\t0\t145\n", "32\t176\t391.9\t0\t176\n", "33\t124\t391.9\t0\t124\n", "34\t148\t391.9\t0\t148\n", "35\t147\t391.9\t0\t147\n", "36\t148\t391.9\t0\t148\n", "37\t135\t391.9\t0\t135\n", "38\t162\t391.9\t0\t162\n", "39\t202\t391.9\t0\t202\n", "40\t188\t391.9\t0\t188\n", "41\t161\t391.9\t0\t161\n", "42\t119\t391.9\t0\t119\n", "43\t199\t391.9\t0\t199\n", "44\t115\t391.9\t0\t115\n", "45\t133\t391.9\t0\t133\n", "46\t158\t391.9\t0\t158\n", "47\t152\t391.9\t0\t152\n", "48\t120\t391.9\t0\t120\n", "49\t94\t391.9\t0\t94\n", "50\t81\t391.9\t0\t81\n", "51\t106\t391.9\t0\t106\n", "52\t122\t391.9\t0\t122\n", "53\t108\t391.9\t0\t108\n", "54\t120\t391.9\t0\t120\n", "55\t91\t391.9\t0\t91\n", "56\t90\t391.9\t0\t90\n", "57\t113\t391.9\t0\t113\n", "58\t131\t391.9\t0\t131\n", "59\t95\t391.9\t0\t95\n", "60\t133\t391.9\t0\t133\n", "61\t166\t391.9\t0\t166\n", "62\t110\t391.9\t0\t110\n", "63\t83\t391.9\t0\t83\n", "64\t110\t391.9\t0\t110\n", "65\t88\t391.9\t0\t88\n", "66\t99\t391.9\t0\t99\n", "67\t83\t391.9\t0\t83\n", "68\t64\t391.9\t0\t64\n", "69\t66\t391.9\t0\t66\n", "70\t62\t391.9\t0\t62\n", "71\t75\t391.9\t0\t75\n", "72\t94\t391.9\t0\t94\n", "73\t84\t391.9\t0\t84\n", "74\t112\t391.9\t0\t112\n", "75\t81\t391.9\t0\t81\n", "76\t113\t391.9\t0\t113\n", "77\t119\t391.9\t0\t119\n", "78\t123\t391.9\t0\t123\n", "79\t124\t391.9\t0\t124\n", "80\t120\t391.9\t0\t120\n", "81\t121\t391.9\t0\t121\n", "82\t193\t391.9\t0\t193\n", "83\t161\t391.9\t0\t161\n", "84\t95\t391.9\t0\t95\n", "85\t119\t391.9\t0\t119\n", "86\t85\t391.9\t0\t85\n", "87\t127\t391.9\t0\t127\n", "88\t130\t391.9\t0\t130\n", "89\t105\t391.9\t0\t105\n", "90\t101\t391.9\t0\t101\n", "91\t80\t391.9\t0\t80\n", "92\t51\t391.9\t0\t51\n", "93\t49\t391.9\t0\t49\n", "94\t59\t391.9\t0\t59\n", "95\t47\t391.9\t0\t47\n", "96\t51\t391.9\t0\t51\n", "97\t89\t391.9\t0\t89\n", "98\t103\t391.9\t0\t103\n", "99\t156\t391.9\t0\t156\n", "100\t132\t391.9\t0\t132\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 414_S49_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/414.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 74.35 s (13 us/read; 4.50 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,575,142\n", "Reads with adapters: 5,210,356 (93.5%)\n", "Reads written (passing filters): 4,860,031 (87.2%)\n", "\n", "Total basepairs processed: 557,514,200 bp\n", "Quality-trimmed: 2,751,738 bp (0.5%)\n", "Total written (filtered): 265,454,402 bp (47.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5111967 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 34.9%\n", " G: 43.3%\n", " T: 21.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t20919\t87111.6\t0\t20919\n", "4\t16159\t21777.9\t0\t16159\n", "5\t13126\t5444.5\t0\t13126\n", "6\t12434\t1361.1\t0\t12434\n", "7\t12632\t340.3\t0\t12632\n", "8\t13548\t85.1\t0\t13548\n", "9\t13692\t85.1\t0\t13692\n", "10\t14047\t85.1\t0\t14047\n", "11\t14740\t85.1\t0\t14740\n", "12\t15645\t85.1\t0\t15645\n", "13\t16898\t85.1\t0\t16898\n", "14\t18215\t85.1\t0\t18215\n", "15\t19354\t85.1\t0\t19354\n", "16\t21232\t85.1\t0\t21232\n", "17\t24569\t85.1\t0\t24569\n", "18\t29439\t85.1\t0\t29439\n", "19\t28145\t85.1\t0\t28145\n", "20\t24913\t85.1\t0\t24913\n", "21\t25170\t85.1\t0\t25170\n", "22\t23831\t85.1\t0\t23831\n", "23\t27667\t85.1\t0\t27667\n", "24\t33442\t85.1\t0\t33442\n", "25\t36591\t85.1\t0\t36591\n", "26\t43353\t85.1\t0\t43353\n", "27\t48316\t85.1\t0\t48316\n", "28\t44318\t85.1\t0\t44318\n", "29\t43075\t85.1\t0\t43075\n", "30\t45918\t85.1\t0\t45918\n", "31\t53014\t85.1\t0\t53014\n", "32\t55003\t85.1\t0\t55003\n", "33\t52910\t85.1\t0\t52910\n", "34\t55097\t85.1\t0\t55097\n", "35\t64796\t85.1\t0\t64796\n", "36\t77119\t85.1\t0\t77119\n", "37\t79980\t85.1\t0\t79980\n", "38\t70569\t85.1\t0\t70569\n", "39\t59730\t85.1\t0\t59730\n", "40\t60795\t85.1\t0\t60795\n", "41\t72098\t85.1\t0\t72098\n", "42\t84201\t85.1\t0\t84201\n", "43\t74597\t85.1\t0\t74597\n", "44\t62411\t85.1\t0\t62411\n", "45\t82070\t85.1\t0\t82070\n", "46\t100791\t85.1\t0\t100791\n", "47\t97788\t85.1\t0\t97788\n", "48\t99241\t85.1\t0\t99241\n", "49\t80677\t85.1\t0\t80677\n", "50\t79905\t85.1\t0\t79905\n", "51\t72209\t85.1\t0\t72209\n", "52\t83912\t85.1\t0\t83912\n", "53\t96550\t85.1\t0\t96550\n", "54\t95637\t85.1\t0\t95637\n", "55\t116301\t85.1\t0\t116301\n", "56\t122074\t85.1\t0\t122074\n", "57\t108692\t85.1\t0\t108692\n", "58\t122141\t85.1\t0\t122141\n", "59\t89620\t85.1\t0\t89620\n", "60\t77152\t85.1\t0\t77152\n", "61\t75656\t85.1\t0\t75656\n", "62\t65784\t85.1\t0\t65784\n", "63\t66597\t85.1\t0\t66597\n", "64\t79058\t85.1\t0\t79058\n", "65\t77802\t85.1\t0\t77802\n", "66\t69440\t85.1\t0\t69440\n", "67\t70696\t85.1\t0\t70696\n", "68\t71975\t85.1\t0\t71975\n", "69\t76989\t85.1\t0\t76989\n", "70\t82350\t85.1\t0\t82350\n", "71\t80428\t85.1\t0\t80428\n", "72\t65044\t85.1\t0\t65044\n", "73\t59822\t85.1\t0\t59822\n", "74\t60324\t85.1\t0\t60324\n", "75\t51645\t85.1\t0\t51645\n", "76\t42877\t85.1\t0\t42877\n", "77\t41516\t85.1\t0\t41516\n", "78\t48356\t85.1\t0\t48356\n", "79\t45850\t85.1\t0\t45850\n", "80\t45641\t85.1\t0\t45641\n", "81\t42872\t85.1\t0\t42872\n", "82\t40690\t85.1\t0\t40690\n", "83\t43875\t85.1\t0\t43875\n", "84\t50695\t85.1\t0\t50695\n", "85\t57276\t85.1\t0\t57276\n", "86\t51097\t85.1\t0\t51097\n", "87\t32909\t85.1\t0\t32909\n", "88\t29176\t85.1\t0\t29176\n", "89\t33811\t85.1\t0\t33811\n", "90\t37682\t85.1\t0\t37682\n", "91\t37463\t85.1\t0\t37463\n", "92\t38030\t85.1\t0\t38030\n", "93\t42677\t85.1\t0\t42677\n", "94\t43127\t85.1\t0\t43127\n", "95\t35807\t85.1\t0\t35807\n", "96\t25386\t85.1\t0\t25386\n", "97\t16177\t85.1\t0\t16177\n", "98\t9539\t85.1\t0\t9539\n", "99\t12274\t85.1\t0\t12274\n", "100\t5086\t85.1\t0\t5086\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 58547 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 87.1%\n", " C: 5.7%\n", " G: 0.0%\n", " T: 7.2%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t3139\t87111.6\t0\t3139\n", "4\t1581\t21777.9\t0\t1581\n", "5\t1262\t5444.5\t0\t1262\n", "6\t1145\t1361.1\t0\t1145\n", "7\t949\t340.3\t0\t949\n", "8\t701\t85.1\t0\t701\n", "9\t670\t85.1\t0\t670\n", "10\t587\t85.1\t0\t587\n", "11\t652\t85.1\t0\t652\n", "12\t537\t85.1\t0\t537\n", "13\t423\t85.1\t0\t423\n", "14\t518\t85.1\t0\t518\n", "15\t448\t85.1\t0\t448\n", "16\t461\t85.1\t0\t461\n", "17\t548\t85.1\t0\t548\n", "18\t732\t85.1\t0\t732\n", "19\t1107\t85.1\t0\t1107\n", "20\t1589\t85.1\t0\t1589\n", "21\t1118\t85.1\t0\t1118\n", "22\t788\t85.1\t0\t788\n", "23\t513\t85.1\t0\t513\n", "24\t508\t85.1\t0\t508\n", "25\t546\t85.1\t0\t546\n", "26\t1160\t85.1\t0\t1160\n", "27\t1106\t85.1\t0\t1106\n", "28\t1155\t85.1\t0\t1155\n", "29\t1616\t85.1\t0\t1616\n", "30\t2859\t85.1\t0\t2859\n", "31\t3276\t85.1\t0\t3276\n", "32\t5224\t85.1\t0\t5224\n", "33\t4481\t85.1\t0\t4481\n", "34\t4221\t85.1\t0\t4221\n", "35\t5849\t85.1\t0\t5849\n", "36\t5543\t85.1\t0\t5543\n", "37\t866\t85.1\t0\t866\n", "38\t43\t85.1\t0\t43\n", "39\t30\t85.1\t0\t30\n", "40\t18\t85.1\t0\t18\n", "41\t19\t85.1\t0\t19\n", "42\t17\t85.1\t0\t17\n", "43\t18\t85.1\t0\t18\n", "44\t17\t85.1\t0\t17\n", "45\t17\t85.1\t0\t17\n", "46\t14\t85.1\t0\t14\n", "47\t21\t85.1\t0\t21\n", "48\t20\t85.1\t0\t20\n", "49\t21\t85.1\t0\t21\n", "50\t21\t85.1\t0\t21\n", "51\t25\t85.1\t0\t25\n", "52\t22\t85.1\t0\t22\n", "53\t19\t85.1\t0\t19\n", "54\t23\t85.1\t0\t23\n", "55\t14\t85.1\t0\t14\n", "56\t7\t85.1\t0\t7\n", "57\t11\t85.1\t0\t11\n", "58\t15\t85.1\t0\t15\n", "59\t5\t85.1\t0\t5\n", "60\t13\t85.1\t0\t13\n", "61\t23\t85.1\t0\t23\n", "62\t17\t85.1\t0\t17\n", "63\t10\t85.1\t0\t10\n", "64\t11\t85.1\t0\t11\n", "65\t6\t85.1\t0\t6\n", "66\t12\t85.1\t0\t12\n", "67\t16\t85.1\t0\t16\n", "68\t5\t85.1\t0\t5\n", "69\t8\t85.1\t0\t8\n", "70\t8\t85.1\t0\t8\n", "71\t4\t85.1\t0\t4\n", "72\t6\t85.1\t0\t6\n", "73\t1\t85.1\t0\t1\n", "74\t3\t85.1\t0\t3\n", "75\t1\t85.1\t0\t1\n", "76\t1\t85.1\t0\t1\n", "77\t3\t85.1\t0\t3\n", "78\t1\t85.1\t0\t1\n", "80\t1\t85.1\t0\t1\n", "81\t1\t85.1\t0\t1\n", "83\t1\t85.1\t0\t1\n", "84\t1\t85.1\t0\t1\n", "85\t1\t85.1\t0\t1\n", "86\t2\t85.1\t0\t2\n", "87\t2\t85.1\t0\t2\n", "88\t3\t85.1\t0\t3\n", "90\t4\t85.1\t0\t4\n", "91\t2\t85.1\t0\t2\n", "92\t4\t85.1\t0\t4\n", "93\t10\t85.1\t0\t10\n", "94\t5\t85.1\t0\t5\n", "95\t13\t85.1\t0\t13\n", "96\t11\t85.1\t0\t11\n", "97\t8\t85.1\t0\t8\n", "98\t14\t85.1\t0\t14\n", "99\t13\t85.1\t0\t13\n", "100\t7\t85.1\t0\t7\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 39842 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 59.2%\n", " C: 14.7%\n", " G: 15.3%\n", " T: 10.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10491\t87111.6\t0\t10491\n", "4\t2084\t21777.9\t0\t2084\n", "5\t733\t5444.5\t0\t733\n", "6\t452\t1361.1\t0\t452\n", "7\t473\t340.3\t0\t473\n", "8\t469\t340.3\t0\t469\n", "9\t451\t340.3\t0\t451\n", "10\t460\t340.3\t0\t460\n", "11\t437\t340.3\t0\t437\n", "12\t607\t340.3\t0\t607\n", "13\t584\t340.3\t0\t584\n", "14\t647\t340.3\t0\t647\n", "15\t673\t340.3\t0\t673\n", "16\t645\t340.3\t0\t645\n", "17\t648\t340.3\t0\t648\n", "18\t630\t340.3\t0\t630\n", "19\t609\t340.3\t0\t609\n", "20\t636\t340.3\t0\t636\n", "21\t562\t340.3\t0\t562\n", "22\t613\t340.3\t0\t613\n", "23\t544\t340.3\t0\t544\n", "24\t484\t340.3\t0\t484\n", "25\t589\t340.3\t0\t589\n", "26\t505\t340.3\t0\t505\n", "27\t642\t340.3\t0\t642\n", "28\t615\t340.3\t0\t615\n", "29\t598\t340.3\t0\t598\n", "30\t547\t340.3\t0\t547\n", "31\t495\t340.3\t0\t495\n", "32\t458\t340.3\t0\t458\n", "33\t459\t340.3\t0\t459\n", "34\t433\t340.3\t0\t433\n", "35\t472\t340.3\t0\t472\n", "36\t393\t340.3\t0\t393\n", "37\t434\t340.3\t0\t434\n", "38\t423\t340.3\t0\t423\n", "39\t398\t340.3\t0\t398\n", "40\t411\t340.3\t0\t411\n", "41\t375\t340.3\t0\t375\n", "42\t299\t340.3\t0\t299\n", "43\t586\t340.3\t0\t586\n", "44\t85\t340.3\t0\t85\n", "45\t324\t340.3\t0\t324\n", "46\t288\t340.3\t0\t288\n", "47\t320\t340.3\t0\t320\n", "48\t273\t340.3\t0\t273\n", "49\t298\t340.3\t0\t298\n", "50\t297\t340.3\t0\t297\n", "51\t268\t340.3\t0\t268\n", "52\t272\t340.3\t0\t272\n", "53\t279\t340.3\t0\t279\n", "54\t211\t340.3\t0\t211\n", "55\t296\t340.3\t0\t296\n", "56\t261\t340.3\t0\t261\n", "57\t201\t340.3\t0\t201\n", "58\t247\t340.3\t0\t247\n", "59\t177\t340.3\t0\t177\n", "60\t181\t340.3\t0\t181\n", "61\t215\t340.3\t0\t215\n", "62\t194\t340.3\t0\t194\n", "63\t145\t340.3\t0\t145\n", "64\t159\t340.3\t0\t159\n", "65\t158\t340.3\t0\t158\n", "66\t172\t340.3\t0\t172\n", "67\t168\t340.3\t0\t168\n", "68\t225\t340.3\t0\t225\n", "69\t31\t340.3\t0\t31\n", "70\t33\t340.3\t0\t33\n", "71\t108\t340.3\t0\t108\n", "72\t125\t340.3\t0\t125\n", "73\t103\t340.3\t0\t103\n", "74\t89\t340.3\t0\t89\n", "75\t41\t340.3\t0\t41\n", "76\t31\t340.3\t0\t31\n", "77\t30\t340.3\t0\t30\n", "78\t17\t340.3\t0\t17\n", "79\t17\t340.3\t0\t17\n", "80\t23\t340.3\t0\t23\n", "81\t27\t340.3\t0\t27\n", "82\t27\t340.3\t0\t27\n", "83\t35\t340.3\t0\t35\n", "84\t24\t340.3\t0\t24\n", "85\t30\t340.3\t0\t30\n", "86\t18\t340.3\t0\t18\n", "87\t30\t340.3\t0\t30\n", "88\t30\t340.3\t0\t30\n", "89\t19\t340.3\t0\t19\n", "90\t25\t340.3\t0\t25\n", "91\t23\t340.3\t0\t23\n", "92\t10\t340.3\t0\t10\n", "93\t16\t340.3\t0\t16\n", "94\t12\t340.3\t0\t12\n", "95\t8\t340.3\t0\t8\n", "96\t11\t340.3\t0\t11\n", "97\t26\t340.3\t0\t26\n", "98\t13\t340.3\t0\t13\n", "99\t18\t340.3\t0\t18\n", "100\t14\t340.3\t0\t14\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 41_S62_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/41.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 105.18 s (13 us/read; 4.73 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,285,971\n", "Reads with adapters: 3,513,243 (42.4%)\n", "Reads written (passing filters): 8,171,671 (98.6%)\n", "\n", "Total basepairs processed: 828,597,100 bp\n", "Quality-trimmed: 1,631,380 bp (0.2%)\n", "Total written (filtered): 721,888,085 bp (87.1%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3264576 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 25.0%\n", " G: 37.2%\n", " T: 37.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t212566\t129468.3\t0\t212566\n", "4\t99414\t32367.1\t0\t99414\n", "5\t71463\t8091.8\t0\t71463\n", "6\t57816\t2022.9\t0\t57816\n", "7\t49721\t505.7\t0\t49721\n", "8\t48684\t126.4\t0\t48684\n", "9\t49807\t126.4\t0\t49807\n", "10\t47997\t126.4\t0\t47997\n", "11\t47180\t126.4\t0\t47180\n", "12\t47326\t126.4\t0\t47326\n", "13\t60072\t126.4\t0\t60072\n", "14\t60589\t126.4\t0\t60589\n", "15\t54216\t126.4\t0\t54216\n", "16\t57405\t126.4\t0\t57405\n", "17\t62143\t126.4\t0\t62143\n", "18\t69979\t126.4\t0\t69979\n", "19\t59024\t126.4\t0\t59024\n", "20\t47345\t126.4\t0\t47345\n", "21\t44525\t126.4\t0\t44525\n", "22\t41241\t126.4\t0\t41241\n", "23\t43495\t126.4\t0\t43495\n", "24\t50126\t126.4\t0\t50126\n", "25\t52312\t126.4\t0\t52312\n", "26\t58339\t126.4\t0\t58339\n", "27\t64884\t126.4\t0\t64884\n", "28\t61824\t126.4\t0\t61824\n", "29\t60387\t126.4\t0\t60387\n", "30\t61680\t126.4\t0\t61680\n", "31\t64357\t126.4\t0\t64357\n", "32\t59607\t126.4\t0\t59607\n", "33\t54744\t126.4\t0\t54744\n", "34\t54059\t126.4\t0\t54059\n", "35\t59126\t126.4\t0\t59126\n", "36\t67991\t126.4\t0\t67991\n", "37\t73500\t126.4\t0\t73500\n", "38\t57071\t126.4\t0\t57071\n", "39\t48046\t126.4\t0\t48046\n", "40\t43256\t126.4\t0\t43256\n", "41\t41623\t126.4\t0\t41623\n", "42\t40805\t126.4\t0\t40805\n", "43\t36871\t126.4\t0\t36871\n", "44\t30543\t126.4\t0\t30543\n", "45\t35027\t126.4\t0\t35027\n", "46\t38769\t126.4\t0\t38769\n", "47\t37241\t126.4\t0\t37241\n", "48\t36581\t126.4\t0\t36581\n", "49\t31034\t126.4\t0\t31034\n", "50\t28897\t126.4\t0\t28897\n", "51\t24980\t126.4\t0\t24980\n", "52\t25465\t126.4\t0\t25465\n", "53\t26883\t126.4\t0\t26883\n", "54\t28241\t126.4\t0\t28241\n", "55\t28175\t126.4\t0\t28175\n", "56\t26894\t126.4\t0\t26894\n", "57\t25734\t126.4\t0\t25734\n", "58\t26872\t126.4\t0\t26872\n", "59\t22174\t126.4\t0\t22174\n", "60\t19037\t126.4\t0\t19037\n", "61\t17157\t126.4\t0\t17157\n", "62\t14915\t126.4\t0\t14915\n", "63\t13783\t126.4\t0\t13783\n", "64\t14500\t126.4\t0\t14500\n", "65\t14075\t126.4\t0\t14075\n", "66\t13035\t126.4\t0\t13035\n", "67\t13482\t126.4\t0\t13482\n", "68\t13161\t126.4\t0\t13161\n", "69\t13929\t126.4\t0\t13929\n", "70\t15360\t126.4\t0\t15360\n", "71\t14916\t126.4\t0\t14916\n", "72\t11418\t126.4\t0\t11418\n", "73\t9524\t126.4\t0\t9524\n", "74\t9228\t126.4\t0\t9228\n", "75\t7763\t126.4\t0\t7763\n", "76\t6675\t126.4\t0\t6675\n", "77\t6509\t126.4\t0\t6509\n", "78\t6626\t126.4\t0\t6626\n", "79\t6487\t126.4\t0\t6487\n", "80\t6591\t126.4\t0\t6591\n", "81\t6362\t126.4\t0\t6362\n", "82\t6129\t126.4\t0\t6129\n", "83\t6550\t126.4\t0\t6550\n", "84\t6508\t126.4\t0\t6508\n", "85\t6984\t126.4\t0\t6984\n", "86\t6792\t126.4\t0\t6792\n", "87\t5649\t126.4\t0\t5649\n", "88\t5647\t126.4\t0\t5647\n", "89\t5427\t126.4\t0\t5427\n", "90\t5323\t126.4\t0\t5323\n", "91\t5383\t126.4\t0\t5383\n", "92\t5257\t126.4\t0\t5257\n", "93\t5186\t126.4\t0\t5186\n", "94\t5247\t126.4\t0\t5247\n", "95\t4592\t126.4\t0\t4592\n", "96\t3851\t126.4\t0\t3851\n", "97\t3015\t126.4\t0\t3015\n", "98\t2320\t126.4\t0\t2320\n", "99\t2145\t126.4\t0\t2145\n", "100\t1912\t126.4\t0\t1912\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 90987 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 48.5%\n", " C: 34.6%\n", " G: 0.0%\n", " T: 16.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t30359\t129468.3\t0\t30359\n", "4\t9850\t32367.1\t0\t9850\n", "5\t8303\t8091.8\t0\t8303\n", "6\t3894\t2022.9\t0\t3894\n", "7\t1010\t505.7\t0\t1010\n", "8\t872\t126.4\t0\t872\n", "9\t898\t126.4\t0\t898\n", "10\t937\t126.4\t0\t937\n", "11\t1150\t126.4\t0\t1150\n", "12\t854\t126.4\t0\t854\n", "13\t708\t126.4\t0\t708\n", "14\t664\t126.4\t0\t664\n", "15\t661\t126.4\t0\t661\n", "16\t570\t126.4\t0\t570\n", "17\t499\t126.4\t0\t499\n", "18\t640\t126.4\t0\t640\n", "19\t479\t126.4\t0\t479\n", "20\t554\t126.4\t0\t554\n", "21\t388\t126.4\t0\t388\n", "22\t374\t126.4\t0\t374\n", "23\t403\t126.4\t0\t403\n", "24\t425\t126.4\t0\t425\n", "25\t550\t126.4\t0\t550\n", "26\t972\t126.4\t0\t972\n", "27\t1043\t126.4\t0\t1043\n", "28\t961\t126.4\t0\t961\n", "29\t961\t126.4\t0\t961\n", "30\t1401\t126.4\t0\t1401\n", "31\t1499\t126.4\t0\t1499\n", "32\t2575\t126.4\t0\t2575\n", "33\t2624\t126.4\t0\t2624\n", "34\t2738\t126.4\t0\t2738\n", "35\t3579\t126.4\t0\t3579\n", "36\t3514\t126.4\t0\t3514\n", "37\t1790\t126.4\t0\t1790\n", "38\t143\t126.4\t0\t143\n", "39\t135\t126.4\t0\t135\n", "40\t34\t126.4\t0\t34\n", "41\t26\t126.4\t0\t26\n", "42\t38\t126.4\t0\t38\n", "43\t22\t126.4\t0\t22\n", "44\t12\t126.4\t0\t12\n", "45\t28\t126.4\t0\t28\n", "46\t38\t126.4\t0\t38\n", "47\t44\t126.4\t0\t44\n", "48\t22\t126.4\t0\t22\n", "49\t38\t126.4\t0\t38\n", "50\t35\t126.4\t0\t35\n", "51\t26\t126.4\t0\t26\n", "52\t48\t126.4\t0\t48\n", "53\t17\t126.4\t0\t17\n", "54\t30\t126.4\t0\t30\n", "55\t38\t126.4\t0\t38\n", "56\t18\t126.4\t0\t18\n", "57\t28\t126.4\t0\t28\n", "58\t28\t126.4\t0\t28\n", "59\t27\t126.4\t0\t27\n", "60\t40\t126.4\t0\t40\n", "61\t13\t126.4\t0\t13\n", "62\t13\t126.4\t0\t13\n", "63\t11\t126.4\t0\t11\n", "64\t12\t126.4\t0\t12\n", "65\t13\t126.4\t0\t13\n", "66\t22\t126.4\t0\t22\n", "67\t8\t126.4\t0\t8\n", "68\t8\t126.4\t0\t8\n", "69\t6\t126.4\t0\t6\n", "70\t1\t126.4\t0\t1\n", "71\t12\t126.4\t0\t12\n", "72\t13\t126.4\t0\t13\n", "73\t12\t126.4\t0\t12\n", "74\t5\t126.4\t0\t5\n", "75\t17\t126.4\t0\t17\n", "76\t8\t126.4\t0\t8\n", "77\t7\t126.4\t0\t7\n", "78\t15\t126.4\t0\t15\n", "79\t10\t126.4\t0\t10\n", "80\t1\t126.4\t0\t1\n", "81\t10\t126.4\t0\t10\n", "82\t12\t126.4\t0\t12\n", "83\t16\t126.4\t0\t16\n", "84\t14\t126.4\t0\t14\n", "85\t7\t126.4\t0\t7\n", "86\t9\t126.4\t0\t9\n", "87\t11\t126.4\t0\t11\n", "88\t25\t126.4\t0\t25\n", "89\t28\t126.4\t0\t28\n", "90\t18\t126.4\t0\t18\n", "91\t35\t126.4\t0\t35\n", "92\t53\t126.4\t0\t53\n", "93\t63\t126.4\t0\t63\n", "94\t69\t126.4\t0\t69\n", "95\t197\t126.4\t0\t197\n", "96\t173\t126.4\t0\t173\n", "97\t134\t126.4\t0\t134\n", "98\t135\t126.4\t0\t135\n", "99\t92\t126.4\t0\t92\n", "100\t65\t126.4\t0\t65\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 157680 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.2%\n", " C: 27.5%\n", " G: 9.0%\n", " T: 22.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t115348\t129468.3\t0\t115348\n", "4\t28638\t32367.1\t0\t28638\n", "5\t4107\t8091.8\t0\t4107\n", "6\t220\t2022.9\t0\t220\n", "7\t116\t505.7\t0\t116\n", "8\t106\t505.7\t0\t106\n", "9\t99\t505.7\t0\t99\n", "10\t144\t505.7\t0\t144\n", "11\t192\t505.7\t0\t192\n", "12\t240\t505.7\t0\t240\n", "13\t365\t505.7\t0\t365\n", "14\t316\t505.7\t0\t316\n", "15\t407\t505.7\t0\t407\n", "16\t329\t505.7\t0\t329\n", "17\t346\t505.7\t0\t346\n", "18\t334\t505.7\t0\t334\n", "19\t339\t505.7\t0\t339\n", "20\t311\t505.7\t0\t311\n", "21\t241\t505.7\t0\t241\n", "22\t176\t505.7\t0\t176\n", "23\t100\t505.7\t0\t100\n", "24\t82\t505.7\t0\t82\n", "25\t113\t505.7\t0\t113\n", "26\t80\t505.7\t0\t80\n", "27\t83\t505.7\t0\t83\n", "28\t92\t505.7\t0\t92\n", "29\t64\t505.7\t0\t64\n", "30\t71\t505.7\t0\t71\n", "31\t62\t505.7\t0\t62\n", "32\t69\t505.7\t0\t69\n", "33\t71\t505.7\t0\t71\n", "34\t54\t505.7\t0\t54\n", "35\t63\t505.7\t0\t63\n", "36\t62\t505.7\t0\t62\n", "37\t65\t505.7\t0\t65\n", "38\t51\t505.7\t0\t51\n", "39\t74\t505.7\t0\t74\n", "40\t96\t505.7\t0\t96\n", "41\t65\t505.7\t0\t65\n", "42\t59\t505.7\t0\t59\n", "43\t90\t505.7\t0\t90\n", "44\t52\t505.7\t0\t52\n", "45\t67\t505.7\t0\t67\n", "46\t88\t505.7\t0\t88\n", "47\t107\t505.7\t0\t107\n", "48\t69\t505.7\t0\t69\n", "49\t61\t505.7\t0\t61\n", "50\t77\t505.7\t0\t77\n", "51\t55\t505.7\t0\t55\n", "52\t60\t505.7\t0\t60\n", "53\t123\t505.7\t0\t123\n", "54\t91\t505.7\t0\t91\n", "55\t67\t505.7\t0\t67\n", "56\t78\t505.7\t0\t78\n", "57\t68\t505.7\t0\t68\n", "58\t73\t505.7\t0\t73\n", "59\t68\t505.7\t0\t68\n", "60\t59\t505.7\t0\t59\n", "61\t92\t505.7\t0\t92\n", "62\t55\t505.7\t0\t55\n", "63\t56\t505.7\t0\t56\n", "64\t30\t505.7\t0\t30\n", "65\t44\t505.7\t0\t44\n", "66\t46\t505.7\t0\t46\n", "67\t55\t505.7\t0\t55\n", "68\t57\t505.7\t0\t57\n", "69\t45\t505.7\t0\t45\n", "70\t52\t505.7\t0\t52\n", "71\t57\t505.7\t0\t57\n", "72\t47\t505.7\t0\t47\n", "73\t41\t505.7\t0\t41\n", "74\t67\t505.7\t0\t67\n", "75\t28\t505.7\t0\t28\n", "76\t45\t505.7\t0\t45\n", "77\t57\t505.7\t0\t57\n", "78\t48\t505.7\t0\t48\n", "79\t70\t505.7\t0\t70\n", "80\t57\t505.7\t0\t57\n", "81\t58\t505.7\t0\t58\n", "82\t74\t505.7\t0\t74\n", "83\t51\t505.7\t0\t51\n", "84\t52\t505.7\t0\t52\n", "85\t54\t505.7\t0\t54\n", "86\t41\t505.7\t0\t41\n", "87\t55\t505.7\t0\t55\n", "88\t60\t505.7\t0\t60\n", "89\t37\t505.7\t0\t37\n", "90\t40\t505.7\t0\t40\n", "91\t44\t505.7\t0\t44\n", "92\t36\t505.7\t0\t36\n", "93\t29\t505.7\t0\t29\n", "94\t54\t505.7\t0\t54\n", "95\t43\t505.7\t0\t43\n", "96\t58\t505.7\t0\t58\n", "97\t106\t505.7\t0\t106\n", "98\t168\t505.7\t0\t168\n", "99\t203\t505.7\t0\t203\n", "100\t165\t505.7\t0\t165\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 421_S22_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/421.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 96.11 s (13 us/read; 4.77 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,638,451\n", "Reads with adapters: 4,035,427 (52.8%)\n", "Reads written (passing filters): 7,424,325 (97.2%)\n", "\n", "Total basepairs processed: 763,845,100 bp\n", "Quality-trimmed: 1,778,900 bp (0.2%)\n", "Total written (filtered): 615,035,988 bp (80.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3808338 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.7%\n", " G: 41.7%\n", " T: 26.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t159525\t119350.8\t0\t159525\n", "4\t85107\t29837.7\t0\t85107\n", "5\t60778\t7459.4\t0\t60778\n", "6\t50474\t1864.9\t0\t50474\n", "7\t44647\t466.2\t0\t44647\n", "8\t44951\t116.6\t0\t44951\n", "9\t44270\t116.6\t0\t44270\n", "10\t43033\t116.6\t0\t43033\n", "11\t43234\t116.6\t0\t43234\n", "12\t43126\t116.6\t0\t43126\n", "13\t45465\t116.6\t0\t45465\n", "14\t47441\t116.6\t0\t47441\n", "15\t47061\t116.6\t0\t47061\n", "16\t48686\t116.6\t0\t48686\n", "17\t52172\t116.6\t0\t52172\n", "18\t60869\t116.6\t0\t60869\n", "19\t58369\t116.6\t0\t58369\n", "20\t47850\t116.6\t0\t47850\n", "21\t46091\t116.6\t0\t46091\n", "22\t41867\t116.6\t0\t41867\n", "23\t45229\t116.6\t0\t45229\n", "24\t52434\t116.6\t0\t52434\n", "25\t54712\t116.6\t0\t54712\n", "26\t62275\t116.6\t0\t62275\n", "27\t68493\t116.6\t0\t68493\n", "28\t61468\t116.6\t0\t61468\n", "29\t56540\t116.6\t0\t56540\n", "30\t58332\t116.6\t0\t58332\n", "31\t65873\t116.6\t0\t65873\n", "32\t63866\t116.6\t0\t63866\n", "33\t61121\t116.6\t0\t61121\n", "34\t58187\t116.6\t0\t58187\n", "35\t67192\t116.6\t0\t67192\n", "36\t77984\t116.6\t0\t77984\n", "37\t75532\t116.6\t0\t75532\n", "38\t62335\t116.6\t0\t62335\n", "39\t55731\t116.6\t0\t55731\n", "40\t53699\t116.6\t0\t53699\n", "41\t59298\t116.6\t0\t59298\n", "42\t66895\t116.6\t0\t66895\n", "43\t56593\t116.6\t0\t56593\n", "44\t43688\t116.6\t0\t43688\n", "45\t55329\t116.6\t0\t55329\n", "46\t64246\t116.6\t0\t64246\n", "47\t59370\t116.6\t0\t59370\n", "48\t57935\t116.6\t0\t57935\n", "49\t46079\t116.6\t0\t46079\n", "50\t45822\t116.6\t0\t45822\n", "51\t36889\t116.6\t0\t36889\n", "52\t40720\t116.6\t0\t40720\n", "53\t45671\t116.6\t0\t45671\n", "54\t51842\t116.6\t0\t51842\n", "55\t41849\t116.6\t0\t41849\n", "56\t41145\t116.6\t0\t41145\n", "57\t40976\t116.6\t0\t40976\n", "58\t46924\t116.6\t0\t46924\n", "59\t43469\t116.6\t0\t43469\n", "60\t34833\t116.6\t0\t34833\n", "61\t30920\t116.6\t0\t30920\n", "62\t25410\t116.6\t0\t25410\n", "63\t24517\t116.6\t0\t24517\n", "64\t28854\t116.6\t0\t28854\n", "65\t26459\t116.6\t0\t26459\n", "66\t21885\t116.6\t0\t21885\n", "67\t22973\t116.6\t0\t22973\n", "68\t23278\t116.6\t0\t23278\n", "69\t24755\t116.6\t0\t24755\n", "70\t27114\t116.6\t0\t27114\n", "71\t26483\t116.6\t0\t26483\n", "72\t19363\t116.6\t0\t19363\n", "73\t16281\t116.6\t0\t16281\n", "74\t15690\t116.6\t0\t15690\n", "75\t14400\t116.6\t0\t14400\n", "76\t11687\t116.6\t0\t11687\n", "77\t12504\t116.6\t0\t12504\n", "78\t15398\t116.6\t0\t15398\n", "79\t13310\t116.6\t0\t13310\n", "80\t12080\t116.6\t0\t12080\n", "81\t12063\t116.6\t0\t12063\n", "82\t11525\t116.6\t0\t11525\n", "83\t11469\t116.6\t0\t11469\n", "84\t13374\t116.6\t0\t13374\n", "85\t15551\t116.6\t0\t15551\n", "86\t14916\t116.6\t0\t14916\n", "87\t10672\t116.6\t0\t10672\n", "88\t9208\t116.6\t0\t9208\n", "89\t9943\t116.6\t0\t9943\n", "90\t10936\t116.6\t0\t10936\n", "91\t11707\t116.6\t0\t11707\n", "92\t11934\t116.6\t0\t11934\n", "93\t12784\t116.6\t0\t12784\n", "94\t11891\t116.6\t0\t11891\n", "95\t9439\t116.6\t0\t9439\n", "96\t6888\t116.6\t0\t6888\n", "97\t4444\t116.6\t0\t4444\n", "98\t2845\t116.6\t0\t2845\n", "99\t4634\t116.6\t0\t4634\n", "100\t3162\t116.6\t0\t3162\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 75394 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 52.7%\n", " C: 31.9%\n", " G: 0.0%\n", " T: 15.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t28632\t119350.8\t0\t28632\n", "4\t9213\t29837.7\t0\t9213\n", "5\t5719\t7459.4\t0\t5719\n", "6\t1511\t1864.9\t0\t1511\n", "7\t357\t466.2\t0\t357\n", "8\t291\t116.6\t0\t291\n", "9\t279\t116.6\t0\t279\n", "10\t265\t116.6\t0\t265\n", "11\t265\t116.6\t0\t265\n", "12\t212\t116.6\t0\t212\n", "13\t240\t116.6\t0\t240\n", "14\t205\t116.6\t0\t205\n", "15\t244\t116.6\t0\t244\n", "16\t258\t116.6\t0\t258\n", "17\t302\t116.6\t0\t302\n", "18\t435\t116.6\t0\t435\n", "19\t749\t116.6\t0\t749\n", "20\t992\t116.6\t0\t992\n", "21\t642\t116.6\t0\t642\n", "22\t412\t116.6\t0\t412\n", "23\t291\t116.6\t0\t291\n", "24\t331\t116.6\t0\t331\n", "25\t354\t116.6\t0\t354\n", "26\t553\t116.6\t0\t553\n", "27\t597\t116.6\t0\t597\n", "28\t673\t116.6\t0\t673\n", "29\t855\t116.6\t0\t855\n", "30\t1527\t116.6\t0\t1527\n", "31\t1767\t116.6\t0\t1767\n", "32\t2468\t116.6\t0\t2468\n", "33\t2430\t116.6\t0\t2430\n", "34\t2573\t116.6\t0\t2573\n", "35\t3440\t116.6\t0\t3440\n", "36\t3145\t116.6\t0\t3145\n", "37\t1126\t116.6\t0\t1126\n", "38\t89\t116.6\t0\t89\n", "39\t52\t116.6\t0\t52\n", "40\t55\t116.6\t0\t55\n", "41\t39\t116.6\t0\t39\n", "42\t49\t116.6\t0\t49\n", "43\t42\t116.6\t0\t42\n", "44\t69\t116.6\t0\t69\n", "45\t40\t116.6\t0\t40\n", "46\t46\t116.6\t0\t46\n", "47\t49\t116.6\t0\t49\n", "48\t57\t116.6\t0\t57\n", "49\t47\t116.6\t0\t47\n", "50\t47\t116.6\t0\t47\n", "51\t37\t116.6\t0\t37\n", "52\t43\t116.6\t0\t43\n", "53\t44\t116.6\t0\t44\n", "54\t47\t116.6\t0\t47\n", "55\t45\t116.6\t0\t45\n", "56\t38\t116.6\t0\t38\n", "57\t36\t116.6\t0\t36\n", "58\t32\t116.6\t0\t32\n", "59\t28\t116.6\t0\t28\n", "60\t19\t116.6\t0\t19\n", "61\t27\t116.6\t0\t27\n", "62\t29\t116.6\t0\t29\n", "63\t33\t116.6\t0\t33\n", "64\t26\t116.6\t0\t26\n", "65\t24\t116.6\t0\t24\n", "66\t22\t116.6\t0\t22\n", "67\t24\t116.6\t0\t24\n", "68\t11\t116.6\t0\t11\n", "69\t25\t116.6\t0\t25\n", "70\t16\t116.6\t0\t16\n", "71\t17\t116.6\t0\t17\n", "72\t23\t116.6\t0\t23\n", "73\t16\t116.6\t0\t16\n", "74\t11\t116.6\t0\t11\n", "75\t15\t116.6\t0\t15\n", "76\t18\t116.6\t0\t18\n", "77\t10\t116.6\t0\t10\n", "78\t15\t116.6\t0\t15\n", "79\t10\t116.6\t0\t10\n", "80\t20\t116.6\t0\t20\n", "81\t11\t116.6\t0\t11\n", "82\t12\t116.6\t0\t12\n", "83\t12\t116.6\t0\t12\n", "84\t14\t116.6\t0\t14\n", "85\t9\t116.6\t0\t9\n", "86\t9\t116.6\t0\t9\n", "87\t17\t116.6\t0\t17\n", "88\t9\t116.6\t0\t9\n", "89\t14\t116.6\t0\t14\n", "90\t9\t116.6\t0\t9\n", "91\t17\t116.6\t0\t17\n", "92\t20\t116.6\t0\t20\n", "93\t21\t116.6\t0\t21\n", "94\t42\t116.6\t0\t42\n", "95\t59\t116.6\t0\t59\n", "96\t56\t116.6\t0\t56\n", "97\t84\t116.6\t0\t84\n", "98\t56\t116.6\t0\t56\n", "99\t50\t116.6\t0\t50\n", "100\t78\t116.6\t0\t78\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 151695 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.1%\n", " C: 22.9%\n", " G: 18.0%\n", " T: 19.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t111974\t119350.8\t0\t111974\n", "4\t21248\t29837.7\t0\t21248\n", "5\t3750\t7459.4\t0\t3750\n", "6\t473\t1864.9\t0\t473\n", "7\t205\t466.2\t0\t205\n", "8\t243\t466.2\t0\t243\n", "9\t235\t466.2\t0\t235\n", "10\t249\t466.2\t0\t249\n", "11\t224\t466.2\t0\t224\n", "12\t249\t466.2\t0\t249\n", "13\t244\t466.2\t0\t244\n", "14\t225\t466.2\t0\t225\n", "15\t261\t466.2\t0\t261\n", "16\t216\t466.2\t0\t216\n", "17\t261\t466.2\t0\t261\n", "18\t249\t466.2\t0\t249\n", "19\t241\t466.2\t0\t241\n", "20\t227\t466.2\t0\t227\n", "21\t214\t466.2\t0\t214\n", "22\t227\t466.2\t0\t227\n", "23\t219\t466.2\t0\t219\n", "24\t173\t466.2\t0\t173\n", "25\t166\t466.2\t0\t166\n", "26\t229\t466.2\t0\t229\n", "27\t178\t466.2\t0\t178\n", "28\t190\t466.2\t0\t190\n", "29\t165\t466.2\t0\t165\n", "30\t199\t466.2\t0\t199\n", "31\t195\t466.2\t0\t195\n", "32\t234\t466.2\t0\t234\n", "33\t185\t466.2\t0\t185\n", "34\t190\t466.2\t0\t190\n", "35\t215\t466.2\t0\t215\n", "36\t204\t466.2\t0\t204\n", "37\t201\t466.2\t0\t201\n", "38\t172\t466.2\t0\t172\n", "39\t187\t466.2\t0\t187\n", "40\t196\t466.2\t0\t196\n", "41\t176\t466.2\t0\t176\n", "42\t155\t466.2\t0\t155\n", "43\t221\t466.2\t0\t221\n", "44\t94\t466.2\t0\t94\n", "45\t177\t466.2\t0\t177\n", "46\t170\t466.2\t0\t170\n", "47\t181\t466.2\t0\t181\n", "48\t129\t466.2\t0\t129\n", "49\t135\t466.2\t0\t135\n", "50\t140\t466.2\t0\t140\n", "51\t123\t466.2\t0\t123\n", "52\t140\t466.2\t0\t140\n", "53\t125\t466.2\t0\t125\n", "54\t133\t466.2\t0\t133\n", "55\t114\t466.2\t0\t114\n", "56\t122\t466.2\t0\t122\n", "57\t114\t466.2\t0\t114\n", "58\t148\t466.2\t0\t148\n", "59\t88\t466.2\t0\t88\n", "60\t160\t466.2\t0\t160\n", "61\t135\t466.2\t0\t135\n", "62\t136\t466.2\t0\t136\n", "63\t128\t466.2\t0\t128\n", "64\t130\t466.2\t0\t130\n", "65\t86\t466.2\t0\t86\n", "66\t113\t466.2\t0\t113\n", "67\t112\t466.2\t0\t112\n", "68\t117\t466.2\t0\t117\n", "69\t76\t466.2\t0\t76\n", "70\t63\t466.2\t0\t63\n", "71\t107\t466.2\t0\t107\n", "72\t113\t466.2\t0\t113\n", "73\t95\t466.2\t0\t95\n", "74\t101\t466.2\t0\t101\n", "75\t100\t466.2\t0\t100\n", "76\t124\t466.2\t0\t124\n", "77\t121\t466.2\t0\t121\n", "78\t146\t466.2\t0\t146\n", "79\t115\t466.2\t0\t115\n", "80\t88\t466.2\t0\t88\n", "81\t98\t466.2\t0\t98\n", "82\t116\t466.2\t0\t116\n", "83\t113\t466.2\t0\t113\n", "84\t114\t466.2\t0\t114\n", "85\t131\t466.2\t0\t131\n", "86\t119\t466.2\t0\t119\n", "87\t115\t466.2\t0\t115\n", "88\t142\t466.2\t0\t142\n", "89\t124\t466.2\t0\t124\n", "90\t98\t466.2\t0\t98\n", "91\t50\t466.2\t0\t50\n", "92\t70\t466.2\t0\t70\n", "93\t68\t466.2\t0\t68\n", "94\t65\t466.2\t0\t65\n", "95\t53\t466.2\t0\t53\n", "96\t62\t466.2\t0\t62\n", "97\t69\t466.2\t0\t69\n", "98\t90\t466.2\t0\t90\n", "99\t124\t466.2\t0\t124\n", "100\t110\t466.2\t0\t110\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 431b_S8_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/431b.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 75.32 s (12 us/read; 5.08 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,371,191\n", "Reads with adapters: 3,245,799 (50.9%)\n", "Reads written (passing filters): 6,226,370 (97.7%)\n", "\n", "Total basepairs processed: 637,119,100 bp\n", "Quality-trimmed: 1,395,866 bp (0.2%)\n", "Total written (filtered): 524,353,071 bp (82.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3063158 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.7%\n", " G: 39.5%\n", " T: 31.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t145438\t99549.9\t0\t145438\n", "4\t79322\t24887.5\t0\t79322\n", "5\t56058\t6221.9\t0\t56058\n", "6\t45322\t1555.5\t0\t45322\n", "7\t37842\t388.9\t0\t37842\n", "8\t35090\t97.2\t0\t35090\n", "9\t34843\t97.2\t0\t34843\n", "10\t34339\t97.2\t0\t34339\n", "11\t34873\t97.2\t0\t34873\n", "12\t36064\t97.2\t0\t36064\n", "13\t45058\t97.2\t0\t45058\n", "14\t45215\t97.2\t0\t45215\n", "15\t39997\t97.2\t0\t39997\n", "16\t41006\t97.2\t0\t41006\n", "17\t44932\t97.2\t0\t44932\n", "18\t51915\t97.2\t0\t51915\n", "19\t47106\t97.2\t0\t47106\n", "20\t40307\t97.2\t0\t40307\n", "21\t39216\t97.2\t0\t39216\n", "22\t36054\t97.2\t0\t36054\n", "23\t37435\t97.2\t0\t37435\n", "24\t44136\t97.2\t0\t44136\n", "25\t45879\t97.2\t0\t45879\n", "26\t51907\t97.2\t0\t51907\n", "27\t57574\t97.2\t0\t57574\n", "28\t54501\t97.2\t0\t54501\n", "29\t51518\t97.2\t0\t51518\n", "30\t52395\t97.2\t0\t52395\n", "31\t55886\t97.2\t0\t55886\n", "32\t53755\t97.2\t0\t53755\n", "33\t50127\t97.2\t0\t50127\n", "34\t49766\t97.2\t0\t49766\n", "35\t55708\t97.2\t0\t55708\n", "36\t67466\t97.2\t0\t67466\n", "37\t75039\t97.2\t0\t75039\n", "38\t56578\t97.2\t0\t56578\n", "39\t45037\t97.2\t0\t45037\n", "40\t43262\t97.2\t0\t43262\n", "41\t45001\t97.2\t0\t45001\n", "42\t50123\t97.2\t0\t50123\n", "43\t42974\t97.2\t0\t42974\n", "44\t35588\t97.2\t0\t35588\n", "45\t42147\t97.2\t0\t42147\n", "46\t48896\t97.2\t0\t48896\n", "47\t45755\t97.2\t0\t45755\n", "48\t44582\t97.2\t0\t44582\n", "49\t38320\t97.2\t0\t38320\n", "50\t35312\t97.2\t0\t35312\n", "51\t30052\t97.2\t0\t30052\n", "52\t30067\t97.2\t0\t30067\n", "53\t31702\t97.2\t0\t31702\n", "54\t35275\t97.2\t0\t35275\n", "55\t37000\t97.2\t0\t37000\n", "56\t33470\t97.2\t0\t33470\n", "57\t31388\t97.2\t0\t31388\n", "58\t36580\t97.2\t0\t36580\n", "59\t29480\t97.2\t0\t29480\n", "60\t24753\t97.2\t0\t24753\n", "61\t21366\t97.2\t0\t21366\n", "62\t17291\t97.2\t0\t17291\n", "63\t16128\t97.2\t0\t16128\n", "64\t17212\t97.2\t0\t17212\n", "65\t16988\t97.2\t0\t16988\n", "66\t15727\t97.2\t0\t15727\n", "67\t15572\t97.2\t0\t15572\n", "68\t15120\t97.2\t0\t15120\n", "69\t15402\t97.2\t0\t15402\n", "70\t16361\t97.2\t0\t16361\n", "71\t15360\t97.2\t0\t15360\n", "72\t12278\t97.2\t0\t12278\n", "73\t10794\t97.2\t0\t10794\n", "74\t10432\t97.2\t0\t10432\n", "75\t9096\t97.2\t0\t9096\n", "76\t7913\t97.2\t0\t7913\n", "77\t7147\t97.2\t0\t7147\n", "78\t7764\t97.2\t0\t7764\n", "79\t7558\t97.2\t0\t7558\n", "80\t7577\t97.2\t0\t7577\n", "81\t7450\t97.2\t0\t7450\n", "82\t6872\t97.2\t0\t6872\n", "83\t7737\t97.2\t0\t7737\n", "84\t8484\t97.2\t0\t8484\n", "85\t9572\t97.2\t0\t9572\n", "86\t9219\t97.2\t0\t9219\n", "87\t7276\t97.2\t0\t7276\n", "88\t7128\t97.2\t0\t7128\n", "89\t7071\t97.2\t0\t7071\n", "90\t7594\t97.2\t0\t7594\n", "91\t7991\t97.2\t0\t7991\n", "92\t8477\t97.2\t0\t8477\n", "93\t8752\t97.2\t0\t8752\n", "94\t8436\t97.2\t0\t8436\n", "95\t7259\t97.2\t0\t7259\n", "96\t5392\t97.2\t0\t5392\n", "97\t3634\t97.2\t0\t3634\n", "98\t2180\t97.2\t0\t2180\n", "99\t1779\t97.2\t0\t1779\n", "100\t1338\t97.2\t0\t1338\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 55102 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 47.8%\n", " C: 33.6%\n", " G: 0.0%\n", " T: 18.5%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t20583\t99549.9\t0\t20583\n", "4\t6621\t24887.5\t0\t6621\n", "5\t4815\t6221.9\t0\t4815\n", "6\t4548\t1555.5\t0\t4548\n", "7\t1192\t388.9\t0\t1192\n", "8\t743\t97.2\t0\t743\n", "9\t662\t97.2\t0\t662\n", "10\t629\t97.2\t0\t629\n", "11\t730\t97.2\t0\t730\n", "12\t558\t97.2\t0\t558\n", "13\t471\t97.2\t0\t471\n", "14\t477\t97.2\t0\t477\n", "15\t380\t97.2\t0\t380\n", "16\t385\t97.2\t0\t385\n", "17\t393\t97.2\t0\t393\n", "18\t483\t97.2\t0\t483\n", "19\t410\t97.2\t0\t410\n", "20\t495\t97.2\t0\t495\n", "21\t326\t97.2\t0\t326\n", "22\t301\t97.2\t0\t301\n", "23\t284\t97.2\t0\t284\n", "24\t355\t97.2\t0\t355\n", "25\t329\t97.2\t0\t329\n", "26\t674\t97.2\t0\t674\n", "27\t633\t97.2\t0\t633\n", "28\t511\t97.2\t0\t511\n", "29\t474\t97.2\t0\t474\n", "30\t576\t97.2\t0\t576\n", "31\t540\t97.2\t0\t540\n", "32\t745\t97.2\t0\t745\n", "33\t653\t97.2\t0\t653\n", "34\t627\t97.2\t0\t627\n", "35\t659\t97.2\t0\t659\n", "36\t679\t97.2\t0\t679\n", "37\t257\t97.2\t0\t257\n", "38\t39\t97.2\t0\t39\n", "39\t27\t97.2\t0\t27\n", "40\t27\t97.2\t0\t27\n", "41\t15\t97.2\t0\t15\n", "42\t24\t97.2\t0\t24\n", "43\t19\t97.2\t0\t19\n", "44\t23\t97.2\t0\t23\n", "45\t18\t97.2\t0\t18\n", "46\t24\t97.2\t0\t24\n", "47\t29\t97.2\t0\t29\n", "48\t24\t97.2\t0\t24\n", "49\t28\t97.2\t0\t28\n", "50\t24\t97.2\t0\t24\n", "51\t21\t97.2\t0\t21\n", "52\t20\t97.2\t0\t20\n", "53\t22\t97.2\t0\t22\n", "54\t22\t97.2\t0\t22\n", "55\t11\t97.2\t0\t11\n", "56\t19\t97.2\t0\t19\n", "57\t24\t97.2\t0\t24\n", "58\t21\t97.2\t0\t21\n", "59\t16\t97.2\t0\t16\n", "60\t10\t97.2\t0\t10\n", "61\t12\t97.2\t0\t12\n", "62\t8\t97.2\t0\t8\n", "63\t8\t97.2\t0\t8\n", "64\t14\t97.2\t0\t14\n", "65\t23\t97.2\t0\t23\n", "66\t15\t97.2\t0\t15\n", "67\t15\t97.2\t0\t15\n", "68\t12\t97.2\t0\t12\n", "69\t10\t97.2\t0\t10\n", "70\t17\t97.2\t0\t17\n", "71\t9\t97.2\t0\t9\n", "72\t8\t97.2\t0\t8\n", "73\t11\t97.2\t0\t11\n", "74\t5\t97.2\t0\t5\n", "75\t12\t97.2\t0\t12\n", "76\t12\t97.2\t0\t12\n", "77\t8\t97.2\t0\t8\n", "78\t8\t97.2\t0\t8\n", "79\t5\t97.2\t0\t5\n", "80\t7\t97.2\t0\t7\n", "81\t16\t97.2\t0\t16\n", "82\t7\t97.2\t0\t7\n", "83\t13\t97.2\t0\t13\n", "84\t9\t97.2\t0\t9\n", "85\t26\t97.2\t0\t26\n", "86\t12\t97.2\t0\t12\n", "87\t17\t97.2\t0\t17\n", "88\t13\t97.2\t0\t13\n", "89\t9\t97.2\t0\t9\n", "90\t13\t97.2\t0\t13\n", "91\t26\t97.2\t0\t26\n", "92\t36\t97.2\t0\t36\n", "93\t68\t97.2\t0\t68\n", "94\t121\t97.2\t0\t121\n", "95\t199\t97.2\t0\t199\n", "96\t163\t97.2\t0\t163\n", "97\t138\t97.2\t0\t138\n", "98\t115\t97.2\t0\t115\n", "99\t66\t97.2\t0\t66\n", "100\t111\t97.2\t0\t111\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 127539 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.6%\n", " C: 22.0%\n", " G: 16.0%\n", " T: 17.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t86429\t99549.9\t0\t86429\n", "4\t16139\t24887.5\t0\t16139\n", "5\t3081\t6221.9\t0\t3081\n", "6\t689\t1555.5\t0\t689\n", "7\t511\t388.9\t0\t511\n", "8\t578\t388.9\t0\t578\n", "9\t528\t388.9\t0\t528\n", "10\t556\t388.9\t0\t556\n", "11\t538\t388.9\t0\t538\n", "12\t563\t388.9\t0\t563\n", "13\t600\t388.9\t0\t600\n", "14\t539\t388.9\t0\t539\n", "15\t591\t388.9\t0\t591\n", "16\t546\t388.9\t0\t546\n", "17\t508\t388.9\t0\t508\n", "18\t534\t388.9\t0\t534\n", "19\t495\t388.9\t0\t495\n", "20\t483\t388.9\t0\t483\n", "21\t473\t388.9\t0\t473\n", "22\t510\t388.9\t0\t510\n", "23\t376\t388.9\t0\t376\n", "24\t393\t388.9\t0\t393\n", "25\t374\t388.9\t0\t374\n", "26\t375\t388.9\t0\t375\n", "27\t408\t388.9\t0\t408\n", "28\t391\t388.9\t0\t391\n", "29\t348\t388.9\t0\t348\n", "30\t349\t388.9\t0\t349\n", "31\t309\t388.9\t0\t309\n", "32\t372\t388.9\t0\t372\n", "33\t251\t388.9\t0\t251\n", "34\t308\t388.9\t0\t308\n", "35\t297\t388.9\t0\t297\n", "36\t258\t388.9\t0\t258\n", "37\t210\t388.9\t0\t210\n", "38\t236\t388.9\t0\t236\n", "39\t249\t388.9\t0\t249\n", "40\t208\t388.9\t0\t208\n", "41\t202\t388.9\t0\t202\n", "42\t173\t388.9\t0\t173\n", "43\t295\t388.9\t0\t295\n", "44\t83\t388.9\t0\t83\n", "45\t183\t388.9\t0\t183\n", "46\t163\t388.9\t0\t163\n", "47\t213\t388.9\t0\t213\n", "48\t169\t388.9\t0\t169\n", "49\t169\t388.9\t0\t169\n", "50\t174\t388.9\t0\t174\n", "51\t147\t388.9\t0\t147\n", "52\t157\t388.9\t0\t157\n", "53\t146\t388.9\t0\t146\n", "54\t136\t388.9\t0\t136\n", "55\t157\t388.9\t0\t157\n", "56\t176\t388.9\t0\t176\n", "57\t124\t388.9\t0\t124\n", "58\t140\t388.9\t0\t140\n", "59\t107\t388.9\t0\t107\n", "60\t112\t388.9\t0\t112\n", "61\t152\t388.9\t0\t152\n", "62\t146\t388.9\t0\t146\n", "63\t90\t388.9\t0\t90\n", "64\t116\t388.9\t0\t116\n", "65\t98\t388.9\t0\t98\n", "66\t116\t388.9\t0\t116\n", "67\t101\t388.9\t0\t101\n", "68\t113\t388.9\t0\t113\n", "69\t61\t388.9\t0\t61\n", "70\t55\t388.9\t0\t55\n", "71\t95\t388.9\t0\t95\n", "72\t107\t388.9\t0\t107\n", "73\t115\t388.9\t0\t115\n", "74\t112\t388.9\t0\t112\n", "75\t89\t388.9\t0\t89\n", "76\t82\t388.9\t0\t82\n", "77\t83\t388.9\t0\t83\n", "78\t81\t388.9\t0\t81\n", "79\t102\t388.9\t0\t102\n", "80\t83\t388.9\t0\t83\n", "81\t99\t388.9\t0\t99\n", "82\t129\t388.9\t0\t129\n", "83\t110\t388.9\t0\t110\n", "84\t94\t388.9\t0\t94\n", "85\t101\t388.9\t0\t101\n", "86\t83\t388.9\t0\t83\n", "87\t81\t388.9\t0\t81\n", "88\t113\t388.9\t0\t113\n", "89\t75\t388.9\t0\t75\n", "90\t72\t388.9\t0\t72\n", "91\t58\t388.9\t0\t58\n", "92\t44\t388.9\t0\t44\n", "93\t42\t388.9\t0\t42\n", "94\t55\t388.9\t0\t55\n", "95\t60\t388.9\t0\t60\n", "96\t67\t388.9\t0\t67\n", "97\t73\t388.9\t0\t73\n", "98\t100\t388.9\t0\t100\n", "99\t142\t388.9\t0\t142\n", "100\t115\t388.9\t0\t115\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 432_S75_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/432.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 64.85 s (11 us/read; 5.58 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,031,981\n", "Reads with adapters: 1,787,621 (29.6%)\n", "Reads written (passing filters): 5,883,347 (97.5%)\n", "\n", "Total basepairs processed: 603,198,100 bp\n", "Quality-trimmed: 943,141 bp (0.2%)\n", "Total written (filtered): 537,207,432 bp (89.1%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 1520330 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 16.0%\n", " G: 64.9%\n", " T: 19.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t121122\t94249.7\t0\t121122\n", "4\t44664\t23562.4\t0\t44664\n", "5\t21015\t5890.6\t0\t21015\n", "6\t14143\t1472.7\t0\t14143\n", "7\t10573\t368.2\t0\t10573\n", "8\t11715\t92.0\t0\t11715\n", "9\t13181\t92.0\t0\t13181\n", "10\t18960\t92.0\t0\t18960\n", "11\t20912\t92.0\t0\t20912\n", "12\t26896\t92.0\t0\t26896\n", "13\t66395\t92.0\t0\t66395\n", "14\t66578\t92.0\t0\t66578\n", "15\t39282\t92.0\t0\t39282\n", "16\t41913\t92.0\t0\t41913\n", "17\t37851\t92.0\t0\t37851\n", "18\t47604\t92.0\t0\t47604\n", "19\t23349\t92.0\t0\t23349\n", "20\t11963\t92.0\t0\t11963\n", "21\t9514\t92.0\t0\t9514\n", "22\t10495\t92.0\t0\t10495\n", "23\t8122\t92.0\t0\t8122\n", "24\t9395\t92.0\t0\t9395\n", "25\t10225\t92.0\t0\t10225\n", "26\t11211\t92.0\t0\t11211\n", "27\t13429\t92.0\t0\t13429\n", "28\t12967\t92.0\t0\t12967\n", "29\t13594\t92.0\t0\t13594\n", "30\t14496\t92.0\t0\t14496\n", "31\t14564\t92.0\t0\t14564\n", "32\t11998\t92.0\t0\t11998\n", "33\t10008\t92.0\t0\t10008\n", "34\t9318\t92.0\t0\t9318\n", "35\t11487\t92.0\t0\t11487\n", "36\t13938\t92.0\t0\t13938\n", "37\t17495\t92.0\t0\t17495\n", "38\t12026\t92.0\t0\t12026\n", "39\t9097\t92.0\t0\t9097\n", "40\t8457\t92.0\t0\t8457\n", "41\t8027\t92.0\t0\t8027\n", "42\t8313\t92.0\t0\t8313\n", "43\t7721\t92.0\t0\t7721\n", "44\t6319\t92.0\t0\t6319\n", "45\t7331\t92.0\t0\t7331\n", "46\t8831\t92.0\t0\t8831\n", "47\t8938\t92.0\t0\t8938\n", "48\t10459\t92.0\t0\t10459\n", "49\t8343\t92.0\t0\t8343\n", "50\t6996\t92.0\t0\t6996\n", "51\t5545\t92.0\t0\t5545\n", "52\t5428\t92.0\t0\t5428\n", "53\t6923\t92.0\t0\t6923\n", "54\t9274\t92.0\t0\t9274\n", "55\t8916\t92.0\t0\t8916\n", "56\t8669\t92.0\t0\t8669\n", "57\t8639\t92.0\t0\t8639\n", "58\t10730\t92.0\t0\t10730\n", "59\t8180\t92.0\t0\t8180\n", "60\t7765\t92.0\t0\t7765\n", "61\t8050\t92.0\t0\t8050\n", "62\t7889\t92.0\t0\t7889\n", "63\t8589\t92.0\t0\t8589\n", "64\t9461\t92.0\t0\t9461\n", "65\t11439\t92.0\t0\t11439\n", "66\t13489\t92.0\t0\t13489\n", "67\t17768\t92.0\t0\t17768\n", "68\t23216\t92.0\t0\t23216\n", "69\t31880\t92.0\t0\t31880\n", "70\t45875\t92.0\t0\t45875\n", "71\t49052\t92.0\t0\t49052\n", "72\t28427\t92.0\t0\t28427\n", "73\t20122\t92.0\t0\t20122\n", "74\t18237\t92.0\t0\t18237\n", "75\t13918\t92.0\t0\t13918\n", "76\t11358\t92.0\t0\t11358\n", "77\t10993\t92.0\t0\t10993\n", "78\t10403\t92.0\t0\t10403\n", "79\t9492\t92.0\t0\t9492\n", "80\t8108\t92.0\t0\t8108\n", "81\t7827\t92.0\t0\t7827\n", "82\t6597\t92.0\t0\t6597\n", "83\t6721\t92.0\t0\t6721\n", "84\t8659\t92.0\t0\t8659\n", "85\t9689\t92.0\t0\t9689\n", "86\t9600\t92.0\t0\t9600\n", "87\t6940\t92.0\t0\t6940\n", "88\t6896\t92.0\t0\t6896\n", "89\t6324\t92.0\t0\t6324\n", "90\t7118\t92.0\t0\t7118\n", "91\t7342\t92.0\t0\t7342\n", "92\t8485\t92.0\t0\t8485\n", "93\t7458\t92.0\t0\t7458\n", "94\t7403\t92.0\t0\t7403\n", "95\t7237\t92.0\t0\t7237\n", "96\t5523\t92.0\t0\t5523\n", "97\t3833\t92.0\t0\t3833\n", "98\t2724\t92.0\t0\t2724\n", "99\t3005\t92.0\t0\t3005\n", "100\t1884\t92.0\t0\t1884\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 151355 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 66.4%\n", " C: 24.3%\n", " G: 0.0%\n", " T: 9.2%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t28846\t94249.7\t0\t28846\n", "4\t9362\t23562.4\t0\t9362\n", "5\t7772\t5890.6\t0\t7772\n", "6\t4648\t1472.7\t0\t4648\n", "7\t2269\t368.2\t0\t2269\n", "8\t1936\t92.0\t0\t1936\n", "9\t2286\t92.0\t0\t2286\n", "10\t2554\t92.0\t0\t2554\n", "11\t3622\t92.0\t0\t3622\n", "12\t2295\t92.0\t0\t2295\n", "13\t1952\t92.0\t0\t1952\n", "14\t1692\t92.0\t0\t1692\n", "15\t1437\t92.0\t0\t1437\n", "16\t1638\t92.0\t0\t1638\n", "17\t1420\t92.0\t0\t1420\n", "18\t2048\t92.0\t0\t2048\n", "19\t1261\t92.0\t0\t1261\n", "20\t1499\t92.0\t0\t1499\n", "21\t1190\t92.0\t0\t1190\n", "22\t1091\t92.0\t0\t1091\n", "23\t1001\t92.0\t0\t1001\n", "24\t1246\t92.0\t0\t1246\n", "25\t1508\t92.0\t0\t1508\n", "26\t3638\t92.0\t0\t3638\n", "27\t4521\t92.0\t0\t4521\n", "28\t4177\t92.0\t0\t4177\n", "29\t3476\t92.0\t0\t3476\n", "30\t4577\t92.0\t0\t4577\n", "31\t4179\t92.0\t0\t4179\n", "32\t6215\t92.0\t0\t6215\n", "33\t5482\t92.0\t0\t5482\n", "34\t5219\t92.0\t0\t5219\n", "35\t6432\t92.0\t0\t6432\n", "36\t7168\t92.0\t0\t7168\n", "37\t3458\t92.0\t0\t3458\n", "38\t214\t92.0\t0\t214\n", "39\t134\t92.0\t0\t134\n", "40\t12\t92.0\t0\t12\n", "41\t16\t92.0\t0\t16\n", "42\t11\t92.0\t0\t11\n", "43\t5\t92.0\t0\t5\n", "44\t8\t92.0\t0\t8\n", "45\t11\t92.0\t0\t11\n", "46\t14\t92.0\t0\t14\n", "47\t12\t92.0\t0\t12\n", "48\t9\t92.0\t0\t9\n", "49\t7\t92.0\t0\t7\n", "50\t16\t92.0\t0\t16\n", "51\t6\t92.0\t0\t6\n", "52\t5\t92.0\t0\t5\n", "53\t4\t92.0\t0\t4\n", "54\t8\t92.0\t0\t8\n", "55\t2\t92.0\t0\t2\n", "56\t18\t92.0\t0\t18\n", "57\t10\t92.0\t0\t10\n", "58\t2\t92.0\t0\t2\n", "59\t9\t92.0\t0\t9\n", "60\t3\t92.0\t0\t3\n", "61\t6\t92.0\t0\t6\n", "62\t5\t92.0\t0\t5\n", "63\t8\t92.0\t0\t8\n", "64\t7\t92.0\t0\t7\n", "65\t30\t92.0\t0\t30\n", "66\t29\t92.0\t0\t29\n", "67\t2\t92.0\t0\t2\n", "68\t1\t92.0\t0\t1\n", "69\t2\t92.0\t0\t2\n", "70\t1\t92.0\t0\t1\n", "71\t1\t92.0\t0\t1\n", "72\t2\t92.0\t0\t2\n", "73\t17\t92.0\t0\t17\n", "74\t1\t92.0\t0\t1\n", "76\t19\t92.0\t0\t19\n", "82\t1\t92.0\t0\t1\n", "84\t4\t92.0\t0\t4\n", "85\t24\t92.0\t0\t24\n", "86\t1\t92.0\t0\t1\n", "87\t3\t92.0\t0\t3\n", "88\t29\t92.0\t0\t29\n", "89\t9\t92.0\t0\t9\n", "90\t12\t92.0\t0\t12\n", "91\t53\t92.0\t0\t53\n", "92\t55\t92.0\t0\t55\n", "93\t96\t92.0\t0\t96\n", "94\t199\t92.0\t0\t199\n", "95\t1400\t92.0\t0\t1400\n", "96\t1198\t92.0\t0\t1198\n", "97\t1281\t92.0\t0\t1281\n", "98\t1301\t92.0\t0\t1301\n", "99\t1174\t92.0\t0\t1174\n", "100\t733\t92.0\t0\t733\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 115936 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.9%\n", " C: 25.8%\n", " G: 11.2%\n", " T: 21.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t89202\t94249.7\t0\t89202\n", "4\t11748\t23562.4\t0\t11748\n", "5\t1456\t5890.6\t0\t1456\n", "6\t146\t1472.7\t0\t146\n", "7\t136\t368.2\t0\t136\n", "8\t77\t368.2\t0\t77\n", "9\t85\t368.2\t0\t85\n", "10\t114\t368.2\t0\t114\n", "11\t153\t368.2\t0\t153\n", "12\t282\t368.2\t0\t282\n", "13\t109\t368.2\t0\t109\n", "14\t191\t368.2\t0\t191\n", "15\t238\t368.2\t0\t238\n", "16\t91\t368.2\t0\t91\n", "17\t132\t368.2\t0\t132\n", "18\t93\t368.2\t0\t93\n", "19\t45\t368.2\t0\t45\n", "20\t224\t368.2\t0\t224\n", "21\t73\t368.2\t0\t73\n", "22\t134\t368.2\t0\t134\n", "23\t189\t368.2\t0\t189\n", "24\t117\t368.2\t0\t117\n", "25\t179\t368.2\t0\t179\n", "26\t97\t368.2\t0\t97\n", "27\t162\t368.2\t0\t162\n", "28\t240\t368.2\t0\t240\n", "29\t148\t368.2\t0\t148\n", "30\t55\t368.2\t0\t55\n", "31\t142\t368.2\t0\t142\n", "32\t170\t368.2\t0\t170\n", "33\t95\t368.2\t0\t95\n", "34\t199\t368.2\t0\t199\n", "35\t36\t368.2\t0\t36\n", "36\t89\t368.2\t0\t89\n", "37\t34\t368.2\t0\t34\n", "38\t45\t368.2\t0\t45\n", "39\t74\t368.2\t0\t74\n", "40\t70\t368.2\t0\t70\n", "41\t65\t368.2\t0\t65\n", "42\t35\t368.2\t0\t35\n", "43\t69\t368.2\t0\t69\n", "44\t33\t368.2\t0\t33\n", "45\t129\t368.2\t0\t129\n", "46\t137\t368.2\t0\t137\n", "47\t126\t368.2\t0\t126\n", "48\t133\t368.2\t0\t133\n", "49\t143\t368.2\t0\t143\n", "50\t236\t368.2\t0\t236\n", "51\t297\t368.2\t0\t297\n", "52\t309\t368.2\t0\t309\n", "53\t414\t368.2\t0\t414\n", "54\t471\t368.2\t0\t471\n", "55\t694\t368.2\t0\t694\n", "56\t679\t368.2\t0\t679\n", "57\t619\t368.2\t0\t619\n", "58\t559\t368.2\t0\t559\n", "59\t411\t368.2\t0\t411\n", "60\t478\t368.2\t0\t478\n", "61\t337\t368.2\t0\t337\n", "62\t286\t368.2\t0\t286\n", "63\t234\t368.2\t0\t234\n", "64\t161\t368.2\t0\t161\n", "65\t104\t368.2\t0\t104\n", "66\t139\t368.2\t0\t139\n", "67\t121\t368.2\t0\t121\n", "68\t84\t368.2\t0\t84\n", "69\t46\t368.2\t0\t46\n", "70\t15\t368.2\t0\t15\n", "71\t57\t368.2\t0\t57\n", "72\t90\t368.2\t0\t90\n", "73\t37\t368.2\t0\t37\n", "74\t166\t368.2\t0\t166\n", "75\t43\t368.2\t0\t43\n", "76\t51\t368.2\t0\t51\n", "77\t9\t368.2\t0\t9\n", "78\t1\t368.2\t0\t1\n", "79\t82\t368.2\t0\t82\n", "80\t53\t368.2\t0\t53\n", "81\t16\t368.2\t0\t16\n", "82\t39\t368.2\t0\t39\n", "83\t71\t368.2\t0\t71\n", "84\t42\t368.2\t0\t42\n", "85\t77\t368.2\t0\t77\n", "86\t54\t368.2\t0\t54\n", "87\t18\t368.2\t0\t18\n", "88\t10\t368.2\t0\t10\n", "89\t43\t368.2\t0\t43\n", "90\t1\t368.2\t0\t1\n", "91\t1\t368.2\t0\t1\n", "92\t57\t368.2\t0\t57\n", "93\t1\t368.2\t0\t1\n", "94\t18\t368.2\t0\t18\n", "95\t38\t368.2\t0\t38\n", "96\t68\t368.2\t0\t68\n", "97\t49\t368.2\t0\t49\n", "98\t102\t368.2\t0\t102\n", "99\t167\t368.2\t0\t167\n", "100\t41\t368.2\t0\t41\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 434_S55_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/434.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 84.00 s (12 us/read; 5.06 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,085,710\n", "Reads with adapters: 4,143,590 (58.5%)\n", "Reads written (passing filters): 6,970,399 (98.4%)\n", "\n", "Total basepairs processed: 708,571,000 bp\n", "Quality-trimmed: 1,608,863 bp (0.2%)\n", "Total written (filtered): 571,273,756 bp (80.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4027349 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 25.3%\n", " G: 34.0%\n", " T: 40.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t175454\t110714.2\t0\t175454\n", "4\t106059\t27678.6\t0\t106059\n", "5\t81558\t6919.6\t0\t81558\n", "6\t63017\t1729.9\t0\t63017\n", "7\t54482\t432.5\t0\t54482\n", "8\t52462\t108.1\t0\t52462\n", "9\t51230\t108.1\t0\t51230\n", "10\t46510\t108.1\t0\t46510\n", "11\t47642\t108.1\t0\t47642\n", "12\t48121\t108.1\t0\t48121\n", "13\t49371\t108.1\t0\t49371\n", "14\t51641\t108.1\t0\t51641\n", "15\t51894\t108.1\t0\t51894\n", "16\t53280\t108.1\t0\t53280\n", "17\t60279\t108.1\t0\t60279\n", "18\t71878\t108.1\t0\t71878\n", "19\t68331\t108.1\t0\t68331\n", "20\t59253\t108.1\t0\t59253\n", "21\t58118\t108.1\t0\t58118\n", "22\t51241\t108.1\t0\t51241\n", "23\t56718\t108.1\t0\t56718\n", "24\t68994\t108.1\t0\t68994\n", "25\t69551\t108.1\t0\t69551\n", "26\t78851\t108.1\t0\t78851\n", "27\t91418\t108.1\t0\t91418\n", "28\t85562\t108.1\t0\t85562\n", "29\t79720\t108.1\t0\t79720\n", "30\t81993\t108.1\t0\t81993\n", "31\t85766\t108.1\t0\t85766\n", "32\t81980\t108.1\t0\t81980\n", "33\t70003\t108.1\t0\t70003\n", "34\t67822\t108.1\t0\t67822\n", "35\t78054\t108.1\t0\t78054\n", "36\t99302\t108.1\t0\t99302\n", "37\t116764\t108.1\t0\t116764\n", "38\t84824\t108.1\t0\t84824\n", "39\t60159\t108.1\t0\t60159\n", "40\t54367\t108.1\t0\t54367\n", "41\t53848\t108.1\t0\t53848\n", "42\t58483\t108.1\t0\t58483\n", "43\t50758\t108.1\t0\t50758\n", "44\t42535\t108.1\t0\t42535\n", "45\t53069\t108.1\t0\t53069\n", "46\t65114\t108.1\t0\t65114\n", "47\t61390\t108.1\t0\t61390\n", "48\t68194\t108.1\t0\t68194\n", "49\t54700\t108.1\t0\t54700\n", "50\t46209\t108.1\t0\t46209\n", "51\t37363\t108.1\t0\t37363\n", "52\t37420\t108.1\t0\t37420\n", "53\t43352\t108.1\t0\t43352\n", "54\t55326\t108.1\t0\t55326\n", "55\t50903\t108.1\t0\t50903\n", "56\t46108\t108.1\t0\t46108\n", "57\t37566\t108.1\t0\t37566\n", "58\t41993\t108.1\t0\t41993\n", "59\t27156\t108.1\t0\t27156\n", "60\t22911\t108.1\t0\t22911\n", "61\t22761\t108.1\t0\t22761\n", "62\t17898\t108.1\t0\t17898\n", "63\t17662\t108.1\t0\t17662\n", "64\t19331\t108.1\t0\t19331\n", "65\t17981\t108.1\t0\t17981\n", "66\t16445\t108.1\t0\t16445\n", "67\t15129\t108.1\t0\t15129\n", "68\t13959\t108.1\t0\t13959\n", "69\t13274\t108.1\t0\t13274\n", "70\t13801\t108.1\t0\t13801\n", "71\t12686\t108.1\t0\t12686\n", "72\t10668\t108.1\t0\t10668\n", "73\t9857\t108.1\t0\t9857\n", "74\t9528\t108.1\t0\t9528\n", "75\t7889\t108.1\t0\t7889\n", "76\t6704\t108.1\t0\t6704\n", "77\t5803\t108.1\t0\t5803\n", "78\t6279\t108.1\t0\t6279\n", "79\t6205\t108.1\t0\t6205\n", "80\t6576\t108.1\t0\t6576\n", "81\t6139\t108.1\t0\t6139\n", "82\t5888\t108.1\t0\t5888\n", "83\t6888\t108.1\t0\t6888\n", "84\t8034\t108.1\t0\t8034\n", "85\t9402\t108.1\t0\t9402\n", "86\t8607\t108.1\t0\t8607\n", "87\t6126\t108.1\t0\t6126\n", "88\t5361\t108.1\t0\t5361\n", "89\t6469\t108.1\t0\t6469\n", "90\t6846\t108.1\t0\t6846\n", "91\t6333\t108.1\t0\t6333\n", "92\t5964\t108.1\t0\t5964\n", "93\t6221\t108.1\t0\t6221\n", "94\t6024\t108.1\t0\t6024\n", "95\t5392\t108.1\t0\t5392\n", "96\t3647\t108.1\t0\t3647\n", "97\t2274\t108.1\t0\t2274\n", "98\t1380\t108.1\t0\t1380\n", "99\t1157\t108.1\t0\t1157\n", "100\t694\t108.1\t0\t694\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 17737 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 61.3%\n", " C: 13.0%\n", " G: 0.0%\n", " T: 25.2%\n", " none/other: 0.5%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t7197\t110714.2\t0\t7197\n", "4\t1518\t27678.6\t0\t1518\n", "5\t387\t6919.6\t0\t387\n", "6\t159\t1729.9\t0\t159\n", "7\t69\t432.5\t0\t69\n", "8\t45\t108.1\t0\t45\n", "9\t41\t108.1\t0\t41\n", "10\t36\t108.1\t0\t36\n", "11\t49\t108.1\t0\t49\n", "12\t45\t108.1\t0\t45\n", "13\t43\t108.1\t0\t43\n", "14\t38\t108.1\t0\t38\n", "15\t36\t108.1\t0\t36\n", "16\t38\t108.1\t0\t38\n", "17\t58\t108.1\t0\t58\n", "18\t72\t108.1\t0\t72\n", "19\t76\t108.1\t0\t76\n", "20\t111\t108.1\t0\t111\n", "21\t101\t108.1\t0\t101\n", "22\t80\t108.1\t0\t80\n", "23\t66\t108.1\t0\t66\n", "24\t74\t108.1\t0\t74\n", "25\t85\t108.1\t0\t85\n", "26\t130\t108.1\t0\t130\n", "27\t150\t108.1\t0\t150\n", "28\t152\t108.1\t0\t152\n", "29\t228\t108.1\t0\t228\n", "30\t450\t108.1\t0\t450\n", "31\t482\t108.1\t0\t482\n", "32\t888\t108.1\t0\t888\n", "33\t800\t108.1\t0\t800\n", "34\t719\t108.1\t0\t719\n", "35\t1043\t108.1\t0\t1043\n", "36\t987\t108.1\t0\t987\n", "37\t364\t108.1\t0\t364\n", "38\t64\t108.1\t0\t64\n", "39\t22\t108.1\t0\t22\n", "40\t16\t108.1\t0\t16\n", "41\t21\t108.1\t0\t21\n", "42\t15\t108.1\t0\t15\n", "43\t15\t108.1\t0\t15\n", "44\t15\t108.1\t0\t15\n", "45\t10\t108.1\t0\t10\n", "46\t14\t108.1\t0\t14\n", "47\t10\t108.1\t0\t10\n", "48\t10\t108.1\t0\t10\n", "49\t9\t108.1\t0\t9\n", "50\t10\t108.1\t0\t10\n", "51\t17\t108.1\t0\t17\n", "52\t5\t108.1\t0\t5\n", "53\t14\t108.1\t0\t14\n", "54\t6\t108.1\t0\t6\n", "55\t10\t108.1\t0\t10\n", "56\t18\t108.1\t0\t18\n", "57\t8\t108.1\t0\t8\n", "58\t7\t108.1\t0\t7\n", "59\t10\t108.1\t0\t10\n", "60\t9\t108.1\t0\t9\n", "61\t5\t108.1\t0\t5\n", "62\t1\t108.1\t0\t1\n", "63\t6\t108.1\t0\t6\n", "64\t5\t108.1\t0\t5\n", "65\t2\t108.1\t0\t2\n", "67\t4\t108.1\t0\t4\n", "68\t2\t108.1\t0\t2\n", "69\t2\t108.1\t0\t2\n", "70\t5\t108.1\t0\t5\n", "71\t3\t108.1\t0\t3\n", "72\t2\t108.1\t0\t2\n", "74\t2\t108.1\t0\t2\n", "75\t1\t108.1\t0\t1\n", "76\t1\t108.1\t0\t1\n", "77\t3\t108.1\t0\t3\n", "78\t2\t108.1\t0\t2\n", "79\t2\t108.1\t0\t2\n", "80\t2\t108.1\t0\t2\n", "81\t3\t108.1\t0\t3\n", "82\t4\t108.1\t0\t4\n", "83\t5\t108.1\t0\t5\n", "84\t5\t108.1\t0\t5\n", "85\t7\t108.1\t0\t7\n", "86\t1\t108.1\t0\t1\n", "87\t4\t108.1\t0\t4\n", "88\t1\t108.1\t0\t1\n", "89\t3\t108.1\t0\t3\n", "90\t5\t108.1\t0\t5\n", "91\t4\t108.1\t0\t4\n", "92\t20\t108.1\t0\t20\n", "93\t34\t108.1\t0\t34\n", "94\t78\t108.1\t0\t78\n", "95\t86\t108.1\t0\t86\n", "96\t53\t108.1\t0\t53\n", "97\t47\t108.1\t0\t47\n", "98\t40\t108.1\t0\t40\n", "99\t50\t108.1\t0\t50\n", "100\t85\t108.1\t0\t85\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 98504 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.9%\n", " C: 20.4%\n", " G: 10.9%\n", " T: 22.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t72233\t110714.2\t0\t72233\n", "4\t16958\t27678.6\t0\t16958\n", "5\t3502\t6919.6\t0\t3502\n", "6\t181\t1729.9\t0\t181\n", "7\t35\t432.5\t0\t35\n", "8\t30\t432.5\t0\t30\n", "9\t28\t432.5\t0\t28\n", "10\t46\t432.5\t0\t46\n", "11\t40\t432.5\t0\t40\n", "12\t43\t432.5\t0\t43\n", "13\t59\t432.5\t0\t59\n", "14\t36\t432.5\t0\t36\n", "15\t40\t432.5\t0\t40\n", "16\t40\t432.5\t0\t40\n", "17\t38\t432.5\t0\t38\n", "18\t31\t432.5\t0\t31\n", "19\t49\t432.5\t0\t49\n", "20\t40\t432.5\t0\t40\n", "21\t37\t432.5\t0\t37\n", "22\t42\t432.5\t0\t42\n", "23\t28\t432.5\t0\t28\n", "24\t48\t432.5\t0\t48\n", "25\t32\t432.5\t0\t32\n", "26\t46\t432.5\t0\t46\n", "27\t38\t432.5\t0\t38\n", "28\t40\t432.5\t0\t40\n", "29\t50\t432.5\t0\t50\n", "30\t61\t432.5\t0\t61\n", "31\t57\t432.5\t0\t57\n", "32\t59\t432.5\t0\t59\n", "33\t76\t432.5\t0\t76\n", "34\t44\t432.5\t0\t44\n", "35\t69\t432.5\t0\t69\n", "36\t48\t432.5\t0\t48\n", "37\t44\t432.5\t0\t44\n", "38\t49\t432.5\t0\t49\n", "39\t55\t432.5\t0\t55\n", "40\t69\t432.5\t0\t69\n", "41\t44\t432.5\t0\t44\n", "42\t39\t432.5\t0\t39\n", "43\t48\t432.5\t0\t48\n", "44\t48\t432.5\t0\t48\n", "45\t48\t432.5\t0\t48\n", "46\t48\t432.5\t0\t48\n", "47\t50\t432.5\t0\t50\n", "48\t62\t432.5\t0\t62\n", "49\t56\t432.5\t0\t56\n", "50\t40\t432.5\t0\t40\n", "51\t46\t432.5\t0\t46\n", "52\t57\t432.5\t0\t57\n", "53\t42\t432.5\t0\t42\n", "54\t45\t432.5\t0\t45\n", "55\t32\t432.5\t0\t32\n", "56\t31\t432.5\t0\t31\n", "57\t24\t432.5\t0\t24\n", "58\t40\t432.5\t0\t40\n", "59\t18\t432.5\t0\t18\n", "60\t40\t432.5\t0\t40\n", "61\t52\t432.5\t0\t52\n", "62\t36\t432.5\t0\t36\n", "63\t53\t432.5\t0\t53\n", "64\t39\t432.5\t0\t39\n", "65\t43\t432.5\t0\t43\n", "66\t30\t432.5\t0\t30\n", "67\t40\t432.5\t0\t40\n", "68\t24\t432.5\t0\t24\n", "69\t57\t432.5\t0\t57\n", "70\t41\t432.5\t0\t41\n", "71\t54\t432.5\t0\t54\n", "72\t82\t432.5\t0\t82\n", "73\t120\t432.5\t0\t120\n", "74\t119\t432.5\t0\t119\n", "75\t58\t432.5\t0\t58\n", "76\t88\t432.5\t0\t88\n", "77\t170\t432.5\t0\t170\n", "78\t105\t432.5\t0\t105\n", "79\t107\t432.5\t0\t107\n", "80\t105\t432.5\t0\t105\n", "81\t137\t432.5\t0\t137\n", "82\t184\t432.5\t0\t184\n", "83\t133\t432.5\t0\t133\n", "84\t96\t432.5\t0\t96\n", "85\t91\t432.5\t0\t91\n", "86\t71\t432.5\t0\t71\n", "87\t86\t432.5\t0\t86\n", "88\t71\t432.5\t0\t71\n", "89\t61\t432.5\t0\t61\n", "90\t73\t432.5\t0\t73\n", "91\t64\t432.5\t0\t64\n", "92\t41\t432.5\t0\t41\n", "93\t45\t432.5\t0\t45\n", "94\t59\t432.5\t0\t59\n", "95\t60\t432.5\t0\t60\n", "96\t67\t432.5\t0\t67\n", "97\t81\t432.5\t0\t81\n", "98\t107\t432.5\t0\t107\n", "99\t140\t432.5\t0\t140\n", "100\t135\t432.5\t0\t135\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 43_S46_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/43.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 89.12 s (12 us/read; 4.91 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,292,981\n", "Reads with adapters: 4,875,970 (66.9%)\n", "Reads written (passing filters): 7,115,207 (97.6%)\n", "\n", "Total basepairs processed: 729,298,100 bp\n", "Quality-trimmed: 2,163,857 bp (0.3%)\n", "Total written (filtered): 550,060,635 bp (75.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4730623 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.8%\n", " G: 40.8%\n", " T: 27.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t137716\t113952.8\t0\t137716\n", "4\t80739\t28488.2\t0\t80739\n", "5\t66560\t7122.1\t0\t66560\n", "6\t54842\t1780.5\t0\t54842\n", "7\t52581\t445.1\t0\t52581\n", "8\t54620\t111.3\t0\t54620\n", "9\t53865\t111.3\t0\t53865\n", "10\t52289\t111.3\t0\t52289\n", "11\t51843\t111.3\t0\t51843\n", "12\t52698\t111.3\t0\t52698\n", "13\t54998\t111.3\t0\t54998\n", "14\t57611\t111.3\t0\t57611\n", "15\t58899\t111.3\t0\t58899\n", "16\t61905\t111.3\t0\t61905\n", "17\t68078\t111.3\t0\t68078\n", "18\t79279\t111.3\t0\t79279\n", "19\t74837\t111.3\t0\t74837\n", "20\t63236\t111.3\t0\t63236\n", "21\t60846\t111.3\t0\t60846\n", "22\t55825\t111.3\t0\t55825\n", "23\t60686\t111.3\t0\t60686\n", "24\t70983\t111.3\t0\t70983\n", "25\t73991\t111.3\t0\t73991\n", "26\t83978\t111.3\t0\t83978\n", "27\t93590\t111.3\t0\t93590\n", "28\t86236\t111.3\t0\t86236\n", "29\t80996\t111.3\t0\t80996\n", "30\t84412\t111.3\t0\t84412\n", "31\t93243\t111.3\t0\t93243\n", "32\t88123\t111.3\t0\t88123\n", "33\t82151\t111.3\t0\t82151\n", "34\t81317\t111.3\t0\t81317\n", "35\t91692\t111.3\t0\t91692\n", "36\t109621\t111.3\t0\t109621\n", "37\t115988\t111.3\t0\t115988\n", "38\t91614\t111.3\t0\t91614\n", "39\t77148\t111.3\t0\t77148\n", "40\t71984\t111.3\t0\t71984\n", "41\t77982\t111.3\t0\t77982\n", "42\t86454\t111.3\t0\t86454\n", "43\t74168\t111.3\t0\t74168\n", "44\t57471\t111.3\t0\t57471\n", "45\t73000\t111.3\t0\t73000\n", "46\t86435\t111.3\t0\t86435\n", "47\t82629\t111.3\t0\t82629\n", "48\t81862\t111.3\t0\t81862\n", "49\t66092\t111.3\t0\t66092\n", "50\t64912\t111.3\t0\t64912\n", "51\t57726\t111.3\t0\t57726\n", "52\t57613\t111.3\t0\t57613\n", "53\t49862\t111.3\t0\t49862\n", "54\t57519\t111.3\t0\t57519\n", "55\t58967\t111.3\t0\t58967\n", "56\t48252\t111.3\t0\t48252\n", "57\t52956\t111.3\t0\t52956\n", "58\t64342\t111.3\t0\t64342\n", "59\t47007\t111.3\t0\t47007\n", "60\t37920\t111.3\t0\t37920\n", "61\t35083\t111.3\t0\t35083\n", "62\t29367\t111.3\t0\t29367\n", "63\t27345\t111.3\t0\t27345\n", "64\t31544\t111.3\t0\t31544\n", "65\t30914\t111.3\t0\t30914\n", "66\t26614\t111.3\t0\t26614\n", "67\t25781\t111.3\t0\t25781\n", "68\t25376\t111.3\t0\t25376\n", "69\t26393\t111.3\t0\t26393\n", "70\t27608\t111.3\t0\t27608\n", "71\t26575\t111.3\t0\t26575\n", "72\t20706\t111.3\t0\t20706\n", "73\t18123\t111.3\t0\t18123\n", "74\t18132\t111.3\t0\t18132\n", "75\t15778\t111.3\t0\t15778\n", "76\t12700\t111.3\t0\t12700\n", "77\t12041\t111.3\t0\t12041\n", "78\t13664\t111.3\t0\t13664\n", "79\t12933\t111.3\t0\t12933\n", "80\t12698\t111.3\t0\t12698\n", "81\t11560\t111.3\t0\t11560\n", "82\t10557\t111.3\t0\t10557\n", "83\t11285\t111.3\t0\t11285\n", "84\t12373\t111.3\t0\t12373\n", "85\t13903\t111.3\t0\t13903\n", "86\t12704\t111.3\t0\t12704\n", "87\t8588\t111.3\t0\t8588\n", "88\t7538\t111.3\t0\t7538\n", "89\t8288\t111.3\t0\t8288\n", "90\t8791\t111.3\t0\t8791\n", "91\t8929\t111.3\t0\t8929\n", "92\t9099\t111.3\t0\t9099\n", "93\t9777\t111.3\t0\t9777\n", "94\t9459\t111.3\t0\t9459\n", "95\t7724\t111.3\t0\t7724\n", "96\t5561\t111.3\t0\t5561\n", "97\t3653\t111.3\t0\t3653\n", "98\t2343\t111.3\t0\t2343\n", "99\t3061\t111.3\t0\t3061\n", "100\t1866\t111.3\t0\t1866\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 34027 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 53.1%\n", " C: 27.0%\n", " G: 0.0%\n", " T: 19.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t16236\t113952.8\t0\t16236\n", "4\t3725\t28488.2\t0\t3725\n", "5\t1256\t7122.1\t0\t1256\n", "6\t773\t1780.5\t0\t773\n", "7\t185\t445.1\t0\t185\n", "8\t144\t111.3\t0\t144\n", "9\t97\t111.3\t0\t97\n", "10\t117\t111.3\t0\t117\n", "11\t116\t111.3\t0\t116\n", "12\t117\t111.3\t0\t117\n", "13\t111\t111.3\t0\t111\n", "14\t111\t111.3\t0\t111\n", "15\t97\t111.3\t0\t97\n", "16\t119\t111.3\t0\t119\n", "17\t136\t111.3\t0\t136\n", "18\t168\t111.3\t0\t168\n", "19\t242\t111.3\t0\t242\n", "20\t359\t111.3\t0\t359\n", "21\t258\t111.3\t0\t258\n", "22\t189\t111.3\t0\t189\n", "23\t153\t111.3\t0\t153\n", "24\t165\t111.3\t0\t165\n", "25\t149\t111.3\t0\t149\n", "26\t238\t111.3\t0\t238\n", "27\t253\t111.3\t0\t253\n", "28\t256\t111.3\t0\t256\n", "29\t309\t111.3\t0\t309\n", "30\t570\t111.3\t0\t570\n", "31\t660\t111.3\t0\t660\n", "32\t893\t111.3\t0\t893\n", "33\t852\t111.3\t0\t852\n", "34\t802\t111.3\t0\t802\n", "35\t1048\t111.3\t0\t1048\n", "36\t1054\t111.3\t0\t1054\n", "37\t339\t111.3\t0\t339\n", "38\t64\t111.3\t0\t64\n", "39\t50\t111.3\t0\t50\n", "40\t54\t111.3\t0\t54\n", "41\t51\t111.3\t0\t51\n", "42\t40\t111.3\t0\t40\n", "43\t41\t111.3\t0\t41\n", "44\t48\t111.3\t0\t48\n", "45\t48\t111.3\t0\t48\n", "46\t39\t111.3\t0\t39\n", "47\t44\t111.3\t0\t44\n", "48\t44\t111.3\t0\t44\n", "49\t38\t111.3\t0\t38\n", "50\t39\t111.3\t0\t39\n", "51\t48\t111.3\t0\t48\n", "52\t37\t111.3\t0\t37\n", "53\t36\t111.3\t0\t36\n", "54\t32\t111.3\t0\t32\n", "55\t41\t111.3\t0\t41\n", "56\t29\t111.3\t0\t29\n", "57\t33\t111.3\t0\t33\n", "58\t34\t111.3\t0\t34\n", "59\t19\t111.3\t0\t19\n", "60\t29\t111.3\t0\t29\n", "61\t31\t111.3\t0\t31\n", "62\t22\t111.3\t0\t22\n", "63\t24\t111.3\t0\t24\n", "64\t16\t111.3\t0\t16\n", "65\t22\t111.3\t0\t22\n", "66\t36\t111.3\t0\t36\n", "67\t13\t111.3\t0\t13\n", "68\t16\t111.3\t0\t16\n", "69\t17\t111.3\t0\t17\n", "70\t19\t111.3\t0\t19\n", "71\t12\t111.3\t0\t12\n", "72\t8\t111.3\t0\t8\n", "73\t11\t111.3\t0\t11\n", "74\t4\t111.3\t0\t4\n", "75\t7\t111.3\t0\t7\n", "76\t18\t111.3\t0\t18\n", "77\t9\t111.3\t0\t9\n", "78\t12\t111.3\t0\t12\n", "79\t4\t111.3\t0\t4\n", "80\t9\t111.3\t0\t9\n", "81\t9\t111.3\t0\t9\n", "82\t6\t111.3\t0\t6\n", "83\t9\t111.3\t0\t9\n", "84\t9\t111.3\t0\t9\n", "85\t7\t111.3\t0\t7\n", "86\t8\t111.3\t0\t8\n", "87\t9\t111.3\t0\t9\n", "88\t4\t111.3\t0\t4\n", "89\t17\t111.3\t0\t17\n", "90\t8\t111.3\t0\t8\n", "91\t6\t111.3\t0\t6\n", "92\t15\t111.3\t0\t15\n", "93\t29\t111.3\t0\t29\n", "94\t48\t111.3\t0\t48\n", "95\t67\t111.3\t0\t67\n", "96\t52\t111.3\t0\t52\n", "97\t49\t111.3\t0\t49\n", "98\t49\t111.3\t0\t49\n", "99\t32\t111.3\t0\t32\n", "100\t49\t111.3\t0\t49\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 111320 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.1%\n", " C: 17.5%\n", " G: 16.9%\n", " T: 24.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t78017\t113952.8\t0\t78017\n", "4\t19377\t28488.2\t0\t19377\n", "5\t3081\t7122.1\t0\t3081\n", "6\t350\t1780.5\t0\t350\n", "7\t146\t445.1\t0\t146\n", "8\t163\t445.1\t0\t163\n", "9\t134\t445.1\t0\t134\n", "10\t162\t445.1\t0\t162\n", "11\t148\t445.1\t0\t148\n", "12\t170\t445.1\t0\t170\n", "13\t160\t445.1\t0\t160\n", "14\t179\t445.1\t0\t179\n", "15\t196\t445.1\t0\t196\n", "16\t169\t445.1\t0\t169\n", "17\t182\t445.1\t0\t182\n", "18\t157\t445.1\t0\t157\n", "19\t187\t445.1\t0\t187\n", "20\t190\t445.1\t0\t190\n", "21\t142\t445.1\t0\t142\n", "22\t144\t445.1\t0\t144\n", "23\t119\t445.1\t0\t119\n", "24\t128\t445.1\t0\t128\n", "25\t151\t445.1\t0\t151\n", "26\t121\t445.1\t0\t121\n", "27\t162\t445.1\t0\t162\n", "28\t138\t445.1\t0\t138\n", "29\t151\t445.1\t0\t151\n", "30\t115\t445.1\t0\t115\n", "31\t145\t445.1\t0\t145\n", "32\t131\t445.1\t0\t131\n", "33\t152\t445.1\t0\t152\n", "34\t110\t445.1\t0\t110\n", "35\t137\t445.1\t0\t137\n", "36\t124\t445.1\t0\t124\n", "37\t119\t445.1\t0\t119\n", "38\t116\t445.1\t0\t116\n", "39\t130\t445.1\t0\t130\n", "40\t143\t445.1\t0\t143\n", "41\t122\t445.1\t0\t122\n", "42\t110\t445.1\t0\t110\n", "43\t151\t445.1\t0\t151\n", "44\t62\t445.1\t0\t62\n", "45\t135\t445.1\t0\t135\n", "46\t121\t445.1\t0\t121\n", "47\t101\t445.1\t0\t101\n", "48\t96\t445.1\t0\t96\n", "49\t111\t445.1\t0\t111\n", "50\t102\t445.1\t0\t102\n", "51\t78\t445.1\t0\t78\n", "52\t85\t445.1\t0\t85\n", "53\t102\t445.1\t0\t102\n", "54\t99\t445.1\t0\t99\n", "55\t83\t445.1\t0\t83\n", "56\t93\t445.1\t0\t93\n", "57\t96\t445.1\t0\t96\n", "58\t81\t445.1\t0\t81\n", "59\t67\t445.1\t0\t67\n", "60\t83\t445.1\t0\t83\n", "61\t88\t445.1\t0\t88\n", "62\t60\t445.1\t0\t60\n", "63\t84\t445.1\t0\t84\n", "64\t100\t445.1\t0\t100\n", "65\t86\t445.1\t0\t86\n", "66\t87\t445.1\t0\t87\n", "67\t77\t445.1\t0\t77\n", "68\t66\t445.1\t0\t66\n", "69\t64\t445.1\t0\t64\n", "70\t55\t445.1\t0\t55\n", "71\t79\t445.1\t0\t79\n", "72\t68\t445.1\t0\t68\n", "73\t90\t445.1\t0\t90\n", "74\t88\t445.1\t0\t88\n", "75\t74\t445.1\t0\t74\n", "76\t67\t445.1\t0\t67\n", "77\t135\t445.1\t0\t135\n", "78\t95\t445.1\t0\t95\n", "79\t105\t445.1\t0\t105\n", "80\t97\t445.1\t0\t97\n", "81\t127\t445.1\t0\t127\n", "82\t137\t445.1\t0\t137\n", "83\t134\t445.1\t0\t134\n", "84\t104\t445.1\t0\t104\n", "85\t77\t445.1\t0\t77\n", "86\t87\t445.1\t0\t87\n", "87\t109\t445.1\t0\t109\n", "88\t108\t445.1\t0\t108\n", "89\t91\t445.1\t0\t91\n", "90\t77\t445.1\t0\t77\n", "91\t65\t445.1\t0\t65\n", "92\t71\t445.1\t0\t71\n", "93\t49\t445.1\t0\t49\n", "94\t66\t445.1\t0\t66\n", "95\t73\t445.1\t0\t73\n", "96\t61\t445.1\t0\t61\n", "97\t78\t445.1\t0\t78\n", "98\t103\t445.1\t0\t103\n", "99\t101\t445.1\t0\t101\n", "100\t113\t445.1\t0\t113\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 441_S73_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/441.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 111.46 s (12 us/read; 4.94 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 9,183,978\n", "Reads with adapters: 7,525,967 (81.9%)\n", "Reads written (passing filters): 8,072,265 (87.9%)\n", "\n", "Total basepairs processed: 918,397,800 bp\n", "Quality-trimmed: 1,684,224 bp (0.2%)\n", "Total written (filtered): 589,344,748 bp (64.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4475506 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.5%\n", " G: 39.4%\n", " T: 30.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t124717\t143499.7\t0\t124717\n", "4\t90079\t35874.9\t0\t90079\n", "5\t75447\t8968.7\t0\t75447\n", "6\t55112\t2242.2\t0\t55112\n", "7\t55200\t560.5\t0\t55200\n", "8\t51430\t140.1\t0\t51430\n", "9\t48773\t140.1\t0\t48773\n", "10\t48740\t140.1\t0\t48740\n", "11\t48522\t140.1\t0\t48522\n", "12\t47414\t140.1\t0\t47414\n", "13\t45939\t140.1\t0\t45939\n", "14\t44450\t140.1\t0\t44450\n", "15\t49372\t140.1\t0\t49372\n", "16\t55986\t140.1\t0\t55986\n", "17\t58873\t140.1\t0\t58873\n", "18\t65663\t140.1\t0\t65663\n", "19\t62317\t140.1\t0\t62317\n", "20\t50879\t140.1\t0\t50879\n", "21\t45133\t140.1\t0\t45133\n", "22\t40257\t140.1\t0\t40257\n", "23\t39862\t140.1\t0\t39862\n", "24\t43904\t140.1\t0\t43904\n", "25\t47140\t140.1\t0\t47140\n", "26\t50136\t140.1\t0\t50136\n", "27\t55861\t140.1\t0\t55861\n", "28\t51624\t140.1\t0\t51624\n", "29\t50156\t140.1\t0\t50156\n", "30\t54475\t140.1\t0\t54475\n", "31\t55542\t140.1\t0\t55542\n", "32\t54778\t140.1\t0\t54778\n", "33\t51991\t140.1\t0\t51991\n", "34\t49495\t140.1\t0\t49495\n", "35\t54590\t140.1\t0\t54590\n", "36\t58007\t140.1\t0\t58007\n", "37\t64358\t140.1\t0\t64358\n", "38\t52823\t140.1\t0\t52823\n", "39\t43428\t140.1\t0\t43428\n", "40\t39827\t140.1\t0\t39827\n", "41\t44002\t140.1\t0\t44002\n", "42\t44832\t140.1\t0\t44832\n", "43\t38334\t140.1\t0\t38334\n", "44\t33298\t140.1\t0\t33298\n", "45\t43335\t140.1\t0\t43335\n", "46\t52927\t140.1\t0\t52927\n", "47\t51933\t140.1\t0\t51933\n", "48\t51936\t140.1\t0\t51936\n", "49\t45400\t140.1\t0\t45400\n", "50\t42438\t140.1\t0\t42438\n", "51\t36760\t140.1\t0\t36760\n", "52\t36330\t140.1\t0\t36330\n", "53\t35984\t140.1\t0\t35984\n", "54\t47650\t140.1\t0\t47650\n", "55\t45381\t140.1\t0\t45381\n", "56\t41734\t140.1\t0\t41734\n", "57\t37793\t140.1\t0\t37793\n", "58\t45976\t140.1\t0\t45976\n", "59\t34653\t140.1\t0\t34653\n", "60\t29467\t140.1\t0\t29467\n", "61\t28049\t140.1\t0\t28049\n", "62\t22100\t140.1\t0\t22100\n", "63\t25609\t140.1\t0\t25609\n", "64\t29593\t140.1\t0\t29593\n", "65\t28748\t140.1\t0\t28748\n", "66\t28275\t140.1\t0\t28275\n", "67\t26907\t140.1\t0\t26907\n", "68\t23692\t140.1\t0\t23692\n", "69\t25618\t140.1\t0\t25618\n", "70\t25638\t140.1\t0\t25638\n", "71\t25105\t140.1\t0\t25105\n", "72\t21791\t140.1\t0\t21791\n", "73\t20314\t140.1\t0\t20314\n", "74\t21901\t140.1\t0\t21901\n", "75\t18738\t140.1\t0\t18738\n", "76\t16172\t140.1\t0\t16172\n", "77\t15410\t140.1\t0\t15410\n", "78\t17986\t140.1\t0\t17986\n", "79\t16627\t140.1\t0\t16627\n", "80\t18367\t140.1\t0\t18367\n", "81\t17577\t140.1\t0\t17577\n", "82\t19060\t140.1\t0\t19060\n", "83\t23063\t140.1\t0\t23063\n", "84\t28997\t140.1\t0\t28997\n", "85\t36262\t140.1\t0\t36262\n", "86\t36791\t140.1\t0\t36791\n", "87\t26110\t140.1\t0\t26110\n", "88\t25568\t140.1\t0\t25568\n", "89\t32988\t140.1\t0\t32988\n", "90\t36434\t140.1\t0\t36434\n", "91\t49505\t140.1\t0\t49505\n", "92\t71788\t140.1\t0\t71788\n", "93\t90870\t140.1\t0\t90870\n", "94\t102629\t140.1\t0\t102629\n", "95\t99348\t140.1\t0\t99348\n", "96\t87117\t140.1\t0\t87117\n", "97\t77590\t140.1\t0\t77590\n", "98\t67381\t140.1\t0\t67381\n", "99\t113114\t140.1\t0\t113114\n", "100\t54211\t140.1\t0\t54211\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 2997020 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 93.0%\n", " C: 2.3%\n", " G: 0.0%\n", " T: 4.7%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t5039\t143499.7\t0\t5039\n", "4\t1232\t35874.9\t0\t1232\n", "5\t610\t8968.7\t0\t610\n", "6\t409\t2242.2\t0\t409\n", "7\t602\t560.5\t0\t602\n", "8\t805\t140.1\t0\t805\n", "9\t586\t140.1\t0\t586\n", "10\t622\t140.1\t0\t622\n", "11\t706\t140.1\t0\t706\n", "12\t416\t140.1\t0\t416\n", "13\t732\t140.1\t0\t732\n", "14\t550\t140.1\t0\t550\n", "15\t672\t140.1\t0\t672\n", "16\t801\t140.1\t0\t801\n", "17\t1310\t140.1\t0\t1310\n", "18\t2227\t140.1\t0\t2227\n", "19\t4195\t140.1\t0\t4195\n", "20\t8342\t140.1\t0\t8342\n", "21\t7438\t140.1\t0\t7438\n", "22\t6707\t140.1\t0\t6707\n", "23\t6225\t140.1\t0\t6225\n", "24\t7621\t140.1\t0\t7621\n", "25\t11833\t140.1\t0\t11833\n", "26\t28667\t140.1\t0\t28667\n", "27\t30813\t140.1\t0\t30813\n", "28\t40894\t140.1\t0\t40894\n", "29\t59713\t140.1\t0\t59713\n", "30\t123575\t140.1\t0\t123575\n", "31\t160043\t140.1\t0\t160043\n", "32\t321892\t140.1\t0\t321892\n", "33\t334141\t140.1\t0\t334141\n", "34\t388497\t140.1\t0\t388497\n", "35\t570361\t140.1\t0\t570361\n", "36\t580791\t140.1\t0\t580791\n", "37\t279946\t140.1\t0\t279946\n", "38\t6725\t140.1\t0\t6725\n", "39\t281\t140.1\t0\t281\n", "40\t24\t140.1\t0\t24\n", "41\t9\t140.1\t0\t9\n", "42\t10\t140.1\t0\t10\n", "43\t5\t140.1\t0\t5\n", "44\t2\t140.1\t0\t2\n", "45\t2\t140.1\t0\t2\n", "46\t2\t140.1\t0\t2\n", "47\t4\t140.1\t0\t4\n", "48\t1\t140.1\t0\t1\n", "49\t3\t140.1\t0\t3\n", "50\t1\t140.1\t0\t1\n", "52\t1\t140.1\t0\t1\n", "56\t1\t140.1\t0\t1\n", "58\t4\t140.1\t0\t4\n", "59\t4\t140.1\t0\t4\n", "64\t2\t140.1\t0\t2\n", "73\t1\t140.1\t0\t1\n", "91\t1\t140.1\t0\t1\n", "92\t1\t140.1\t0\t1\n", "93\t178\t140.1\t0\t178\n", "94\t143\t140.1\t0\t143\n", "95\t160\t140.1\t0\t160\n", "96\t27\t140.1\t0\t27\n", "97\t202\t140.1\t0\t202\n", "98\t1\t140.1\t0\t1\n", "99\t120\t140.1\t0\t120\n", "100\t92\t140.1\t0\t92\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 53441 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 50.5%\n", " C: 13.5%\n", " G: 15.5%\n", " T: 20.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t32865\t143499.7\t0\t32865\n", "4\t8133\t35874.9\t0\t8133\n", "5\t1403\t8968.7\t0\t1403\n", "6\t133\t2242.2\t0\t133\n", "7\t18\t560.5\t0\t18\n", "8\t143\t560.5\t0\t143\n", "9\t156\t560.5\t0\t156\n", "10\t3\t560.5\t0\t3\n", "11\t13\t560.5\t0\t13\n", "12\t5\t560.5\t0\t5\n", "13\t8\t560.5\t0\t8\n", "14\t4\t560.5\t0\t4\n", "15\t4\t560.5\t0\t4\n", "16\t5\t560.5\t0\t5\n", "17\t4\t560.5\t0\t4\n", "18\t100\t560.5\t0\t100\n", "19\t2\t560.5\t0\t2\n", "20\t184\t560.5\t0\t184\n", "21\t1\t560.5\t0\t1\n", "22\t36\t560.5\t0\t36\n", "23\t7\t560.5\t0\t7\n", "24\t167\t560.5\t0\t167\n", "25\t2\t560.5\t0\t2\n", "26\t8\t560.5\t0\t8\n", "27\t3\t560.5\t0\t3\n", "28\t7\t560.5\t0\t7\n", "29\t130\t560.5\t0\t130\n", "30\t19\t560.5\t0\t19\n", "31\t93\t560.5\t0\t93\n", "32\t133\t560.5\t0\t133\n", "33\t296\t560.5\t0\t296\n", "34\t1\t560.5\t0\t1\n", "35\t1\t560.5\t0\t1\n", "36\t1\t560.5\t0\t1\n", "38\t1\t560.5\t0\t1\n", "39\t7\t560.5\t0\t7\n", "40\t107\t560.5\t0\t107\n", "41\t430\t560.5\t0\t430\n", "42\t118\t560.5\t0\t118\n", "43\t7\t560.5\t0\t7\n", "44\t4\t560.5\t0\t4\n", "45\t125\t560.5\t0\t125\n", "46\t21\t560.5\t0\t21\n", "47\t154\t560.5\t0\t154\n", "48\t5\t560.5\t0\t5\n", "49\t38\t560.5\t0\t38\n", "50\t260\t560.5\t0\t260\n", "51\t9\t560.5\t0\t9\n", "52\t115\t560.5\t0\t115\n", "53\t559\t560.5\t0\t559\n", "54\t4\t560.5\t0\t4\n", "55\t153\t560.5\t0\t153\n", "56\t211\t560.5\t0\t211\n", "57\t148\t560.5\t0\t148\n", "58\t29\t560.5\t0\t29\n", "59\t145\t560.5\t0\t145\n", "60\t237\t560.5\t0\t237\n", "61\t303\t560.5\t0\t303\n", "62\t237\t560.5\t0\t237\n", "63\t20\t560.5\t0\t20\n", "64\t41\t560.5\t0\t41\n", "65\t67\t560.5\t0\t67\n", "66\t317\t560.5\t0\t317\n", "67\t102\t560.5\t0\t102\n", "68\t423\t560.5\t0\t423\n", "69\t33\t560.5\t0\t33\n", "70\t49\t560.5\t0\t49\n", "71\t112\t560.5\t0\t112\n", "72\t321\t560.5\t0\t321\n", "73\t145\t560.5\t0\t145\n", "74\t257\t560.5\t0\t257\n", "75\t39\t560.5\t0\t39\n", "76\t362\t560.5\t0\t362\n", "77\t125\t560.5\t0\t125\n", "78\t251\t560.5\t0\t251\n", "79\t137\t560.5\t0\t137\n", "80\t100\t560.5\t0\t100\n", "81\t438\t560.5\t0\t438\n", "82\t105\t560.5\t0\t105\n", "83\t379\t560.5\t0\t379\n", "84\t155\t560.5\t0\t155\n", "85\t85\t560.5\t0\t85\n", "86\t280\t560.5\t0\t280\n", "87\t43\t560.5\t0\t43\n", "88\t198\t560.5\t0\t198\n", "89\t190\t560.5\t0\t190\n", "90\t347\t560.5\t0\t347\n", "91\t250\t560.5\t0\t250\n", "92\t7\t560.5\t0\t7\n", "93\t146\t560.5\t0\t146\n", "94\t2\t560.5\t0\t2\n", "95\t5\t560.5\t0\t5\n", "96\t70\t560.5\t0\t70\n", "97\t99\t560.5\t0\t99\n", "98\t163\t560.5\t0\t163\n", "99\t16\t560.5\t0\t16\n", "100\t47\t560.5\t0\t47\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 442b_S60_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/442b.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 64.06 s (12 us/read; 5.09 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,438,425\n", "Reads with adapters: 3,323,348 (61.1%)\n", "Reads written (passing filters): 5,025,993 (92.4%)\n", "\n", "Total basepairs processed: 543,842,500 bp\n", "Quality-trimmed: 2,671,938 bp (0.5%)\n", "Total written (filtered): 384,778,202 bp (70.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3204728 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 23.6%\n", " G: 43.4%\n", " T: 33.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t92808\t84975.4\t0\t92808\n", "4\t44125\t21243.8\t0\t44125\n", "5\t30336\t5311.0\t0\t30336\n", "6\t24236\t1327.7\t0\t24236\n", "7\t21281\t331.9\t0\t21281\n", "8\t19378\t83.0\t0\t19378\n", "9\t19894\t83.0\t0\t19894\n", "10\t20695\t83.0\t0\t20695\n", "11\t21918\t83.0\t0\t21918\n", "12\t23827\t83.0\t0\t23827\n", "13\t37903\t83.0\t0\t37903\n", "14\t37047\t83.0\t0\t37047\n", "15\t28247\t83.0\t0\t28247\n", "16\t29413\t83.0\t0\t29413\n", "17\t30610\t83.0\t0\t30610\n", "18\t37475\t83.0\t0\t37475\n", "19\t28909\t83.0\t0\t28909\n", "20\t22543\t83.0\t0\t22543\n", "21\t21383\t83.0\t0\t21383\n", "22\t19863\t83.0\t0\t19863\n", "23\t22294\t83.0\t0\t22294\n", "24\t25617\t83.0\t0\t25617\n", "25\t26544\t83.0\t0\t26544\n", "26\t31495\t83.0\t0\t31495\n", "27\t37054\t83.0\t0\t37054\n", "28\t37986\t83.0\t0\t37986\n", "29\t41222\t83.0\t0\t41222\n", "30\t46066\t83.0\t0\t46066\n", "31\t48233\t83.0\t0\t48233\n", "32\t44363\t83.0\t0\t44363\n", "33\t37620\t83.0\t0\t37620\n", "34\t35434\t83.0\t0\t35434\n", "35\t40763\t83.0\t0\t40763\n", "36\t47684\t83.0\t0\t47684\n", "37\t51346\t83.0\t0\t51346\n", "38\t46588\t83.0\t0\t46588\n", "39\t42794\t83.0\t0\t42794\n", "40\t41827\t83.0\t0\t41827\n", "41\t38057\t83.0\t0\t38057\n", "42\t41744\t83.0\t0\t41744\n", "43\t37214\t83.0\t0\t37214\n", "44\t32909\t83.0\t0\t32909\n", "45\t43864\t83.0\t0\t43864\n", "46\t55373\t83.0\t0\t55373\n", "47\t54360\t83.0\t0\t54360\n", "48\t57151\t83.0\t0\t57151\n", "49\t45774\t83.0\t0\t45774\n", "50\t41419\t83.0\t0\t41419\n", "51\t37589\t83.0\t0\t37589\n", "52\t38747\t83.0\t0\t38747\n", "53\t39897\t83.0\t0\t39897\n", "54\t47185\t83.0\t0\t47185\n", "55\t56040\t83.0\t0\t56040\n", "56\t52289\t83.0\t0\t52289\n", "57\t49702\t83.0\t0\t49702\n", "58\t59926\t83.0\t0\t59926\n", "59\t46663\t83.0\t0\t46663\n", "60\t36972\t83.0\t0\t36972\n", "61\t36610\t83.0\t0\t36610\n", "62\t30956\t83.0\t0\t30956\n", "63\t30939\t83.0\t0\t30939\n", "64\t34196\t83.0\t0\t34196\n", "65\t35469\t83.0\t0\t35469\n", "66\t34347\t83.0\t0\t34347\n", "67\t35356\t83.0\t0\t35356\n", "68\t33023\t83.0\t0\t33023\n", "69\t33860\t83.0\t0\t33860\n", "70\t37276\t83.0\t0\t37276\n", "71\t37277\t83.0\t0\t37277\n", "72\t30304\t83.0\t0\t30304\n", "73\t28345\t83.0\t0\t28345\n", "74\t29765\t83.0\t0\t29765\n", "75\t25428\t83.0\t0\t25428\n", "76\t22303\t83.0\t0\t22303\n", "77\t21455\t83.0\t0\t21455\n", "78\t23691\t83.0\t0\t23691\n", "79\t23979\t83.0\t0\t23979\n", "80\t25211\t83.0\t0\t25211\n", "81\t23749\t83.0\t0\t23749\n", "82\t23268\t83.0\t0\t23268\n", "83\t24440\t83.0\t0\t24440\n", "84\t25503\t83.0\t0\t25503\n", "85\t26782\t83.0\t0\t26782\n", "86\t25913\t83.0\t0\t25913\n", "87\t21737\t83.0\t0\t21737\n", "88\t21502\t83.0\t0\t21502\n", "89\t21710\t83.0\t0\t21710\n", "90\t21780\t83.0\t0\t21780\n", "91\t21176\t83.0\t0\t21176\n", "92\t19767\t83.0\t0\t19767\n", "93\t17935\t83.0\t0\t17935\n", "94\t15863\t83.0\t0\t15863\n", "95\t13193\t83.0\t0\t13193\n", "96\t10121\t83.0\t0\t10121\n", "97\t7836\t83.0\t0\t7836\n", "98\t6767\t83.0\t0\t6767\n", "99\t8881\t83.0\t0\t8881\n", "100\t7319\t83.0\t0\t7319\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 34600 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 46.6%\n", " C: 37.2%\n", " G: 0.0%\n", " T: 16.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13326\t84975.4\t0\t13326\n", "4\t3994\t21243.8\t0\t3994\n", "5\t2441\t5311.0\t0\t2441\n", "6\t1100\t1327.7\t0\t1100\n", "7\t431\t331.9\t0\t431\n", "8\t316\t83.0\t0\t316\n", "9\t353\t83.0\t0\t353\n", "10\t262\t83.0\t0\t262\n", "11\t382\t83.0\t0\t382\n", "12\t299\t83.0\t0\t299\n", "13\t240\t83.0\t0\t240\n", "14\t264\t83.0\t0\t264\n", "15\t243\t83.0\t0\t243\n", "16\t260\t83.0\t0\t260\n", "17\t249\t83.0\t0\t249\n", "18\t353\t83.0\t0\t353\n", "19\t422\t83.0\t0\t422\n", "20\t746\t83.0\t0\t746\n", "21\t450\t83.0\t0\t450\n", "22\t323\t83.0\t0\t323\n", "23\t260\t83.0\t0\t260\n", "24\t248\t83.0\t0\t248\n", "25\t262\t83.0\t0\t262\n", "26\t419\t83.0\t0\t419\n", "27\t407\t83.0\t0\t407\n", "28\t355\t83.0\t0\t355\n", "29\t350\t83.0\t0\t350\n", "30\t477\t83.0\t0\t477\n", "31\t364\t83.0\t0\t364\n", "32\t623\t83.0\t0\t623\n", "33\t713\t83.0\t0\t713\n", "34\t664\t83.0\t0\t664\n", "35\t741\t83.0\t0\t741\n", "36\t780\t83.0\t0\t780\n", "37\t435\t83.0\t0\t435\n", "38\t47\t83.0\t0\t47\n", "39\t38\t83.0\t0\t38\n", "40\t18\t83.0\t0\t18\n", "41\t17\t83.0\t0\t17\n", "42\t13\t83.0\t0\t13\n", "43\t14\t83.0\t0\t14\n", "44\t13\t83.0\t0\t13\n", "45\t9\t83.0\t0\t9\n", "46\t12\t83.0\t0\t12\n", "47\t12\t83.0\t0\t12\n", "48\t10\t83.0\t0\t10\n", "49\t8\t83.0\t0\t8\n", "50\t15\t83.0\t0\t15\n", "51\t7\t83.0\t0\t7\n", "52\t12\t83.0\t0\t12\n", "53\t12\t83.0\t0\t12\n", "54\t10\t83.0\t0\t10\n", "55\t17\t83.0\t0\t17\n", "56\t10\t83.0\t0\t10\n", "57\t15\t83.0\t0\t15\n", "58\t8\t83.0\t0\t8\n", "59\t7\t83.0\t0\t7\n", "60\t7\t83.0\t0\t7\n", "61\t6\t83.0\t0\t6\n", "62\t9\t83.0\t0\t9\n", "63\t5\t83.0\t0\t5\n", "64\t5\t83.0\t0\t5\n", "65\t5\t83.0\t0\t5\n", "66\t4\t83.0\t0\t4\n", "67\t5\t83.0\t0\t5\n", "68\t6\t83.0\t0\t6\n", "69\t5\t83.0\t0\t5\n", "70\t8\t83.0\t0\t8\n", "71\t7\t83.0\t0\t7\n", "72\t5\t83.0\t0\t5\n", "73\t3\t83.0\t0\t3\n", "74\t2\t83.0\t0\t2\n", "75\t3\t83.0\t0\t3\n", "77\t2\t83.0\t0\t2\n", "78\t4\t83.0\t0\t4\n", "79\t5\t83.0\t0\t5\n", "80\t6\t83.0\t0\t6\n", "81\t4\t83.0\t0\t4\n", "82\t2\t83.0\t0\t2\n", "83\t4\t83.0\t0\t4\n", "84\t9\t83.0\t0\t9\n", "85\t2\t83.0\t0\t2\n", "86\t7\t83.0\t0\t7\n", "87\t6\t83.0\t0\t6\n", "88\t4\t83.0\t0\t4\n", "89\t5\t83.0\t0\t5\n", "90\t10\t83.0\t0\t10\n", "91\t3\t83.0\t0\t3\n", "92\t16\t83.0\t0\t16\n", "93\t27\t83.0\t0\t27\n", "94\t43\t83.0\t0\t43\n", "95\t88\t83.0\t0\t88\n", "96\t89\t83.0\t0\t89\n", "97\t84\t83.0\t0\t84\n", "98\t72\t83.0\t0\t72\n", "99\t69\t83.0\t0\t69\n", "100\t78\t83.0\t0\t78\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 84020 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.7%\n", " C: 19.7%\n", " G: 12.8%\n", " T: 26.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t60417\t84975.4\t0\t60417\n", "4\t13017\t21243.8\t0\t13017\n", "5\t1517\t5311.0\t0\t1517\n", "6\t258\t1327.7\t0\t258\n", "7\t186\t331.9\t0\t186\n", "8\t158\t331.9\t0\t158\n", "9\t147\t331.9\t0\t147\n", "10\t153\t331.9\t0\t153\n", "11\t152\t331.9\t0\t152\n", "12\t158\t331.9\t0\t158\n", "13\t144\t331.9\t0\t144\n", "14\t157\t331.9\t0\t157\n", "15\t180\t331.9\t0\t180\n", "16\t166\t331.9\t0\t166\n", "17\t162\t331.9\t0\t162\n", "18\t174\t331.9\t0\t174\n", "19\t153\t331.9\t0\t153\n", "20\t162\t331.9\t0\t162\n", "21\t121\t331.9\t0\t121\n", "22\t114\t331.9\t0\t114\n", "23\t111\t331.9\t0\t111\n", "24\t93\t331.9\t0\t93\n", "25\t109\t331.9\t0\t109\n", "26\t131\t331.9\t0\t131\n", "27\t123\t331.9\t0\t123\n", "28\t120\t331.9\t0\t120\n", "29\t89\t331.9\t0\t89\n", "30\t125\t331.9\t0\t125\n", "31\t121\t331.9\t0\t121\n", "32\t138\t331.9\t0\t138\n", "33\t112\t331.9\t0\t112\n", "34\t106\t331.9\t0\t106\n", "35\t111\t331.9\t0\t111\n", "36\t99\t331.9\t0\t99\n", "37\t125\t331.9\t0\t125\n", "38\t86\t331.9\t0\t86\n", "39\t138\t331.9\t0\t138\n", "40\t85\t331.9\t0\t85\n", "41\t106\t331.9\t0\t106\n", "42\t101\t331.9\t0\t101\n", "43\t129\t331.9\t0\t129\n", "44\t47\t331.9\t0\t47\n", "45\t93\t331.9\t0\t93\n", "46\t99\t331.9\t0\t99\n", "47\t92\t331.9\t0\t92\n", "48\t91\t331.9\t0\t91\n", "49\t96\t331.9\t0\t96\n", "50\t93\t331.9\t0\t93\n", "51\t78\t331.9\t0\t78\n", "52\t105\t331.9\t0\t105\n", "53\t110\t331.9\t0\t110\n", "54\t100\t331.9\t0\t100\n", "55\t105\t331.9\t0\t105\n", "56\t122\t331.9\t0\t122\n", "57\t87\t331.9\t0\t87\n", "58\t153\t331.9\t0\t153\n", "59\t104\t331.9\t0\t104\n", "60\t131\t331.9\t0\t131\n", "61\t132\t331.9\t0\t132\n", "62\t111\t331.9\t0\t111\n", "63\t63\t331.9\t0\t63\n", "64\t129\t331.9\t0\t129\n", "65\t84\t331.9\t0\t84\n", "66\t95\t331.9\t0\t95\n", "67\t76\t331.9\t0\t76\n", "68\t65\t331.9\t0\t65\n", "69\t38\t331.9\t0\t38\n", "70\t38\t331.9\t0\t38\n", "71\t47\t331.9\t0\t47\n", "72\t54\t331.9\t0\t54\n", "73\t38\t331.9\t0\t38\n", "74\t49\t331.9\t0\t49\n", "75\t52\t331.9\t0\t52\n", "76\t64\t331.9\t0\t64\n", "77\t56\t331.9\t0\t56\n", "78\t31\t331.9\t0\t31\n", "79\t29\t331.9\t0\t29\n", "80\t47\t331.9\t0\t47\n", "81\t54\t331.9\t0\t54\n", "82\t42\t331.9\t0\t42\n", "83\t50\t331.9\t0\t50\n", "84\t43\t331.9\t0\t43\n", "85\t42\t331.9\t0\t42\n", "86\t34\t331.9\t0\t34\n", "87\t38\t331.9\t0\t38\n", "88\t90\t331.9\t0\t90\n", "89\t71\t331.9\t0\t71\n", "90\t48\t331.9\t0\t48\n", "91\t29\t331.9\t0\t29\n", "92\t27\t331.9\t0\t27\n", "93\t35\t331.9\t0\t35\n", "94\t22\t331.9\t0\t22\n", "95\t17\t331.9\t0\t17\n", "96\t32\t331.9\t0\t32\n", "97\t57\t331.9\t0\t57\n", "98\t65\t331.9\t0\t65\n", "99\t95\t331.9\t0\t95\n", "100\t71\t331.9\t0\t71\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 443_S36_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/443.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 78.13 s (13 us/read; 4.74 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,168,835\n", "Reads with adapters: 3,652,396 (59.2%)\n", "Reads written (passing filters): 6,046,395 (98.0%)\n", "\n", "Total basepairs processed: 616,883,500 bp\n", "Quality-trimmed: 1,522,829 bp (0.2%)\n", "Total written (filtered): 488,143,753 bp (79.1%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3520409 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.3%\n", " G: 36.1%\n", " T: 36.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t146376\t96388.0\t0\t146376\n", "4\t81736\t24097.0\t0\t81736\n", "5\t61737\t6024.3\t0\t61737\n", "6\t49339\t1506.1\t0\t49339\n", "7\t44256\t376.5\t0\t44256\n", "8\t45285\t94.1\t0\t45285\n", "9\t42666\t94.1\t0\t42666\n", "10\t39908\t94.1\t0\t39908\n", "11\t40753\t94.1\t0\t40753\n", "12\t41211\t94.1\t0\t41211\n", "13\t43868\t94.1\t0\t43868\n", "14\t44262\t94.1\t0\t44262\n", "15\t43864\t94.1\t0\t43864\n", "16\t46961\t94.1\t0\t46961\n", "17\t51783\t94.1\t0\t51783\n", "18\t60204\t94.1\t0\t60204\n", "19\t54047\t94.1\t0\t54047\n", "20\t45373\t94.1\t0\t45373\n", "21\t44154\t94.1\t0\t44154\n", "22\t41266\t94.1\t0\t41266\n", "23\t45721\t94.1\t0\t45721\n", "24\t53226\t94.1\t0\t53226\n", "25\t52904\t94.1\t0\t52904\n", "26\t59623\t94.1\t0\t59623\n", "27\t67914\t94.1\t0\t67914\n", "28\t62152\t94.1\t0\t62152\n", "29\t59889\t94.1\t0\t59889\n", "30\t64319\t94.1\t0\t64319\n", "31\t68510\t94.1\t0\t68510\n", "32\t67019\t94.1\t0\t67019\n", "33\t60209\t94.1\t0\t60209\n", "34\t56141\t94.1\t0\t56141\n", "35\t64280\t94.1\t0\t64280\n", "36\t76316\t94.1\t0\t76316\n", "37\t81662\t94.1\t0\t81662\n", "38\t67930\t94.1\t0\t67930\n", "39\t52367\t94.1\t0\t52367\n", "40\t49904\t94.1\t0\t49904\n", "41\t50558\t94.1\t0\t50558\n", "42\t54792\t94.1\t0\t54792\n", "43\t48493\t94.1\t0\t48493\n", "44\t40041\t94.1\t0\t40041\n", "45\t51333\t94.1\t0\t51333\n", "46\t61793\t94.1\t0\t61793\n", "47\t56857\t94.1\t0\t56857\n", "48\t57150\t94.1\t0\t57150\n", "49\t43110\t94.1\t0\t43110\n", "50\t40317\t94.1\t0\t40317\n", "51\t36329\t94.1\t0\t36329\n", "52\t37654\t94.1\t0\t37654\n", "53\t40898\t94.1\t0\t40898\n", "54\t47167\t94.1\t0\t47167\n", "55\t51388\t94.1\t0\t51388\n", "56\t47913\t94.1\t0\t47913\n", "57\t37715\t94.1\t0\t37715\n", "58\t36269\t94.1\t0\t36269\n", "59\t30189\t94.1\t0\t30189\n", "60\t26465\t94.1\t0\t26465\n", "61\t25974\t94.1\t0\t25974\n", "62\t20922\t94.1\t0\t20922\n", "63\t20293\t94.1\t0\t20293\n", "64\t23669\t94.1\t0\t23669\n", "65\t23267\t94.1\t0\t23267\n", "66\t20670\t94.1\t0\t20670\n", "67\t19803\t94.1\t0\t19803\n", "68\t19020\t94.1\t0\t19020\n", "69\t19051\t94.1\t0\t19051\n", "70\t19867\t94.1\t0\t19867\n", "71\t18702\t94.1\t0\t18702\n", "72\t14867\t94.1\t0\t14867\n", "73\t13752\t94.1\t0\t13752\n", "74\t13830\t94.1\t0\t13830\n", "75\t11318\t94.1\t0\t11318\n", "76\t9570\t94.1\t0\t9570\n", "77\t8550\t94.1\t0\t8550\n", "78\t9476\t94.1\t0\t9476\n", "79\t9056\t94.1\t0\t9056\n", "80\t8901\t94.1\t0\t8901\n", "81\t7986\t94.1\t0\t7986\n", "82\t7612\t94.1\t0\t7612\n", "83\t8265\t94.1\t0\t8265\n", "84\t9028\t94.1\t0\t9028\n", "85\t10363\t94.1\t0\t10363\n", "86\t9324\t94.1\t0\t9324\n", "87\t6209\t94.1\t0\t6209\n", "88\t5697\t94.1\t0\t5697\n", "89\t5924\t94.1\t0\t5924\n", "90\t6090\t94.1\t0\t6090\n", "91\t6258\t94.1\t0\t6258\n", "92\t5663\t94.1\t0\t5663\n", "93\t5636\t94.1\t0\t5636\n", "94\t5223\t94.1\t0\t5223\n", "95\t4382\t94.1\t0\t4382\n", "96\t3385\t94.1\t0\t3385\n", "97\t2407\t94.1\t0\t2407\n", "98\t1635\t94.1\t0\t1635\n", "99\t1795\t94.1\t0\t1795\n", "100\t1403\t94.1\t0\t1403\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 17430 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 55.3%\n", " C: 17.1%\n", " G: 0.0%\n", " T: 27.5%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t8689\t96388.0\t0\t8689\n", "4\t1804\t24097.0\t0\t1804\n", "5\t598\t6024.3\t0\t598\n", "6\t286\t1506.1\t0\t286\n", "7\t135\t376.5\t0\t135\n", "8\t100\t94.1\t0\t100\n", "9\t114\t94.1\t0\t114\n", "10\t71\t94.1\t0\t71\n", "11\t88\t94.1\t0\t88\n", "12\t88\t94.1\t0\t88\n", "13\t94\t94.1\t0\t94\n", "14\t83\t94.1\t0\t83\n", "15\t77\t94.1\t0\t77\n", "16\t68\t94.1\t0\t68\n", "17\t92\t94.1\t0\t92\n", "18\t98\t94.1\t0\t98\n", "19\t162\t94.1\t0\t162\n", "20\t244\t94.1\t0\t244\n", "21\t203\t94.1\t0\t203\n", "22\t149\t94.1\t0\t149\n", "23\t101\t94.1\t0\t101\n", "24\t92\t94.1\t0\t92\n", "25\t93\t94.1\t0\t93\n", "26\t119\t94.1\t0\t119\n", "27\t137\t94.1\t0\t137\n", "28\t100\t94.1\t0\t100\n", "29\t128\t94.1\t0\t128\n", "30\t181\t94.1\t0\t181\n", "31\t251\t94.1\t0\t251\n", "32\t383\t94.1\t0\t383\n", "33\t338\t94.1\t0\t338\n", "34\t393\t94.1\t0\t393\n", "35\t509\t94.1\t0\t509\n", "36\t462\t94.1\t0\t462\n", "37\t198\t94.1\t0\t198\n", "38\t30\t94.1\t0\t30\n", "39\t24\t94.1\t0\t24\n", "40\t23\t94.1\t0\t23\n", "41\t19\t94.1\t0\t19\n", "42\t19\t94.1\t0\t19\n", "43\t14\t94.1\t0\t14\n", "44\t16\t94.1\t0\t16\n", "45\t15\t94.1\t0\t15\n", "46\t16\t94.1\t0\t16\n", "47\t16\t94.1\t0\t16\n", "48\t12\t94.1\t0\t12\n", "49\t23\t94.1\t0\t23\n", "50\t24\t94.1\t0\t24\n", "51\t13\t94.1\t0\t13\n", "52\t23\t94.1\t0\t23\n", "53\t9\t94.1\t0\t9\n", "54\t9\t94.1\t0\t9\n", "55\t13\t94.1\t0\t13\n", "56\t7\t94.1\t0\t7\n", "57\t13\t94.1\t0\t13\n", "58\t14\t94.1\t0\t14\n", "59\t9\t94.1\t0\t9\n", "60\t10\t94.1\t0\t10\n", "61\t3\t94.1\t0\t3\n", "62\t6\t94.1\t0\t6\n", "63\t10\t94.1\t0\t10\n", "64\t3\t94.1\t0\t3\n", "65\t4\t94.1\t0\t4\n", "66\t4\t94.1\t0\t4\n", "67\t10\t94.1\t0\t10\n", "68\t5\t94.1\t0\t5\n", "69\t8\t94.1\t0\t8\n", "70\t2\t94.1\t0\t2\n", "71\t3\t94.1\t0\t3\n", "72\t2\t94.1\t0\t2\n", "73\t5\t94.1\t0\t5\n", "74\t6\t94.1\t0\t6\n", "75\t2\t94.1\t0\t2\n", "76\t2\t94.1\t0\t2\n", "77\t2\t94.1\t0\t2\n", "78\t2\t94.1\t0\t2\n", "79\t2\t94.1\t0\t2\n", "80\t3\t94.1\t0\t3\n", "81\t1\t94.1\t0\t1\n", "82\t4\t94.1\t0\t4\n", "83\t2\t94.1\t0\t2\n", "84\t3\t94.1\t0\t3\n", "85\t7\t94.1\t0\t7\n", "86\t1\t94.1\t0\t1\n", "87\t10\t94.1\t0\t10\n", "88\t2\t94.1\t0\t2\n", "89\t2\t94.1\t0\t2\n", "90\t4\t94.1\t0\t4\n", "91\t4\t94.1\t0\t4\n", "92\t6\t94.1\t0\t6\n", "93\t14\t94.1\t0\t14\n", "94\t31\t94.1\t0\t31\n", "95\t35\t94.1\t0\t35\n", "96\t24\t94.1\t0\t24\n", "97\t12\t94.1\t0\t12\n", "98\t34\t94.1\t0\t34\n", "99\t23\t94.1\t0\t23\n", "100\t28\t94.1\t0\t28\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 114557 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.8%\n", " C: 17.6%\n", " G: 12.3%\n", " T: 27.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t78745\t96388.0\t0\t78745\n", "4\t20950\t24097.0\t0\t20950\n", "5\t3757\t6024.3\t0\t3757\n", "6\t291\t1506.1\t0\t291\n", "7\t147\t376.5\t0\t147\n", "8\t134\t376.5\t0\t134\n", "9\t117\t376.5\t0\t117\n", "10\t175\t376.5\t0\t175\n", "11\t152\t376.5\t0\t152\n", "12\t152\t376.5\t0\t152\n", "13\t181\t376.5\t0\t181\n", "14\t143\t376.5\t0\t143\n", "15\t169\t376.5\t0\t169\n", "16\t140\t376.5\t0\t140\n", "17\t148\t376.5\t0\t148\n", "18\t154\t376.5\t0\t154\n", "19\t118\t376.5\t0\t118\n", "20\t146\t376.5\t0\t146\n", "21\t133\t376.5\t0\t133\n", "22\t130\t376.5\t0\t130\n", "23\t116\t376.5\t0\t116\n", "24\t111\t376.5\t0\t111\n", "25\t100\t376.5\t0\t100\n", "26\t111\t376.5\t0\t111\n", "27\t118\t376.5\t0\t118\n", "28\t115\t376.5\t0\t115\n", "29\t124\t376.5\t0\t124\n", "30\t129\t376.5\t0\t129\n", "31\t112\t376.5\t0\t112\n", "32\t133\t376.5\t0\t133\n", "33\t108\t376.5\t0\t108\n", "34\t124\t376.5\t0\t124\n", "35\t133\t376.5\t0\t133\n", "36\t130\t376.5\t0\t130\n", "37\t158\t376.5\t0\t158\n", "38\t159\t376.5\t0\t159\n", "39\t209\t376.5\t0\t209\n", "40\t175\t376.5\t0\t175\n", "41\t142\t376.5\t0\t142\n", "42\t101\t376.5\t0\t101\n", "43\t131\t376.5\t0\t131\n", "44\t101\t376.5\t0\t101\n", "45\t119\t376.5\t0\t119\n", "46\t152\t376.5\t0\t152\n", "47\t129\t376.5\t0\t129\n", "48\t122\t376.5\t0\t122\n", "49\t94\t376.5\t0\t94\n", "50\t101\t376.5\t0\t101\n", "51\t85\t376.5\t0\t85\n", "52\t94\t376.5\t0\t94\n", "53\t103\t376.5\t0\t103\n", "54\t102\t376.5\t0\t102\n", "55\t93\t376.5\t0\t93\n", "56\t85\t376.5\t0\t85\n", "57\t69\t376.5\t0\t69\n", "58\t109\t376.5\t0\t109\n", "59\t118\t376.5\t0\t118\n", "60\t124\t376.5\t0\t124\n", "61\t111\t376.5\t0\t111\n", "62\t107\t376.5\t0\t107\n", "63\t81\t376.5\t0\t81\n", "64\t82\t376.5\t0\t82\n", "65\t108\t376.5\t0\t108\n", "66\t89\t376.5\t0\t89\n", "67\t76\t376.5\t0\t76\n", "68\t78\t376.5\t0\t78\n", "69\t57\t376.5\t0\t57\n", "70\t64\t376.5\t0\t64\n", "71\t75\t376.5\t0\t75\n", "72\t100\t376.5\t0\t100\n", "73\t125\t376.5\t0\t125\n", "74\t129\t376.5\t0\t129\n", "75\t65\t376.5\t0\t65\n", "76\t116\t376.5\t0\t116\n", "77\t127\t376.5\t0\t127\n", "78\t128\t376.5\t0\t128\n", "79\t108\t376.5\t0\t108\n", "80\t116\t376.5\t0\t116\n", "81\t138\t376.5\t0\t138\n", "82\t216\t376.5\t0\t216\n", "83\t141\t376.5\t0\t141\n", "84\t112\t376.5\t0\t112\n", "85\t108\t376.5\t0\t108\n", "86\t75\t376.5\t0\t75\n", "87\t100\t376.5\t0\t100\n", "88\t135\t376.5\t0\t135\n", "89\t104\t376.5\t0\t104\n", "90\t62\t376.5\t0\t62\n", "91\t68\t376.5\t0\t68\n", "92\t45\t376.5\t0\t45\n", "93\t54\t376.5\t0\t54\n", "94\t50\t376.5\t0\t50\n", "95\t41\t376.5\t0\t41\n", "96\t58\t376.5\t0\t58\n", "97\t93\t376.5\t0\t93\n", "98\t115\t376.5\t0\t115\n", "99\t143\t376.5\t0\t143\n", "100\t136\t376.5\t0\t136\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 444_S34_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/444.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 103.81 s (13 us/read; 4.66 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,059,379\n", "Reads with adapters: 4,713,281 (58.5%)\n", "Reads written (passing filters): 7,946,834 (98.6%)\n", "\n", "Total basepairs processed: 805,937,900 bp\n", "Quality-trimmed: 1,970,436 bp (0.2%)\n", "Total written (filtered): 651,610,586 bp (80.9%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4588869 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 26.6%\n", " G: 33.2%\n", " T: 40.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t207726\t125927.8\t0\t207726\n", "4\t124893\t31481.9\t0\t124893\n", "5\t94867\t7870.5\t0\t94867\n", "6\t74418\t1967.6\t0\t74418\n", "7\t66260\t491.9\t0\t66260\n", "8\t64056\t123.0\t0\t64056\n", "9\t62909\t123.0\t0\t62909\n", "10\t58553\t123.0\t0\t58553\n", "11\t59646\t123.0\t0\t59646\n", "12\t58768\t123.0\t0\t58768\n", "13\t59496\t123.0\t0\t59496\n", "14\t61335\t123.0\t0\t61335\n", "15\t61952\t123.0\t0\t61952\n", "16\t64575\t123.0\t0\t64575\n", "17\t73679\t123.0\t0\t73679\n", "18\t86080\t123.0\t0\t86080\n", "19\t80167\t123.0\t0\t80167\n", "20\t67458\t123.0\t0\t67458\n", "21\t65458\t123.0\t0\t65458\n", "22\t58891\t123.0\t0\t58891\n", "23\t65859\t123.0\t0\t65859\n", "24\t76870\t123.0\t0\t76870\n", "25\t76650\t123.0\t0\t76650\n", "26\t86591\t123.0\t0\t86591\n", "27\t99396\t123.0\t0\t99396\n", "28\t91146\t123.0\t0\t91146\n", "29\t86998\t123.0\t0\t86998\n", "30\t90359\t123.0\t0\t90359\n", "31\t94383\t123.0\t0\t94383\n", "32\t91964\t123.0\t0\t91964\n", "33\t79774\t123.0\t0\t79774\n", "34\t74551\t123.0\t0\t74551\n", "35\t84357\t123.0\t0\t84357\n", "36\t100067\t123.0\t0\t100067\n", "37\t102679\t123.0\t0\t102679\n", "38\t85916\t123.0\t0\t85916\n", "39\t67861\t123.0\t0\t67861\n", "40\t62306\t123.0\t0\t62306\n", "41\t62800\t123.0\t0\t62800\n", "42\t68890\t123.0\t0\t68890\n", "43\t61654\t123.0\t0\t61654\n", "44\t51068\t123.0\t0\t51068\n", "45\t67123\t123.0\t0\t67123\n", "46\t81557\t123.0\t0\t81557\n", "47\t76394\t123.0\t0\t76394\n", "48\t79283\t123.0\t0\t79283\n", "49\t63510\t123.0\t0\t63510\n", "50\t55839\t123.0\t0\t55839\n", "51\t46808\t123.0\t0\t46808\n", "52\t42035\t123.0\t0\t42035\n", "53\t42478\t123.0\t0\t42478\n", "54\t50671\t123.0\t0\t50671\n", "55\t54109\t123.0\t0\t54109\n", "56\t48372\t123.0\t0\t48372\n", "57\t42047\t123.0\t0\t42047\n", "58\t46291\t123.0\t0\t46291\n", "59\t36484\t123.0\t0\t36484\n", "60\t29949\t123.0\t0\t29949\n", "61\t28206\t123.0\t0\t28206\n", "62\t23423\t123.0\t0\t23423\n", "63\t24686\t123.0\t0\t24686\n", "64\t27897\t123.0\t0\t27897\n", "65\t22023\t123.0\t0\t22023\n", "66\t18918\t123.0\t0\t18918\n", "67\t19529\t123.0\t0\t19529\n", "68\t17715\t123.0\t0\t17715\n", "69\t17840\t123.0\t0\t17840\n", "70\t20262\t123.0\t0\t20262\n", "71\t17367\t123.0\t0\t17367\n", "72\t13135\t123.0\t0\t13135\n", "73\t9733\t123.0\t0\t9733\n", "74\t8463\t123.0\t0\t8463\n", "75\t7637\t123.0\t0\t7637\n", "76\t6366\t123.0\t0\t6366\n", "77\t7023\t123.0\t0\t7023\n", "78\t8748\t123.0\t0\t8748\n", "79\t6845\t123.0\t0\t6845\n", "80\t6215\t123.0\t0\t6215\n", "81\t6302\t123.0\t0\t6302\n", "82\t6146\t123.0\t0\t6146\n", "83\t5871\t123.0\t0\t5871\n", "84\t7483\t123.0\t0\t7483\n", "85\t9579\t123.0\t0\t9579\n", "86\t10185\t123.0\t0\t10185\n", "87\t6953\t123.0\t0\t6953\n", "88\t5554\t123.0\t0\t5554\n", "89\t5640\t123.0\t0\t5640\n", "90\t6075\t123.0\t0\t6075\n", "91\t5722\t123.0\t0\t5722\n", "92\t5252\t123.0\t0\t5252\n", "93\t5016\t123.0\t0\t5016\n", "94\t4477\t123.0\t0\t4477\n", "95\t3840\t123.0\t0\t3840\n", "96\t2580\t123.0\t0\t2580\n", "97\t1584\t123.0\t0\t1584\n", "98\t968\t123.0\t0\t968\n", "99\t774\t123.0\t0\t774\n", "100\t561\t123.0\t0\t561\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 17377 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 58.9%\n", " C: 13.3%\n", " G: 0.0%\n", " T: 27.6%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t7111\t125927.8\t0\t7111\n", "4\t1642\t31481.9\t0\t1642\n", "5\t425\t7870.5\t0\t425\n", "6\t146\t1967.6\t0\t146\n", "7\t100\t491.9\t0\t100\n", "8\t72\t123.0\t0\t72\n", "9\t66\t123.0\t0\t66\n", "10\t48\t123.0\t0\t48\n", "11\t59\t123.0\t0\t59\n", "12\t52\t123.0\t0\t52\n", "13\t60\t123.0\t0\t60\n", "14\t57\t123.0\t0\t57\n", "15\t57\t123.0\t0\t57\n", "16\t46\t123.0\t0\t46\n", "17\t59\t123.0\t0\t59\n", "18\t70\t123.0\t0\t70\n", "19\t117\t123.0\t0\t117\n", "20\t117\t123.0\t0\t117\n", "21\t72\t123.0\t0\t72\n", "22\t64\t123.0\t0\t64\n", "23\t72\t123.0\t0\t72\n", "24\t94\t123.0\t0\t94\n", "25\t86\t123.0\t0\t86\n", "26\t104\t123.0\t0\t104\n", "27\t133\t123.0\t0\t133\n", "28\t157\t123.0\t0\t157\n", "29\t232\t123.0\t0\t232\n", "30\t432\t123.0\t0\t432\n", "31\t495\t123.0\t0\t495\n", "32\t716\t123.0\t0\t716\n", "33\t733\t123.0\t0\t733\n", "34\t863\t123.0\t0\t863\n", "35\t1087\t123.0\t0\t1087\n", "36\t787\t123.0\t0\t787\n", "37\t302\t123.0\t0\t302\n", "38\t71\t123.0\t0\t71\n", "39\t14\t123.0\t0\t14\n", "40\t21\t123.0\t0\t21\n", "41\t14\t123.0\t0\t14\n", "42\t17\t123.0\t0\t17\n", "43\t15\t123.0\t0\t15\n", "44\t10\t123.0\t0\t10\n", "45\t5\t123.0\t0\t5\n", "46\t7\t123.0\t0\t7\n", "47\t13\t123.0\t0\t13\n", "48\t10\t123.0\t0\t10\n", "49\t7\t123.0\t0\t7\n", "50\t12\t123.0\t0\t12\n", "51\t5\t123.0\t0\t5\n", "52\t5\t123.0\t0\t5\n", "53\t5\t123.0\t0\t5\n", "54\t9\t123.0\t0\t9\n", "55\t7\t123.0\t0\t7\n", "56\t7\t123.0\t0\t7\n", "57\t4\t123.0\t0\t4\n", "58\t6\t123.0\t0\t6\n", "59\t5\t123.0\t0\t5\n", "60\t3\t123.0\t0\t3\n", "61\t2\t123.0\t0\t2\n", "62\t2\t123.0\t0\t2\n", "63\t4\t123.0\t0\t4\n", "64\t1\t123.0\t0\t1\n", "65\t4\t123.0\t0\t4\n", "66\t2\t123.0\t0\t2\n", "67\t2\t123.0\t0\t2\n", "71\t1\t123.0\t0\t1\n", "73\t1\t123.0\t0\t1\n", "74\t1\t123.0\t0\t1\n", "75\t1\t123.0\t0\t1\n", "76\t1\t123.0\t0\t1\n", "77\t1\t123.0\t0\t1\n", "78\t2\t123.0\t0\t2\n", "81\t3\t123.0\t0\t3\n", "82\t3\t123.0\t0\t3\n", "83\t2\t123.0\t0\t2\n", "85\t1\t123.0\t0\t1\n", "87\t1\t123.0\t0\t1\n", "88\t1\t123.0\t0\t1\n", "89\t1\t123.0\t0\t1\n", "90\t5\t123.0\t0\t5\n", "91\t1\t123.0\t0\t1\n", "92\t3\t123.0\t0\t3\n", "93\t30\t123.0\t0\t30\n", "94\t60\t123.0\t0\t60\n", "95\t59\t123.0\t0\t59\n", "96\t22\t123.0\t0\t22\n", "97\t29\t123.0\t0\t29\n", "98\t24\t123.0\t0\t24\n", "99\t30\t123.0\t0\t30\n", "100\t72\t123.0\t0\t72\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 107035 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 49.8%\n", " C: 14.3%\n", " G: 11.5%\n", " T: 24.3%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t75520\t125927.8\t0\t75520\n", "4\t20275\t31481.9\t0\t20275\n", "5\t4967\t7870.5\t0\t4967\n", "6\t157\t1967.6\t0\t157\n", "7\t48\t491.9\t0\t48\n", "8\t67\t491.9\t0\t67\n", "9\t59\t491.9\t0\t59\n", "10\t69\t491.9\t0\t69\n", "11\t69\t491.9\t0\t69\n", "12\t68\t491.9\t0\t68\n", "13\t60\t491.9\t0\t60\n", "14\t48\t491.9\t0\t48\n", "15\t44\t491.9\t0\t44\n", "16\t27\t491.9\t0\t27\n", "17\t45\t491.9\t0\t45\n", "18\t38\t491.9\t0\t38\n", "19\t44\t491.9\t0\t44\n", "20\t48\t491.9\t0\t48\n", "21\t39\t491.9\t0\t39\n", "22\t44\t491.9\t0\t44\n", "23\t23\t491.9\t0\t23\n", "24\t40\t491.9\t0\t40\n", "25\t43\t491.9\t0\t43\n", "26\t35\t491.9\t0\t35\n", "27\t47\t491.9\t0\t47\n", "28\t38\t491.9\t0\t38\n", "29\t41\t491.9\t0\t41\n", "30\t41\t491.9\t0\t41\n", "31\t55\t491.9\t0\t55\n", "32\t50\t491.9\t0\t50\n", "33\t45\t491.9\t0\t45\n", "34\t47\t491.9\t0\t47\n", "35\t39\t491.9\t0\t39\n", "36\t42\t491.9\t0\t42\n", "37\t40\t491.9\t0\t40\n", "38\t39\t491.9\t0\t39\n", "39\t57\t491.9\t0\t57\n", "40\t65\t491.9\t0\t65\n", "41\t45\t491.9\t0\t45\n", "42\t38\t491.9\t0\t38\n", "43\t39\t491.9\t0\t39\n", "44\t51\t491.9\t0\t51\n", "45\t47\t491.9\t0\t47\n", "46\t58\t491.9\t0\t58\n", "47\t44\t491.9\t0\t44\n", "48\t52\t491.9\t0\t52\n", "49\t37\t491.9\t0\t37\n", "50\t41\t491.9\t0\t41\n", "51\t43\t491.9\t0\t43\n", "52\t65\t491.9\t0\t65\n", "53\t40\t491.9\t0\t40\n", "54\t51\t491.9\t0\t51\n", "55\t35\t491.9\t0\t35\n", "56\t38\t491.9\t0\t38\n", "57\t43\t491.9\t0\t43\n", "58\t50\t491.9\t0\t50\n", "59\t32\t491.9\t0\t32\n", "60\t50\t491.9\t0\t50\n", "61\t57\t491.9\t0\t57\n", "62\t49\t491.9\t0\t49\n", "63\t60\t491.9\t0\t60\n", "64\t67\t491.9\t0\t67\n", "65\t43\t491.9\t0\t43\n", "66\t60\t491.9\t0\t60\n", "67\t51\t491.9\t0\t51\n", "68\t30\t491.9\t0\t30\n", "69\t42\t491.9\t0\t42\n", "70\t35\t491.9\t0\t35\n", "71\t52\t491.9\t0\t52\n", "72\t99\t491.9\t0\t99\n", "73\t146\t491.9\t0\t146\n", "74\t151\t491.9\t0\t151\n", "75\t87\t491.9\t0\t87\n", "76\t98\t491.9\t0\t98\n", "77\t141\t491.9\t0\t141\n", "78\t133\t491.9\t0\t133\n", "79\t126\t491.9\t0\t126\n", "80\t145\t491.9\t0\t145\n", "81\t160\t491.9\t0\t160\n", "82\t175\t491.9\t0\t175\n", "83\t163\t491.9\t0\t163\n", "84\t93\t491.9\t0\t93\n", "85\t101\t491.9\t0\t101\n", "86\t88\t491.9\t0\t88\n", "87\t81\t491.9\t0\t81\n", "88\t92\t491.9\t0\t92\n", "89\t60\t491.9\t0\t60\n", "90\t55\t491.9\t0\t55\n", "91\t50\t491.9\t0\t50\n", "92\t52\t491.9\t0\t52\n", "93\t38\t491.9\t0\t38\n", "94\t46\t491.9\t0\t46\n", "95\t63\t491.9\t0\t63\n", "96\t53\t491.9\t0\t53\n", "97\t114\t491.9\t0\t114\n", "98\t124\t491.9\t0\t124\n", "99\t139\t491.9\t0\t139\n", "100\t194\t491.9\t0\t194\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 445_S45_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/445.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 84.00 s (13 us/read; 4.74 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,632,469\n", "Reads with adapters: 3,655,257 (55.1%)\n", "Reads written (passing filters): 6,518,991 (98.3%)\n", "\n", "Total basepairs processed: 663,246,900 bp\n", "Quality-trimmed: 1,510,255 bp (0.2%)\n", "Total written (filtered): 541,275,173 bp (81.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3497921 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.0%\n", " G: 39.2%\n", " T: 29.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t157062\t103632.3\t0\t157062\n", "4\t89565\t25908.1\t0\t89565\n", "5\t68203\t6477.0\t0\t68203\n", "6\t55269\t1619.3\t0\t55269\n", "7\t49145\t404.8\t0\t49145\n", "8\t48422\t101.2\t0\t48422\n", "9\t47738\t101.2\t0\t47738\n", "10\t46120\t101.2\t0\t46120\n", "11\t46527\t101.2\t0\t46527\n", "12\t46679\t101.2\t0\t46679\n", "13\t49560\t101.2\t0\t49560\n", "14\t50850\t101.2\t0\t50850\n", "15\t49711\t101.2\t0\t49711\n", "16\t51495\t101.2\t0\t51495\n", "17\t54878\t101.2\t0\t54878\n", "18\t63783\t101.2\t0\t63783\n", "19\t61175\t101.2\t0\t61175\n", "20\t50741\t101.2\t0\t50741\n", "21\t48143\t101.2\t0\t48143\n", "22\t43686\t101.2\t0\t43686\n", "23\t46990\t101.2\t0\t46990\n", "24\t54347\t101.2\t0\t54347\n", "25\t56301\t101.2\t0\t56301\n", "26\t62890\t101.2\t0\t62890\n", "27\t67756\t101.2\t0\t67756\n", "28\t61821\t101.2\t0\t61821\n", "29\t60890\t101.2\t0\t60890\n", "30\t61687\t101.2\t0\t61687\n", "31\t66385\t101.2\t0\t66385\n", "32\t63034\t101.2\t0\t63034\n", "33\t58092\t101.2\t0\t58092\n", "34\t56249\t101.2\t0\t56249\n", "35\t63251\t101.2\t0\t63251\n", "36\t72452\t101.2\t0\t72452\n", "37\t73227\t101.2\t0\t73227\n", "38\t59903\t101.2\t0\t59903\n", "39\t50957\t101.2\t0\t50957\n", "40\t49452\t101.2\t0\t49452\n", "41\t53444\t101.2\t0\t53444\n", "42\t57045\t101.2\t0\t57045\n", "43\t50372\t101.2\t0\t50372\n", "44\t41541\t101.2\t0\t41541\n", "45\t52173\t101.2\t0\t52173\n", "46\t61411\t101.2\t0\t61411\n", "47\t52322\t101.2\t0\t52322\n", "48\t50883\t101.2\t0\t50883\n", "49\t42016\t101.2\t0\t42016\n", "50\t40566\t101.2\t0\t40566\n", "51\t36488\t101.2\t0\t36488\n", "52\t36831\t101.2\t0\t36831\n", "53\t36119\t101.2\t0\t36119\n", "54\t36713\t101.2\t0\t36713\n", "55\t36907\t101.2\t0\t36907\n", "56\t36372\t101.2\t0\t36372\n", "57\t36264\t101.2\t0\t36264\n", "58\t37729\t101.2\t0\t37729\n", "59\t32416\t101.2\t0\t32416\n", "60\t26114\t101.2\t0\t26114\n", "61\t22977\t101.2\t0\t22977\n", "62\t19134\t101.2\t0\t19134\n", "63\t18570\t101.2\t0\t18570\n", "64\t20624\t101.2\t0\t20624\n", "65\t19232\t101.2\t0\t19232\n", "66\t15723\t101.2\t0\t15723\n", "67\t16068\t101.2\t0\t16068\n", "68\t15866\t101.2\t0\t15866\n", "69\t16493\t101.2\t0\t16493\n", "70\t17752\t101.2\t0\t17752\n", "71\t16682\t101.2\t0\t16682\n", "72\t12632\t101.2\t0\t12632\n", "73\t10022\t101.2\t0\t10022\n", "74\t9525\t101.2\t0\t9525\n", "75\t8505\t101.2\t0\t8505\n", "76\t6767\t101.2\t0\t6767\n", "77\t7050\t101.2\t0\t7050\n", "78\t8639\t101.2\t0\t8639\n", "79\t7365\t101.2\t0\t7365\n", "80\t6759\t101.2\t0\t6759\n", "81\t6766\t101.2\t0\t6766\n", "82\t6162\t101.2\t0\t6162\n", "83\t6192\t101.2\t0\t6192\n", "84\t7339\t101.2\t0\t7339\n", "85\t8150\t101.2\t0\t8150\n", "86\t8075\t101.2\t0\t8075\n", "87\t5947\t101.2\t0\t5947\n", "88\t5410\t101.2\t0\t5410\n", "89\t5296\t101.2\t0\t5296\n", "90\t5687\t101.2\t0\t5687\n", "91\t6048\t101.2\t0\t6048\n", "92\t6008\t101.2\t0\t6008\n", "93\t6174\t101.2\t0\t6174\n", "94\t5739\t101.2\t0\t5739\n", "95\t4822\t101.2\t0\t4822\n", "96\t3514\t101.2\t0\t3514\n", "97\t2199\t101.2\t0\t2199\n", "98\t1359\t101.2\t0\t1359\n", "99\t1546\t101.2\t0\t1546\n", "100\t941\t101.2\t0\t941\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 30822 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 47.0%\n", " C: 27.1%\n", " G: 0.0%\n", " T: 25.8%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t16301\t103632.3\t0\t16301\n", "4\t3695\t25908.1\t0\t3695\n", "5\t1209\t6477.0\t0\t1209\n", "6\t755\t1619.3\t0\t755\n", "7\t140\t404.8\t0\t140\n", "8\t108\t101.2\t0\t108\n", "9\t102\t101.2\t0\t102\n", "10\t93\t101.2\t0\t93\n", "11\t88\t101.2\t0\t88\n", "12\t85\t101.2\t0\t85\n", "13\t83\t101.2\t0\t83\n", "14\t98\t101.2\t0\t98\n", "15\t97\t101.2\t0\t97\n", "16\t98\t101.2\t0\t98\n", "17\t91\t101.2\t0\t91\n", "18\t118\t101.2\t0\t118\n", "19\t169\t101.2\t0\t169\n", "20\t211\t101.2\t0\t211\n", "21\t167\t101.2\t0\t167\n", "22\t125\t101.2\t0\t125\n", "23\t103\t101.2\t0\t103\n", "24\t88\t101.2\t0\t88\n", "25\t112\t101.2\t0\t112\n", "26\t163\t101.2\t0\t163\n", "27\t172\t101.2\t0\t172\n", "28\t178\t101.2\t0\t178\n", "29\t207\t101.2\t0\t207\n", "30\t370\t101.2\t0\t370\n", "31\t415\t101.2\t0\t415\n", "32\t609\t101.2\t0\t609\n", "33\t602\t101.2\t0\t602\n", "34\t619\t101.2\t0\t619\n", "35\t736\t101.2\t0\t736\n", "36\t607\t101.2\t0\t607\n", "37\t222\t101.2\t0\t222\n", "38\t56\t101.2\t0\t56\n", "39\t47\t101.2\t0\t47\n", "40\t44\t101.2\t0\t44\n", "41\t35\t101.2\t0\t35\n", "42\t47\t101.2\t0\t47\n", "43\t45\t101.2\t0\t45\n", "44\t36\t101.2\t0\t36\n", "45\t44\t101.2\t0\t44\n", "46\t25\t101.2\t0\t25\n", "47\t27\t101.2\t0\t27\n", "48\t34\t101.2\t0\t34\n", "49\t33\t101.2\t0\t33\n", "50\t41\t101.2\t0\t41\n", "51\t33\t101.2\t0\t33\n", "52\t21\t101.2\t0\t21\n", "53\t25\t101.2\t0\t25\n", "54\t25\t101.2\t0\t25\n", "55\t18\t101.2\t0\t18\n", "56\t24\t101.2\t0\t24\n", "57\t23\t101.2\t0\t23\n", "58\t27\t101.2\t0\t27\n", "59\t24\t101.2\t0\t24\n", "60\t24\t101.2\t0\t24\n", "61\t23\t101.2\t0\t23\n", "62\t18\t101.2\t0\t18\n", "63\t14\t101.2\t0\t14\n", "64\t17\t101.2\t0\t17\n", "65\t14\t101.2\t0\t14\n", "66\t19\t101.2\t0\t19\n", "67\t11\t101.2\t0\t11\n", "68\t16\t101.2\t0\t16\n", "69\t22\t101.2\t0\t22\n", "70\t19\t101.2\t0\t19\n", "71\t9\t101.2\t0\t9\n", "72\t11\t101.2\t0\t11\n", "73\t11\t101.2\t0\t11\n", "74\t14\t101.2\t0\t14\n", "75\t8\t101.2\t0\t8\n", "76\t14\t101.2\t0\t14\n", "77\t8\t101.2\t0\t8\n", "78\t8\t101.2\t0\t8\n", "79\t11\t101.2\t0\t11\n", "80\t10\t101.2\t0\t10\n", "81\t15\t101.2\t0\t15\n", "82\t15\t101.2\t0\t15\n", "83\t10\t101.2\t0\t10\n", "84\t7\t101.2\t0\t7\n", "85\t9\t101.2\t0\t9\n", "86\t8\t101.2\t0\t8\n", "87\t7\t101.2\t0\t7\n", "88\t14\t101.2\t0\t14\n", "89\t11\t101.2\t0\t11\n", "90\t18\t101.2\t0\t18\n", "91\t16\t101.2\t0\t16\n", "92\t32\t101.2\t0\t32\n", "93\t57\t101.2\t0\t57\n", "94\t80\t101.2\t0\t80\n", "95\t84\t101.2\t0\t84\n", "96\t81\t101.2\t0\t81\n", "97\t97\t101.2\t0\t97\n", "98\t55\t101.2\t0\t55\n", "99\t35\t101.2\t0\t35\n", "100\t100\t101.2\t0\t100\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 126514 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.9%\n", " C: 20.5%\n", " G: 17.3%\n", " T: 21.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t93638\t103632.3\t0\t93638\n", "4\t19650\t25908.1\t0\t19650\n", "5\t3231\t6477.0\t0\t3231\n", "6\t335\t1619.3\t0\t335\n", "7\t132\t404.8\t0\t132\n", "8\t106\t404.8\t0\t106\n", "9\t119\t404.8\t0\t119\n", "10\t132\t404.8\t0\t132\n", "11\t122\t404.8\t0\t122\n", "12\t131\t404.8\t0\t131\n", "13\t116\t404.8\t0\t116\n", "14\t150\t404.8\t0\t150\n", "15\t116\t404.8\t0\t116\n", "16\t112\t404.8\t0\t112\n", "17\t135\t404.8\t0\t135\n", "18\t126\t404.8\t0\t126\n", "19\t104\t404.8\t0\t104\n", "20\t95\t404.8\t0\t95\n", "21\t142\t404.8\t0\t142\n", "22\t88\t404.8\t0\t88\n", "23\t102\t404.8\t0\t102\n", "24\t103\t404.8\t0\t103\n", "25\t100\t404.8\t0\t100\n", "26\t113\t404.8\t0\t113\n", "27\t102\t404.8\t0\t102\n", "28\t125\t404.8\t0\t125\n", "29\t101\t404.8\t0\t101\n", "30\t131\t404.8\t0\t131\n", "31\t123\t404.8\t0\t123\n", "32\t105\t404.8\t0\t105\n", "33\t115\t404.8\t0\t115\n", "34\t92\t404.8\t0\t92\n", "35\t118\t404.8\t0\t118\n", "36\t67\t404.8\t0\t67\n", "37\t102\t404.8\t0\t102\n", "38\t134\t404.8\t0\t134\n", "39\t160\t404.8\t0\t160\n", "40\t151\t404.8\t0\t151\n", "41\t112\t404.8\t0\t112\n", "42\t101\t404.8\t0\t101\n", "43\t119\t404.8\t0\t119\n", "44\t93\t404.8\t0\t93\n", "45\t119\t404.8\t0\t119\n", "46\t118\t404.8\t0\t118\n", "47\t112\t404.8\t0\t112\n", "48\t86\t404.8\t0\t86\n", "49\t94\t404.8\t0\t94\n", "50\t77\t404.8\t0\t77\n", "51\t85\t404.8\t0\t85\n", "52\t79\t404.8\t0\t79\n", "53\t85\t404.8\t0\t85\n", "54\t85\t404.8\t0\t85\n", "55\t77\t404.8\t0\t77\n", "56\t75\t404.8\t0\t75\n", "57\t98\t404.8\t0\t98\n", "58\t90\t404.8\t0\t90\n", "59\t80\t404.8\t0\t80\n", "60\t91\t404.8\t0\t91\n", "61\t92\t404.8\t0\t92\n", "62\t57\t404.8\t0\t57\n", "63\t81\t404.8\t0\t81\n", "64\t89\t404.8\t0\t89\n", "65\t79\t404.8\t0\t79\n", "66\t91\t404.8\t0\t91\n", "67\t76\t404.8\t0\t76\n", "68\t66\t404.8\t0\t66\n", "69\t87\t404.8\t0\t87\n", "70\t70\t404.8\t0\t70\n", "71\t78\t404.8\t0\t78\n", "72\t91\t404.8\t0\t91\n", "73\t93\t404.8\t0\t93\n", "74\t102\t404.8\t0\t102\n", "75\t109\t404.8\t0\t109\n", "76\t111\t404.8\t0\t111\n", "77\t142\t404.8\t0\t142\n", "78\t107\t404.8\t0\t107\n", "79\t94\t404.8\t0\t94\n", "80\t118\t404.8\t0\t118\n", "81\t138\t404.8\t0\t138\n", "82\t158\t404.8\t0\t158\n", "83\t117\t404.8\t0\t117\n", "84\t117\t404.8\t0\t117\n", "85\t125\t404.8\t0\t125\n", "86\t78\t404.8\t0\t78\n", "87\t118\t404.8\t0\t118\n", "88\t138\t404.8\t0\t138\n", "89\t92\t404.8\t0\t92\n", "90\t90\t404.8\t0\t90\n", "91\t85\t404.8\t0\t85\n", "92\t52\t404.8\t0\t52\n", "93\t65\t404.8\t0\t65\n", "94\t76\t404.8\t0\t76\n", "95\t60\t404.8\t0\t60\n", "96\t67\t404.8\t0\t67\n", "97\t83\t404.8\t0\t83\n", "98\t89\t404.8\t0\t89\n", "99\t123\t404.8\t0\t123\n", "100\t110\t404.8\t0\t110\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 44_S71_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/44.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 18.30 s (13 us/read; 4.48 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 1,365,492\n", "Reads with adapters: 1,298,152 (95.1%)\n", "Reads written (passing filters): 990,849 (72.6%)\n", "\n", "Total basepairs processed: 136,549,200 bp\n", "Quality-trimmed: 844,379 bp (0.6%)\n", "Total written (filtered): 57,377,280 bp (42.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 700563 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 35.7%\n", " G: 43.7%\n", " T: 20.5%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t3741\t21335.8\t0\t3741\n", "4\t2823\t5334.0\t0\t2823\n", "5\t1060\t1333.5\t0\t1060\n", "6\t906\t333.4\t0\t906\n", "7\t830\t83.3\t0\t830\n", "8\t933\t20.8\t0\t933\n", "9\t887\t20.8\t0\t887\n", "10\t880\t20.8\t0\t880\n", "11\t937\t20.8\t0\t937\n", "12\t892\t20.8\t0\t892\n", "13\t1099\t20.8\t0\t1099\n", "14\t1192\t20.8\t0\t1192\n", "15\t1210\t20.8\t0\t1210\n", "16\t1345\t20.8\t0\t1345\n", "17\t1509\t20.8\t0\t1509\n", "18\t1872\t20.8\t0\t1872\n", "19\t2045\t20.8\t0\t2045\n", "20\t2101\t20.8\t0\t2101\n", "21\t2208\t20.8\t0\t2208\n", "22\t1956\t20.8\t0\t1956\n", "23\t1687\t20.8\t0\t1687\n", "24\t1936\t20.8\t0\t1936\n", "25\t2020\t20.8\t0\t2020\n", "26\t2092\t20.8\t0\t2092\n", "27\t2419\t20.8\t0\t2419\n", "28\t2197\t20.8\t0\t2197\n", "29\t2156\t20.8\t0\t2156\n", "30\t2362\t20.8\t0\t2362\n", "31\t2777\t20.8\t0\t2777\n", "32\t2298\t20.8\t0\t2298\n", "33\t2322\t20.8\t0\t2322\n", "34\t2511\t20.8\t0\t2511\n", "35\t2840\t20.8\t0\t2840\n", "36\t3200\t20.8\t0\t3200\n", "37\t3216\t20.8\t0\t3216\n", "38\t2749\t20.8\t0\t2749\n", "39\t2342\t20.8\t0\t2342\n", "40\t2678\t20.8\t0\t2678\n", "41\t2644\t20.8\t0\t2644\n", "42\t3058\t20.8\t0\t3058\n", "43\t2839\t20.8\t0\t2839\n", "44\t2373\t20.8\t0\t2373\n", "45\t3137\t20.8\t0\t3137\n", "46\t3989\t20.8\t0\t3989\n", "47\t3864\t20.8\t0\t3864\n", "48\t4102\t20.8\t0\t4102\n", "49\t3866\t20.8\t0\t3866\n", "50\t3993\t20.8\t0\t3993\n", "51\t3900\t20.8\t0\t3900\n", "52\t4226\t20.8\t0\t4226\n", "53\t4576\t20.8\t0\t4576\n", "54\t5715\t20.8\t0\t5715\n", "55\t6649\t20.8\t0\t6649\n", "56\t6119\t20.8\t0\t6119\n", "57\t5864\t20.8\t0\t5864\n", "58\t6524\t20.8\t0\t6524\n", "59\t5984\t20.8\t0\t5984\n", "60\t5172\t20.8\t0\t5172\n", "61\t4967\t20.8\t0\t4967\n", "62\t5174\t20.8\t0\t5174\n", "63\t5844\t20.8\t0\t5844\n", "64\t6825\t20.8\t0\t6825\n", "65\t6500\t20.8\t0\t6500\n", "66\t7004\t20.8\t0\t7004\n", "67\t9769\t20.8\t0\t9769\n", "68\t11581\t20.8\t0\t11581\n", "69\t13960\t20.8\t0\t13960\n", "70\t14428\t20.8\t0\t14428\n", "71\t12416\t20.8\t0\t12416\n", "72\t9375\t20.8\t0\t9375\n", "73\t7709\t20.8\t0\t7709\n", "74\t7926\t20.8\t0\t7926\n", "75\t9387\t20.8\t0\t9387\n", "76\t10774\t20.8\t0\t10774\n", "77\t11828\t20.8\t0\t11828\n", "78\t12866\t20.8\t0\t12866\n", "79\t10230\t20.8\t0\t10230\n", "80\t9813\t20.8\t0\t9813\n", "81\t9779\t20.8\t0\t9779\n", "82\t9112\t20.8\t0\t9112\n", "83\t10311\t20.8\t0\t10311\n", "84\t12964\t20.8\t0\t12964\n", "85\t14308\t20.8\t0\t14308\n", "86\t13258\t20.8\t0\t13258\n", "87\t9796\t20.8\t0\t9796\n", "88\t8183\t20.8\t0\t8183\n", "89\t8606\t20.8\t0\t8606\n", "90\t9535\t20.8\t0\t9535\n", "91\t12229\t20.8\t0\t12229\n", "92\t18261\t20.8\t0\t18261\n", "93\t28985\t20.8\t0\t28985\n", "94\t31332\t20.8\t0\t31332\n", "95\t29411\t20.8\t0\t29411\n", "96\t25876\t20.8\t0\t25876\n", "97\t19882\t20.8\t0\t19882\n", "98\t17022\t20.8\t0\t17022\n", "99\t36000\t20.8\t0\t36000\n", "100\t24515\t20.8\t0\t24515\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 319070 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 88.8%\n", " C: 5.5%\n", " G: 0.0%\n", " T: 5.7%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t2320\t21335.8\t0\t2320\n", "4\t1974\t5334.0\t0\t1974\n", "5\t2016\t1333.5\t0\t2016\n", "6\t1707\t333.4\t0\t1707\n", "7\t3904\t83.3\t0\t3904\n", "8\t3224\t20.8\t0\t3224\n", "9\t2971\t20.8\t0\t2971\n", "10\t2697\t20.8\t0\t2697\n", "11\t2772\t20.8\t0\t2772\n", "12\t2699\t20.8\t0\t2699\n", "13\t2542\t20.8\t0\t2542\n", "14\t2240\t20.8\t0\t2240\n", "15\t2192\t20.8\t0\t2192\n", "16\t2931\t20.8\t0\t2931\n", "17\t5139\t20.8\t0\t5139\n", "18\t13998\t20.8\t0\t13998\n", "19\t31455\t20.8\t0\t31455\n", "20\t35696\t20.8\t0\t35696\n", "21\t23371\t20.8\t0\t23371\n", "22\t15053\t20.8\t0\t15053\n", "23\t9493\t20.8\t0\t9493\n", "24\t6790\t20.8\t0\t6790\n", "25\t5018\t20.8\t0\t5018\n", "26\t4327\t20.8\t0\t4327\n", "27\t3797\t20.8\t0\t3797\n", "28\t4479\t20.8\t0\t4479\n", "29\t6534\t20.8\t0\t6534\n", "30\t11216\t20.8\t0\t11216\n", "31\t14245\t20.8\t0\t14245\n", "32\t17602\t20.8\t0\t17602\n", "33\t15811\t20.8\t0\t15811\n", "34\t17970\t20.8\t0\t17970\n", "35\t22789\t20.8\t0\t22789\n", "36\t14764\t20.8\t0\t14764\n", "37\t2826\t20.8\t0\t2826\n", "38\t101\t20.8\t0\t101\n", "39\t26\t20.8\t0\t26\n", "40\t14\t20.8\t0\t14\n", "41\t26\t20.8\t0\t26\n", "42\t24\t20.8\t0\t24\n", "43\t32\t20.8\t0\t32\n", "44\t17\t20.8\t0\t17\n", "45\t12\t20.8\t0\t12\n", "46\t33\t20.8\t0\t33\n", "47\t47\t20.8\t0\t47\n", "48\t22\t20.8\t0\t22\n", "49\t10\t20.8\t0\t10\n", "50\t4\t20.8\t0\t4\n", "51\t9\t20.8\t0\t9\n", "52\t7\t20.8\t0\t7\n", "53\t5\t20.8\t0\t5\n", "54\t3\t20.8\t0\t3\n", "55\t1\t20.8\t0\t1\n", "56\t2\t20.8\t0\t2\n", "60\t15\t20.8\t0\t15\n", "61\t2\t20.8\t0\t2\n", "62\t1\t20.8\t0\t1\n", "63\t2\t20.8\t0\t2\n", "64\t7\t20.8\t0\t7\n", "65\t1\t20.8\t0\t1\n", "66\t1\t20.8\t0\t1\n", "68\t1\t20.8\t0\t1\n", "70\t2\t20.8\t0\t2\n", "71\t1\t20.8\t0\t1\n", "91\t9\t20.8\t0\t9\n", "92\t2\t20.8\t0\t2\n", "93\t2\t20.8\t0\t2\n", "94\t15\t20.8\t0\t15\n", "95\t19\t20.8\t0\t19\n", "96\t10\t20.8\t0\t10\n", "97\t15\t20.8\t0\t15\n", "98\t8\t20.8\t0\t8\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 278519 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 19.1%\n", " C: 25.2%\n", " G: 35.4%\n", " T: 20.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t1264\t21335.8\t0\t1264\n", "4\t379\t5334.0\t0\t379\n", "5\t302\t1333.5\t0\t302\n", "6\t266\t333.4\t0\t266\n", "7\t371\t83.3\t0\t371\n", "8\t340\t83.3\t0\t340\n", "9\t355\t83.3\t0\t355\n", "10\t531\t83.3\t0\t531\n", "11\t495\t83.3\t0\t495\n", "12\t501\t83.3\t0\t501\n", "13\t447\t83.3\t0\t447\n", "14\t476\t83.3\t0\t476\n", "15\t454\t83.3\t0\t454\n", "16\t688\t83.3\t0\t688\n", "17\t512\t83.3\t0\t512\n", "18\t614\t83.3\t0\t614\n", "19\t581\t83.3\t0\t581\n", "20\t456\t83.3\t0\t456\n", "21\t630\t83.3\t0\t630\n", "22\t646\t83.3\t0\t646\n", "23\t712\t83.3\t0\t712\n", "24\t534\t83.3\t0\t534\n", "25\t709\t83.3\t0\t709\n", "26\t895\t83.3\t0\t895\n", "27\t1171\t83.3\t0\t1171\n", "28\t1301\t83.3\t0\t1301\n", "29\t1264\t83.3\t0\t1264\n", "30\t2007\t83.3\t0\t2007\n", "31\t1784\t83.3\t0\t1784\n", "32\t2511\t83.3\t0\t2511\n", "33\t2513\t83.3\t0\t2513\n", "34\t2974\t83.3\t0\t2974\n", "35\t3220\t83.3\t0\t3220\n", "36\t2803\t83.3\t0\t2803\n", "37\t3633\t83.3\t0\t3633\n", "38\t2544\t83.3\t0\t2544\n", "39\t3478\t83.3\t0\t3478\n", "40\t2960\t83.3\t0\t2960\n", "41\t2266\t83.3\t0\t2266\n", "42\t2352\t83.3\t0\t2352\n", "43\t4852\t83.3\t0\t4852\n", "44\t920\t83.3\t0\t920\n", "45\t2744\t83.3\t0\t2744\n", "46\t5632\t83.3\t0\t5632\n", "47\t1828\t83.3\t0\t1828\n", "48\t598\t83.3\t0\t598\n", "49\t3132\t83.3\t0\t3132\n", "50\t2543\t83.3\t0\t2543\n", "51\t1285\t83.3\t0\t1285\n", "52\t3684\t83.3\t0\t3684\n", "53\t6531\t83.3\t0\t6531\n", "54\t2410\t83.3\t0\t2410\n", "55\t5656\t83.3\t0\t5656\n", "56\t3264\t83.3\t0\t3264\n", "57\t17222\t83.3\t0\t17222\n", "58\t4761\t83.3\t0\t4761\n", "59\t5387\t83.3\t0\t5387\n", "60\t45654\t83.3\t0\t45654\n", "61\t8147\t83.3\t0\t8147\n", "62\t8224\t83.3\t0\t8224\n", "63\t9241\t83.3\t0\t9241\n", "64\t38590\t83.3\t0\t38590\n", "65\t1477\t83.3\t0\t1477\n", "66\t6122\t83.3\t0\t6122\n", "67\t6814\t83.3\t0\t6814\n", "68\t5943\t83.3\t0\t5943\n", "69\t600\t83.3\t0\t600\n", "70\t922\t83.3\t0\t922\n", "71\t3162\t83.3\t0\t3162\n", "72\t2879\t83.3\t0\t2879\n", "73\t2640\t83.3\t0\t2640\n", "74\t2269\t83.3\t0\t2269\n", "75\t1355\t83.3\t0\t1355\n", "76\t437\t83.3\t0\t437\n", "77\t156\t83.3\t0\t156\n", "78\t80\t83.3\t0\t80\n", "79\t66\t83.3\t0\t66\n", "80\t85\t83.3\t0\t85\n", "81\t95\t83.3\t0\t95\n", "82\t83\t83.3\t0\t83\n", "83\t106\t83.3\t0\t106\n", "84\t171\t83.3\t0\t171\n", "85\t334\t83.3\t0\t334\n", "86\t821\t83.3\t0\t821\n", "87\t915\t83.3\t0\t915\n", "88\t2706\t83.3\t0\t2706\n", "89\t1863\t83.3\t0\t1863\n", "90\t944\t83.3\t0\t944\n", "91\t660\t83.3\t0\t660\n", "92\t283\t83.3\t0\t283\n", "93\t147\t83.3\t0\t147\n", "94\t36\t83.3\t0\t36\n", "95\t34\t83.3\t0\t34\n", "96\t33\t83.3\t0\t33\n", "97\t5\t83.3\t0\t5\n", "98\t7\t83.3\t0\t7\n", "99\t25\t83.3\t0\t25\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 451_S28_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/451.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 117.94 s (13 us/read; 4.63 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 9,109,762\n", "Reads with adapters: 5,563,041 (61.1%)\n", "Reads written (passing filters): 8,825,897 (96.9%)\n", "\n", "Total basepairs processed: 910,976,200 bp\n", "Quality-trimmed: 2,621,775 bp (0.3%)\n", "Total written (filtered): 691,860,676 bp (75.9%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5370545 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.0%\n", " G: 37.2%\n", " T: 33.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t179316\t142340.0\t0\t179316\n", "4\t108250\t35585.0\t0\t108250\n", "5\t80078\t8896.3\t0\t80078\n", "6\t62593\t2224.1\t0\t62593\n", "7\t54660\t556.0\t0\t54660\n", "8\t53032\t139.0\t0\t53032\n", "9\t52742\t139.0\t0\t52742\n", "10\t51511\t139.0\t0\t51511\n", "11\t50888\t139.0\t0\t50888\n", "12\t51427\t139.0\t0\t51427\n", "13\t53141\t139.0\t0\t53141\n", "14\t54332\t139.0\t0\t54332\n", "15\t54371\t139.0\t0\t54371\n", "16\t57471\t139.0\t0\t57471\n", "17\t64579\t139.0\t0\t64579\n", "18\t76424\t139.0\t0\t76424\n", "19\t72164\t139.0\t0\t72164\n", "20\t61055\t139.0\t0\t61055\n", "21\t60953\t139.0\t0\t60953\n", "22\t54876\t139.0\t0\t54876\n", "23\t60726\t139.0\t0\t60726\n", "24\t71868\t139.0\t0\t71868\n", "25\t72614\t139.0\t0\t72614\n", "26\t83709\t139.0\t0\t83709\n", "27\t94355\t139.0\t0\t94355\n", "28\t85504\t139.0\t0\t85504\n", "29\t81359\t139.0\t0\t81359\n", "30\t83197\t139.0\t0\t83197\n", "31\t91087\t139.0\t0\t91087\n", "32\t92062\t139.0\t0\t92062\n", "33\t82879\t139.0\t0\t82879\n", "34\t79119\t139.0\t0\t79119\n", "35\t90317\t139.0\t0\t90317\n", "36\t107089\t139.0\t0\t107089\n", "37\t110326\t139.0\t0\t110326\n", "38\t92394\t139.0\t0\t92394\n", "39\t78091\t139.0\t0\t78091\n", "40\t69395\t139.0\t0\t69395\n", "41\t76729\t139.0\t0\t76729\n", "42\t90356\t139.0\t0\t90356\n", "43\t78875\t139.0\t0\t78875\n", "44\t64416\t139.0\t0\t64416\n", "45\t83177\t139.0\t0\t83177\n", "46\t101271\t139.0\t0\t101271\n", "47\t94660\t139.0\t0\t94660\n", "48\t98997\t139.0\t0\t98997\n", "49\t79691\t139.0\t0\t79691\n", "50\t80053\t139.0\t0\t80053\n", "51\t68930\t139.0\t0\t68930\n", "52\t66700\t139.0\t0\t66700\n", "53\t62810\t139.0\t0\t62810\n", "54\t75579\t139.0\t0\t75579\n", "55\t84517\t139.0\t0\t84517\n", "56\t71816\t139.0\t0\t71816\n", "57\t72281\t139.0\t0\t72281\n", "58\t86434\t139.0\t0\t86434\n", "59\t68485\t139.0\t0\t68485\n", "60\t58841\t139.0\t0\t58841\n", "61\t53234\t139.0\t0\t53234\n", "62\t41736\t139.0\t0\t41736\n", "63\t39203\t139.0\t0\t39203\n", "64\t44330\t139.0\t0\t44330\n", "65\t45348\t139.0\t0\t45348\n", "66\t40609\t139.0\t0\t40609\n", "67\t39305\t139.0\t0\t39305\n", "68\t37402\t139.0\t0\t37402\n", "69\t38097\t139.0\t0\t38097\n", "70\t39077\t139.0\t0\t39077\n", "71\t37343\t139.0\t0\t37343\n", "72\t30415\t139.0\t0\t30415\n", "73\t28111\t139.0\t0\t28111\n", "74\t28429\t139.0\t0\t28429\n", "75\t24402\t139.0\t0\t24402\n", "76\t20422\t139.0\t0\t20422\n", "77\t18018\t139.0\t0\t18018\n", "78\t20067\t139.0\t0\t20067\n", "79\t19338\t139.0\t0\t19338\n", "80\t19463\t139.0\t0\t19463\n", "81\t17590\t139.0\t0\t17590\n", "82\t16993\t139.0\t0\t16993\n", "83\t17798\t139.0\t0\t17798\n", "84\t19667\t139.0\t0\t19667\n", "85\t21726\t139.0\t0\t21726\n", "86\t20079\t139.0\t0\t20079\n", "87\t14246\t139.0\t0\t14246\n", "88\t12792\t139.0\t0\t12792\n", "89\t13617\t139.0\t0\t13617\n", "90\t14912\t139.0\t0\t14912\n", "91\t15327\t139.0\t0\t15327\n", "92\t15178\t139.0\t0\t15178\n", "93\t16037\t139.0\t0\t16037\n", "94\t14441\t139.0\t0\t14441\n", "95\t11587\t139.0\t0\t11587\n", "96\t8142\t139.0\t0\t8142\n", "97\t5247\t139.0\t0\t5247\n", "98\t2766\t139.0\t0\t2766\n", "99\t2239\t139.0\t0\t2239\n", "100\t1240\t139.0\t0\t1240\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 41051 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 64.8%\n", " C: 14.5%\n", " G: 0.0%\n", " T: 20.7%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13956\t142340.0\t0\t13956\n", "4\t3722\t35585.0\t0\t3722\n", "5\t1478\t8896.3\t0\t1478\n", "6\t829\t2224.1\t0\t829\n", "7\t460\t556.0\t0\t460\n", "8\t390\t139.0\t0\t390\n", "9\t371\t139.0\t0\t371\n", "10\t352\t139.0\t0\t352\n", "11\t350\t139.0\t0\t350\n", "12\t313\t139.0\t0\t313\n", "13\t288\t139.0\t0\t288\n", "14\t282\t139.0\t0\t282\n", "15\t254\t139.0\t0\t254\n", "16\t280\t139.0\t0\t280\n", "17\t268\t139.0\t0\t268\n", "18\t350\t139.0\t0\t350\n", "19\t439\t139.0\t0\t439\n", "20\t633\t139.0\t0\t633\n", "21\t437\t139.0\t0\t437\n", "22\t299\t139.0\t0\t299\n", "23\t228\t139.0\t0\t228\n", "24\t258\t139.0\t0\t258\n", "25\t278\t139.0\t0\t278\n", "26\t517\t139.0\t0\t517\n", "27\t484\t139.0\t0\t484\n", "28\t502\t139.0\t0\t502\n", "29\t537\t139.0\t0\t537\n", "30\t945\t139.0\t0\t945\n", "31\t1013\t139.0\t0\t1013\n", "32\t1485\t139.0\t0\t1485\n", "33\t1441\t139.0\t0\t1441\n", "34\t1447\t139.0\t0\t1447\n", "35\t1808\t139.0\t0\t1808\n", "36\t2151\t139.0\t0\t2151\n", "37\t872\t139.0\t0\t872\n", "38\t66\t139.0\t0\t66\n", "39\t36\t139.0\t0\t36\n", "40\t28\t139.0\t0\t28\n", "41\t24\t139.0\t0\t24\n", "42\t22\t139.0\t0\t22\n", "43\t12\t139.0\t0\t12\n", "44\t20\t139.0\t0\t20\n", "45\t24\t139.0\t0\t24\n", "46\t21\t139.0\t0\t21\n", "47\t16\t139.0\t0\t16\n", "48\t11\t139.0\t0\t11\n", "49\t21\t139.0\t0\t21\n", "50\t20\t139.0\t0\t20\n", "51\t25\t139.0\t0\t25\n", "52\t24\t139.0\t0\t24\n", "53\t21\t139.0\t0\t21\n", "54\t12\t139.0\t0\t12\n", "55\t21\t139.0\t0\t21\n", "56\t11\t139.0\t0\t11\n", "57\t16\t139.0\t0\t16\n", "58\t16\t139.0\t0\t16\n", "59\t18\t139.0\t0\t18\n", "60\t15\t139.0\t0\t15\n", "61\t14\t139.0\t0\t14\n", "62\t19\t139.0\t0\t19\n", "63\t13\t139.0\t0\t13\n", "64\t14\t139.0\t0\t14\n", "65\t14\t139.0\t0\t14\n", "66\t16\t139.0\t0\t16\n", "67\t16\t139.0\t0\t16\n", "68\t11\t139.0\t0\t11\n", "69\t11\t139.0\t0\t11\n", "70\t9\t139.0\t0\t9\n", "71\t12\t139.0\t0\t12\n", "72\t8\t139.0\t0\t8\n", "73\t9\t139.0\t0\t9\n", "74\t4\t139.0\t0\t4\n", "75\t8\t139.0\t0\t8\n", "76\t7\t139.0\t0\t7\n", "77\t7\t139.0\t0\t7\n", "78\t6\t139.0\t0\t6\n", "79\t4\t139.0\t0\t4\n", "80\t1\t139.0\t0\t1\n", "81\t4\t139.0\t0\t4\n", "82\t6\t139.0\t0\t6\n", "83\t11\t139.0\t0\t11\n", "84\t6\t139.0\t0\t6\n", "85\t7\t139.0\t0\t7\n", "86\t7\t139.0\t0\t7\n", "87\t4\t139.0\t0\t4\n", "88\t9\t139.0\t0\t9\n", "89\t7\t139.0\t0\t7\n", "90\t8\t139.0\t0\t8\n", "91\t5\t139.0\t0\t5\n", "92\t23\t139.0\t0\t23\n", "93\t38\t139.0\t0\t38\n", "94\t71\t139.0\t0\t71\n", "95\t91\t139.0\t0\t91\n", "96\t63\t139.0\t0\t63\n", "97\t56\t139.0\t0\t56\n", "98\t65\t139.0\t0\t65\n", "99\t65\t139.0\t0\t65\n", "100\t85\t139.0\t0\t85\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 151445 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.8%\n", " C: 20.4%\n", " G: 15.0%\n", " T: 19.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t100771\t142340.0\t0\t100771\n", "4\t20461\t35585.0\t0\t20461\n", "5\t4531\t8896.3\t0\t4531\n", "6\t732\t2224.1\t0\t732\n", "7\t523\t556.0\t0\t523\n", "8\t601\t556.0\t0\t601\n", "9\t524\t556.0\t0\t524\n", "10\t566\t556.0\t0\t566\n", "11\t549\t556.0\t0\t549\n", "12\t620\t556.0\t0\t620\n", "13\t568\t556.0\t0\t568\n", "14\t570\t556.0\t0\t570\n", "15\t599\t556.0\t0\t599\n", "16\t620\t556.0\t0\t620\n", "17\t566\t556.0\t0\t566\n", "18\t582\t556.0\t0\t582\n", "19\t530\t556.0\t0\t530\n", "20\t547\t556.0\t0\t547\n", "21\t525\t556.0\t0\t525\n", "22\t477\t556.0\t0\t477\n", "23\t421\t556.0\t0\t421\n", "24\t484\t556.0\t0\t484\n", "25\t447\t556.0\t0\t447\n", "26\t387\t556.0\t0\t387\n", "27\t435\t556.0\t0\t435\n", "28\t464\t556.0\t0\t464\n", "29\t383\t556.0\t0\t383\n", "30\t429\t556.0\t0\t429\n", "31\t458\t556.0\t0\t458\n", "32\t449\t556.0\t0\t449\n", "33\t339\t556.0\t0\t339\n", "34\t414\t556.0\t0\t414\n", "35\t351\t556.0\t0\t351\n", "36\t362\t556.0\t0\t362\n", "37\t310\t556.0\t0\t310\n", "38\t353\t556.0\t0\t353\n", "39\t366\t556.0\t0\t366\n", "40\t329\t556.0\t0\t329\n", "41\t310\t556.0\t0\t310\n", "42\t269\t556.0\t0\t269\n", "43\t415\t556.0\t0\t415\n", "44\t138\t556.0\t0\t138\n", "45\t286\t556.0\t0\t286\n", "46\t295\t556.0\t0\t295\n", "47\t259\t556.0\t0\t259\n", "48\t288\t556.0\t0\t288\n", "49\t228\t556.0\t0\t228\n", "50\t215\t556.0\t0\t215\n", "51\t237\t556.0\t0\t237\n", "52\t195\t556.0\t0\t195\n", "53\t228\t556.0\t0\t228\n", "54\t188\t556.0\t0\t188\n", "55\t156\t556.0\t0\t156\n", "56\t171\t556.0\t0\t171\n", "57\t150\t556.0\t0\t150\n", "58\t152\t556.0\t0\t152\n", "59\t117\t556.0\t0\t117\n", "60\t142\t556.0\t0\t142\n", "61\t160\t556.0\t0\t160\n", "62\t162\t556.0\t0\t162\n", "63\t132\t556.0\t0\t132\n", "64\t114\t556.0\t0\t114\n", "65\t130\t556.0\t0\t130\n", "66\t120\t556.0\t0\t120\n", "67\t118\t556.0\t0\t118\n", "68\t151\t556.0\t0\t151\n", "69\t90\t556.0\t0\t90\n", "70\t78\t556.0\t0\t78\n", "71\t113\t556.0\t0\t113\n", "72\t110\t556.0\t0\t110\n", "73\t121\t556.0\t0\t121\n", "74\t150\t556.0\t0\t150\n", "75\t77\t556.0\t0\t77\n", "76\t97\t556.0\t0\t97\n", "77\t131\t556.0\t0\t131\n", "78\t78\t556.0\t0\t78\n", "79\t93\t556.0\t0\t93\n", "80\t107\t556.0\t0\t107\n", "81\t120\t556.0\t0\t120\n", "82\t203\t556.0\t0\t203\n", "83\t158\t556.0\t0\t158\n", "84\t117\t556.0\t0\t117\n", "85\t106\t556.0\t0\t106\n", "86\t102\t556.0\t0\t102\n", "87\t94\t556.0\t0\t94\n", "88\t109\t556.0\t0\t109\n", "89\t100\t556.0\t0\t100\n", "90\t71\t556.0\t0\t71\n", "91\t75\t556.0\t0\t75\n", "92\t68\t556.0\t0\t68\n", "93\t81\t556.0\t0\t81\n", "94\t68\t556.0\t0\t68\n", "95\t59\t556.0\t0\t59\n", "96\t62\t556.0\t0\t62\n", "97\t87\t556.0\t0\t87\n", "98\t102\t556.0\t0\t102\n", "99\t112\t556.0\t0\t112\n", "100\t137\t556.0\t0\t137\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 452b_S2_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/452b.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 68.98 s (12 us/read; 4.83 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,550,931\n", "Reads with adapters: 2,900,298 (52.2%)\n", "Reads written (passing filters): 5,437,883 (98.0%)\n", "\n", "Total basepairs processed: 555,093,100 bp\n", "Quality-trimmed: 1,321,087 bp (0.2%)\n", "Total written (filtered): 450,699,427 bp (81.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2745887 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.1%\n", " G: 40.9%\n", " T: 29.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t120776\t86733.3\t0\t120776\n", "4\t60720\t21683.3\t0\t60720\n", "5\t43795\t5420.8\t0\t43795\n", "6\t35940\t1355.2\t0\t35940\n", "7\t30655\t338.8\t0\t30655\n", "8\t30991\t84.7\t0\t30991\n", "9\t30129\t84.7\t0\t30129\n", "10\t28816\t84.7\t0\t28816\n", "11\t29858\t84.7\t0\t29858\n", "12\t30281\t84.7\t0\t30281\n", "13\t34127\t84.7\t0\t34127\n", "14\t35011\t84.7\t0\t35011\n", "15\t33213\t84.7\t0\t33213\n", "16\t35619\t84.7\t0\t35619\n", "17\t37964\t84.7\t0\t37964\n", "18\t43170\t84.7\t0\t43170\n", "19\t40394\t84.7\t0\t40394\n", "20\t34277\t84.7\t0\t34277\n", "21\t33216\t84.7\t0\t33216\n", "22\t30679\t84.7\t0\t30679\n", "23\t33184\t84.7\t0\t33184\n", "24\t38365\t84.7\t0\t38365\n", "25\t39878\t84.7\t0\t39878\n", "26\t44851\t84.7\t0\t44851\n", "27\t49158\t84.7\t0\t49158\n", "28\t45731\t84.7\t0\t45731\n", "29\t43629\t84.7\t0\t43629\n", "30\t45235\t84.7\t0\t45235\n", "31\t49278\t84.7\t0\t49278\n", "32\t47227\t84.7\t0\t47227\n", "33\t43838\t84.7\t0\t43838\n", "34\t44162\t84.7\t0\t44162\n", "35\t50097\t84.7\t0\t50097\n", "36\t58794\t84.7\t0\t58794\n", "37\t63937\t84.7\t0\t63937\n", "38\t50202\t84.7\t0\t50202\n", "39\t41564\t84.7\t0\t41564\n", "40\t39766\t84.7\t0\t39766\n", "41\t43372\t84.7\t0\t43372\n", "42\t47790\t84.7\t0\t47790\n", "43\t41231\t84.7\t0\t41231\n", "44\t34006\t84.7\t0\t34006\n", "45\t41599\t84.7\t0\t41599\n", "46\t48231\t84.7\t0\t48231\n", "47\t46269\t84.7\t0\t46269\n", "48\t44112\t84.7\t0\t44112\n", "49\t35851\t84.7\t0\t35851\n", "50\t32979\t84.7\t0\t32979\n", "51\t30648\t84.7\t0\t30648\n", "52\t29650\t84.7\t0\t29650\n", "53\t29450\t84.7\t0\t29450\n", "54\t36212\t84.7\t0\t36212\n", "55\t40265\t84.7\t0\t40265\n", "56\t32779\t84.7\t0\t32779\n", "57\t29939\t84.7\t0\t29939\n", "58\t31726\t84.7\t0\t31726\n", "59\t26780\t84.7\t0\t26780\n", "60\t23254\t84.7\t0\t23254\n", "61\t21447\t84.7\t0\t21447\n", "62\t17956\t84.7\t0\t17956\n", "63\t17624\t84.7\t0\t17624\n", "64\t19472\t84.7\t0\t19472\n", "65\t18631\t84.7\t0\t18631\n", "66\t16318\t84.7\t0\t16318\n", "67\t16353\t84.7\t0\t16353\n", "68\t16602\t84.7\t0\t16602\n", "69\t17037\t84.7\t0\t17037\n", "70\t18365\t84.7\t0\t18365\n", "71\t17480\t84.7\t0\t17480\n", "72\t13830\t84.7\t0\t13830\n", "73\t12027\t84.7\t0\t12027\n", "74\t11706\t84.7\t0\t11706\n", "75\t10028\t84.7\t0\t10028\n", "76\t8385\t84.7\t0\t8385\n", "77\t8240\t84.7\t0\t8240\n", "78\t9343\t84.7\t0\t9343\n", "79\t8644\t84.7\t0\t8644\n", "80\t8311\t84.7\t0\t8311\n", "81\t7743\t84.7\t0\t7743\n", "82\t7087\t84.7\t0\t7087\n", "83\t7222\t84.7\t0\t7222\n", "84\t7872\t84.7\t0\t7872\n", "85\t8405\t84.7\t0\t8405\n", "86\t7765\t84.7\t0\t7765\n", "87\t5831\t84.7\t0\t5831\n", "88\t5162\t84.7\t0\t5162\n", "89\t5241\t84.7\t0\t5241\n", "90\t5543\t84.7\t0\t5543\n", "91\t5641\t84.7\t0\t5641\n", "92\t5670\t84.7\t0\t5670\n", "93\t5548\t84.7\t0\t5548\n", "94\t4992\t84.7\t0\t4992\n", "95\t4251\t84.7\t0\t4251\n", "96\t3097\t84.7\t0\t3097\n", "97\t2161\t84.7\t0\t2161\n", "98\t1441\t84.7\t0\t1441\n", "99\t1627\t84.7\t0\t1627\n", "100\t1119\t84.7\t0\t1119\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 39347 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.6%\n", " C: 35.5%\n", " G: 0.0%\n", " T: 18.9%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t18775\t86733.3\t0\t18775\n", "4\t5232\t21683.3\t0\t5232\n", "5\t2906\t5420.8\t0\t2906\n", "6\t1799\t1355.2\t0\t1799\n", "7\t470\t338.8\t0\t470\n", "8\t361\t84.7\t0\t361\n", "9\t327\t84.7\t0\t327\n", "10\t285\t84.7\t0\t285\n", "11\t277\t84.7\t0\t277\n", "12\t282\t84.7\t0\t282\n", "13\t228\t84.7\t0\t228\n", "14\t266\t84.7\t0\t266\n", "15\t223\t84.7\t0\t223\n", "16\t196\t84.7\t0\t196\n", "17\t213\t84.7\t0\t213\n", "18\t238\t84.7\t0\t238\n", "19\t328\t84.7\t0\t328\n", "20\t381\t84.7\t0\t381\n", "21\t309\t84.7\t0\t309\n", "22\t231\t84.7\t0\t231\n", "23\t188\t84.7\t0\t188\n", "24\t190\t84.7\t0\t190\n", "25\t215\t84.7\t0\t215\n", "26\t319\t84.7\t0\t319\n", "27\t304\t84.7\t0\t304\n", "28\t216\t84.7\t0\t216\n", "29\t260\t84.7\t0\t260\n", "30\t272\t84.7\t0\t272\n", "31\t280\t84.7\t0\t280\n", "32\t490\t84.7\t0\t490\n", "33\t416\t84.7\t0\t416\n", "34\t417\t84.7\t0\t417\n", "35\t527\t84.7\t0\t527\n", "36\t540\t84.7\t0\t540\n", "37\t220\t84.7\t0\t220\n", "38\t24\t84.7\t0\t24\n", "39\t34\t84.7\t0\t34\n", "40\t22\t84.7\t0\t22\n", "41\t18\t84.7\t0\t18\n", "42\t23\t84.7\t0\t23\n", "43\t23\t84.7\t0\t23\n", "44\t24\t84.7\t0\t24\n", "45\t16\t84.7\t0\t16\n", "46\t29\t84.7\t0\t29\n", "47\t31\t84.7\t0\t31\n", "48\t23\t84.7\t0\t23\n", "49\t21\t84.7\t0\t21\n", "50\t18\t84.7\t0\t18\n", "51\t18\t84.7\t0\t18\n", "52\t16\t84.7\t0\t16\n", "53\t15\t84.7\t0\t15\n", "54\t20\t84.7\t0\t20\n", "55\t19\t84.7\t0\t19\n", "56\t15\t84.7\t0\t15\n", "57\t9\t84.7\t0\t9\n", "58\t12\t84.7\t0\t12\n", "59\t14\t84.7\t0\t14\n", "60\t22\t84.7\t0\t22\n", "61\t15\t84.7\t0\t15\n", "62\t16\t84.7\t0\t16\n", "63\t10\t84.7\t0\t10\n", "64\t9\t84.7\t0\t9\n", "65\t9\t84.7\t0\t9\n", "66\t13\t84.7\t0\t13\n", "67\t14\t84.7\t0\t14\n", "68\t9\t84.7\t0\t9\n", "69\t9\t84.7\t0\t9\n", "70\t10\t84.7\t0\t10\n", "71\t14\t84.7\t0\t14\n", "72\t16\t84.7\t0\t16\n", "73\t10\t84.7\t0\t10\n", "74\t7\t84.7\t0\t7\n", "75\t16\t84.7\t0\t16\n", "76\t5\t84.7\t0\t5\n", "77\t4\t84.7\t0\t4\n", "78\t4\t84.7\t0\t4\n", "79\t2\t84.7\t0\t2\n", "80\t9\t84.7\t0\t9\n", "81\t7\t84.7\t0\t7\n", "82\t10\t84.7\t0\t10\n", "83\t9\t84.7\t0\t9\n", "84\t4\t84.7\t0\t4\n", "85\t8\t84.7\t0\t8\n", "86\t8\t84.7\t0\t8\n", "87\t6\t84.7\t0\t6\n", "88\t8\t84.7\t0\t8\n", "89\t5\t84.7\t0\t5\n", "90\t6\t84.7\t0\t6\n", "91\t6\t84.7\t0\t6\n", "92\t16\t84.7\t0\t16\n", "93\t43\t84.7\t0\t43\n", "94\t49\t84.7\t0\t49\n", "95\t59\t84.7\t0\t59\n", "96\t71\t84.7\t0\t71\n", "97\t58\t84.7\t0\t58\n", "98\t32\t84.7\t0\t32\n", "99\t40\t84.7\t0\t40\n", "100\t54\t84.7\t0\t54\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 115064 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.0%\n", " C: 22.0%\n", " G: 16.1%\n", " T: 22.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t79663\t86733.3\t0\t79663\n", "4\t17159\t21683.3\t0\t17159\n", "5\t2618\t5420.8\t0\t2618\n", "6\t435\t1355.2\t0\t435\n", "7\t233\t338.8\t0\t233\n", "8\t256\t338.8\t0\t256\n", "9\t245\t338.8\t0\t245\n", "10\t273\t338.8\t0\t273\n", "11\t245\t338.8\t0\t245\n", "12\t300\t338.8\t0\t300\n", "13\t253\t338.8\t0\t253\n", "14\t267\t338.8\t0\t267\n", "15\t309\t338.8\t0\t309\n", "16\t267\t338.8\t0\t267\n", "17\t328\t338.8\t0\t328\n", "18\t279\t338.8\t0\t279\n", "19\t264\t338.8\t0\t264\n", "20\t268\t338.8\t0\t268\n", "21\t268\t338.8\t0\t268\n", "22\t263\t338.8\t0\t263\n", "23\t246\t338.8\t0\t246\n", "24\t220\t338.8\t0\t220\n", "25\t242\t338.8\t0\t242\n", "26\t219\t338.8\t0\t219\n", "27\t200\t338.8\t0\t200\n", "28\t246\t338.8\t0\t246\n", "29\t222\t338.8\t0\t222\n", "30\t221\t338.8\t0\t221\n", "31\t250\t338.8\t0\t250\n", "32\t226\t338.8\t0\t226\n", "33\t234\t338.8\t0\t234\n", "34\t225\t338.8\t0\t225\n", "35\t235\t338.8\t0\t235\n", "36\t173\t338.8\t0\t173\n", "37\t243\t338.8\t0\t243\n", "38\t211\t338.8\t0\t211\n", "39\t186\t338.8\t0\t186\n", "40\t249\t338.8\t0\t249\n", "41\t159\t338.8\t0\t159\n", "42\t167\t338.8\t0\t167\n", "43\t284\t338.8\t0\t284\n", "44\t82\t338.8\t0\t82\n", "45\t198\t338.8\t0\t198\n", "46\t174\t338.8\t0\t174\n", "47\t186\t338.8\t0\t186\n", "48\t162\t338.8\t0\t162\n", "49\t171\t338.8\t0\t171\n", "50\t154\t338.8\t0\t154\n", "51\t153\t338.8\t0\t153\n", "52\t149\t338.8\t0\t149\n", "53\t166\t338.8\t0\t166\n", "54\t129\t338.8\t0\t129\n", "55\t149\t338.8\t0\t149\n", "56\t162\t338.8\t0\t162\n", "57\t113\t338.8\t0\t113\n", "58\t143\t338.8\t0\t143\n", "59\t118\t338.8\t0\t118\n", "60\t144\t338.8\t0\t144\n", "61\t182\t338.8\t0\t182\n", "62\t136\t338.8\t0\t136\n", "63\t111\t338.8\t0\t111\n", "64\t115\t338.8\t0\t115\n", "65\t101\t338.8\t0\t101\n", "66\t103\t338.8\t0\t103\n", "67\t97\t338.8\t0\t97\n", "68\t109\t338.8\t0\t109\n", "69\t65\t338.8\t0\t65\n", "70\t62\t338.8\t0\t62\n", "71\t90\t338.8\t0\t90\n", "72\t93\t338.8\t0\t93\n", "73\t98\t338.8\t0\t98\n", "74\t100\t338.8\t0\t100\n", "75\t71\t338.8\t0\t71\n", "76\t74\t338.8\t0\t74\n", "77\t99\t338.8\t0\t99\n", "78\t81\t338.8\t0\t81\n", "79\t106\t338.8\t0\t106\n", "80\t94\t338.8\t0\t94\n", "81\t89\t338.8\t0\t89\n", "82\t117\t338.8\t0\t117\n", "83\t104\t338.8\t0\t104\n", "84\t85\t338.8\t0\t85\n", "85\t69\t338.8\t0\t69\n", "86\t76\t338.8\t0\t76\n", "87\t104\t338.8\t0\t104\n", "88\t147\t338.8\t0\t147\n", "89\t111\t338.8\t0\t111\n", "90\t108\t338.8\t0\t108\n", "91\t69\t338.8\t0\t69\n", "92\t45\t338.8\t0\t45\n", "93\t55\t338.8\t0\t55\n", "94\t52\t338.8\t0\t52\n", "95\t46\t338.8\t0\t46\n", "96\t40\t338.8\t0\t40\n", "97\t66\t338.8\t0\t66\n", "98\t71\t338.8\t0\t71\n", "99\t127\t338.8\t0\t127\n", "100\t92\t338.8\t0\t92\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 453_S12_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/453.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 69.50 s (13 us/read; 4.62 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,346,302\n", "Reads with adapters: 3,507,741 (65.6%)\n", "Reads written (passing filters): 5,209,585 (97.4%)\n", "\n", "Total basepairs processed: 534,630,200 bp\n", "Quality-trimmed: 1,578,257 bp (0.3%)\n", "Total written (filtered): 407,401,492 bp (76.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3404545 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.6%\n", " G: 39.7%\n", " T: 28.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t109525\t83536.0\t0\t109525\n", "4\t67102\t20884.0\t0\t67102\n", "5\t55061\t5221.0\t0\t55061\n", "6\t44413\t1305.2\t0\t44413\n", "7\t42179\t326.3\t0\t42179\n", "8\t41866\t81.6\t0\t41866\n", "9\t41165\t81.6\t0\t41165\n", "10\t39868\t81.6\t0\t39868\n", "11\t40419\t81.6\t0\t40419\n", "12\t40877\t81.6\t0\t40877\n", "13\t43156\t81.6\t0\t43156\n", "14\t44524\t81.6\t0\t44524\n", "15\t43581\t81.6\t0\t43581\n", "16\t44418\t81.6\t0\t44418\n", "17\t47588\t81.6\t0\t47588\n", "18\t56787\t81.6\t0\t56787\n", "19\t55671\t81.6\t0\t55671\n", "20\t46078\t81.6\t0\t46078\n", "21\t46689\t81.6\t0\t46689\n", "22\t40889\t81.6\t0\t40889\n", "23\t44252\t81.6\t0\t44252\n", "24\t51626\t81.6\t0\t51626\n", "25\t51727\t81.6\t0\t51727\n", "26\t59820\t81.6\t0\t59820\n", "27\t68918\t81.6\t0\t68918\n", "28\t62185\t81.6\t0\t62185\n", "29\t55417\t81.6\t0\t55417\n", "30\t59771\t81.6\t0\t59771\n", "31\t68149\t81.6\t0\t68149\n", "32\t59252\t81.6\t0\t59252\n", "33\t56990\t81.6\t0\t56990\n", "34\t52328\t81.6\t0\t52328\n", "35\t62006\t81.6\t0\t62006\n", "36\t75843\t81.6\t0\t75843\n", "37\t71941\t81.6\t0\t71941\n", "38\t61711\t81.6\t0\t61711\n", "39\t49119\t81.6\t0\t49119\n", "40\t47350\t81.6\t0\t47350\n", "41\t52207\t81.6\t0\t52207\n", "42\t58674\t81.6\t0\t58674\n", "43\t51441\t81.6\t0\t51441\n", "44\t38887\t81.6\t0\t38887\n", "45\t51844\t81.6\t0\t51844\n", "46\t63787\t81.6\t0\t63787\n", "47\t60215\t81.6\t0\t60215\n", "48\t60310\t81.6\t0\t60310\n", "49\t45546\t81.6\t0\t45546\n", "50\t42996\t81.6\t0\t42996\n", "51\t38715\t81.6\t0\t38715\n", "52\t35981\t81.6\t0\t35981\n", "53\t41250\t81.6\t0\t41250\n", "54\t49667\t81.6\t0\t49667\n", "55\t39628\t81.6\t0\t39628\n", "56\t41641\t81.6\t0\t41641\n", "57\t44965\t81.6\t0\t44965\n", "58\t46814\t81.6\t0\t46814\n", "59\t31960\t81.6\t0\t31960\n", "60\t25265\t81.6\t0\t25265\n", "61\t25460\t81.6\t0\t25460\n", "62\t21208\t81.6\t0\t21208\n", "63\t21800\t81.6\t0\t21800\n", "64\t26532\t81.6\t0\t26532\n", "65\t21625\t81.6\t0\t21625\n", "66\t17091\t81.6\t0\t17091\n", "67\t18587\t81.6\t0\t18587\n", "68\t17721\t81.6\t0\t17721\n", "69\t18219\t81.6\t0\t18219\n", "70\t21202\t81.6\t0\t21202\n", "71\t19735\t81.6\t0\t19735\n", "72\t13486\t81.6\t0\t13486\n", "73\t9782\t81.6\t0\t9782\n", "74\t8643\t81.6\t0\t8643\n", "75\t8024\t81.6\t0\t8024\n", "76\t6209\t81.6\t0\t6209\n", "77\t7773\t81.6\t0\t7773\n", "78\t10413\t81.6\t0\t10413\n", "79\t7800\t81.6\t0\t7800\n", "80\t6956\t81.6\t0\t6956\n", "81\t7335\t81.6\t0\t7335\n", "82\t6651\t81.6\t0\t6651\n", "83\t6431\t81.6\t0\t6431\n", "84\t8151\t81.6\t0\t8151\n", "85\t10341\t81.6\t0\t10341\n", "86\t10444\t81.6\t0\t10444\n", "87\t6680\t81.6\t0\t6680\n", "88\t5455\t81.6\t0\t5455\n", "89\t6115\t81.6\t0\t6115\n", "90\t6890\t81.6\t0\t6890\n", "91\t7060\t81.6\t0\t7060\n", "92\t7385\t81.6\t0\t7385\n", "93\t8099\t81.6\t0\t8099\n", "94\t8001\t81.6\t0\t8001\n", "95\t6856\t81.6\t0\t6856\n", "96\t5046\t81.6\t0\t5046\n", "97\t3151\t81.6\t0\t3151\n", "98\t1696\t81.6\t0\t1696\n", "99\t1563\t81.6\t0\t1563\n", "100\t875\t81.6\t0\t875\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 22007 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 57.2%\n", " C: 19.9%\n", " G: 0.0%\n", " T: 22.7%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9333\t83536.0\t0\t9333\n", "4\t2324\t20884.0\t0\t2324\n", "5\t671\t5221.0\t0\t671\n", "6\t367\t1305.2\t0\t367\n", "7\t162\t326.3\t0\t162\n", "8\t105\t81.6\t0\t105\n", "9\t127\t81.6\t0\t127\n", "10\t100\t81.6\t0\t100\n", "11\t100\t81.6\t0\t100\n", "12\t105\t81.6\t0\t105\n", "13\t91\t81.6\t0\t91\n", "14\t91\t81.6\t0\t91\n", "15\t104\t81.6\t0\t104\n", "16\t106\t81.6\t0\t106\n", "17\t112\t81.6\t0\t112\n", "18\t120\t81.6\t0\t120\n", "19\t137\t81.6\t0\t137\n", "20\t136\t81.6\t0\t136\n", "21\t122\t81.6\t0\t122\n", "22\t92\t81.6\t0\t92\n", "23\t97\t81.6\t0\t97\n", "24\t135\t81.6\t0\t135\n", "25\t156\t81.6\t0\t156\n", "26\t209\t81.6\t0\t209\n", "27\t229\t81.6\t0\t229\n", "28\t242\t81.6\t0\t242\n", "29\t295\t81.6\t0\t295\n", "30\t489\t81.6\t0\t489\n", "31\t569\t81.6\t0\t569\n", "32\t777\t81.6\t0\t777\n", "33\t713\t81.6\t0\t713\n", "34\t805\t81.6\t0\t805\n", "35\t856\t81.6\t0\t856\n", "36\t607\t81.6\t0\t607\n", "37\t143\t81.6\t0\t143\n", "38\t29\t81.6\t0\t29\n", "39\t25\t81.6\t0\t25\n", "40\t36\t81.6\t0\t36\n", "41\t35\t81.6\t0\t35\n", "42\t19\t81.6\t0\t19\n", "43\t32\t81.6\t0\t32\n", "44\t26\t81.6\t0\t26\n", "45\t23\t81.6\t0\t23\n", "46\t29\t81.6\t0\t29\n", "47\t19\t81.6\t0\t19\n", "48\t28\t81.6\t0\t28\n", "49\t22\t81.6\t0\t22\n", "50\t31\t81.6\t0\t31\n", "51\t19\t81.6\t0\t19\n", "52\t29\t81.6\t0\t29\n", "53\t15\t81.6\t0\t15\n", "54\t14\t81.6\t0\t14\n", "55\t13\t81.6\t0\t13\n", "56\t19\t81.6\t0\t19\n", "57\t13\t81.6\t0\t13\n", "58\t15\t81.6\t0\t15\n", "59\t17\t81.6\t0\t17\n", "60\t16\t81.6\t0\t16\n", "61\t13\t81.6\t0\t13\n", "62\t16\t81.6\t0\t16\n", "63\t10\t81.6\t0\t10\n", "64\t22\t81.6\t0\t22\n", "65\t13\t81.6\t0\t13\n", "66\t8\t81.6\t0\t8\n", "67\t13\t81.6\t0\t13\n", "68\t9\t81.6\t0\t9\n", "69\t12\t81.6\t0\t12\n", "70\t10\t81.6\t0\t10\n", "71\t7\t81.6\t0\t7\n", "72\t6\t81.6\t0\t6\n", "73\t5\t81.6\t0\t5\n", "74\t4\t81.6\t0\t4\n", "75\t11\t81.6\t0\t11\n", "76\t5\t81.6\t0\t5\n", "77\t2\t81.6\t0\t2\n", "78\t5\t81.6\t0\t5\n", "79\t5\t81.6\t0\t5\n", "80\t6\t81.6\t0\t6\n", "81\t4\t81.6\t0\t4\n", "82\t5\t81.6\t0\t5\n", "83\t2\t81.6\t0\t2\n", "84\t11\t81.6\t0\t11\n", "85\t7\t81.6\t0\t7\n", "86\t9\t81.6\t0\t9\n", "87\t5\t81.6\t0\t5\n", "88\t7\t81.6\t0\t7\n", "89\t12\t81.6\t0\t12\n", "90\t5\t81.6\t0\t5\n", "91\t9\t81.6\t0\t9\n", "92\t18\t81.6\t0\t18\n", "93\t44\t81.6\t0\t44\n", "94\t71\t81.6\t0\t71\n", "95\t53\t81.6\t0\t53\n", "96\t40\t81.6\t0\t40\n", "97\t49\t81.6\t0\t49\n", "98\t37\t81.6\t0\t37\n", "99\t26\t81.6\t0\t26\n", "100\t60\t81.6\t0\t60\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 81189 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.7%\n", " C: 18.2%\n", " G: 17.7%\n", " T: 20.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t55712\t83536.0\t0\t55712\n", "4\t12573\t20884.0\t0\t12573\n", "5\t2274\t5221.0\t0\t2274\n", "6\t302\t1305.2\t0\t302\n", "7\t184\t326.3\t0\t184\n", "8\t194\t326.3\t0\t194\n", "9\t168\t326.3\t0\t168\n", "10\t189\t326.3\t0\t189\n", "11\t186\t326.3\t0\t186\n", "12\t198\t326.3\t0\t198\n", "13\t201\t326.3\t0\t201\n", "14\t211\t326.3\t0\t211\n", "15\t257\t326.3\t0\t257\n", "16\t219\t326.3\t0\t219\n", "17\t192\t326.3\t0\t192\n", "18\t158\t326.3\t0\t158\n", "19\t163\t326.3\t0\t163\n", "20\t147\t326.3\t0\t147\n", "21\t166\t326.3\t0\t166\n", "22\t159\t326.3\t0\t159\n", "23\t135\t326.3\t0\t135\n", "24\t132\t326.3\t0\t132\n", "25\t124\t326.3\t0\t124\n", "26\t161\t326.3\t0\t161\n", "27\t161\t326.3\t0\t161\n", "28\t147\t326.3\t0\t147\n", "29\t145\t326.3\t0\t145\n", "30\t131\t326.3\t0\t131\n", "31\t146\t326.3\t0\t146\n", "32\t129\t326.3\t0\t129\n", "33\t143\t326.3\t0\t143\n", "34\t137\t326.3\t0\t137\n", "35\t125\t326.3\t0\t125\n", "36\t131\t326.3\t0\t131\n", "37\t113\t326.3\t0\t113\n", "38\t118\t326.3\t0\t118\n", "39\t148\t326.3\t0\t148\n", "40\t136\t326.3\t0\t136\n", "41\t139\t326.3\t0\t139\n", "42\t97\t326.3\t0\t97\n", "43\t130\t326.3\t0\t130\n", "44\t57\t326.3\t0\t57\n", "45\t119\t326.3\t0\t119\n", "46\t133\t326.3\t0\t133\n", "47\t120\t326.3\t0\t120\n", "48\t73\t326.3\t0\t73\n", "49\t86\t326.3\t0\t86\n", "50\t76\t326.3\t0\t76\n", "51\t67\t326.3\t0\t67\n", "52\t71\t326.3\t0\t71\n", "53\t85\t326.3\t0\t85\n", "54\t72\t326.3\t0\t72\n", "55\t68\t326.3\t0\t68\n", "56\t67\t326.3\t0\t67\n", "57\t63\t326.3\t0\t63\n", "58\t70\t326.3\t0\t70\n", "59\t73\t326.3\t0\t73\n", "60\t69\t326.3\t0\t69\n", "61\t91\t326.3\t0\t91\n", "62\t54\t326.3\t0\t54\n", "63\t75\t326.3\t0\t75\n", "64\t82\t326.3\t0\t82\n", "65\t65\t326.3\t0\t65\n", "66\t52\t326.3\t0\t52\n", "67\t64\t326.3\t0\t64\n", "68\t72\t326.3\t0\t72\n", "69\t65\t326.3\t0\t65\n", "70\t43\t326.3\t0\t43\n", "71\t57\t326.3\t0\t57\n", "72\t61\t326.3\t0\t61\n", "73\t83\t326.3\t0\t83\n", "74\t87\t326.3\t0\t87\n", "75\t91\t326.3\t0\t91\n", "76\t77\t326.3\t0\t77\n", "77\t106\t326.3\t0\t106\n", "78\t102\t326.3\t0\t102\n", "79\t90\t326.3\t0\t90\n", "80\t111\t326.3\t0\t111\n", "81\t127\t326.3\t0\t127\n", "82\t139\t326.3\t0\t139\n", "83\t118\t326.3\t0\t118\n", "84\t78\t326.3\t0\t78\n", "85\t85\t326.3\t0\t85\n", "86\t71\t326.3\t0\t71\n", "87\t90\t326.3\t0\t90\n", "88\t102\t326.3\t0\t102\n", "89\t69\t326.3\t0\t69\n", "90\t56\t326.3\t0\t56\n", "91\t59\t326.3\t0\t59\n", "92\t47\t326.3\t0\t47\n", "93\t35\t326.3\t0\t35\n", "94\t69\t326.3\t0\t69\n", "95\t51\t326.3\t0\t51\n", "96\t66\t326.3\t0\t66\n", "97\t59\t326.3\t0\t59\n", "98\t98\t326.3\t0\t98\n", "99\t107\t326.3\t0\t107\n", "100\t85\t326.3\t0\t85\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 45_S63_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/45.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 92.25 s (13 us/read; 4.70 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,231,064\n", "Reads with adapters: 4,872,208 (67.4%)\n", "Reads written (passing filters): 6,994,794 (96.7%)\n", "\n", "Total basepairs processed: 723,106,400 bp\n", "Quality-trimmed: 2,470,549 bp (0.3%)\n", "Total written (filtered): 534,685,910 bp (73.9%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4661828 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 32.1%\n", " G: 39.5%\n", " T: 28.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t126343\t112985.4\t0\t126343\n", "4\t67294\t28246.3\t0\t67294\n", "5\t55437\t7061.6\t0\t55437\n", "6\t45815\t1765.4\t0\t45815\n", "7\t44736\t441.3\t0\t44736\n", "8\t46722\t110.3\t0\t46722\n", "9\t48546\t110.3\t0\t48546\n", "10\t47793\t110.3\t0\t47793\n", "11\t50967\t110.3\t0\t50967\n", "12\t49662\t110.3\t0\t49662\n", "13\t57134\t110.3\t0\t57134\n", "14\t57792\t110.3\t0\t57792\n", "15\t59243\t110.3\t0\t59243\n", "16\t63187\t110.3\t0\t63187\n", "17\t66397\t110.3\t0\t66397\n", "18\t74997\t110.3\t0\t74997\n", "19\t66480\t110.3\t0\t66480\n", "20\t55187\t110.3\t0\t55187\n", "21\t53358\t110.3\t0\t53358\n", "22\t49711\t110.3\t0\t49711\n", "23\t56256\t110.3\t0\t56256\n", "24\t65849\t110.3\t0\t65849\n", "25\t69977\t110.3\t0\t69977\n", "26\t82145\t110.3\t0\t82145\n", "27\t94047\t110.3\t0\t94047\n", "28\t84232\t110.3\t0\t84232\n", "29\t76719\t110.3\t0\t76719\n", "30\t77090\t110.3\t0\t77090\n", "31\t83039\t110.3\t0\t83039\n", "32\t85389\t110.3\t0\t85389\n", "33\t79664\t110.3\t0\t79664\n", "34\t81194\t110.3\t0\t81194\n", "35\t90537\t110.3\t0\t90537\n", "36\t106427\t110.3\t0\t106427\n", "37\t117416\t110.3\t0\t117416\n", "38\t93286\t110.3\t0\t93286\n", "39\t76029\t110.3\t0\t76029\n", "40\t69446\t110.3\t0\t69446\n", "41\t71464\t110.3\t0\t71464\n", "42\t73901\t110.3\t0\t73901\n", "43\t65042\t110.3\t0\t65042\n", "44\t54767\t110.3\t0\t54767\n", "45\t66716\t110.3\t0\t66716\n", "46\t76928\t110.3\t0\t76928\n", "47\t68589\t110.3\t0\t68589\n", "48\t68557\t110.3\t0\t68557\n", "49\t58843\t110.3\t0\t58843\n", "50\t57674\t110.3\t0\t57674\n", "51\t51055\t110.3\t0\t51055\n", "52\t54128\t110.3\t0\t54128\n", "53\t53828\t110.3\t0\t53828\n", "54\t58635\t110.3\t0\t58635\n", "55\t61512\t110.3\t0\t61512\n", "56\t62723\t110.3\t0\t62723\n", "57\t59762\t110.3\t0\t59762\n", "58\t60118\t110.3\t0\t60118\n", "59\t48976\t110.3\t0\t48976\n", "60\t43533\t110.3\t0\t43533\n", "61\t39287\t110.3\t0\t39287\n", "62\t32770\t110.3\t0\t32770\n", "63\t32367\t110.3\t0\t32367\n", "64\t36449\t110.3\t0\t36449\n", "65\t35720\t110.3\t0\t35720\n", "66\t31151\t110.3\t0\t31151\n", "67\t32195\t110.3\t0\t32195\n", "68\t31864\t110.3\t0\t31864\n", "69\t34301\t110.3\t0\t34301\n", "70\t35799\t110.3\t0\t35799\n", "71\t33819\t110.3\t0\t33819\n", "72\t26266\t110.3\t0\t26266\n", "73\t24022\t110.3\t0\t24022\n", "74\t24352\t110.3\t0\t24352\n", "75\t21003\t110.3\t0\t21003\n", "76\t17351\t110.3\t0\t17351\n", "77\t16139\t110.3\t0\t16139\n", "78\t17712\t110.3\t0\t17712\n", "79\t16325\t110.3\t0\t16325\n", "80\t16507\t110.3\t0\t16507\n", "81\t15134\t110.3\t0\t15134\n", "82\t14042\t110.3\t0\t14042\n", "83\t14487\t110.3\t0\t14487\n", "84\t16363\t110.3\t0\t16363\n", "85\t18107\t110.3\t0\t18107\n", "86\t16206\t110.3\t0\t16206\n", "87\t10556\t110.3\t0\t10556\n", "88\t9934\t110.3\t0\t9934\n", "89\t10372\t110.3\t0\t10372\n", "90\t10899\t110.3\t0\t10899\n", "91\t10291\t110.3\t0\t10291\n", "92\t9566\t110.3\t0\t9566\n", "93\t9873\t110.3\t0\t9873\n", "94\t9177\t110.3\t0\t9177\n", "95\t8364\t110.3\t0\t8364\n", "96\t6900\t110.3\t0\t6900\n", "97\t5561\t110.3\t0\t5561\n", "98\t5102\t110.3\t0\t5102\n", "99\t7107\t110.3\t0\t7107\n", "100\t6094\t110.3\t0\t6094\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 80689 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 64.2%\n", " C: 19.0%\n", " G: 0.0%\n", " T: 16.8%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t15925\t112985.4\t0\t15925\n", "4\t5258\t28246.3\t0\t5258\n", "5\t3060\t7061.6\t0\t3060\n", "6\t822\t1765.4\t0\t822\n", "7\t286\t441.3\t0\t286\n", "8\t288\t110.3\t0\t288\n", "9\t238\t110.3\t0\t238\n", "10\t259\t110.3\t0\t259\n", "11\t261\t110.3\t0\t261\n", "12\t236\t110.3\t0\t236\n", "13\t260\t110.3\t0\t260\n", "14\t240\t110.3\t0\t240\n", "15\t244\t110.3\t0\t244\n", "16\t273\t110.3\t0\t273\n", "17\t321\t110.3\t0\t321\n", "18\t546\t110.3\t0\t546\n", "19\t943\t110.3\t0\t943\n", "20\t1915\t110.3\t0\t1915\n", "21\t1195\t110.3\t0\t1195\n", "22\t786\t110.3\t0\t786\n", "23\t518\t110.3\t0\t518\n", "24\t458\t110.3\t0\t458\n", "25\t420\t110.3\t0\t420\n", "26\t505\t110.3\t0\t505\n", "27\t569\t110.3\t0\t569\n", "28\t737\t110.3\t0\t737\n", "29\t1152\t110.3\t0\t1152\n", "30\t2163\t110.3\t0\t2163\n", "31\t2546\t110.3\t0\t2546\n", "32\t4092\t110.3\t0\t4092\n", "33\t4223\t110.3\t0\t4223\n", "34\t4863\t110.3\t0\t4863\n", "35\t6458\t110.3\t0\t6458\n", "36\t6522\t110.3\t0\t6522\n", "37\t3472\t110.3\t0\t3472\n", "38\t350\t110.3\t0\t350\n", "39\t339\t110.3\t0\t339\n", "40\t265\t110.3\t0\t265\n", "41\t237\t110.3\t0\t237\n", "42\t251\t110.3\t0\t251\n", "43\t219\t110.3\t0\t219\n", "44\t217\t110.3\t0\t217\n", "45\t238\t110.3\t0\t238\n", "46\t230\t110.3\t0\t230\n", "47\t218\t110.3\t0\t218\n", "48\t218\t110.3\t0\t218\n", "49\t251\t110.3\t0\t251\n", "50\t248\t110.3\t0\t248\n", "51\t197\t110.3\t0\t197\n", "52\t195\t110.3\t0\t195\n", "53\t168\t110.3\t0\t168\n", "54\t131\t110.3\t0\t131\n", "55\t149\t110.3\t0\t149\n", "56\t143\t110.3\t0\t143\n", "57\t129\t110.3\t0\t129\n", "58\t125\t110.3\t0\t125\n", "59\t145\t110.3\t0\t145\n", "60\t109\t110.3\t0\t109\n", "61\t138\t110.3\t0\t138\n", "62\t160\t110.3\t0\t160\n", "63\t178\t110.3\t0\t178\n", "64\t140\t110.3\t0\t140\n", "65\t145\t110.3\t0\t145\n", "66\t113\t110.3\t0\t113\n", "67\t86\t110.3\t0\t86\n", "68\t114\t110.3\t0\t114\n", "69\t89\t110.3\t0\t89\n", "70\t102\t110.3\t0\t102\n", "71\t94\t110.3\t0\t94\n", "72\t55\t110.3\t0\t55\n", "73\t76\t110.3\t0\t76\n", "74\t67\t110.3\t0\t67\n", "75\t48\t110.3\t0\t48\n", "76\t41\t110.3\t0\t41\n", "77\t30\t110.3\t0\t30\n", "78\t17\t110.3\t0\t17\n", "79\t30\t110.3\t0\t30\n", "80\t42\t110.3\t0\t42\n", "81\t29\t110.3\t0\t29\n", "82\t30\t110.3\t0\t30\n", "83\t31\t110.3\t0\t31\n", "84\t43\t110.3\t0\t43\n", "85\t32\t110.3\t0\t32\n", "86\t34\t110.3\t0\t34\n", "87\t53\t110.3\t0\t53\n", "88\t29\t110.3\t0\t29\n", "89\t46\t110.3\t0\t46\n", "90\t60\t110.3\t0\t60\n", "91\t86\t110.3\t0\t86\n", "92\t91\t110.3\t0\t91\n", "93\t164\t110.3\t0\t164\n", "94\t240\t110.3\t0\t240\n", "95\t249\t110.3\t0\t249\n", "96\t216\t110.3\t0\t216\n", "97\t208\t110.3\t0\t208\n", "98\t178\t110.3\t0\t178\n", "99\t154\t110.3\t0\t154\n", "100\t125\t110.3\t0\t125\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 129691 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 36.6%\n", " C: 15.7%\n", " G: 15.0%\n", " T: 32.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t83668\t112985.4\t0\t83668\n", "4\t22700\t28246.3\t0\t22700\n", "5\t1906\t7061.6\t0\t1906\n", "6\t360\t1765.4\t0\t360\n", "7\t225\t441.3\t0\t225\n", "8\t197\t441.3\t0\t197\n", "9\t202\t441.3\t0\t202\n", "10\t226\t441.3\t0\t226\n", "11\t248\t441.3\t0\t248\n", "12\t410\t441.3\t0\t410\n", "13\t610\t441.3\t0\t610\n", "14\t576\t441.3\t0\t576\n", "15\t567\t441.3\t0\t567\n", "16\t481\t441.3\t0\t481\n", "17\t565\t441.3\t0\t565\n", "18\t413\t441.3\t0\t413\n", "19\t440\t441.3\t0\t440\n", "20\t507\t441.3\t0\t507\n", "21\t431\t441.3\t0\t431\n", "22\t343\t441.3\t0\t343\n", "23\t259\t441.3\t0\t259\n", "24\t190\t441.3\t0\t190\n", "25\t253\t441.3\t0\t253\n", "26\t245\t441.3\t0\t245\n", "27\t245\t441.3\t0\t245\n", "28\t317\t441.3\t0\t317\n", "29\t255\t441.3\t0\t255\n", "30\t253\t441.3\t0\t253\n", "31\t285\t441.3\t0\t285\n", "32\t304\t441.3\t0\t304\n", "33\t227\t441.3\t0\t227\n", "34\t339\t441.3\t0\t339\n", "35\t272\t441.3\t0\t272\n", "36\t203\t441.3\t0\t203\n", "37\t236\t441.3\t0\t236\n", "38\t229\t441.3\t0\t229\n", "39\t264\t441.3\t0\t264\n", "40\t266\t441.3\t0\t266\n", "41\t204\t441.3\t0\t204\n", "42\t201\t441.3\t0\t201\n", "43\t277\t441.3\t0\t277\n", "44\t64\t441.3\t0\t64\n", "45\t162\t441.3\t0\t162\n", "46\t227\t441.3\t0\t227\n", "47\t250\t441.3\t0\t250\n", "48\t179\t441.3\t0\t179\n", "49\t189\t441.3\t0\t189\n", "50\t210\t441.3\t0\t210\n", "51\t166\t441.3\t0\t166\n", "52\t165\t441.3\t0\t165\n", "53\t168\t441.3\t0\t168\n", "54\t155\t441.3\t0\t155\n", "55\t203\t441.3\t0\t203\n", "56\t256\t441.3\t0\t256\n", "57\t300\t441.3\t0\t300\n", "58\t565\t441.3\t0\t565\n", "59\t308\t441.3\t0\t308\n", "60\t582\t441.3\t0\t582\n", "61\t588\t441.3\t0\t588\n", "62\t432\t441.3\t0\t432\n", "63\t268\t441.3\t0\t268\n", "64\t509\t441.3\t0\t509\n", "65\t283\t441.3\t0\t283\n", "66\t266\t441.3\t0\t266\n", "67\t150\t441.3\t0\t150\n", "68\t128\t441.3\t0\t128\n", "69\t50\t441.3\t0\t50\n", "70\t68\t441.3\t0\t68\n", "71\t82\t441.3\t0\t82\n", "72\t84\t441.3\t0\t84\n", "73\t97\t441.3\t0\t97\n", "74\t78\t441.3\t0\t78\n", "75\t87\t441.3\t0\t87\n", "76\t49\t441.3\t0\t49\n", "77\t70\t441.3\t0\t70\n", "78\t48\t441.3\t0\t48\n", "79\t65\t441.3\t0\t65\n", "80\t77\t441.3\t0\t77\n", "81\t57\t441.3\t0\t57\n", "82\t57\t441.3\t0\t57\n", "83\t52\t441.3\t0\t52\n", "84\t45\t441.3\t0\t45\n", "85\t68\t441.3\t0\t68\n", "86\t58\t441.3\t0\t58\n", "87\t83\t441.3\t0\t83\n", "88\t145\t441.3\t0\t145\n", "89\t122\t441.3\t0\t122\n", "90\t70\t441.3\t0\t70\n", "91\t75\t441.3\t0\t75\n", "92\t50\t441.3\t0\t50\n", "93\t62\t441.3\t0\t62\n", "94\t61\t441.3\t0\t61\n", "95\t73\t441.3\t0\t73\n", "96\t60\t441.3\t0\t60\n", "97\t142\t441.3\t0\t142\n", "98\t114\t441.3\t0\t114\n", "99\t143\t441.3\t0\t143\n", "100\t127\t441.3\t0\t127\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 461b_S31_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/461b.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 58.44 s (13 us/read; 4.76 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 4,635,478\n", "Reads with adapters: 2,444,359 (52.7%)\n", "Reads written (passing filters): 4,537,377 (97.9%)\n", "\n", "Total basepairs processed: 463,547,800 bp\n", "Quality-trimmed: 1,374,482 bp (0.3%)\n", "Total written (filtered): 383,110,243 bp (82.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2342395 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.4%\n", " G: 35.6%\n", " T: 37.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t117791\t72429.3\t0\t117791\n", "4\t69252\t18107.3\t0\t69252\n", "5\t50410\t4526.8\t0\t50410\n", "6\t40845\t1131.7\t0\t40845\n", "7\t34598\t282.9\t0\t34598\n", "8\t32063\t70.7\t0\t32063\n", "9\t31457\t70.7\t0\t31457\n", "10\t29929\t70.7\t0\t29929\n", "11\t29876\t70.7\t0\t29876\n", "12\t30711\t70.7\t0\t30711\n", "13\t32830\t70.7\t0\t32830\n", "14\t34152\t70.7\t0\t34152\n", "15\t33318\t70.7\t0\t33318\n", "16\t34904\t70.7\t0\t34904\n", "17\t38294\t70.7\t0\t38294\n", "18\t44371\t70.7\t0\t44371\n", "19\t40368\t70.7\t0\t40368\n", "20\t33609\t70.7\t0\t33609\n", "21\t33323\t70.7\t0\t33323\n", "22\t29804\t70.7\t0\t29804\n", "23\t31959\t70.7\t0\t31959\n", "24\t37416\t70.7\t0\t37416\n", "25\t38015\t70.7\t0\t38015\n", "26\t43539\t70.7\t0\t43539\n", "27\t47983\t70.7\t0\t47983\n", "28\t44085\t70.7\t0\t44085\n", "29\t41235\t70.7\t0\t41235\n", "30\t42173\t70.7\t0\t42173\n", "31\t45818\t70.7\t0\t45818\n", "32\t43844\t70.7\t0\t43844\n", "33\t40685\t70.7\t0\t40685\n", "34\t39689\t70.7\t0\t39689\n", "35\t44470\t70.7\t0\t44470\n", "36\t52715\t70.7\t0\t52715\n", "37\t56657\t70.7\t0\t56657\n", "38\t42732\t70.7\t0\t42732\n", "39\t34921\t70.7\t0\t34921\n", "40\t32021\t70.7\t0\t32021\n", "41\t33954\t70.7\t0\t33954\n", "42\t35602\t70.7\t0\t35602\n", "43\t30955\t70.7\t0\t30955\n", "44\t24322\t70.7\t0\t24322\n", "45\t30448\t70.7\t0\t30448\n", "46\t34984\t70.7\t0\t34984\n", "47\t32387\t70.7\t0\t32387\n", "48\t31204\t70.7\t0\t31204\n", "49\t26417\t70.7\t0\t26417\n", "50\t24912\t70.7\t0\t24912\n", "51\t23181\t70.7\t0\t23181\n", "52\t23600\t70.7\t0\t23600\n", "53\t23216\t70.7\t0\t23216\n", "54\t22727\t70.7\t0\t22727\n", "55\t21498\t70.7\t0\t21498\n", "56\t19935\t70.7\t0\t19935\n", "57\t18325\t70.7\t0\t18325\n", "58\t18684\t70.7\t0\t18684\n", "59\t15735\t70.7\t0\t15735\n", "60\t14220\t70.7\t0\t14220\n", "61\t13324\t70.7\t0\t13324\n", "62\t11422\t70.7\t0\t11422\n", "63\t10895\t70.7\t0\t10895\n", "64\t11475\t70.7\t0\t11475\n", "65\t11408\t70.7\t0\t11408\n", "66\t10349\t70.7\t0\t10349\n", "67\t10282\t70.7\t0\t10282\n", "68\t9727\t70.7\t0\t9727\n", "69\t9768\t70.7\t0\t9768\n", "70\t9963\t70.7\t0\t9963\n", "71\t9283\t70.7\t0\t9283\n", "72\t7690\t70.7\t0\t7690\n", "73\t6502\t70.7\t0\t6502\n", "74\t6762\t70.7\t0\t6762\n", "75\t5929\t70.7\t0\t5929\n", "76\t5376\t70.7\t0\t5376\n", "77\t4970\t70.7\t0\t4970\n", "78\t5306\t70.7\t0\t5306\n", "79\t5239\t70.7\t0\t5239\n", "80\t5169\t70.7\t0\t5169\n", "81\t5232\t70.7\t0\t5232\n", "82\t4954\t70.7\t0\t4954\n", "83\t5269\t70.7\t0\t5269\n", "84\t5881\t70.7\t0\t5881\n", "85\t6608\t70.7\t0\t6608\n", "86\t6144\t70.7\t0\t6144\n", "87\t4962\t70.7\t0\t4962\n", "88\t4759\t70.7\t0\t4759\n", "89\t4814\t70.7\t0\t4814\n", "90\t5072\t70.7\t0\t5072\n", "91\t4884\t70.7\t0\t4884\n", "92\t4860\t70.7\t0\t4860\n", "93\t4690\t70.7\t0\t4690\n", "94\t4299\t70.7\t0\t4299\n", "95\t3642\t70.7\t0\t3642\n", "96\t2621\t70.7\t0\t2621\n", "97\t1775\t70.7\t0\t1775\n", "98\t1186\t70.7\t0\t1186\n", "99\t992\t70.7\t0\t992\n", "100\t744\t70.7\t0\t744\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 23518 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.3%\n", " C: 32.9%\n", " G: 0.0%\n", " T: 21.6%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10595\t72429.3\t0\t10595\n", "4\t2974\t18107.3\t0\t2974\n", "5\t1988\t4526.8\t0\t1988\n", "6\t1121\t1131.7\t0\t1121\n", "7\t186\t282.9\t0\t186\n", "8\t148\t70.7\t0\t148\n", "9\t122\t70.7\t0\t122\n", "10\t136\t70.7\t0\t136\n", "11\t145\t70.7\t0\t145\n", "12\t131\t70.7\t0\t131\n", "13\t90\t70.7\t0\t90\n", "14\t96\t70.7\t0\t96\n", "15\t84\t70.7\t0\t84\n", "16\t91\t70.7\t0\t91\n", "17\t83\t70.7\t0\t83\n", "18\t90\t70.7\t0\t90\n", "19\t92\t70.7\t0\t92\n", "20\t110\t70.7\t0\t110\n", "21\t100\t70.7\t0\t100\n", "22\t86\t70.7\t0\t86\n", "23\t82\t70.7\t0\t82\n", "24\t77\t70.7\t0\t77\n", "25\t82\t70.7\t0\t82\n", "26\t186\t70.7\t0\t186\n", "27\t125\t70.7\t0\t125\n", "28\t148\t70.7\t0\t148\n", "29\t169\t70.7\t0\t169\n", "30\t303\t70.7\t0\t303\n", "31\t297\t70.7\t0\t297\n", "32\t502\t70.7\t0\t502\n", "33\t442\t70.7\t0\t442\n", "34\t462\t70.7\t0\t462\n", "35\t580\t70.7\t0\t580\n", "36\t494\t70.7\t0\t494\n", "37\t184\t70.7\t0\t184\n", "38\t28\t70.7\t0\t28\n", "39\t19\t70.7\t0\t19\n", "40\t13\t70.7\t0\t13\n", "41\t10\t70.7\t0\t10\n", "42\t8\t70.7\t0\t8\n", "43\t9\t70.7\t0\t9\n", "44\t10\t70.7\t0\t10\n", "45\t5\t70.7\t0\t5\n", "46\t10\t70.7\t0\t10\n", "47\t9\t70.7\t0\t9\n", "48\t12\t70.7\t0\t12\n", "49\t12\t70.7\t0\t12\n", "50\t12\t70.7\t0\t12\n", "51\t7\t70.7\t0\t7\n", "52\t14\t70.7\t0\t14\n", "53\t7\t70.7\t0\t7\n", "54\t12\t70.7\t0\t12\n", "55\t10\t70.7\t0\t10\n", "56\t11\t70.7\t0\t11\n", "57\t12\t70.7\t0\t12\n", "58\t11\t70.7\t0\t11\n", "59\t6\t70.7\t0\t6\n", "60\t8\t70.7\t0\t8\n", "61\t7\t70.7\t0\t7\n", "62\t4\t70.7\t0\t4\n", "63\t6\t70.7\t0\t6\n", "64\t3\t70.7\t0\t3\n", "65\t4\t70.7\t0\t4\n", "66\t7\t70.7\t0\t7\n", "67\t3\t70.7\t0\t3\n", "68\t3\t70.7\t0\t3\n", "69\t5\t70.7\t0\t5\n", "70\t2\t70.7\t0\t2\n", "71\t9\t70.7\t0\t9\n", "72\t3\t70.7\t0\t3\n", "73\t7\t70.7\t0\t7\n", "74\t2\t70.7\t0\t2\n", "75\t2\t70.7\t0\t2\n", "76\t2\t70.7\t0\t2\n", "77\t6\t70.7\t0\t6\n", "78\t1\t70.7\t0\t1\n", "79\t3\t70.7\t0\t3\n", "80\t4\t70.7\t0\t4\n", "82\t4\t70.7\t0\t4\n", "83\t4\t70.7\t0\t4\n", "84\t2\t70.7\t0\t2\n", "85\t3\t70.7\t0\t3\n", "86\t4\t70.7\t0\t4\n", "87\t1\t70.7\t0\t1\n", "88\t5\t70.7\t0\t5\n", "89\t3\t70.7\t0\t3\n", "90\t4\t70.7\t0\t4\n", "91\t6\t70.7\t0\t6\n", "92\t14\t70.7\t0\t14\n", "93\t36\t70.7\t0\t36\n", "94\t86\t70.7\t0\t86\n", "95\t89\t70.7\t0\t89\n", "96\t74\t70.7\t0\t74\n", "97\t56\t70.7\t0\t56\n", "98\t56\t70.7\t0\t56\n", "99\t54\t70.7\t0\t54\n", "100\t78\t70.7\t0\t78\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 78446 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.5%\n", " C: 21.5%\n", " G: 12.8%\n", " T: 24.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t56336\t72429.3\t0\t56336\n", "4\t12288\t18107.3\t0\t12288\n", "5\t2270\t4526.8\t0\t2270\n", "6\t205\t1131.7\t0\t205\n", "7\t135\t282.9\t0\t135\n", "8\t142\t282.9\t0\t142\n", "9\t111\t282.9\t0\t111\n", "10\t123\t282.9\t0\t123\n", "11\t124\t282.9\t0\t124\n", "12\t161\t282.9\t0\t161\n", "13\t188\t282.9\t0\t188\n", "14\t212\t282.9\t0\t212\n", "15\t214\t282.9\t0\t214\n", "16\t201\t282.9\t0\t201\n", "17\t210\t282.9\t0\t210\n", "18\t189\t282.9\t0\t189\n", "19\t213\t282.9\t0\t213\n", "20\t234\t282.9\t0\t234\n", "21\t193\t282.9\t0\t193\n", "22\t160\t282.9\t0\t160\n", "23\t125\t282.9\t0\t125\n", "24\t112\t282.9\t0\t112\n", "25\t118\t282.9\t0\t118\n", "26\t112\t282.9\t0\t112\n", "27\t119\t282.9\t0\t119\n", "28\t106\t282.9\t0\t106\n", "29\t86\t282.9\t0\t86\n", "30\t108\t282.9\t0\t108\n", "31\t87\t282.9\t0\t87\n", "32\t78\t282.9\t0\t78\n", "33\t81\t282.9\t0\t81\n", "34\t86\t282.9\t0\t86\n", "35\t76\t282.9\t0\t76\n", "36\t75\t282.9\t0\t75\n", "37\t55\t282.9\t0\t55\n", "38\t77\t282.9\t0\t77\n", "39\t83\t282.9\t0\t83\n", "40\t82\t282.9\t0\t82\n", "41\t68\t282.9\t0\t68\n", "42\t48\t282.9\t0\t48\n", "43\t77\t282.9\t0\t77\n", "44\t36\t282.9\t0\t36\n", "45\t60\t282.9\t0\t60\n", "46\t63\t282.9\t0\t63\n", "47\t62\t282.9\t0\t62\n", "48\t47\t282.9\t0\t47\n", "49\t47\t282.9\t0\t47\n", "50\t52\t282.9\t0\t52\n", "51\t44\t282.9\t0\t44\n", "52\t36\t282.9\t0\t36\n", "53\t53\t282.9\t0\t53\n", "54\t48\t282.9\t0\t48\n", "55\t64\t282.9\t0\t64\n", "56\t48\t282.9\t0\t48\n", "57\t55\t282.9\t0\t55\n", "58\t52\t282.9\t0\t52\n", "59\t47\t282.9\t0\t47\n", "60\t42\t282.9\t0\t42\n", "61\t54\t282.9\t0\t54\n", "62\t51\t282.9\t0\t51\n", "63\t38\t282.9\t0\t38\n", "64\t35\t282.9\t0\t35\n", "65\t37\t282.9\t0\t37\n", "66\t36\t282.9\t0\t36\n", "67\t34\t282.9\t0\t34\n", "68\t31\t282.9\t0\t31\n", "69\t35\t282.9\t0\t35\n", "70\t24\t282.9\t0\t24\n", "71\t39\t282.9\t0\t39\n", "72\t40\t282.9\t0\t40\n", "73\t46\t282.9\t0\t46\n", "74\t37\t282.9\t0\t37\n", "75\t32\t282.9\t0\t32\n", "76\t44\t282.9\t0\t44\n", "77\t65\t282.9\t0\t65\n", "78\t54\t282.9\t0\t54\n", "79\t58\t282.9\t0\t58\n", "80\t46\t282.9\t0\t46\n", "81\t52\t282.9\t0\t52\n", "82\t65\t282.9\t0\t65\n", "83\t46\t282.9\t0\t46\n", "84\t60\t282.9\t0\t60\n", "85\t47\t282.9\t0\t47\n", "86\t52\t282.9\t0\t52\n", "87\t47\t282.9\t0\t47\n", "88\t44\t282.9\t0\t44\n", "89\t40\t282.9\t0\t40\n", "90\t41\t282.9\t0\t41\n", "91\t27\t282.9\t0\t27\n", "92\t32\t282.9\t0\t32\n", "93\t32\t282.9\t0\t32\n", "94\t37\t282.9\t0\t37\n", "95\t33\t282.9\t0\t33\n", "96\t41\t282.9\t0\t41\n", "97\t57\t282.9\t0\t57\n", "98\t66\t282.9\t0\t66\n", "99\t83\t282.9\t0\t83\n", "100\t84\t282.9\t0\t84\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 462b_S64_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/462b.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 133.29 s (13 us/read; 4.58 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 10,172,164\n", "Reads with adapters: 7,420,011 (72.9%)\n", "Reads written (passing filters): 9,643,294 (94.8%)\n", "\n", "Total basepairs processed: 1,017,216,400 bp\n", "Quality-trimmed: 3,866,285 bp (0.4%)\n", "Total written (filtered): 700,385,559 bp (68.9%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 7203294 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.0%\n", " G: 40.4%\n", " T: 32.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t173372\t158940.1\t0\t173372\n", "4\t111587\t39735.0\t0\t111587\n", "5\t85286\t9933.8\t0\t85286\n", "6\t70027\t2483.4\t0\t70027\n", "7\t60571\t620.9\t0\t60571\n", "8\t55401\t155.2\t0\t55401\n", "9\t54687\t155.2\t0\t54687\n", "10\t54219\t155.2\t0\t54219\n", "11\t56571\t155.2\t0\t56571\n", "12\t59258\t155.2\t0\t59258\n", "13\t74950\t155.2\t0\t74950\n", "14\t75115\t155.2\t0\t75115\n", "15\t70643\t155.2\t0\t70643\n", "16\t75406\t155.2\t0\t75406\n", "17\t81173\t155.2\t0\t81173\n", "18\t94216\t155.2\t0\t94216\n", "19\t82303\t155.2\t0\t82303\n", "20\t66040\t155.2\t0\t66040\n", "21\t64137\t155.2\t0\t64137\n", "22\t60097\t155.2\t0\t60097\n", "23\t68507\t155.2\t0\t68507\n", "24\t84035\t155.2\t0\t84035\n", "25\t87748\t155.2\t0\t87748\n", "26\t105136\t155.2\t0\t105136\n", "27\t118207\t155.2\t0\t118207\n", "28\t112698\t155.2\t0\t112698\n", "29\t112572\t155.2\t0\t112572\n", "30\t120635\t155.2\t0\t120635\n", "31\t130167\t155.2\t0\t130167\n", "32\t124531\t155.2\t0\t124531\n", "33\t111305\t155.2\t0\t111305\n", "34\t108346\t155.2\t0\t108346\n", "35\t129975\t155.2\t0\t129975\n", "36\t153669\t155.2\t0\t153669\n", "37\t163916\t155.2\t0\t163916\n", "38\t132957\t155.2\t0\t132957\n", "39\t109718\t155.2\t0\t109718\n", "40\t103320\t155.2\t0\t103320\n", "41\t104359\t155.2\t0\t104359\n", "42\t113965\t155.2\t0\t113965\n", "43\t100250\t155.2\t0\t100250\n", "44\t84703\t155.2\t0\t84703\n", "45\t112319\t155.2\t0\t112319\n", "46\t138478\t155.2\t0\t138478\n", "47\t131729\t155.2\t0\t131729\n", "48\t130815\t155.2\t0\t130815\n", "49\t106897\t155.2\t0\t106897\n", "50\t97521\t155.2\t0\t97521\n", "51\t87988\t155.2\t0\t87988\n", "52\t102131\t155.2\t0\t102131\n", "53\t115687\t155.2\t0\t115687\n", "54\t112372\t155.2\t0\t112372\n", "55\t104911\t155.2\t0\t104911\n", "56\t104501\t155.2\t0\t104501\n", "57\t102768\t155.2\t0\t102768\n", "58\t111240\t155.2\t0\t111240\n", "59\t84365\t155.2\t0\t84365\n", "60\t70598\t155.2\t0\t70598\n", "61\t68571\t155.2\t0\t68571\n", "62\t56846\t155.2\t0\t56846\n", "63\t56887\t155.2\t0\t56887\n", "64\t65348\t155.2\t0\t65348\n", "65\t64755\t155.2\t0\t64755\n", "66\t57950\t155.2\t0\t57950\n", "67\t58264\t155.2\t0\t58264\n", "68\t56292\t155.2\t0\t56292\n", "69\t57293\t155.2\t0\t57293\n", "70\t62875\t155.2\t0\t62875\n", "71\t61436\t155.2\t0\t61436\n", "72\t46178\t155.2\t0\t46178\n", "73\t41877\t155.2\t0\t41877\n", "74\t42540\t155.2\t0\t42540\n", "75\t36368\t155.2\t0\t36368\n", "76\t30707\t155.2\t0\t30707\n", "77\t28616\t155.2\t0\t28616\n", "78\t32950\t155.2\t0\t32950\n", "79\t31873\t155.2\t0\t31873\n", "80\t33787\t155.2\t0\t33787\n", "81\t31739\t155.2\t0\t31739\n", "82\t29923\t155.2\t0\t29923\n", "83\t32920\t155.2\t0\t32920\n", "84\t37833\t155.2\t0\t37833\n", "85\t43270\t155.2\t0\t43270\n", "86\t40391\t155.2\t0\t40391\n", "87\t28769\t155.2\t0\t28769\n", "88\t26541\t155.2\t0\t26541\n", "89\t28131\t155.2\t0\t28131\n", "90\t28588\t155.2\t0\t28588\n", "91\t27737\t155.2\t0\t27737\n", "92\t25593\t155.2\t0\t25593\n", "93\t25582\t155.2\t0\t25582\n", "94\t22789\t155.2\t0\t22789\n", "95\t19627\t155.2\t0\t19627\n", "96\t14277\t155.2\t0\t14277\n", "97\t9850\t155.2\t0\t9850\n", "98\t6481\t155.2\t0\t6481\n", "99\t7526\t155.2\t0\t7526\n", "100\t4216\t155.2\t0\t4216\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 118576 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 84.3%\n", " C: 7.5%\n", " G: 0.0%\n", " T: 8.1%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10279\t158940.1\t0\t10279\n", "4\t2607\t39735.0\t0\t2607\n", "5\t1379\t9933.8\t0\t1379\n", "6\t485\t2483.4\t0\t485\n", "7\t231\t620.9\t0\t231\n", "8\t211\t155.2\t0\t211\n", "9\t221\t155.2\t0\t221\n", "10\t215\t155.2\t0\t215\n", "11\t274\t155.2\t0\t274\n", "12\t213\t155.2\t0\t213\n", "13\t201\t155.2\t0\t201\n", "14\t196\t155.2\t0\t196\n", "15\t196\t155.2\t0\t196\n", "16\t233\t155.2\t0\t233\n", "17\t239\t155.2\t0\t239\n", "18\t351\t155.2\t0\t351\n", "19\t488\t155.2\t0\t488\n", "20\t836\t155.2\t0\t836\n", "21\t636\t155.2\t0\t636\n", "22\t478\t155.2\t0\t478\n", "23\t426\t155.2\t0\t426\n", "24\t560\t155.2\t0\t560\n", "25\t751\t155.2\t0\t751\n", "26\t1421\t155.2\t0\t1421\n", "27\t1575\t155.2\t0\t1575\n", "28\t1916\t155.2\t0\t1916\n", "29\t2820\t155.2\t0\t2820\n", "30\t5457\t155.2\t0\t5457\n", "31\t6693\t155.2\t0\t6693\n", "32\t11542\t155.2\t0\t11542\n", "33\t11451\t155.2\t0\t11451\n", "34\t12643\t155.2\t0\t12643\n", "35\t16229\t155.2\t0\t16229\n", "36\t16470\t155.2\t0\t16470\n", "37\t6903\t155.2\t0\t6903\n", "38\t295\t155.2\t0\t295\n", "39\t137\t155.2\t0\t137\n", "40\t19\t155.2\t0\t19\n", "41\t13\t155.2\t0\t13\n", "42\t5\t155.2\t0\t5\n", "43\t15\t155.2\t0\t15\n", "44\t15\t155.2\t0\t15\n", "45\t14\t155.2\t0\t14\n", "46\t15\t155.2\t0\t15\n", "47\t6\t155.2\t0\t6\n", "48\t13\t155.2\t0\t13\n", "49\t11\t155.2\t0\t11\n", "50\t12\t155.2\t0\t12\n", "51\t14\t155.2\t0\t14\n", "52\t18\t155.2\t0\t18\n", "53\t10\t155.2\t0\t10\n", "54\t9\t155.2\t0\t9\n", "55\t10\t155.2\t0\t10\n", "56\t12\t155.2\t0\t12\n", "57\t7\t155.2\t0\t7\n", "58\t4\t155.2\t0\t4\n", "59\t7\t155.2\t0\t7\n", "60\t2\t155.2\t0\t2\n", "61\t3\t155.2\t0\t3\n", "62\t6\t155.2\t0\t6\n", "63\t5\t155.2\t0\t5\n", "64\t5\t155.2\t0\t5\n", "65\t4\t155.2\t0\t4\n", "66\t4\t155.2\t0\t4\n", "67\t2\t155.2\t0\t2\n", "68\t1\t155.2\t0\t1\n", "69\t3\t155.2\t0\t3\n", "70\t4\t155.2\t0\t4\n", "71\t3\t155.2\t0\t3\n", "72\t6\t155.2\t0\t6\n", "73\t3\t155.2\t0\t3\n", "74\t1\t155.2\t0\t1\n", "75\t3\t155.2\t0\t3\n", "76\t3\t155.2\t0\t3\n", "77\t2\t155.2\t0\t2\n", "79\t5\t155.2\t0\t5\n", "80\t1\t155.2\t0\t1\n", "81\t1\t155.2\t0\t1\n", "82\t5\t155.2\t0\t5\n", "83\t5\t155.2\t0\t5\n", "84\t3\t155.2\t0\t3\n", "85\t2\t155.2\t0\t2\n", "86\t6\t155.2\t0\t6\n", "87\t1\t155.2\t0\t1\n", "88\t2\t155.2\t0\t2\n", "89\t3\t155.2\t0\t3\n", "90\t9\t155.2\t0\t9\n", "91\t12\t155.2\t0\t12\n", "92\t21\t155.2\t0\t21\n", "93\t80\t155.2\t0\t80\n", "94\t187\t155.2\t0\t187\n", "95\t184\t155.2\t0\t184\n", "96\t105\t155.2\t0\t105\n", "97\t124\t155.2\t0\t124\n", "98\t72\t155.2\t0\t72\n", "99\t75\t155.2\t0\t75\n", "100\t126\t155.2\t0\t126\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 98141 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.0%\n", " C: 16.8%\n", " G: 10.7%\n", " T: 32.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t69830\t158940.1\t0\t69830\n", "4\t19350\t39735.0\t0\t19350\n", "5\t2221\t9933.8\t0\t2221\n", "6\t167\t2483.4\t0\t167\n", "7\t80\t620.9\t0\t80\n", "8\t86\t620.9\t0\t86\n", "9\t67\t620.9\t0\t67\n", "10\t82\t620.9\t0\t82\n", "11\t90\t620.9\t0\t90\n", "12\t109\t620.9\t0\t109\n", "13\t132\t620.9\t0\t132\n", "14\t105\t620.9\t0\t105\n", "15\t106\t620.9\t0\t106\n", "16\t113\t620.9\t0\t113\n", "17\t98\t620.9\t0\t98\n", "18\t94\t620.9\t0\t94\n", "19\t103\t620.9\t0\t103\n", "20\t108\t620.9\t0\t108\n", "21\t83\t620.9\t0\t83\n", "22\t89\t620.9\t0\t89\n", "23\t49\t620.9\t0\t49\n", "24\t60\t620.9\t0\t60\n", "25\t66\t620.9\t0\t66\n", "26\t73\t620.9\t0\t73\n", "27\t78\t620.9\t0\t78\n", "28\t66\t620.9\t0\t66\n", "29\t89\t620.9\t0\t89\n", "30\t75\t620.9\t0\t75\n", "31\t61\t620.9\t0\t61\n", "32\t65\t620.9\t0\t65\n", "33\t46\t620.9\t0\t46\n", "34\t50\t620.9\t0\t50\n", "35\t73\t620.9\t0\t73\n", "36\t48\t620.9\t0\t48\n", "37\t65\t620.9\t0\t65\n", "38\t60\t620.9\t0\t60\n", "39\t87\t620.9\t0\t87\n", "40\t68\t620.9\t0\t68\n", "41\t47\t620.9\t0\t47\n", "42\t43\t620.9\t0\t43\n", "43\t75\t620.9\t0\t75\n", "44\t58\t620.9\t0\t58\n", "45\t62\t620.9\t0\t62\n", "46\t78\t620.9\t0\t78\n", "47\t80\t620.9\t0\t80\n", "48\t83\t620.9\t0\t83\n", "49\t55\t620.9\t0\t55\n", "50\t63\t620.9\t0\t63\n", "51\t79\t620.9\t0\t79\n", "52\t59\t620.9\t0\t59\n", "53\t77\t620.9\t0\t77\n", "54\t67\t620.9\t0\t67\n", "55\t65\t620.9\t0\t65\n", "56\t67\t620.9\t0\t67\n", "57\t63\t620.9\t0\t63\n", "58\t74\t620.9\t0\t74\n", "59\t54\t620.9\t0\t54\n", "60\t101\t620.9\t0\t101\n", "61\t94\t620.9\t0\t94\n", "62\t69\t620.9\t0\t69\n", "63\t46\t620.9\t0\t46\n", "64\t56\t620.9\t0\t56\n", "65\t52\t620.9\t0\t52\n", "66\t50\t620.9\t0\t50\n", "67\t43\t620.9\t0\t43\n", "68\t45\t620.9\t0\t45\n", "69\t35\t620.9\t0\t35\n", "70\t33\t620.9\t0\t33\n", "71\t33\t620.9\t0\t33\n", "72\t51\t620.9\t0\t51\n", "73\t44\t620.9\t0\t44\n", "74\t73\t620.9\t0\t73\n", "75\t39\t620.9\t0\t39\n", "76\t46\t620.9\t0\t46\n", "77\t103\t620.9\t0\t103\n", "78\t71\t620.9\t0\t71\n", "79\t70\t620.9\t0\t70\n", "80\t58\t620.9\t0\t58\n", "81\t57\t620.9\t0\t57\n", "82\t102\t620.9\t0\t102\n", "83\t75\t620.9\t0\t75\n", "84\t63\t620.9\t0\t63\n", "85\t45\t620.9\t0\t45\n", "86\t74\t620.9\t0\t74\n", "87\t71\t620.9\t0\t71\n", "88\t87\t620.9\t0\t87\n", "89\t71\t620.9\t0\t71\n", "90\t51\t620.9\t0\t51\n", "91\t54\t620.9\t0\t54\n", "92\t59\t620.9\t0\t59\n", "93\t45\t620.9\t0\t45\n", "94\t41\t620.9\t0\t41\n", "95\t28\t620.9\t0\t28\n", "96\t49\t620.9\t0\t49\n", "97\t86\t620.9\t0\t86\n", "98\t114\t620.9\t0\t114\n", "99\t130\t620.9\t0\t130\n", "100\t86\t620.9\t0\t86\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 46_S66_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/46.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 94.83 s (13 us/read; 4.80 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,585,419\n", "Reads with adapters: 3,849,914 (50.8%)\n", "Reads written (passing filters): 7,381,449 (97.3%)\n", "\n", "Total basepairs processed: 758,541,900 bp\n", "Quality-trimmed: 2,339,776 bp (0.3%)\n", "Total written (filtered): 613,924,407 bp (80.9%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3636215 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 26.2%\n", " G: 38.1%\n", " T: 35.7%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t164056\t118522.2\t0\t164056\n", "4\t81907\t29630.5\t0\t81907\n", "5\t56888\t7407.6\t0\t56888\n", "6\t45579\t1851.9\t0\t45579\n", "7\t38021\t463.0\t0\t38021\n", "8\t36117\t115.7\t0\t36117\n", "9\t35748\t115.7\t0\t35748\n", "10\t34296\t115.7\t0\t34296\n", "11\t35301\t115.7\t0\t35301\n", "12\t35712\t115.7\t0\t35712\n", "13\t42898\t115.7\t0\t42898\n", "14\t44052\t115.7\t0\t44052\n", "15\t41123\t115.7\t0\t41123\n", "16\t44387\t115.7\t0\t44387\n", "17\t44976\t115.7\t0\t44976\n", "18\t53561\t115.7\t0\t53561\n", "19\t50355\t115.7\t0\t50355\n", "20\t40486\t115.7\t0\t40486\n", "21\t38985\t115.7\t0\t38985\n", "22\t36081\t115.7\t0\t36081\n", "23\t40776\t115.7\t0\t40776\n", "24\t47286\t115.7\t0\t47286\n", "25\t48600\t115.7\t0\t48600\n", "26\t55832\t115.7\t0\t55832\n", "27\t63739\t115.7\t0\t63739\n", "28\t59666\t115.7\t0\t59666\n", "29\t59857\t115.7\t0\t59857\n", "30\t62387\t115.7\t0\t62387\n", "31\t66688\t115.7\t0\t66688\n", "32\t62731\t115.7\t0\t62731\n", "33\t58384\t115.7\t0\t58384\n", "34\t59007\t115.7\t0\t59007\n", "35\t65091\t115.7\t0\t65091\n", "36\t75450\t115.7\t0\t75450\n", "37\t82808\t115.7\t0\t82808\n", "38\t68247\t115.7\t0\t68247\n", "39\t58918\t115.7\t0\t58918\n", "40\t55159\t115.7\t0\t55159\n", "41\t53127\t115.7\t0\t53127\n", "42\t55797\t115.7\t0\t55797\n", "43\t49087\t115.7\t0\t49087\n", "44\t41863\t115.7\t0\t41863\n", "45\t51284\t115.7\t0\t51284\n", "46\t60077\t115.7\t0\t60077\n", "47\t57504\t115.7\t0\t57504\n", "48\t55566\t115.7\t0\t55566\n", "49\t45266\t115.7\t0\t45266\n", "50\t42487\t115.7\t0\t42487\n", "51\t38369\t115.7\t0\t38369\n", "52\t44785\t115.7\t0\t44785\n", "53\t51649\t115.7\t0\t51649\n", "54\t53405\t115.7\t0\t53405\n", "55\t51238\t115.7\t0\t51238\n", "56\t41042\t115.7\t0\t41042\n", "57\t38602\t115.7\t0\t38602\n", "58\t40645\t115.7\t0\t40645\n", "59\t36305\t115.7\t0\t36305\n", "60\t32362\t115.7\t0\t32362\n", "61\t29926\t115.7\t0\t29926\n", "62\t25226\t115.7\t0\t25226\n", "63\t24617\t115.7\t0\t24617\n", "64\t27136\t115.7\t0\t27136\n", "65\t26287\t115.7\t0\t26287\n", "66\t25104\t115.7\t0\t25104\n", "67\t25049\t115.7\t0\t25049\n", "68\t24360\t115.7\t0\t24360\n", "69\t25757\t115.7\t0\t25757\n", "70\t26986\t115.7\t0\t26986\n", "71\t25363\t115.7\t0\t25363\n", "72\t20249\t115.7\t0\t20249\n", "73\t19088\t115.7\t0\t19088\n", "74\t18707\t115.7\t0\t18707\n", "75\t16139\t115.7\t0\t16139\n", "76\t13832\t115.7\t0\t13832\n", "77\t12827\t115.7\t0\t12827\n", "78\t13579\t115.7\t0\t13579\n", "79\t13379\t115.7\t0\t13379\n", "80\t13176\t115.7\t0\t13176\n", "81\t12452\t115.7\t0\t12452\n", "82\t11375\t115.7\t0\t11375\n", "83\t11924\t115.7\t0\t11924\n", "84\t12504\t115.7\t0\t12504\n", "85\t13047\t115.7\t0\t13047\n", "86\t12054\t115.7\t0\t12054\n", "87\t9220\t115.7\t0\t9220\n", "88\t8637\t115.7\t0\t8637\n", "89\t8542\t115.7\t0\t8542\n", "90\t8618\t115.7\t0\t8618\n", "91\t8186\t115.7\t0\t8186\n", "92\t7589\t115.7\t0\t7589\n", "93\t7589\t115.7\t0\t7589\n", "94\t7022\t115.7\t0\t7022\n", "95\t6872\t115.7\t0\t6872\n", "96\t6217\t115.7\t0\t6217\n", "97\t5637\t115.7\t0\t5637\n", "98\t5799\t115.7\t0\t5799\n", "99\t7652\t115.7\t0\t7652\n", "100\t6877\t115.7\t0\t6877\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 70559 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 46.6%\n", " C: 37.9%\n", " G: 0.0%\n", " T: 15.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t22943\t118522.2\t0\t22943\n", "4\t8429\t29630.5\t0\t8429\n", "5\t8473\t7407.6\t0\t8473\n", "6\t2590\t1851.9\t0\t2590\n", "7\t811\t463.0\t0\t811\n", "8\t724\t115.7\t0\t724\n", "9\t609\t115.7\t0\t609\n", "10\t570\t115.7\t0\t570\n", "11\t697\t115.7\t0\t697\n", "12\t509\t115.7\t0\t509\n", "13\t538\t115.7\t0\t538\n", "14\t540\t115.7\t0\t540\n", "15\t436\t115.7\t0\t436\n", "16\t432\t115.7\t0\t432\n", "17\t339\t115.7\t0\t339\n", "18\t473\t115.7\t0\t473\n", "19\t478\t115.7\t0\t478\n", "20\t877\t115.7\t0\t877\n", "21\t606\t115.7\t0\t606\n", "22\t451\t115.7\t0\t451\n", "23\t380\t115.7\t0\t380\n", "24\t359\t115.7\t0\t359\n", "25\t338\t115.7\t0\t338\n", "26\t450\t115.7\t0\t450\n", "27\t488\t115.7\t0\t488\n", "28\t404\t115.7\t0\t404\n", "29\t457\t115.7\t0\t457\n", "30\t795\t115.7\t0\t795\n", "31\t927\t115.7\t0\t927\n", "32\t1412\t115.7\t0\t1412\n", "33\t1653\t115.7\t0\t1653\n", "34\t1890\t115.7\t0\t1890\n", "35\t2682\t115.7\t0\t2682\n", "36\t2595\t115.7\t0\t2595\n", "37\t1446\t115.7\t0\t1446\n", "38\t152\t115.7\t0\t152\n", "39\t121\t115.7\t0\t121\n", "40\t74\t115.7\t0\t74\n", "41\t65\t115.7\t0\t65\n", "42\t55\t115.7\t0\t55\n", "43\t66\t115.7\t0\t66\n", "44\t66\t115.7\t0\t66\n", "45\t45\t115.7\t0\t45\n", "46\t69\t115.7\t0\t69\n", "47\t52\t115.7\t0\t52\n", "48\t48\t115.7\t0\t48\n", "49\t39\t115.7\t0\t39\n", "50\t64\t115.7\t0\t64\n", "51\t65\t115.7\t0\t65\n", "52\t64\t115.7\t0\t64\n", "53\t85\t115.7\t0\t85\n", "54\t63\t115.7\t0\t63\n", "55\t56\t115.7\t0\t56\n", "56\t49\t115.7\t0\t49\n", "57\t56\t115.7\t0\t56\n", "58\t48\t115.7\t0\t48\n", "59\t56\t115.7\t0\t56\n", "60\t61\t115.7\t0\t61\n", "61\t47\t115.7\t0\t47\n", "62\t51\t115.7\t0\t51\n", "63\t52\t115.7\t0\t52\n", "64\t44\t115.7\t0\t44\n", "65\t34\t115.7\t0\t34\n", "66\t35\t115.7\t0\t35\n", "67\t47\t115.7\t0\t47\n", "68\t31\t115.7\t0\t31\n", "69\t24\t115.7\t0\t24\n", "70\t21\t115.7\t0\t21\n", "71\t26\t115.7\t0\t26\n", "72\t24\t115.7\t0\t24\n", "73\t19\t115.7\t0\t19\n", "74\t19\t115.7\t0\t19\n", "75\t7\t115.7\t0\t7\n", "76\t9\t115.7\t0\t9\n", "77\t4\t115.7\t0\t4\n", "78\t10\t115.7\t0\t10\n", "79\t5\t115.7\t0\t5\n", "80\t24\t115.7\t0\t24\n", "81\t13\t115.7\t0\t13\n", "82\t9\t115.7\t0\t9\n", "83\t11\t115.7\t0\t11\n", "84\t3\t115.7\t0\t3\n", "85\t5\t115.7\t0\t5\n", "86\t7\t115.7\t0\t7\n", "87\t3\t115.7\t0\t3\n", "88\t2\t115.7\t0\t2\n", "89\t9\t115.7\t0\t9\n", "90\t8\t115.7\t0\t8\n", "91\t14\t115.7\t0\t14\n", "92\t44\t115.7\t0\t44\n", "93\t38\t115.7\t0\t38\n", "94\t80\t115.7\t0\t80\n", "95\t137\t115.7\t0\t137\n", "96\t74\t115.7\t0\t74\n", "97\t53\t115.7\t0\t53\n", "98\t86\t115.7\t0\t86\n", "99\t57\t115.7\t0\t57\n", "100\t53\t115.7\t0\t53\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 143140 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 36.6%\n", " C: 22.9%\n", " G: 10.7%\n", " T: 29.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t100320\t118522.2\t0\t100320\n", "4\t25920\t29630.5\t0\t25920\n", "5\t2800\t7407.6\t0\t2800\n", "6\t267\t1851.9\t0\t267\n", "7\t153\t463.0\t0\t153\n", "8\t160\t463.0\t0\t160\n", "9\t149\t463.0\t0\t149\n", "10\t167\t463.0\t0\t167\n", "11\t113\t463.0\t0\t113\n", "12\t193\t463.0\t0\t193\n", "13\t226\t463.0\t0\t226\n", "14\t246\t463.0\t0\t246\n", "15\t232\t463.0\t0\t232\n", "16\t247\t463.0\t0\t247\n", "17\t271\t463.0\t0\t271\n", "18\t234\t463.0\t0\t234\n", "19\t219\t463.0\t0\t219\n", "20\t251\t463.0\t0\t251\n", "21\t195\t463.0\t0\t195\n", "22\t216\t463.0\t0\t216\n", "23\t156\t463.0\t0\t156\n", "24\t99\t463.0\t0\t99\n", "25\t89\t463.0\t0\t89\n", "26\t130\t463.0\t0\t130\n", "27\t179\t463.0\t0\t179\n", "28\t115\t463.0\t0\t115\n", "29\t141\t463.0\t0\t141\n", "30\t146\t463.0\t0\t146\n", "31\t175\t463.0\t0\t175\n", "32\t196\t463.0\t0\t196\n", "33\t199\t463.0\t0\t199\n", "34\t149\t463.0\t0\t149\n", "35\t204\t463.0\t0\t204\n", "36\t164\t463.0\t0\t164\n", "37\t153\t463.0\t0\t153\n", "38\t133\t463.0\t0\t133\n", "39\t196\t463.0\t0\t196\n", "40\t186\t463.0\t0\t186\n", "41\t139\t463.0\t0\t139\n", "42\t146\t463.0\t0\t146\n", "43\t185\t463.0\t0\t185\n", "44\t92\t463.0\t0\t92\n", "45\t152\t463.0\t0\t152\n", "46\t136\t463.0\t0\t136\n", "47\t123\t463.0\t0\t123\n", "48\t86\t463.0\t0\t86\n", "49\t116\t463.0\t0\t116\n", "50\t128\t463.0\t0\t128\n", "51\t115\t463.0\t0\t115\n", "52\t123\t463.0\t0\t123\n", "53\t149\t463.0\t0\t149\n", "54\t117\t463.0\t0\t117\n", "55\t154\t463.0\t0\t154\n", "56\t165\t463.0\t0\t165\n", "57\t208\t463.0\t0\t208\n", "58\t397\t463.0\t0\t397\n", "59\t212\t463.0\t0\t212\n", "60\t377\t463.0\t0\t377\n", "61\t427\t463.0\t0\t427\n", "62\t348\t463.0\t0\t348\n", "63\t179\t463.0\t0\t179\n", "64\t361\t463.0\t0\t361\n", "65\t284\t463.0\t0\t284\n", "66\t228\t463.0\t0\t228\n", "67\t120\t463.0\t0\t120\n", "68\t111\t463.0\t0\t111\n", "69\t70\t463.0\t0\t70\n", "70\t48\t463.0\t0\t48\n", "71\t72\t463.0\t0\t72\n", "72\t86\t463.0\t0\t86\n", "73\t70\t463.0\t0\t70\n", "74\t117\t463.0\t0\t117\n", "75\t41\t463.0\t0\t41\n", "76\t78\t463.0\t0\t78\n", "77\t81\t463.0\t0\t81\n", "78\t74\t463.0\t0\t74\n", "79\t54\t463.0\t0\t54\n", "80\t60\t463.0\t0\t60\n", "81\t44\t463.0\t0\t44\n", "82\t102\t463.0\t0\t102\n", "83\t79\t463.0\t0\t79\n", "84\t51\t463.0\t0\t51\n", "85\t39\t463.0\t0\t39\n", "86\t43\t463.0\t0\t43\n", "87\t77\t463.0\t0\t77\n", "88\t165\t463.0\t0\t165\n", "89\t144\t463.0\t0\t144\n", "90\t77\t463.0\t0\t77\n", "91\t48\t463.0\t0\t48\n", "92\t45\t463.0\t0\t45\n", "93\t40\t463.0\t0\t40\n", "94\t66\t463.0\t0\t66\n", "95\t56\t463.0\t0\t56\n", "96\t41\t463.0\t0\t41\n", "97\t89\t463.0\t0\t89\n", "98\t85\t463.0\t0\t85\n", "99\t142\t463.0\t0\t142\n", "100\t89\t463.0\t0\t89\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 471b_S51_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/471b.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 82.29 s (13 us/read; 4.65 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,376,976\n", "Reads with adapters: 3,490,456 (54.7%)\n", "Reads written (passing filters): 6,249,764 (98.0%)\n", "\n", "Total basepairs processed: 637,697,600 bp\n", "Quality-trimmed: 1,594,100 bp (0.2%)\n", "Total written (filtered): 520,142,921 bp (81.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3345831 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.0%\n", " G: 38.0%\n", " T: 33.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t155100\t99640.2\t0\t155100\n", "4\t90666\t24910.1\t0\t90666\n", "5\t68498\t6227.5\t0\t68498\n", "6\t55252\t1556.9\t0\t55252\n", "7\t46399\t389.2\t0\t46399\n", "8\t43868\t97.3\t0\t43868\n", "9\t42364\t97.3\t0\t42364\n", "10\t40891\t97.3\t0\t40891\n", "11\t41118\t97.3\t0\t41118\n", "12\t42828\t97.3\t0\t42828\n", "13\t48935\t97.3\t0\t48935\n", "14\t49591\t97.3\t0\t49591\n", "15\t46209\t97.3\t0\t46209\n", "16\t48214\t97.3\t0\t48214\n", "17\t52419\t97.3\t0\t52419\n", "18\t60769\t97.3\t0\t60769\n", "19\t55820\t97.3\t0\t55820\n", "20\t46282\t97.3\t0\t46282\n", "21\t44797\t97.3\t0\t44797\n", "22\t40866\t97.3\t0\t40866\n", "23\t43513\t97.3\t0\t43513\n", "24\t50992\t97.3\t0\t50992\n", "25\t53088\t97.3\t0\t53088\n", "26\t59710\t97.3\t0\t59710\n", "27\t66248\t97.3\t0\t66248\n", "28\t61063\t97.3\t0\t61063\n", "29\t57553\t97.3\t0\t57553\n", "30\t58798\t97.3\t0\t58798\n", "31\t64106\t97.3\t0\t64106\n", "32\t60368\t97.3\t0\t60368\n", "33\t56442\t97.3\t0\t56442\n", "34\t56317\t97.3\t0\t56317\n", "35\t63487\t97.3\t0\t63487\n", "36\t73654\t97.3\t0\t73654\n", "37\t78331\t97.3\t0\t78331\n", "38\t59987\t97.3\t0\t59987\n", "39\t49946\t97.3\t0\t49946\n", "40\t46952\t97.3\t0\t46952\n", "41\t49803\t97.3\t0\t49803\n", "42\t53362\t97.3\t0\t53362\n", "43\t46596\t97.3\t0\t46596\n", "44\t37600\t97.3\t0\t37600\n", "45\t45933\t97.3\t0\t45933\n", "46\t54079\t97.3\t0\t54079\n", "47\t50919\t97.3\t0\t50919\n", "48\t49264\t97.3\t0\t49264\n", "49\t40025\t97.3\t0\t40025\n", "50\t37590\t97.3\t0\t37590\n", "51\t33891\t97.3\t0\t33891\n", "52\t32672\t97.3\t0\t32672\n", "53\t31888\t97.3\t0\t31888\n", "54\t34969\t97.3\t0\t34969\n", "55\t36838\t97.3\t0\t36838\n", "56\t33143\t97.3\t0\t33143\n", "57\t33681\t97.3\t0\t33681\n", "58\t34466\t97.3\t0\t34466\n", "59\t25915\t97.3\t0\t25915\n", "60\t21663\t97.3\t0\t21663\n", "61\t20605\t97.3\t0\t20605\n", "62\t17681\t97.3\t0\t17681\n", "63\t16682\t97.3\t0\t16682\n", "64\t18386\t97.3\t0\t18386\n", "65\t17506\t97.3\t0\t17506\n", "66\t15761\t97.3\t0\t15761\n", "67\t15517\t97.3\t0\t15517\n", "68\t15230\t97.3\t0\t15230\n", "69\t15624\t97.3\t0\t15624\n", "70\t16547\t97.3\t0\t16547\n", "71\t15503\t97.3\t0\t15503\n", "72\t12085\t97.3\t0\t12085\n", "73\t10131\t97.3\t0\t10131\n", "74\t10011\t97.3\t0\t10011\n", "75\t8841\t97.3\t0\t8841\n", "76\t7417\t97.3\t0\t7417\n", "77\t7125\t97.3\t0\t7125\n", "78\t8380\t97.3\t0\t8380\n", "79\t7907\t97.3\t0\t7907\n", "80\t7624\t97.3\t0\t7624\n", "81\t7452\t97.3\t0\t7452\n", "82\t6955\t97.3\t0\t6955\n", "83\t7375\t97.3\t0\t7375\n", "84\t8186\t97.3\t0\t8186\n", "85\t9186\t97.3\t0\t9186\n", "86\t8889\t97.3\t0\t8889\n", "87\t6833\t97.3\t0\t6833\n", "88\t6312\t97.3\t0\t6312\n", "89\t6225\t97.3\t0\t6225\n", "90\t6635\t97.3\t0\t6635\n", "91\t6865\t97.3\t0\t6865\n", "92\t6536\t97.3\t0\t6536\n", "93\t6894\t97.3\t0\t6894\n", "94\t5997\t97.3\t0\t5997\n", "95\t5082\t97.3\t0\t5082\n", "96\t3777\t97.3\t0\t3777\n", "97\t2366\t97.3\t0\t2366\n", "98\t1485\t97.3\t0\t1485\n", "99\t1476\t97.3\t0\t1476\n", "100\t1004\t97.3\t0\t1004\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 36505 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 49.6%\n", " C: 29.4%\n", " G: 0.0%\n", " T: 20.9%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t15503\t99640.2\t0\t15503\n", "4\t3869\t24910.1\t0\t3869\n", "5\t2384\t6227.5\t0\t2384\n", "6\t1877\t1556.9\t0\t1877\n", "7\t304\t389.2\t0\t304\n", "8\t263\t97.3\t0\t263\n", "9\t231\t97.3\t0\t231\n", "10\t218\t97.3\t0\t218\n", "11\t248\t97.3\t0\t248\n", "12\t157\t97.3\t0\t157\n", "13\t177\t97.3\t0\t177\n", "14\t184\t97.3\t0\t184\n", "15\t176\t97.3\t0\t176\n", "16\t161\t97.3\t0\t161\n", "17\t148\t97.3\t0\t148\n", "18\t196\t97.3\t0\t196\n", "19\t231\t97.3\t0\t231\n", "20\t234\t97.3\t0\t234\n", "21\t203\t97.3\t0\t203\n", "22\t198\t97.3\t0\t198\n", "23\t144\t97.3\t0\t144\n", "24\t188\t97.3\t0\t188\n", "25\t251\t97.3\t0\t251\n", "26\t409\t97.3\t0\t409\n", "27\t350\t97.3\t0\t350\n", "28\t335\t97.3\t0\t335\n", "29\t370\t97.3\t0\t370\n", "30\t591\t97.3\t0\t591\n", "31\t608\t97.3\t0\t608\n", "32\t1041\t97.3\t0\t1041\n", "33\t843\t97.3\t0\t843\n", "34\t858\t97.3\t0\t858\n", "35\t1084\t97.3\t0\t1084\n", "36\t953\t97.3\t0\t953\n", "37\t294\t97.3\t0\t294\n", "38\t30\t97.3\t0\t30\n", "39\t20\t97.3\t0\t20\n", "40\t15\t97.3\t0\t15\n", "41\t22\t97.3\t0\t22\n", "42\t16\t97.3\t0\t16\n", "43\t11\t97.3\t0\t11\n", "44\t12\t97.3\t0\t12\n", "45\t12\t97.3\t0\t12\n", "46\t13\t97.3\t0\t13\n", "47\t13\t97.3\t0\t13\n", "48\t16\t97.3\t0\t16\n", "49\t9\t97.3\t0\t9\n", "50\t11\t97.3\t0\t11\n", "51\t16\t97.3\t0\t16\n", "52\t7\t97.3\t0\t7\n", "53\t17\t97.3\t0\t17\n", "54\t15\t97.3\t0\t15\n", "55\t9\t97.3\t0\t9\n", "56\t12\t97.3\t0\t12\n", "57\t9\t97.3\t0\t9\n", "58\t12\t97.3\t0\t12\n", "59\t16\t97.3\t0\t16\n", "60\t8\t97.3\t0\t8\n", "61\t9\t97.3\t0\t9\n", "62\t4\t97.3\t0\t4\n", "63\t9\t97.3\t0\t9\n", "64\t2\t97.3\t0\t2\n", "65\t4\t97.3\t0\t4\n", "66\t15\t97.3\t0\t15\n", "67\t9\t97.3\t0\t9\n", "68\t10\t97.3\t0\t10\n", "69\t10\t97.3\t0\t10\n", "70\t5\t97.3\t0\t5\n", "71\t7\t97.3\t0\t7\n", "72\t10\t97.3\t0\t10\n", "73\t5\t97.3\t0\t5\n", "74\t3\t97.3\t0\t3\n", "75\t4\t97.3\t0\t4\n", "76\t4\t97.3\t0\t4\n", "77\t4\t97.3\t0\t4\n", "78\t7\t97.3\t0\t7\n", "79\t7\t97.3\t0\t7\n", "80\t5\t97.3\t0\t5\n", "81\t3\t97.3\t0\t3\n", "82\t7\t97.3\t0\t7\n", "83\t1\t97.3\t0\t1\n", "84\t6\t97.3\t0\t6\n", "86\t10\t97.3\t0\t10\n", "87\t2\t97.3\t0\t2\n", "88\t4\t97.3\t0\t4\n", "89\t6\t97.3\t0\t6\n", "90\t10\t97.3\t0\t10\n", "91\t13\t97.3\t0\t13\n", "92\t29\t97.3\t0\t29\n", "93\t43\t97.3\t0\t43\n", "94\t102\t97.3\t0\t102\n", "95\t123\t97.3\t0\t123\n", "96\t93\t97.3\t0\t93\n", "97\t89\t97.3\t0\t89\n", "98\t75\t97.3\t0\t75\n", "99\t50\t97.3\t0\t50\n", "100\t104\t97.3\t0\t104\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 108120 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.3%\n", " C: 21.0%\n", " G: 14.5%\n", " T: 22.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t78274\t99640.2\t0\t78274\n", "4\t16147\t24910.1\t0\t16147\n", "5\t2744\t6227.5\t0\t2744\n", "6\t303\t1556.9\t0\t303\n", "7\t191\t389.2\t0\t191\n", "8\t197\t389.2\t0\t197\n", "9\t197\t389.2\t0\t197\n", "10\t197\t389.2\t0\t197\n", "11\t193\t389.2\t0\t193\n", "12\t213\t389.2\t0\t213\n", "13\t245\t389.2\t0\t245\n", "14\t234\t389.2\t0\t234\n", "15\t229\t389.2\t0\t229\n", "16\t235\t389.2\t0\t235\n", "17\t230\t389.2\t0\t230\n", "18\t240\t389.2\t0\t240\n", "19\t206\t389.2\t0\t206\n", "20\t193\t389.2\t0\t193\n", "21\t210\t389.2\t0\t210\n", "22\t194\t389.2\t0\t194\n", "23\t191\t389.2\t0\t191\n", "24\t158\t389.2\t0\t158\n", "25\t159\t389.2\t0\t159\n", "26\t144\t389.2\t0\t144\n", "27\t153\t389.2\t0\t153\n", "28\t121\t389.2\t0\t121\n", "29\t165\t389.2\t0\t165\n", "30\t134\t389.2\t0\t134\n", "31\t140\t389.2\t0\t140\n", "32\t133\t389.2\t0\t133\n", "33\t125\t389.2\t0\t125\n", "34\t150\t389.2\t0\t150\n", "35\t125\t389.2\t0\t125\n", "36\t117\t389.2\t0\t117\n", "37\t127\t389.2\t0\t127\n", "38\t103\t389.2\t0\t103\n", "39\t156\t389.2\t0\t156\n", "40\t130\t389.2\t0\t130\n", "41\t138\t389.2\t0\t138\n", "42\t77\t389.2\t0\t77\n", "43\t122\t389.2\t0\t122\n", "44\t65\t389.2\t0\t65\n", "45\t98\t389.2\t0\t98\n", "46\t102\t389.2\t0\t102\n", "47\t79\t389.2\t0\t79\n", "48\t95\t389.2\t0\t95\n", "49\t79\t389.2\t0\t79\n", "50\t94\t389.2\t0\t94\n", "51\t92\t389.2\t0\t92\n", "52\t89\t389.2\t0\t89\n", "53\t96\t389.2\t0\t96\n", "54\t66\t389.2\t0\t66\n", "55\t88\t389.2\t0\t88\n", "56\t61\t389.2\t0\t61\n", "57\t65\t389.2\t0\t65\n", "58\t67\t389.2\t0\t67\n", "59\t58\t389.2\t0\t58\n", "60\t67\t389.2\t0\t67\n", "61\t87\t389.2\t0\t87\n", "62\t65\t389.2\t0\t65\n", "63\t71\t389.2\t0\t71\n", "64\t67\t389.2\t0\t67\n", "65\t66\t389.2\t0\t66\n", "66\t71\t389.2\t0\t71\n", "67\t64\t389.2\t0\t64\n", "68\t60\t389.2\t0\t60\n", "69\t43\t389.2\t0\t43\n", "70\t45\t389.2\t0\t45\n", "71\t69\t389.2\t0\t69\n", "72\t74\t389.2\t0\t74\n", "73\t89\t389.2\t0\t89\n", "74\t93\t389.2\t0\t93\n", "75\t71\t389.2\t0\t71\n", "76\t86\t389.2\t0\t86\n", "77\t106\t389.2\t0\t106\n", "78\t84\t389.2\t0\t84\n", "79\t79\t389.2\t0\t79\n", "80\t90\t389.2\t0\t90\n", "81\t95\t389.2\t0\t95\n", "82\t104\t389.2\t0\t104\n", "83\t101\t389.2\t0\t101\n", "84\t81\t389.2\t0\t81\n", "85\t82\t389.2\t0\t82\n", "86\t64\t389.2\t0\t64\n", "87\t85\t389.2\t0\t85\n", "88\t79\t389.2\t0\t79\n", "89\t62\t389.2\t0\t62\n", "90\t56\t389.2\t0\t56\n", "91\t63\t389.2\t0\t63\n", "92\t57\t389.2\t0\t57\n", "93\t34\t389.2\t0\t34\n", "94\t73\t389.2\t0\t73\n", "95\t71\t389.2\t0\t71\n", "96\t54\t389.2\t0\t54\n", "97\t66\t389.2\t0\t66\n", "98\t88\t389.2\t0\t88\n", "99\t102\t389.2\t0\t102\n", "100\t122\t389.2\t0\t122\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 472b_S48_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/472b.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 86.12 s (14 us/read; 4.38 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,292,167\n", "Reads with adapters: 4,179,944 (66.4%)\n", "Reads written (passing filters): 6,074,913 (96.5%)\n", "\n", "Total basepairs processed: 629,216,700 bp\n", "Quality-trimmed: 2,051,069 bp (0.3%)\n", "Total written (filtered): 467,111,106 bp (74.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4070599 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.5%\n", " G: 37.3%\n", " T: 32.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t122323\t98315.1\t0\t122323\n", "4\t72567\t24578.8\t0\t72567\n", "5\t55518\t6144.7\t0\t55518\n", "6\t47169\t1536.2\t0\t47169\n", "7\t41930\t384.0\t0\t41930\n", "8\t40958\t96.0\t0\t40958\n", "9\t40894\t96.0\t0\t40894\n", "10\t39871\t96.0\t0\t39871\n", "11\t39986\t96.0\t0\t39986\n", "12\t41753\t96.0\t0\t41753\n", "13\t46543\t96.0\t0\t46543\n", "14\t48101\t96.0\t0\t48101\n", "15\t46034\t96.0\t0\t46034\n", "16\t48708\t96.0\t0\t48708\n", "17\t54295\t96.0\t0\t54295\n", "18\t62639\t96.0\t0\t62639\n", "19\t58786\t96.0\t0\t58786\n", "20\t49766\t96.0\t0\t49766\n", "21\t48559\t96.0\t0\t48559\n", "22\t44136\t96.0\t0\t44136\n", "23\t46955\t96.0\t0\t46955\n", "24\t54755\t96.0\t0\t54755\n", "25\t57210\t96.0\t0\t57210\n", "26\t65416\t96.0\t0\t65416\n", "27\t74843\t96.0\t0\t74843\n", "28\t68377\t96.0\t0\t68377\n", "29\t64015\t96.0\t0\t64015\n", "30\t66471\t96.0\t0\t66471\n", "31\t73215\t96.0\t0\t73215\n", "32\t70072\t96.0\t0\t70072\n", "33\t67136\t96.0\t0\t67136\n", "34\t66191\t96.0\t0\t66191\n", "35\t75722\t96.0\t0\t75722\n", "36\t89570\t96.0\t0\t89570\n", "37\t94157\t96.0\t0\t94157\n", "38\t73755\t96.0\t0\t73755\n", "39\t61340\t96.0\t0\t61340\n", "40\t59324\t96.0\t0\t59324\n", "41\t65176\t96.0\t0\t65176\n", "42\t72804\t96.0\t0\t72804\n", "43\t63647\t96.0\t0\t63647\n", "44\t51517\t96.0\t0\t51517\n", "45\t66338\t96.0\t0\t66338\n", "46\t81058\t96.0\t0\t81058\n", "47\t77600\t96.0\t0\t77600\n", "48\t75251\t96.0\t0\t75251\n", "49\t58061\t96.0\t0\t58061\n", "50\t54510\t96.0\t0\t54510\n", "51\t47109\t96.0\t0\t47109\n", "52\t48217\t96.0\t0\t48217\n", "53\t50954\t96.0\t0\t50954\n", "54\t55840\t96.0\t0\t55840\n", "55\t55148\t96.0\t0\t55148\n", "56\t48294\t96.0\t0\t48294\n", "57\t45037\t96.0\t0\t45037\n", "58\t53622\t96.0\t0\t53622\n", "59\t48012\t96.0\t0\t48012\n", "60\t39985\t96.0\t0\t39985\n", "61\t34744\t96.0\t0\t34744\n", "62\t28676\t96.0\t0\t28676\n", "63\t27776\t96.0\t0\t27776\n", "64\t32143\t96.0\t0\t32143\n", "65\t29092\t96.0\t0\t29092\n", "66\t24367\t96.0\t0\t24367\n", "67\t25692\t96.0\t0\t25692\n", "68\t25265\t96.0\t0\t25265\n", "69\t26288\t96.0\t0\t26288\n", "70\t28834\t96.0\t0\t28834\n", "71\t26852\t96.0\t0\t26852\n", "72\t19788\t96.0\t0\t19788\n", "73\t15855\t96.0\t0\t15855\n", "74\t14684\t96.0\t0\t14684\n", "75\t13211\t96.0\t0\t13211\n", "76\t10950\t96.0\t0\t10950\n", "77\t11634\t96.0\t0\t11634\n", "78\t14168\t96.0\t0\t14168\n", "79\t12624\t96.0\t0\t12624\n", "80\t11947\t96.0\t0\t11947\n", "81\t11958\t96.0\t0\t11958\n", "82\t10977\t96.0\t0\t10977\n", "83\t11150\t96.0\t0\t11150\n", "84\t13122\t96.0\t0\t13122\n", "85\t15384\t96.0\t0\t15384\n", "86\t15237\t96.0\t0\t15237\n", "87\t11746\t96.0\t0\t11746\n", "88\t10119\t96.0\t0\t10119\n", "89\t10172\t96.0\t0\t10172\n", "90\t11488\t96.0\t0\t11488\n", "91\t12063\t96.0\t0\t12063\n", "92\t12346\t96.0\t0\t12346\n", "93\t12818\t96.0\t0\t12818\n", "94\t11736\t96.0\t0\t11736\n", "95\t9699\t96.0\t0\t9699\n", "96\t7029\t96.0\t0\t7029\n", "97\t4455\t96.0\t0\t4455\n", "98\t2704\t96.0\t0\t2704\n", "99\t3058\t96.0\t0\t3058\n", "100\t1508\t96.0\t0\t1508\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27886 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 51.9%\n", " C: 28.7%\n", " G: 0.0%\n", " T: 19.2%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t11200\t98315.1\t0\t11200\n", "4\t3123\t24578.8\t0\t3123\n", "5\t1962\t6144.7\t0\t1962\n", "6\t1293\t1536.2\t0\t1293\n", "7\t228\t384.0\t0\t228\n", "8\t169\t96.0\t0\t169\n", "9\t162\t96.0\t0\t162\n", "10\t125\t96.0\t0\t125\n", "11\t126\t96.0\t0\t126\n", "12\t127\t96.0\t0\t127\n", "13\t109\t96.0\t0\t109\n", "14\t118\t96.0\t0\t118\n", "15\t108\t96.0\t0\t108\n", "16\t128\t96.0\t0\t128\n", "17\t133\t96.0\t0\t133\n", "18\t157\t96.0\t0\t157\n", "19\t195\t96.0\t0\t195\n", "20\t247\t96.0\t0\t247\n", "21\t159\t96.0\t0\t159\n", "22\t135\t96.0\t0\t135\n", "23\t114\t96.0\t0\t114\n", "24\t124\t96.0\t0\t124\n", "25\t145\t96.0\t0\t145\n", "26\t224\t96.0\t0\t224\n", "27\t236\t96.0\t0\t236\n", "28\t269\t96.0\t0\t269\n", "29\t313\t96.0\t0\t313\n", "30\t518\t96.0\t0\t518\n", "31\t607\t96.0\t0\t607\n", "32\t954\t96.0\t0\t954\n", "33\t761\t96.0\t0\t761\n", "34\t801\t96.0\t0\t801\n", "35\t955\t96.0\t0\t955\n", "36\t766\t96.0\t0\t766\n", "37\t232\t96.0\t0\t232\n", "38\t22\t96.0\t0\t22\n", "39\t16\t96.0\t0\t16\n", "40\t12\t96.0\t0\t12\n", "41\t6\t96.0\t0\t6\n", "42\t14\t96.0\t0\t14\n", "43\t15\t96.0\t0\t15\n", "44\t8\t96.0\t0\t8\n", "45\t14\t96.0\t0\t14\n", "46\t8\t96.0\t0\t8\n", "47\t8\t96.0\t0\t8\n", "48\t9\t96.0\t0\t9\n", "49\t12\t96.0\t0\t12\n", "50\t8\t96.0\t0\t8\n", "51\t21\t96.0\t0\t21\n", "52\t11\t96.0\t0\t11\n", "53\t8\t96.0\t0\t8\n", "54\t14\t96.0\t0\t14\n", "55\t8\t96.0\t0\t8\n", "56\t9\t96.0\t0\t9\n", "57\t14\t96.0\t0\t14\n", "58\t11\t96.0\t0\t11\n", "59\t8\t96.0\t0\t8\n", "60\t10\t96.0\t0\t10\n", "61\t7\t96.0\t0\t7\n", "62\t9\t96.0\t0\t9\n", "63\t5\t96.0\t0\t5\n", "64\t2\t96.0\t0\t2\n", "65\t4\t96.0\t0\t4\n", "66\t4\t96.0\t0\t4\n", "67\t9\t96.0\t0\t9\n", "68\t3\t96.0\t0\t3\n", "69\t5\t96.0\t0\t5\n", "70\t7\t96.0\t0\t7\n", "71\t9\t96.0\t0\t9\n", "73\t5\t96.0\t0\t5\n", "74\t5\t96.0\t0\t5\n", "75\t2\t96.0\t0\t2\n", "76\t1\t96.0\t0\t1\n", "77\t1\t96.0\t0\t1\n", "78\t4\t96.0\t0\t4\n", "79\t5\t96.0\t0\t5\n", "80\t2\t96.0\t0\t2\n", "81\t8\t96.0\t0\t8\n", "82\t4\t96.0\t0\t4\n", "83\t6\t96.0\t0\t6\n", "84\t8\t96.0\t0\t8\n", "85\t6\t96.0\t0\t6\n", "86\t7\t96.0\t0\t7\n", "87\t4\t96.0\t0\t4\n", "88\t2\t96.0\t0\t2\n", "89\t2\t96.0\t0\t2\n", "90\t4\t96.0\t0\t4\n", "91\t10\t96.0\t0\t10\n", "92\t19\t96.0\t0\t19\n", "93\t29\t96.0\t0\t29\n", "94\t66\t96.0\t0\t66\n", "95\t54\t96.0\t0\t54\n", "96\t56\t96.0\t0\t56\n", "97\t72\t96.0\t0\t72\n", "98\t52\t96.0\t0\t52\n", "99\t34\t96.0\t0\t34\n", "100\t65\t96.0\t0\t65\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 81459 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.4%\n", " C: 20.0%\n", " G: 13.6%\n", " T: 22.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t57377\t98315.1\t0\t57377\n", "4\t11969\t24578.8\t0\t11969\n", "5\t2120\t6144.7\t0\t2120\n", "6\t252\t1536.2\t0\t252\n", "7\t161\t384.0\t0\t161\n", "8\t169\t384.0\t0\t169\n", "9\t175\t384.0\t0\t175\n", "10\t209\t384.0\t0\t209\n", "11\t214\t384.0\t0\t214\n", "12\t237\t384.0\t0\t237\n", "13\t281\t384.0\t0\t281\n", "14\t252\t384.0\t0\t252\n", "15\t230\t384.0\t0\t230\n", "16\t241\t384.0\t0\t241\n", "17\t260\t384.0\t0\t260\n", "18\t227\t384.0\t0\t227\n", "19\t263\t384.0\t0\t263\n", "20\t204\t384.0\t0\t204\n", "21\t218\t384.0\t0\t218\n", "22\t187\t384.0\t0\t187\n", "23\t146\t384.0\t0\t146\n", "24\t141\t384.0\t0\t141\n", "25\t164\t384.0\t0\t164\n", "26\t161\t384.0\t0\t161\n", "27\t164\t384.0\t0\t164\n", "28\t143\t384.0\t0\t143\n", "29\t153\t384.0\t0\t153\n", "30\t121\t384.0\t0\t121\n", "31\t156\t384.0\t0\t156\n", "32\t146\t384.0\t0\t146\n", "33\t143\t384.0\t0\t143\n", "34\t120\t384.0\t0\t120\n", "35\t106\t384.0\t0\t106\n", "36\t143\t384.0\t0\t143\n", "37\t130\t384.0\t0\t130\n", "38\t99\t384.0\t0\t99\n", "39\t116\t384.0\t0\t116\n", "40\t109\t384.0\t0\t109\n", "41\t71\t384.0\t0\t71\n", "42\t81\t384.0\t0\t81\n", "43\t138\t384.0\t0\t138\n", "44\t44\t384.0\t0\t44\n", "45\t78\t384.0\t0\t78\n", "46\t92\t384.0\t0\t92\n", "47\t79\t384.0\t0\t79\n", "48\t73\t384.0\t0\t73\n", "49\t84\t384.0\t0\t84\n", "50\t83\t384.0\t0\t83\n", "51\t68\t384.0\t0\t68\n", "52\t65\t384.0\t0\t65\n", "53\t67\t384.0\t0\t67\n", "54\t64\t384.0\t0\t64\n", "55\t75\t384.0\t0\t75\n", "56\t70\t384.0\t0\t70\n", "57\t75\t384.0\t0\t75\n", "58\t67\t384.0\t0\t67\n", "59\t45\t384.0\t0\t45\n", "60\t64\t384.0\t0\t64\n", "61\t67\t384.0\t0\t67\n", "62\t39\t384.0\t0\t39\n", "63\t50\t384.0\t0\t50\n", "64\t56\t384.0\t0\t56\n", "65\t51\t384.0\t0\t51\n", "66\t57\t384.0\t0\t57\n", "67\t40\t384.0\t0\t40\n", "68\t58\t384.0\t0\t58\n", "69\t35\t384.0\t0\t35\n", "70\t38\t384.0\t0\t38\n", "71\t33\t384.0\t0\t33\n", "72\t44\t384.0\t0\t44\n", "73\t58\t384.0\t0\t58\n", "74\t69\t384.0\t0\t69\n", "75\t56\t384.0\t0\t56\n", "76\t58\t384.0\t0\t58\n", "77\t66\t384.0\t0\t66\n", "78\t67\t384.0\t0\t67\n", "79\t77\t384.0\t0\t77\n", "80\t75\t384.0\t0\t75\n", "81\t54\t384.0\t0\t54\n", "82\t99\t384.0\t0\t99\n", "83\t76\t384.0\t0\t76\n", "84\t64\t384.0\t0\t64\n", "85\t60\t384.0\t0\t60\n", "86\t56\t384.0\t0\t56\n", "87\t75\t384.0\t0\t75\n", "88\t56\t384.0\t0\t56\n", "89\t49\t384.0\t0\t49\n", "90\t49\t384.0\t0\t49\n", "91\t59\t384.0\t0\t59\n", "92\t33\t384.0\t0\t33\n", "93\t44\t384.0\t0\t44\n", "94\t48\t384.0\t0\t48\n", "95\t30\t384.0\t0\t30\n", "96\t55\t384.0\t0\t55\n", "97\t61\t384.0\t0\t61\n", "98\t72\t384.0\t0\t72\n", "99\t64\t384.0\t0\t64\n", "100\t71\t384.0\t0\t71\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 473_S20_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/473.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 86.59 s (13 us/read; 4.60 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,643,017\n", "Reads with adapters: 3,348,997 (50.4%)\n", "Reads written (passing filters): 6,549,731 (98.6%)\n", "\n", "Total basepairs processed: 664,301,700 bp\n", "Quality-trimmed: 1,269,590 bp (0.2%)\n", "Total written (filtered): 561,776,988 bp (84.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3195215 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.9%\n", " G: 36.9%\n", " T: 34.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t174778\t103797.1\t0\t174778\n", "4\t104371\t25949.3\t0\t104371\n", "5\t78954\t6487.3\t0\t78954\n", "6\t62401\t1621.8\t0\t62401\n", "7\t53337\t405.5\t0\t53337\n", "8\t50333\t101.4\t0\t50333\n", "9\t48976\t101.4\t0\t48976\n", "10\t46337\t101.4\t0\t46337\n", "11\t46547\t101.4\t0\t46547\n", "12\t47560\t101.4\t0\t47560\n", "13\t49473\t101.4\t0\t49473\n", "14\t50337\t101.4\t0\t50337\n", "15\t48958\t101.4\t0\t48958\n", "16\t50966\t101.4\t0\t50966\n", "17\t56011\t101.4\t0\t56011\n", "18\t64224\t101.4\t0\t64224\n", "19\t58849\t101.4\t0\t58849\n", "20\t48442\t101.4\t0\t48442\n", "21\t47299\t101.4\t0\t47299\n", "22\t42119\t101.4\t0\t42119\n", "23\t45893\t101.4\t0\t45893\n", "24\t54267\t101.4\t0\t54267\n", "25\t54563\t101.4\t0\t54563\n", "26\t61687\t101.4\t0\t61687\n", "27\t68572\t101.4\t0\t68572\n", "28\t60705\t101.4\t0\t60705\n", "29\t57744\t101.4\t0\t57744\n", "30\t58042\t101.4\t0\t58042\n", "31\t61914\t101.4\t0\t61914\n", "32\t59963\t101.4\t0\t59963\n", "33\t53192\t101.4\t0\t53192\n", "34\t51022\t101.4\t0\t51022\n", "35\t57571\t101.4\t0\t57571\n", "36\t66962\t101.4\t0\t66962\n", "37\t69440\t101.4\t0\t69440\n", "38\t55215\t101.4\t0\t55215\n", "39\t44948\t101.4\t0\t44948\n", "40\t40638\t101.4\t0\t40638\n", "41\t43236\t101.4\t0\t43236\n", "42\t47670\t101.4\t0\t47670\n", "43\t40555\t101.4\t0\t40555\n", "44\t31381\t101.4\t0\t31381\n", "45\t39206\t101.4\t0\t39206\n", "46\t47951\t101.4\t0\t47951\n", "47\t45524\t101.4\t0\t45524\n", "48\t44667\t101.4\t0\t44667\n", "49\t34256\t101.4\t0\t34256\n", "50\t31637\t101.4\t0\t31637\n", "51\t26775\t101.4\t0\t26775\n", "52\t27007\t101.4\t0\t27007\n", "53\t29181\t101.4\t0\t29181\n", "54\t32382\t101.4\t0\t32382\n", "55\t27056\t101.4\t0\t27056\n", "56\t27003\t101.4\t0\t27003\n", "57\t26710\t101.4\t0\t26710\n", "58\t28324\t101.4\t0\t28324\n", "59\t20850\t101.4\t0\t20850\n", "60\t17305\t101.4\t0\t17305\n", "61\t16248\t101.4\t0\t16248\n", "62\t13093\t101.4\t0\t13093\n", "63\t12285\t101.4\t0\t12285\n", "64\t13784\t101.4\t0\t13784\n", "65\t13065\t101.4\t0\t13065\n", "66\t11705\t101.4\t0\t11705\n", "67\t11278\t101.4\t0\t11278\n", "68\t10570\t101.4\t0\t10570\n", "69\t10703\t101.4\t0\t10703\n", "70\t10983\t101.4\t0\t10983\n", "71\t10362\t101.4\t0\t10362\n", "72\t8173\t101.4\t0\t8173\n", "73\t7289\t101.4\t0\t7289\n", "74\t7321\t101.4\t0\t7321\n", "75\t6188\t101.4\t0\t6188\n", "76\t5322\t101.4\t0\t5322\n", "77\t4748\t101.4\t0\t4748\n", "78\t5403\t101.4\t0\t5403\n", "79\t5091\t101.4\t0\t5091\n", "80\t4985\t101.4\t0\t4985\n", "81\t4950\t101.4\t0\t4950\n", "82\t4762\t101.4\t0\t4762\n", "83\t5148\t101.4\t0\t5148\n", "84\t5835\t101.4\t0\t5835\n", "85\t6600\t101.4\t0\t6600\n", "86\t6176\t101.4\t0\t6176\n", "87\t4744\t101.4\t0\t4744\n", "88\t4358\t101.4\t0\t4358\n", "89\t4714\t101.4\t0\t4714\n", "90\t4924\t101.4\t0\t4924\n", "91\t5010\t101.4\t0\t5010\n", "92\t4985\t101.4\t0\t4985\n", "93\t5228\t101.4\t0\t5228\n", "94\t5036\t101.4\t0\t5036\n", "95\t4417\t101.4\t0\t4417\n", "96\t3227\t101.4\t0\t3227\n", "97\t2159\t101.4\t0\t2159\n", "98\t1322\t101.4\t0\t1322\n", "99\t883\t101.4\t0\t883\n", "100\t855\t101.4\t0\t855\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28004 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 47.4%\n", " C: 24.9%\n", " G: 0.0%\n", " T: 27.5%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t14000\t103797.1\t0\t14000\n", "4\t3370\t25949.3\t0\t3370\n", "5\t1079\t6487.3\t0\t1079\n", "6\t484\t1621.8\t0\t484\n", "7\t138\t405.5\t0\t138\n", "8\t113\t101.4\t0\t113\n", "9\t88\t101.4\t0\t88\n", "10\t89\t101.4\t0\t89\n", "11\t82\t101.4\t0\t82\n", "12\t88\t101.4\t0\t88\n", "13\t84\t101.4\t0\t84\n", "14\t82\t101.4\t0\t82\n", "15\t86\t101.4\t0\t86\n", "16\t65\t101.4\t0\t65\n", "17\t79\t101.4\t0\t79\n", "18\t96\t101.4\t0\t96\n", "19\t79\t101.4\t0\t79\n", "20\t115\t101.4\t0\t115\n", "21\t107\t101.4\t0\t107\n", "22\t101\t101.4\t0\t101\n", "23\t78\t101.4\t0\t78\n", "24\t90\t101.4\t0\t90\n", "25\t118\t101.4\t0\t118\n", "26\t152\t101.4\t0\t152\n", "27\t178\t101.4\t0\t178\n", "28\t170\t101.4\t0\t170\n", "29\t208\t101.4\t0\t208\n", "30\t309\t101.4\t0\t309\n", "31\t386\t101.4\t0\t386\n", "32\t585\t101.4\t0\t585\n", "33\t584\t101.4\t0\t584\n", "34\t624\t101.4\t0\t624\n", "35\t821\t101.4\t0\t821\n", "36\t751\t101.4\t0\t751\n", "37\t360\t101.4\t0\t360\n", "38\t113\t101.4\t0\t113\n", "39\t50\t101.4\t0\t50\n", "40\t37\t101.4\t0\t37\n", "41\t37\t101.4\t0\t37\n", "42\t31\t101.4\t0\t31\n", "43\t19\t101.4\t0\t19\n", "44\t37\t101.4\t0\t37\n", "45\t33\t101.4\t0\t33\n", "46\t32\t101.4\t0\t32\n", "47\t31\t101.4\t0\t31\n", "48\t40\t101.4\t0\t40\n", "49\t24\t101.4\t0\t24\n", "50\t38\t101.4\t0\t38\n", "51\t35\t101.4\t0\t35\n", "52\t31\t101.4\t0\t31\n", "53\t26\t101.4\t0\t26\n", "54\t30\t101.4\t0\t30\n", "55\t27\t101.4\t0\t27\n", "56\t22\t101.4\t0\t22\n", "57\t17\t101.4\t0\t17\n", "58\t25\t101.4\t0\t25\n", "59\t22\t101.4\t0\t22\n", "60\t21\t101.4\t0\t21\n", "61\t17\t101.4\t0\t17\n", "62\t9\t101.4\t0\t9\n", "63\t13\t101.4\t0\t13\n", "64\t24\t101.4\t0\t24\n", "65\t14\t101.4\t0\t14\n", "66\t14\t101.4\t0\t14\n", "67\t9\t101.4\t0\t9\n", "68\t10\t101.4\t0\t10\n", "69\t8\t101.4\t0\t8\n", "70\t9\t101.4\t0\t9\n", "71\t9\t101.4\t0\t9\n", "72\t13\t101.4\t0\t13\n", "73\t6\t101.4\t0\t6\n", "74\t6\t101.4\t0\t6\n", "75\t10\t101.4\t0\t10\n", "76\t5\t101.4\t0\t5\n", "77\t4\t101.4\t0\t4\n", "78\t14\t101.4\t0\t14\n", "79\t11\t101.4\t0\t11\n", "80\t11\t101.4\t0\t11\n", "81\t6\t101.4\t0\t6\n", "82\t10\t101.4\t0\t10\n", "83\t10\t101.4\t0\t10\n", "84\t14\t101.4\t0\t14\n", "85\t16\t101.4\t0\t16\n", "86\t14\t101.4\t0\t14\n", "87\t7\t101.4\t0\t7\n", "88\t12\t101.4\t0\t12\n", "89\t20\t101.4\t0\t20\n", "90\t14\t101.4\t0\t14\n", "91\t9\t101.4\t0\t9\n", "92\t32\t101.4\t0\t32\n", "93\t83\t101.4\t0\t83\n", "94\t128\t101.4\t0\t128\n", "95\t174\t101.4\t0\t174\n", "96\t135\t101.4\t0\t135\n", "97\t140\t101.4\t0\t140\n", "98\t119\t101.4\t0\t119\n", "99\t82\t101.4\t0\t82\n", "100\t146\t101.4\t0\t146\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 125778 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.0%\n", " C: 20.3%\n", " G: 15.4%\n", " T: 21.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t93003\t103797.1\t0\t93003\n", "4\t18971\t25949.3\t0\t18971\n", "5\t3667\t6487.3\t0\t3667\n", "6\t299\t1621.8\t0\t299\n", "7\t135\t405.5\t0\t135\n", "8\t159\t405.5\t0\t159\n", "9\t155\t405.5\t0\t155\n", "10\t192\t405.5\t0\t192\n", "11\t142\t405.5\t0\t142\n", "12\t152\t405.5\t0\t152\n", "13\t168\t405.5\t0\t168\n", "14\t155\t405.5\t0\t155\n", "15\t171\t405.5\t0\t171\n", "16\t151\t405.5\t0\t151\n", "17\t177\t405.5\t0\t177\n", "18\t148\t405.5\t0\t148\n", "19\t162\t405.5\t0\t162\n", "20\t175\t405.5\t0\t175\n", "21\t138\t405.5\t0\t138\n", "22\t140\t405.5\t0\t140\n", "23\t121\t405.5\t0\t121\n", "24\t103\t405.5\t0\t103\n", "25\t126\t405.5\t0\t126\n", "26\t108\t405.5\t0\t108\n", "27\t109\t405.5\t0\t109\n", "28\t120\t405.5\t0\t120\n", "29\t103\t405.5\t0\t103\n", "30\t126\t405.5\t0\t126\n", "31\t144\t405.5\t0\t144\n", "32\t138\t405.5\t0\t138\n", "33\t104\t405.5\t0\t104\n", "34\t107\t405.5\t0\t107\n", "35\t115\t405.5\t0\t115\n", "36\t101\t405.5\t0\t101\n", "37\t118\t405.5\t0\t118\n", "38\t99\t405.5\t0\t99\n", "39\t131\t405.5\t0\t131\n", "40\t125\t405.5\t0\t125\n", "41\t133\t405.5\t0\t133\n", "42\t108\t405.5\t0\t108\n", "43\t100\t405.5\t0\t100\n", "44\t74\t405.5\t0\t74\n", "45\t105\t405.5\t0\t105\n", "46\t104\t405.5\t0\t104\n", "47\t103\t405.5\t0\t103\n", "48\t76\t405.5\t0\t76\n", "49\t96\t405.5\t0\t96\n", "50\t74\t405.5\t0\t74\n", "51\t71\t405.5\t0\t71\n", "52\t96\t405.5\t0\t96\n", "53\t91\t405.5\t0\t91\n", "54\t68\t405.5\t0\t68\n", "55\t64\t405.5\t0\t64\n", "56\t49\t405.5\t0\t49\n", "57\t66\t405.5\t0\t66\n", "58\t63\t405.5\t0\t63\n", "59\t68\t405.5\t0\t68\n", "60\t59\t405.5\t0\t59\n", "61\t81\t405.5\t0\t81\n", "62\t95\t405.5\t0\t95\n", "63\t79\t405.5\t0\t79\n", "64\t64\t405.5\t0\t64\n", "65\t55\t405.5\t0\t55\n", "66\t69\t405.5\t0\t69\n", "67\t76\t405.5\t0\t76\n", "68\t69\t405.5\t0\t69\n", "69\t63\t405.5\t0\t63\n", "70\t56\t405.5\t0\t56\n", "71\t66\t405.5\t0\t66\n", "72\t77\t405.5\t0\t77\n", "73\t70\t405.5\t0\t70\n", "74\t94\t405.5\t0\t94\n", "75\t102\t405.5\t0\t102\n", "76\t99\t405.5\t0\t99\n", "77\t106\t405.5\t0\t106\n", "78\t102\t405.5\t0\t102\n", "79\t101\t405.5\t0\t101\n", "80\t116\t405.5\t0\t116\n", "81\t121\t405.5\t0\t121\n", "82\t135\t405.5\t0\t135\n", "83\t123\t405.5\t0\t123\n", "84\t107\t405.5\t0\t107\n", "85\t92\t405.5\t0\t92\n", "86\t97\t405.5\t0\t97\n", "87\t105\t405.5\t0\t105\n", "88\t93\t405.5\t0\t93\n", "89\t79\t405.5\t0\t79\n", "90\t75\t405.5\t0\t75\n", "91\t67\t405.5\t0\t67\n", "92\t56\t405.5\t0\t56\n", "93\t70\t405.5\t0\t70\n", "94\t78\t405.5\t0\t78\n", "95\t67\t405.5\t0\t67\n", "96\t63\t405.5\t0\t63\n", "97\t90\t405.5\t0\t90\n", "98\t104\t405.5\t0\t104\n", "99\t135\t405.5\t0\t135\n", "100\t155\t405.5\t0\t155\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 474_S14_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/474.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 108.39 s (13 us/read; 4.71 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,501,340\n", "Reads with adapters: 4,077,610 (48.0%)\n", "Reads written (passing filters): 8,402,514 (98.8%)\n", "\n", "Total basepairs processed: 850,134,000 bp\n", "Quality-trimmed: 1,667,527 bp (0.2%)\n", "Total written (filtered): 720,289,180 bp (84.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3886625 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.5%\n", " G: 34.9%\n", " T: 37.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t217331\t132833.4\t0\t217331\n", "4\t119636\t33208.4\t0\t119636\n", "5\t85444\t8302.1\t0\t85444\n", "6\t65739\t2075.5\t0\t65739\n", "7\t56081\t518.9\t0\t56081\n", "8\t54708\t129.7\t0\t54708\n", "9\t53110\t129.7\t0\t53110\n", "10\t50246\t129.7\t0\t50246\n", "11\t51114\t129.7\t0\t51114\n", "12\t51084\t129.7\t0\t51084\n", "13\t52109\t129.7\t0\t52109\n", "14\t53709\t129.7\t0\t53709\n", "15\t53801\t129.7\t0\t53801\n", "16\t56372\t129.7\t0\t56372\n", "17\t62713\t129.7\t0\t62713\n", "18\t72127\t129.7\t0\t72127\n", "19\t66364\t129.7\t0\t66364\n", "20\t55034\t129.7\t0\t55034\n", "21\t53638\t129.7\t0\t53638\n", "22\t47658\t129.7\t0\t47658\n", "23\t54648\t129.7\t0\t54648\n", "24\t62897\t129.7\t0\t62897\n", "25\t63230\t129.7\t0\t63230\n", "26\t71244\t129.7\t0\t71244\n", "27\t78971\t129.7\t0\t78971\n", "28\t71383\t129.7\t0\t71383\n", "29\t68762\t129.7\t0\t68762\n", "30\t71262\t129.7\t0\t71262\n", "31\t75997\t129.7\t0\t75997\n", "32\t73536\t129.7\t0\t73536\n", "33\t64903\t129.7\t0\t64903\n", "34\t61114\t129.7\t0\t61114\n", "35\t69367\t129.7\t0\t69367\n", "36\t80571\t129.7\t0\t80571\n", "37\t81549\t129.7\t0\t81549\n", "38\t67556\t129.7\t0\t67556\n", "39\t56626\t129.7\t0\t56626\n", "40\t51338\t129.7\t0\t51338\n", "41\t52644\t129.7\t0\t52644\n", "42\t57669\t129.7\t0\t57669\n", "43\t51557\t129.7\t0\t51557\n", "44\t41828\t129.7\t0\t41828\n", "45\t54215\t129.7\t0\t54215\n", "46\t65408\t129.7\t0\t65408\n", "47\t61711\t129.7\t0\t61711\n", "48\t62265\t129.7\t0\t62265\n", "49\t48519\t129.7\t0\t48519\n", "50\t46142\t129.7\t0\t46142\n", "51\t42905\t129.7\t0\t42905\n", "52\t41061\t129.7\t0\t41061\n", "53\t35053\t129.7\t0\t35053\n", "54\t35384\t129.7\t0\t35384\n", "55\t43657\t129.7\t0\t43657\n", "56\t42357\t129.7\t0\t42357\n", "57\t37380\t129.7\t0\t37380\n", "58\t40368\t129.7\t0\t40368\n", "59\t31415\t129.7\t0\t31415\n", "60\t26126\t129.7\t0\t26126\n", "61\t24515\t129.7\t0\t24515\n", "62\t20115\t129.7\t0\t20115\n", "63\t19008\t129.7\t0\t19008\n", "64\t20766\t129.7\t0\t20766\n", "65\t20452\t129.7\t0\t20452\n", "66\t17136\t129.7\t0\t17136\n", "67\t16657\t129.7\t0\t16657\n", "68\t15699\t129.7\t0\t15699\n", "69\t15432\t129.7\t0\t15432\n", "70\t16194\t129.7\t0\t16194\n", "71\t14862\t129.7\t0\t14862\n", "72\t12148\t129.7\t0\t12148\n", "73\t10555\t129.7\t0\t10555\n", "74\t10435\t129.7\t0\t10435\n", "75\t8587\t129.7\t0\t8587\n", "76\t7047\t129.7\t0\t7047\n", "77\t6651\t129.7\t0\t6651\n", "78\t7432\t129.7\t0\t7432\n", "79\t6898\t129.7\t0\t6898\n", "80\t6796\t129.7\t0\t6796\n", "81\t6470\t129.7\t0\t6470\n", "82\t6087\t129.7\t0\t6087\n", "83\t6352\t129.7\t0\t6352\n", "84\t6959\t129.7\t0\t6959\n", "85\t7758\t129.7\t0\t7758\n", "86\t7326\t129.7\t0\t7326\n", "87\t5404\t129.7\t0\t5404\n", "88\t5122\t129.7\t0\t5122\n", "89\t4947\t129.7\t0\t4947\n", "90\t5079\t129.7\t0\t5079\n", "91\t4912\t129.7\t0\t4912\n", "92\t4588\t129.7\t0\t4588\n", "93\t4292\t129.7\t0\t4292\n", "94\t3804\t129.7\t0\t3804\n", "95\t3056\t129.7\t0\t3056\n", "96\t2370\t129.7\t0\t2370\n", "97\t1597\t129.7\t0\t1597\n", "98\t1042\t129.7\t0\t1042\n", "99\t807\t129.7\t0\t807\n", "100\t632\t129.7\t0\t632\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 26302 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.9%\n", " C: 18.6%\n", " G: 0.0%\n", " T: 35.2%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t16342\t132833.4\t0\t16342\n", "4\t3242\t33208.4\t0\t3242\n", "5\t861\t8302.1\t0\t861\n", "6\t263\t2075.5\t0\t263\n", "7\t122\t518.9\t0\t122\n", "8\t99\t129.7\t0\t99\n", "9\t82\t129.7\t0\t82\n", "10\t64\t129.7\t0\t64\n", "11\t73\t129.7\t0\t73\n", "12\t69\t129.7\t0\t69\n", "13\t76\t129.7\t0\t76\n", "14\t76\t129.7\t0\t76\n", "15\t74\t129.7\t0\t74\n", "16\t74\t129.7\t0\t74\n", "17\t75\t129.7\t0\t75\n", "18\t86\t129.7\t0\t86\n", "19\t112\t129.7\t0\t112\n", "20\t111\t129.7\t0\t111\n", "21\t106\t129.7\t0\t106\n", "22\t66\t129.7\t0\t66\n", "23\t88\t129.7\t0\t88\n", "24\t72\t129.7\t0\t72\n", "25\t69\t129.7\t0\t69\n", "26\t93\t129.7\t0\t93\n", "27\t82\t129.7\t0\t82\n", "28\t73\t129.7\t0\t73\n", "29\t114\t129.7\t0\t114\n", "30\t151\t129.7\t0\t151\n", "31\t210\t129.7\t0\t210\n", "32\t312\t129.7\t0\t312\n", "33\t256\t129.7\t0\t256\n", "34\t263\t129.7\t0\t263\n", "35\t382\t129.7\t0\t382\n", "36\t380\t129.7\t0\t380\n", "37\t155\t129.7\t0\t155\n", "38\t38\t129.7\t0\t38\n", "39\t37\t129.7\t0\t37\n", "40\t27\t129.7\t0\t27\n", "41\t20\t129.7\t0\t20\n", "42\t25\t129.7\t0\t25\n", "43\t23\t129.7\t0\t23\n", "44\t34\t129.7\t0\t34\n", "45\t26\t129.7\t0\t26\n", "46\t21\t129.7\t0\t21\n", "47\t37\t129.7\t0\t37\n", "48\t36\t129.7\t0\t36\n", "49\t33\t129.7\t0\t33\n", "50\t21\t129.7\t0\t21\n", "51\t21\t129.7\t0\t21\n", "52\t14\t129.7\t0\t14\n", "53\t20\t129.7\t0\t20\n", "54\t12\t129.7\t0\t12\n", "55\t19\t129.7\t0\t19\n", "56\t16\t129.7\t0\t16\n", "57\t21\t129.7\t0\t21\n", "58\t19\t129.7\t0\t19\n", "59\t14\t129.7\t0\t14\n", "60\t18\t129.7\t0\t18\n", "61\t28\t129.7\t0\t28\n", "62\t23\t129.7\t0\t23\n", "63\t18\t129.7\t0\t18\n", "64\t18\t129.7\t0\t18\n", "65\t10\t129.7\t0\t10\n", "66\t10\t129.7\t0\t10\n", "67\t12\t129.7\t0\t12\n", "68\t15\t129.7\t0\t15\n", "69\t22\t129.7\t0\t22\n", "70\t10\t129.7\t0\t10\n", "71\t18\t129.7\t0\t18\n", "72\t9\t129.7\t0\t9\n", "73\t8\t129.7\t0\t8\n", "74\t10\t129.7\t0\t10\n", "75\t4\t129.7\t0\t4\n", "76\t5\t129.7\t0\t5\n", "77\t12\t129.7\t0\t12\n", "78\t4\t129.7\t0\t4\n", "79\t5\t129.7\t0\t5\n", "80\t9\t129.7\t0\t9\n", "81\t5\t129.7\t0\t5\n", "82\t17\t129.7\t0\t17\n", "83\t6\t129.7\t0\t6\n", "84\t8\t129.7\t0\t8\n", "85\t9\t129.7\t0\t9\n", "86\t2\t129.7\t0\t2\n", "87\t5\t129.7\t0\t5\n", "88\t9\t129.7\t0\t9\n", "89\t7\t129.7\t0\t7\n", "90\t8\t129.7\t0\t8\n", "91\t11\t129.7\t0\t11\n", "92\t19\t129.7\t0\t19\n", "93\t58\t129.7\t0\t58\n", "94\t76\t129.7\t0\t76\n", "95\t66\t129.7\t0\t66\n", "96\t65\t129.7\t0\t65\n", "97\t80\t129.7\t0\t80\n", "98\t59\t129.7\t0\t59\n", "99\t85\t129.7\t0\t85\n", "100\t132\t129.7\t0\t132\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 164683 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.7%\n", " C: 20.2%\n", " G: 14.3%\n", " T: 23.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t122147\t132833.4\t0\t122147\n", "4\t26772\t33208.4\t0\t26772\n", "5\t5385\t8302.1\t0\t5385\n", "6\t352\t2075.5\t0\t352\n", "7\t99\t518.9\t0\t99\n", "8\t105\t518.9\t0\t105\n", "9\t108\t518.9\t0\t108\n", "10\t112\t518.9\t0\t112\n", "11\t95\t518.9\t0\t95\n", "12\t118\t518.9\t0\t118\n", "13\t117\t518.9\t0\t117\n", "14\t109\t518.9\t0\t109\n", "15\t114\t518.9\t0\t114\n", "16\t126\t518.9\t0\t126\n", "17\t107\t518.9\t0\t107\n", "18\t96\t518.9\t0\t96\n", "19\t137\t518.9\t0\t137\n", "20\t101\t518.9\t0\t101\n", "21\t87\t518.9\t0\t87\n", "22\t84\t518.9\t0\t84\n", "23\t74\t518.9\t0\t74\n", "24\t86\t518.9\t0\t86\n", "25\t88\t518.9\t0\t88\n", "26\t100\t518.9\t0\t100\n", "27\t117\t518.9\t0\t117\n", "28\t101\t518.9\t0\t101\n", "29\t98\t518.9\t0\t98\n", "30\t112\t518.9\t0\t112\n", "31\t103\t518.9\t0\t103\n", "32\t106\t518.9\t0\t106\n", "33\t95\t518.9\t0\t95\n", "34\t84\t518.9\t0\t84\n", "35\t109\t518.9\t0\t109\n", "36\t114\t518.9\t0\t114\n", "37\t99\t518.9\t0\t99\n", "38\t136\t518.9\t0\t136\n", "39\t172\t518.9\t0\t172\n", "40\t160\t518.9\t0\t160\n", "41\t130\t518.9\t0\t130\n", "42\t82\t518.9\t0\t82\n", "43\t97\t518.9\t0\t97\n", "44\t113\t518.9\t0\t113\n", "45\t104\t518.9\t0\t104\n", "46\t128\t518.9\t0\t128\n", "47\t118\t518.9\t0\t118\n", "48\t82\t518.9\t0\t82\n", "49\t105\t518.9\t0\t105\n", "50\t103\t518.9\t0\t103\n", "51\t97\t518.9\t0\t97\n", "52\t107\t518.9\t0\t107\n", "53\t90\t518.9\t0\t90\n", "54\t106\t518.9\t0\t106\n", "55\t84\t518.9\t0\t84\n", "56\t59\t518.9\t0\t59\n", "57\t62\t518.9\t0\t62\n", "58\t101\t518.9\t0\t101\n", "59\t61\t518.9\t0\t61\n", "60\t104\t518.9\t0\t104\n", "61\t111\t518.9\t0\t111\n", "62\t103\t518.9\t0\t103\n", "63\t82\t518.9\t0\t82\n", "64\t79\t518.9\t0\t79\n", "65\t59\t518.9\t0\t59\n", "66\t68\t518.9\t0\t68\n", "67\t81\t518.9\t0\t81\n", "68\t64\t518.9\t0\t64\n", "69\t72\t518.9\t0\t72\n", "70\t80\t518.9\t0\t80\n", "71\t84\t518.9\t0\t84\n", "72\t87\t518.9\t0\t87\n", "73\t111\t518.9\t0\t111\n", "74\t115\t518.9\t0\t115\n", "75\t111\t518.9\t0\t111\n", "76\t111\t518.9\t0\t111\n", "77\t152\t518.9\t0\t152\n", "78\t114\t518.9\t0\t114\n", "79\t127\t518.9\t0\t127\n", "80\t142\t518.9\t0\t142\n", "81\t160\t518.9\t0\t160\n", "82\t252\t518.9\t0\t252\n", "83\t159\t518.9\t0\t159\n", "84\t155\t518.9\t0\t155\n", "85\t107\t518.9\t0\t107\n", "86\t97\t518.9\t0\t97\n", "87\t115\t518.9\t0\t115\n", "88\t141\t518.9\t0\t141\n", "89\t130\t518.9\t0\t130\n", "90\t93\t518.9\t0\t93\n", "91\t90\t518.9\t0\t90\n", "92\t65\t518.9\t0\t65\n", "93\t63\t518.9\t0\t63\n", "94\t65\t518.9\t0\t65\n", "95\t63\t518.9\t0\t63\n", "96\t70\t518.9\t0\t70\n", "97\t117\t518.9\t0\t117\n", "98\t152\t518.9\t0\t152\n", "99\t169\t518.9\t0\t169\n", "100\t209\t518.9\t0\t209\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 475_S16_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/475.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 91.43 s (12 us/read; 4.84 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,373,472\n", "Reads with adapters: 3,719,893 (50.4%)\n", "Reads written (passing filters): 7,267,714 (98.6%)\n", "\n", "Total basepairs processed: 737,347,200 bp\n", "Quality-trimmed: 1,626,973 bp (0.2%)\n", "Total written (filtered): 610,096,197 bp (82.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3555785 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.3%\n", " G: 33.6%\n", " T: 37.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t180414\t115210.5\t0\t180414\n", "4\t98495\t28802.6\t0\t98495\n", "5\t69329\t7200.7\t0\t69329\n", "6\t53873\t1800.2\t0\t53873\n", "7\t47042\t450.0\t0\t47042\n", "8\t46278\t112.5\t0\t46278\n", "9\t45279\t112.5\t0\t45279\n", "10\t42221\t112.5\t0\t42221\n", "11\t42429\t112.5\t0\t42429\n", "12\t42819\t112.5\t0\t42819\n", "13\t43662\t112.5\t0\t43662\n", "14\t44864\t112.5\t0\t44864\n", "15\t46034\t112.5\t0\t46034\n", "16\t48236\t112.5\t0\t48236\n", "17\t54117\t112.5\t0\t54117\n", "18\t62419\t112.5\t0\t62419\n", "19\t56717\t112.5\t0\t56717\n", "20\t46868\t112.5\t0\t46868\n", "21\t44531\t112.5\t0\t44531\n", "22\t40991\t112.5\t0\t40991\n", "23\t44802\t112.5\t0\t44802\n", "24\t50977\t112.5\t0\t50977\n", "25\t52005\t112.5\t0\t52005\n", "26\t58330\t112.5\t0\t58330\n", "27\t64590\t112.5\t0\t64590\n", "28\t58181\t112.5\t0\t58181\n", "29\t55615\t112.5\t0\t55615\n", "30\t57566\t112.5\t0\t57566\n", "31\t61144\t112.5\t0\t61144\n", "32\t63001\t112.5\t0\t63001\n", "33\t57956\t112.5\t0\t57956\n", "34\t55259\t112.5\t0\t55259\n", "35\t62435\t112.5\t0\t62435\n", "36\t71928\t112.5\t0\t71928\n", "37\t72210\t112.5\t0\t72210\n", "38\t62231\t112.5\t0\t62231\n", "39\t48150\t112.5\t0\t48150\n", "40\t47118\t112.5\t0\t47118\n", "41\t50859\t112.5\t0\t50859\n", "42\t56494\t112.5\t0\t56494\n", "43\t49906\t112.5\t0\t49906\n", "44\t41430\t112.5\t0\t41430\n", "45\t52637\t112.5\t0\t52637\n", "46\t63334\t112.5\t0\t63334\n", "47\t59714\t112.5\t0\t59714\n", "48\t57587\t112.5\t0\t57587\n", "49\t44334\t112.5\t0\t44334\n", "50\t41883\t112.5\t0\t41883\n", "51\t42958\t112.5\t0\t42958\n", "52\t44806\t112.5\t0\t44806\n", "53\t44732\t112.5\t0\t44732\n", "54\t41369\t112.5\t0\t41369\n", "55\t43357\t112.5\t0\t43357\n", "56\t36049\t112.5\t0\t36049\n", "57\t39485\t112.5\t0\t39485\n", "58\t44522\t112.5\t0\t44522\n", "59\t35185\t112.5\t0\t35185\n", "60\t29107\t112.5\t0\t29107\n", "61\t28124\t112.5\t0\t28124\n", "62\t23141\t112.5\t0\t23141\n", "63\t22377\t112.5\t0\t22377\n", "64\t26337\t112.5\t0\t26337\n", "65\t25115\t112.5\t0\t25115\n", "66\t20175\t112.5\t0\t20175\n", "67\t20340\t112.5\t0\t20340\n", "68\t19782\t112.5\t0\t19782\n", "69\t20238\t112.5\t0\t20238\n", "70\t21503\t112.5\t0\t21503\n", "71\t20217\t112.5\t0\t20217\n", "72\t15108\t112.5\t0\t15108\n", "73\t12686\t112.5\t0\t12686\n", "74\t12205\t112.5\t0\t12205\n", "75\t10591\t112.5\t0\t10591\n", "76\t8249\t112.5\t0\t8249\n", "77\t8314\t112.5\t0\t8314\n", "78\t10017\t112.5\t0\t10017\n", "79\t8600\t112.5\t0\t8600\n", "80\t8024\t112.5\t0\t8024\n", "81\t7655\t112.5\t0\t7655\n", "82\t7048\t112.5\t0\t7048\n", "83\t7160\t112.5\t0\t7160\n", "84\t8280\t112.5\t0\t8280\n", "85\t9282\t112.5\t0\t9282\n", "86\t8620\t112.5\t0\t8620\n", "87\t5825\t112.5\t0\t5825\n", "88\t5192\t112.5\t0\t5192\n", "89\t5167\t112.5\t0\t5167\n", "90\t5295\t112.5\t0\t5295\n", "91\t5187\t112.5\t0\t5187\n", "92\t4431\t112.5\t0\t4431\n", "93\t4049\t112.5\t0\t4049\n", "94\t3393\t112.5\t0\t3393\n", "95\t2897\t112.5\t0\t2897\n", "96\t1978\t112.5\t0\t1978\n", "97\t1337\t112.5\t0\t1337\n", "98\t806\t112.5\t0\t806\n", "99\t714\t112.5\t0\t714\n", "100\t462\t112.5\t0\t462\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 23308 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 47.2%\n", " C: 18.1%\n", " G: 0.0%\n", " T: 34.6%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t14179\t115210.5\t0\t14179\n", "4\t2866\t28802.6\t0\t2866\n", "5\t701\t7200.7\t0\t701\n", "6\t248\t1800.2\t0\t248\n", "7\t126\t450.0\t0\t126\n", "8\t96\t112.5\t0\t96\n", "9\t83\t112.5\t0\t83\n", "10\t84\t112.5\t0\t84\n", "11\t76\t112.5\t0\t76\n", "12\t64\t112.5\t0\t64\n", "13\t56\t112.5\t0\t56\n", "14\t67\t112.5\t0\t67\n", "15\t76\t112.5\t0\t76\n", "16\t67\t112.5\t0\t67\n", "17\t75\t112.5\t0\t75\n", "18\t80\t112.5\t0\t80\n", "19\t136\t112.5\t0\t136\n", "20\t112\t112.5\t0\t112\n", "21\t94\t112.5\t0\t94\n", "22\t85\t112.5\t0\t85\n", "23\t81\t112.5\t0\t81\n", "24\t80\t112.5\t0\t80\n", "25\t67\t112.5\t0\t67\n", "26\t94\t112.5\t0\t94\n", "27\t119\t112.5\t0\t119\n", "28\t92\t112.5\t0\t92\n", "29\t110\t112.5\t0\t110\n", "30\t180\t112.5\t0\t180\n", "31\t182\t112.5\t0\t182\n", "32\t307\t112.5\t0\t307\n", "33\t294\t112.5\t0\t294\n", "34\t342\t112.5\t0\t342\n", "35\t445\t112.5\t0\t445\n", "36\t449\t112.5\t0\t449\n", "37\t191\t112.5\t0\t191\n", "38\t41\t112.5\t0\t41\n", "39\t29\t112.5\t0\t29\n", "40\t29\t112.5\t0\t29\n", "41\t17\t112.5\t0\t17\n", "42\t18\t112.5\t0\t18\n", "43\t21\t112.5\t0\t21\n", "44\t27\t112.5\t0\t27\n", "45\t22\t112.5\t0\t22\n", "46\t20\t112.5\t0\t20\n", "47\t22\t112.5\t0\t22\n", "48\t25\t112.5\t0\t25\n", "49\t21\t112.5\t0\t21\n", "50\t17\t112.5\t0\t17\n", "51\t27\t112.5\t0\t27\n", "52\t19\t112.5\t0\t19\n", "53\t17\t112.5\t0\t17\n", "54\t12\t112.5\t0\t12\n", "55\t10\t112.5\t0\t10\n", "56\t11\t112.5\t0\t11\n", "57\t18\t112.5\t0\t18\n", "58\t11\t112.5\t0\t11\n", "59\t8\t112.5\t0\t8\n", "60\t9\t112.5\t0\t9\n", "61\t16\t112.5\t0\t16\n", "62\t7\t112.5\t0\t7\n", "63\t8\t112.5\t0\t8\n", "64\t9\t112.5\t0\t9\n", "65\t7\t112.5\t0\t7\n", "66\t13\t112.5\t0\t13\n", "67\t9\t112.5\t0\t9\n", "68\t7\t112.5\t0\t7\n", "69\t9\t112.5\t0\t9\n", "70\t8\t112.5\t0\t8\n", "71\t5\t112.5\t0\t5\n", "73\t4\t112.5\t0\t4\n", "74\t4\t112.5\t0\t4\n", "75\t9\t112.5\t0\t9\n", "76\t5\t112.5\t0\t5\n", "77\t1\t112.5\t0\t1\n", "78\t3\t112.5\t0\t3\n", "79\t3\t112.5\t0\t3\n", "80\t4\t112.5\t0\t4\n", "81\t7\t112.5\t0\t7\n", "83\t1\t112.5\t0\t1\n", "84\t3\t112.5\t0\t3\n", "85\t1\t112.5\t0\t1\n", "86\t6\t112.5\t0\t6\n", "87\t5\t112.5\t0\t5\n", "88\t2\t112.5\t0\t2\n", "89\t1\t112.5\t0\t1\n", "90\t2\t112.5\t0\t2\n", "91\t8\t112.5\t0\t8\n", "92\t11\t112.5\t0\t11\n", "93\t18\t112.5\t0\t18\n", "94\t55\t112.5\t0\t55\n", "95\t38\t112.5\t0\t38\n", "96\t29\t112.5\t0\t29\n", "97\t19\t112.5\t0\t19\n", "98\t30\t112.5\t0\t30\n", "99\t45\t112.5\t0\t45\n", "100\t41\t112.5\t0\t41\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 140800 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.4%\n", " C: 19.9%\n", " G: 14.3%\n", " T: 23.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t101201\t115210.5\t0\t101201\n", "4\t23160\t28802.6\t0\t23160\n", "5\t4941\t7200.7\t0\t4941\n", "6\t279\t1800.2\t0\t279\n", "7\t108\t450.0\t0\t108\n", "8\t133\t450.0\t0\t133\n", "9\t129\t450.0\t0\t129\n", "10\t131\t450.0\t0\t131\n", "11\t141\t450.0\t0\t141\n", "12\t144\t450.0\t0\t144\n", "13\t132\t450.0\t0\t132\n", "14\t122\t450.0\t0\t122\n", "15\t109\t450.0\t0\t109\n", "16\t88\t450.0\t0\t88\n", "17\t113\t450.0\t0\t113\n", "18\t132\t450.0\t0\t132\n", "19\t124\t450.0\t0\t124\n", "20\t138\t450.0\t0\t138\n", "21\t133\t450.0\t0\t133\n", "22\t127\t450.0\t0\t127\n", "23\t127\t450.0\t0\t127\n", "24\t111\t450.0\t0\t111\n", "25\t108\t450.0\t0\t108\n", "26\t102\t450.0\t0\t102\n", "27\t123\t450.0\t0\t123\n", "28\t119\t450.0\t0\t119\n", "29\t84\t450.0\t0\t84\n", "30\t109\t450.0\t0\t109\n", "31\t107\t450.0\t0\t107\n", "32\t125\t450.0\t0\t125\n", "33\t107\t450.0\t0\t107\n", "34\t92\t450.0\t0\t92\n", "35\t107\t450.0\t0\t107\n", "36\t116\t450.0\t0\t116\n", "37\t126\t450.0\t0\t126\n", "38\t132\t450.0\t0\t132\n", "39\t193\t450.0\t0\t193\n", "40\t173\t450.0\t0\t173\n", "41\t173\t450.0\t0\t173\n", "42\t100\t450.0\t0\t100\n", "43\t177\t450.0\t0\t177\n", "44\t125\t450.0\t0\t125\n", "45\t138\t450.0\t0\t138\n", "46\t192\t450.0\t0\t192\n", "47\t153\t450.0\t0\t153\n", "48\t130\t450.0\t0\t130\n", "49\t174\t450.0\t0\t174\n", "50\t127\t450.0\t0\t127\n", "51\t90\t450.0\t0\t90\n", "52\t104\t450.0\t0\t104\n", "53\t122\t450.0\t0\t122\n", "54\t113\t450.0\t0\t113\n", "55\t89\t450.0\t0\t89\n", "56\t105\t450.0\t0\t105\n", "57\t109\t450.0\t0\t109\n", "58\t104\t450.0\t0\t104\n", "59\t81\t450.0\t0\t81\n", "60\t106\t450.0\t0\t106\n", "61\t139\t450.0\t0\t139\n", "62\t91\t450.0\t0\t91\n", "63\t108\t450.0\t0\t108\n", "64\t90\t450.0\t0\t90\n", "65\t73\t450.0\t0\t73\n", "66\t81\t450.0\t0\t81\n", "67\t122\t450.0\t0\t122\n", "68\t90\t450.0\t0\t90\n", "69\t84\t450.0\t0\t84\n", "70\t64\t450.0\t0\t64\n", "71\t88\t450.0\t0\t88\n", "72\t135\t450.0\t0\t135\n", "73\t143\t450.0\t0\t143\n", "74\t171\t450.0\t0\t171\n", "75\t128\t450.0\t0\t128\n", "76\t143\t450.0\t0\t143\n", "77\t198\t450.0\t0\t198\n", "78\t149\t450.0\t0\t149\n", "79\t157\t450.0\t0\t157\n", "80\t142\t450.0\t0\t142\n", "81\t149\t450.0\t0\t149\n", "82\t222\t450.0\t0\t222\n", "83\t191\t450.0\t0\t191\n", "84\t124\t450.0\t0\t124\n", "85\t94\t450.0\t0\t94\n", "86\t90\t450.0\t0\t90\n", "87\t106\t450.0\t0\t106\n", "88\t155\t450.0\t0\t155\n", "89\t125\t450.0\t0\t125\n", "90\t73\t450.0\t0\t73\n", "91\t90\t450.0\t0\t90\n", "92\t38\t450.0\t0\t38\n", "93\t43\t450.0\t0\t43\n", "94\t59\t450.0\t0\t59\n", "95\t68\t450.0\t0\t68\n", "96\t64\t450.0\t0\t64\n", "97\t86\t450.0\t0\t86\n", "98\t112\t450.0\t0\t112\n", "99\t133\t450.0\t0\t133\n", "100\t124\t450.0\t0\t124\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 476_S17_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/476.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 62.07 s (13 us/read; 4.56 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 4,715,521\n", "Reads with adapters: 2,835,156 (60.1%)\n", "Reads written (passing filters): 4,670,118 (99.0%)\n", "\n", "Total basepairs processed: 471,552,100 bp\n", "Quality-trimmed: 1,089,298 bp (0.2%)\n", "Total written (filtered): 385,672,514 bp (81.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2767279 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.4%\n", " G: 31.8%\n", " T: 39.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t129866\t73680.0\t0\t129866\n", "4\t81735\t18420.0\t0\t81735\n", "5\t64150\t4605.0\t0\t64150\n", "6\t50952\t1151.3\t0\t50952\n", "7\t46073\t287.8\t0\t46073\n", "8\t46613\t72.0\t0\t46613\n", "9\t45092\t72.0\t0\t45092\n", "10\t42150\t72.0\t0\t42150\n", "11\t43380\t72.0\t0\t43380\n", "12\t42224\t72.0\t0\t42224\n", "13\t42634\t72.0\t0\t42634\n", "14\t43977\t72.0\t0\t43977\n", "15\t44515\t72.0\t0\t44515\n", "16\t45877\t72.0\t0\t45877\n", "17\t52589\t72.0\t0\t52589\n", "18\t62464\t72.0\t0\t62464\n", "19\t57573\t72.0\t0\t57573\n", "20\t47455\t72.0\t0\t47455\n", "21\t44314\t72.0\t0\t44314\n", "22\t38870\t72.0\t0\t38870\n", "23\t42767\t72.0\t0\t42767\n", "24\t49475\t72.0\t0\t49475\n", "25\t49364\t72.0\t0\t49364\n", "26\t55459\t72.0\t0\t55459\n", "27\t61414\t72.0\t0\t61414\n", "28\t55136\t72.0\t0\t55136\n", "29\t52435\t72.0\t0\t52435\n", "30\t54286\t72.0\t0\t54286\n", "31\t57430\t72.0\t0\t57430\n", "32\t53842\t72.0\t0\t53842\n", "33\t49404\t72.0\t0\t49404\n", "34\t44590\t72.0\t0\t44590\n", "35\t50565\t72.0\t0\t50565\n", "36\t57891\t72.0\t0\t57891\n", "37\t54314\t72.0\t0\t54314\n", "38\t46232\t72.0\t0\t46232\n", "39\t37793\t72.0\t0\t37793\n", "40\t35572\t72.0\t0\t35572\n", "41\t36577\t72.0\t0\t36577\n", "42\t39687\t72.0\t0\t39687\n", "43\t34858\t72.0\t0\t34858\n", "44\t27675\t72.0\t0\t27675\n", "45\t35797\t72.0\t0\t35797\n", "46\t43578\t72.0\t0\t43578\n", "47\t43063\t72.0\t0\t43063\n", "48\t42966\t72.0\t0\t42966\n", "49\t34641\t72.0\t0\t34641\n", "50\t29331\t72.0\t0\t29331\n", "51\t25298\t72.0\t0\t25298\n", "52\t24266\t72.0\t0\t24266\n", "53\t27953\t72.0\t0\t27953\n", "54\t26685\t72.0\t0\t26685\n", "55\t27263\t72.0\t0\t27263\n", "56\t23965\t72.0\t0\t23965\n", "57\t20919\t72.0\t0\t20919\n", "58\t21759\t72.0\t0\t21759\n", "59\t16658\t72.0\t0\t16658\n", "60\t15136\t72.0\t0\t15136\n", "61\t14335\t72.0\t0\t14335\n", "62\t11156\t72.0\t0\t11156\n", "63\t10430\t72.0\t0\t10430\n", "64\t11630\t72.0\t0\t11630\n", "65\t11074\t72.0\t0\t11074\n", "66\t9476\t72.0\t0\t9476\n", "67\t9049\t72.0\t0\t9049\n", "68\t8274\t72.0\t0\t8274\n", "69\t8122\t72.0\t0\t8122\n", "70\t8475\t72.0\t0\t8475\n", "71\t7944\t72.0\t0\t7944\n", "72\t6111\t72.0\t0\t6111\n", "73\t5264\t72.0\t0\t5264\n", "74\t5093\t72.0\t0\t5093\n", "75\t4191\t72.0\t0\t4191\n", "76\t3409\t72.0\t0\t3409\n", "77\t3047\t72.0\t0\t3047\n", "78\t3441\t72.0\t0\t3441\n", "79\t3237\t72.0\t0\t3237\n", "80\t3248\t72.0\t0\t3248\n", "81\t3037\t72.0\t0\t3037\n", "82\t2810\t72.0\t0\t2810\n", "83\t2988\t72.0\t0\t2988\n", "84\t3366\t72.0\t0\t3366\n", "85\t3925\t72.0\t0\t3925\n", "86\t3875\t72.0\t0\t3875\n", "87\t2660\t72.0\t0\t2660\n", "88\t2274\t72.0\t0\t2274\n", "89\t2577\t72.0\t0\t2577\n", "90\t2486\t72.0\t0\t2486\n", "91\t2160\t72.0\t0\t2160\n", "92\t2068\t72.0\t0\t2068\n", "93\t1922\t72.0\t0\t1922\n", "94\t1675\t72.0\t0\t1675\n", "95\t1365\t72.0\t0\t1365\n", "96\t936\t72.0\t0\t936\n", "97\t638\t72.0\t0\t638\n", "98\t403\t72.0\t0\t403\n", "99\t326\t72.0\t0\t326\n", "100\t235\t72.0\t0\t235\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 7637 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 51.1%\n", " C: 15.1%\n", " G: 0.0%\n", " T: 33.6%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t3956\t73680.0\t0\t3956\n", "4\t750\t18420.0\t0\t750\n", "5\t210\t4605.0\t0\t210\n", "6\t83\t1151.3\t0\t83\n", "7\t34\t287.8\t0\t34\n", "8\t35\t72.0\t0\t35\n", "9\t25\t72.0\t0\t25\n", "10\t26\t72.0\t0\t26\n", "11\t28\t72.0\t0\t28\n", "12\t24\t72.0\t0\t24\n", "13\t27\t72.0\t0\t27\n", "14\t29\t72.0\t0\t29\n", "15\t24\t72.0\t0\t24\n", "16\t17\t72.0\t0\t17\n", "17\t32\t72.0\t0\t32\n", "18\t34\t72.0\t0\t34\n", "19\t33\t72.0\t0\t33\n", "20\t49\t72.0\t0\t49\n", "21\t32\t72.0\t0\t32\n", "22\t20\t72.0\t0\t20\n", "23\t28\t72.0\t0\t28\n", "24\t26\t72.0\t0\t26\n", "25\t32\t72.0\t0\t32\n", "26\t44\t72.0\t0\t44\n", "27\t39\t72.0\t0\t39\n", "28\t44\t72.0\t0\t44\n", "29\t66\t72.0\t0\t66\n", "30\t109\t72.0\t0\t109\n", "31\t139\t72.0\t0\t139\n", "32\t218\t72.0\t0\t218\n", "33\t239\t72.0\t0\t239\n", "34\t232\t72.0\t0\t232\n", "35\t304\t72.0\t0\t304\n", "36\t280\t72.0\t0\t280\n", "37\t109\t72.0\t0\t109\n", "38\t15\t72.0\t0\t15\n", "39\t11\t72.0\t0\t11\n", "40\t5\t72.0\t0\t5\n", "41\t5\t72.0\t0\t5\n", "42\t4\t72.0\t0\t4\n", "43\t6\t72.0\t0\t6\n", "44\t6\t72.0\t0\t6\n", "45\t3\t72.0\t0\t3\n", "46\t6\t72.0\t0\t6\n", "47\t2\t72.0\t0\t2\n", "48\t5\t72.0\t0\t5\n", "49\t2\t72.0\t0\t2\n", "50\t3\t72.0\t0\t3\n", "51\t1\t72.0\t0\t1\n", "52\t1\t72.0\t0\t1\n", "53\t3\t72.0\t0\t3\n", "54\t3\t72.0\t0\t3\n", "55\t4\t72.0\t0\t4\n", "56\t2\t72.0\t0\t2\n", "57\t3\t72.0\t0\t3\n", "58\t3\t72.0\t0\t3\n", "59\t2\t72.0\t0\t2\n", "60\t2\t72.0\t0\t2\n", "61\t4\t72.0\t0\t4\n", "62\t1\t72.0\t0\t1\n", "63\t1\t72.0\t0\t1\n", "64\t4\t72.0\t0\t4\n", "65\t1\t72.0\t0\t1\n", "66\t2\t72.0\t0\t2\n", "67\t3\t72.0\t0\t3\n", "69\t2\t72.0\t0\t2\n", "72\t1\t72.0\t0\t1\n", "74\t1\t72.0\t0\t1\n", "75\t1\t72.0\t0\t1\n", "76\t1\t72.0\t0\t1\n", "78\t1\t72.0\t0\t1\n", "82\t2\t72.0\t0\t2\n", "83\t1\t72.0\t0\t1\n", "84\t1\t72.0\t0\t1\n", "85\t1\t72.0\t0\t1\n", "86\t1\t72.0\t0\t1\n", "87\t1\t72.0\t0\t1\n", "90\t2\t72.0\t0\t2\n", "92\t2\t72.0\t0\t2\n", "93\t16\t72.0\t0\t16\n", "94\t26\t72.0\t0\t26\n", "95\t12\t72.0\t0\t12\n", "96\t15\t72.0\t0\t15\n", "97\t15\t72.0\t0\t15\n", "98\t7\t72.0\t0\t7\n", "99\t18\t72.0\t0\t18\n", "100\t20\t72.0\t0\t20\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 60240 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 53.1%\n", " C: 13.4%\n", " G: 11.8%\n", " T: 21.7%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t41569\t73680.0\t0\t41569\n", "4\t10947\t18420.0\t0\t10947\n", "5\t3694\t4605.0\t0\t3694\n", "6\t91\t1151.3\t0\t91\n", "7\t28\t287.8\t0\t28\n", "8\t35\t287.8\t0\t35\n", "9\t29\t287.8\t0\t29\n", "10\t35\t287.8\t0\t35\n", "11\t31\t287.8\t0\t31\n", "12\t37\t287.8\t0\t37\n", "13\t33\t287.8\t0\t33\n", "14\t23\t287.8\t0\t23\n", "15\t20\t287.8\t0\t20\n", "16\t17\t287.8\t0\t17\n", "17\t16\t287.8\t0\t16\n", "18\t17\t287.8\t0\t17\n", "19\t28\t287.8\t0\t28\n", "20\t13\t287.8\t0\t13\n", "21\t22\t287.8\t0\t22\n", "22\t23\t287.8\t0\t23\n", "23\t20\t287.8\t0\t20\n", "24\t12\t287.8\t0\t12\n", "25\t23\t287.8\t0\t23\n", "26\t21\t287.8\t0\t21\n", "27\t24\t287.8\t0\t24\n", "28\t18\t287.8\t0\t18\n", "29\t30\t287.8\t0\t30\n", "30\t18\t287.8\t0\t18\n", "31\t24\t287.8\t0\t24\n", "32\t17\t287.8\t0\t17\n", "33\t15\t287.8\t0\t15\n", "34\t12\t287.8\t0\t12\n", "35\t20\t287.8\t0\t20\n", "36\t22\t287.8\t0\t22\n", "37\t20\t287.8\t0\t20\n", "38\t21\t287.8\t0\t21\n", "39\t34\t287.8\t0\t34\n", "40\t31\t287.8\t0\t31\n", "41\t22\t287.8\t0\t22\n", "42\t24\t287.8\t0\t24\n", "43\t34\t287.8\t0\t34\n", "44\t17\t287.8\t0\t17\n", "45\t34\t287.8\t0\t34\n", "46\t40\t287.8\t0\t40\n", "47\t24\t287.8\t0\t24\n", "48\t31\t287.8\t0\t31\n", "49\t42\t287.8\t0\t42\n", "50\t38\t287.8\t0\t38\n", "51\t22\t287.8\t0\t22\n", "52\t28\t287.8\t0\t28\n", "53\t19\t287.8\t0\t19\n", "54\t14\t287.8\t0\t14\n", "55\t21\t287.8\t0\t21\n", "56\t16\t287.8\t0\t16\n", "57\t27\t287.8\t0\t27\n", "58\t25\t287.8\t0\t25\n", "59\t20\t287.8\t0\t20\n", "60\t37\t287.8\t0\t37\n", "61\t46\t287.8\t0\t46\n", "62\t29\t287.8\t0\t29\n", "63\t34\t287.8\t0\t34\n", "64\t26\t287.8\t0\t26\n", "65\t29\t287.8\t0\t29\n", "66\t29\t287.8\t0\t29\n", "67\t30\t287.8\t0\t30\n", "68\t21\t287.8\t0\t21\n", "69\t17\t287.8\t0\t17\n", "70\t20\t287.8\t0\t20\n", "71\t26\t287.8\t0\t26\n", "72\t56\t287.8\t0\t56\n", "73\t138\t287.8\t0\t138\n", "74\t161\t287.8\t0\t161\n", "75\t135\t287.8\t0\t135\n", "76\t117\t287.8\t0\t117\n", "77\t189\t287.8\t0\t189\n", "78\t113\t287.8\t0\t113\n", "79\t96\t287.8\t0\t96\n", "80\t94\t287.8\t0\t94\n", "81\t116\t287.8\t0\t116\n", "82\t128\t287.8\t0\t128\n", "83\t115\t287.8\t0\t115\n", "84\t83\t287.8\t0\t83\n", "85\t61\t287.8\t0\t61\n", "86\t46\t287.8\t0\t46\n", "87\t71\t287.8\t0\t71\n", "88\t65\t287.8\t0\t65\n", "89\t33\t287.8\t0\t33\n", "90\t40\t287.8\t0\t40\n", "91\t39\t287.8\t0\t39\n", "92\t23\t287.8\t0\t23\n", "93\t19\t287.8\t0\t19\n", "94\t32\t287.8\t0\t32\n", "95\t27\t287.8\t0\t27\n", "96\t25\t287.8\t0\t25\n", "97\t38\t287.8\t0\t38\n", "98\t57\t287.8\t0\t57\n", "99\t75\t287.8\t0\t75\n", "100\t116\t287.8\t0\t116\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 477_S37_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/477.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 81.75 s (12 us/read; 4.82 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,572,156\n", "Reads with adapters: 3,148,710 (47.9%)\n", "Reads written (passing filters): 6,454,707 (98.2%)\n", "\n", "Total basepairs processed: 657,215,600 bp\n", "Quality-trimmed: 1,275,564 bp (0.2%)\n", "Total written (filtered): 554,326,238 bp (84.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2963264 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.2%\n", " G: 40.6%\n", " T: 28.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t160340\t102689.9\t0\t160340\n", "4\t83898\t25672.5\t0\t83898\n", "5\t59728\t6418.1\t0\t59728\n", "6\t47931\t1604.5\t0\t47931\n", "7\t42660\t401.1\t0\t42660\n", "8\t42583\t100.3\t0\t42583\n", "9\t41205\t100.3\t0\t41205\n", "10\t40548\t100.3\t0\t40548\n", "11\t41650\t100.3\t0\t41650\n", "12\t41998\t100.3\t0\t41998\n", "13\t47972\t100.3\t0\t47972\n", "14\t48775\t100.3\t0\t48775\n", "15\t44975\t100.3\t0\t44975\n", "16\t46742\t100.3\t0\t46742\n", "17\t48905\t100.3\t0\t48905\n", "18\t56414\t100.3\t0\t56414\n", "19\t51105\t100.3\t0\t51105\n", "20\t42628\t100.3\t0\t42628\n", "21\t40257\t100.3\t0\t40257\n", "22\t36911\t100.3\t0\t36911\n", "23\t39336\t100.3\t0\t39336\n", "24\t45584\t100.3\t0\t45584\n", "25\t46472\t100.3\t0\t46472\n", "26\t51968\t100.3\t0\t51968\n", "27\t55391\t100.3\t0\t55391\n", "28\t49978\t100.3\t0\t49978\n", "29\t47237\t100.3\t0\t47237\n", "30\t48140\t100.3\t0\t48140\n", "31\t51743\t100.3\t0\t51743\n", "32\t51248\t100.3\t0\t51248\n", "33\t46738\t100.3\t0\t46738\n", "34\t45438\t100.3\t0\t45438\n", "35\t50548\t100.3\t0\t50548\n", "36\t57320\t100.3\t0\t57320\n", "37\t59635\t100.3\t0\t59635\n", "38\t48128\t100.3\t0\t48128\n", "39\t41161\t100.3\t0\t41161\n", "40\t38715\t100.3\t0\t38715\n", "41\t42766\t100.3\t0\t42766\n", "42\t47457\t100.3\t0\t47457\n", "43\t41194\t100.3\t0\t41194\n", "44\t32094\t100.3\t0\t32094\n", "45\t39496\t100.3\t0\t39496\n", "46\t45907\t100.3\t0\t45907\n", "47\t41593\t100.3\t0\t41593\n", "48\t40897\t100.3\t0\t40897\n", "49\t32845\t100.3\t0\t32845\n", "50\t31934\t100.3\t0\t31934\n", "51\t27492\t100.3\t0\t27492\n", "52\t29255\t100.3\t0\t29255\n", "53\t28534\t100.3\t0\t28534\n", "54\t27767\t100.3\t0\t27767\n", "55\t30762\t100.3\t0\t30762\n", "56\t28944\t100.3\t0\t28944\n", "57\t26408\t100.3\t0\t26408\n", "58\t28523\t100.3\t0\t28523\n", "59\t23517\t100.3\t0\t23517\n", "60\t20299\t100.3\t0\t20299\n", "61\t18397\t100.3\t0\t18397\n", "62\t15095\t100.3\t0\t15095\n", "63\t14529\t100.3\t0\t14529\n", "64\t16145\t100.3\t0\t16145\n", "65\t15815\t100.3\t0\t15815\n", "66\t14311\t100.3\t0\t14311\n", "67\t13908\t100.3\t0\t13908\n", "68\t13838\t100.3\t0\t13838\n", "69\t14430\t100.3\t0\t14430\n", "70\t15323\t100.3\t0\t15323\n", "71\t14657\t100.3\t0\t14657\n", "72\t11458\t100.3\t0\t11458\n", "73\t10126\t100.3\t0\t10126\n", "74\t10214\t100.3\t0\t10214\n", "75\t8961\t100.3\t0\t8961\n", "76\t7454\t100.3\t0\t7454\n", "77\t7251\t100.3\t0\t7251\n", "78\t7962\t100.3\t0\t7962\n", "79\t7787\t100.3\t0\t7787\n", "80\t7655\t100.3\t0\t7655\n", "81\t7225\t100.3\t0\t7225\n", "82\t6768\t100.3\t0\t6768\n", "83\t7121\t100.3\t0\t7121\n", "84\t8125\t100.3\t0\t8125\n", "85\t8626\t100.3\t0\t8626\n", "86\t8045\t100.3\t0\t8045\n", "87\t5958\t100.3\t0\t5958\n", "88\t5735\t100.3\t0\t5735\n", "89\t5896\t100.3\t0\t5896\n", "90\t6132\t100.3\t0\t6132\n", "91\t6313\t100.3\t0\t6313\n", "92\t6213\t100.3\t0\t6213\n", "93\t6363\t100.3\t0\t6363\n", "94\t5662\t100.3\t0\t5662\n", "95\t4661\t100.3\t0\t4661\n", "96\t3372\t100.3\t0\t3372\n", "97\t2269\t100.3\t0\t2269\n", "98\t1388\t100.3\t0\t1388\n", "99\t1400\t100.3\t0\t1400\n", "100\t987\t100.3\t0\t987\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 38347 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.4%\n", " C: 29.8%\n", " G: 0.0%\n", " T: 26.7%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t23021\t102689.9\t0\t23021\n", "4\t4731\t25672.5\t0\t4731\n", "5\t1649\t6418.1\t0\t1649\n", "6\t965\t1604.5\t0\t965\n", "7\t113\t401.1\t0\t113\n", "8\t100\t100.3\t0\t100\n", "9\t69\t100.3\t0\t69\n", "10\t67\t100.3\t0\t67\n", "11\t76\t100.3\t0\t76\n", "12\t85\t100.3\t0\t85\n", "13\t81\t100.3\t0\t81\n", "14\t74\t100.3\t0\t74\n", "15\t89\t100.3\t0\t89\n", "16\t74\t100.3\t0\t74\n", "17\t92\t100.3\t0\t92\n", "18\t91\t100.3\t0\t91\n", "19\t138\t100.3\t0\t138\n", "20\t236\t100.3\t0\t236\n", "21\t163\t100.3\t0\t163\n", "22\t112\t100.3\t0\t112\n", "23\t91\t100.3\t0\t91\n", "24\t82\t100.3\t0\t82\n", "25\t86\t100.3\t0\t86\n", "26\t123\t100.3\t0\t123\n", "27\t119\t100.3\t0\t119\n", "28\t150\t100.3\t0\t150\n", "29\t191\t100.3\t0\t191\n", "30\t286\t100.3\t0\t286\n", "31\t327\t100.3\t0\t327\n", "32\t502\t100.3\t0\t502\n", "33\t445\t100.3\t0\t445\n", "34\t427\t100.3\t0\t427\n", "35\t535\t100.3\t0\t535\n", "36\t505\t100.3\t0\t505\n", "37\t183\t100.3\t0\t183\n", "38\t65\t100.3\t0\t65\n", "39\t64\t100.3\t0\t64\n", "40\t54\t100.3\t0\t54\n", "41\t48\t100.3\t0\t48\n", "42\t55\t100.3\t0\t55\n", "43\t48\t100.3\t0\t48\n", "44\t45\t100.3\t0\t45\n", "45\t41\t100.3\t0\t41\n", "46\t44\t100.3\t0\t44\n", "47\t47\t100.3\t0\t47\n", "48\t43\t100.3\t0\t43\n", "49\t50\t100.3\t0\t50\n", "50\t42\t100.3\t0\t42\n", "51\t38\t100.3\t0\t38\n", "52\t41\t100.3\t0\t41\n", "53\t65\t100.3\t0\t65\n", "54\t21\t100.3\t0\t21\n", "55\t41\t100.3\t0\t41\n", "56\t46\t100.3\t0\t46\n", "57\t30\t100.3\t0\t30\n", "58\t36\t100.3\t0\t36\n", "59\t35\t100.3\t0\t35\n", "60\t28\t100.3\t0\t28\n", "61\t25\t100.3\t0\t25\n", "62\t31\t100.3\t0\t31\n", "63\t37\t100.3\t0\t37\n", "64\t26\t100.3\t0\t26\n", "65\t22\t100.3\t0\t22\n", "66\t26\t100.3\t0\t26\n", "67\t24\t100.3\t0\t24\n", "68\t21\t100.3\t0\t21\n", "69\t24\t100.3\t0\t24\n", "70\t27\t100.3\t0\t27\n", "71\t18\t100.3\t0\t18\n", "72\t18\t100.3\t0\t18\n", "73\t22\t100.3\t0\t22\n", "74\t16\t100.3\t0\t16\n", "75\t11\t100.3\t0\t11\n", "76\t18\t100.3\t0\t18\n", "77\t14\t100.3\t0\t14\n", "78\t12\t100.3\t0\t12\n", "79\t12\t100.3\t0\t12\n", "80\t13\t100.3\t0\t13\n", "81\t16\t100.3\t0\t16\n", "82\t8\t100.3\t0\t8\n", "83\t9\t100.3\t0\t9\n", "84\t15\t100.3\t0\t15\n", "85\t12\t100.3\t0\t12\n", "86\t17\t100.3\t0\t17\n", "87\t15\t100.3\t0\t15\n", "88\t9\t100.3\t0\t9\n", "89\t11\t100.3\t0\t11\n", "90\t14\t100.3\t0\t14\n", "91\t18\t100.3\t0\t18\n", "92\t35\t100.3\t0\t35\n", "93\t57\t100.3\t0\t57\n", "94\t72\t100.3\t0\t72\n", "95\t86\t100.3\t0\t86\n", "96\t111\t100.3\t0\t111\n", "97\t93\t100.3\t0\t93\n", "98\t70\t100.3\t0\t70\n", "99\t64\t100.3\t0\t64\n", "100\t93\t100.3\t0\t93\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 147099 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 38.4%\n", " C: 22.4%\n", " G: 18.6%\n", " T: 20.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t110778\t102689.9\t0\t110778\n", "4\t21664\t25672.5\t0\t21664\n", "5\t3639\t6418.1\t0\t3639\n", "6\t327\t1604.5\t0\t327\n", "7\t102\t401.1\t0\t102\n", "8\t94\t401.1\t0\t94\n", "9\t112\t401.1\t0\t112\n", "10\t100\t401.1\t0\t100\n", "11\t107\t401.1\t0\t107\n", "12\t119\t401.1\t0\t119\n", "13\t95\t401.1\t0\t95\n", "14\t98\t401.1\t0\t98\n", "15\t113\t401.1\t0\t113\n", "16\t107\t401.1\t0\t107\n", "17\t115\t401.1\t0\t115\n", "18\t126\t401.1\t0\t126\n", "19\t84\t401.1\t0\t84\n", "20\t102\t401.1\t0\t102\n", "21\t104\t401.1\t0\t104\n", "22\t92\t401.1\t0\t92\n", "23\t118\t401.1\t0\t118\n", "24\t71\t401.1\t0\t71\n", "25\t78\t401.1\t0\t78\n", "26\t104\t401.1\t0\t104\n", "27\t89\t401.1\t0\t89\n", "28\t91\t401.1\t0\t91\n", "29\t106\t401.1\t0\t106\n", "30\t106\t401.1\t0\t106\n", "31\t99\t401.1\t0\t99\n", "32\t108\t401.1\t0\t108\n", "33\t119\t401.1\t0\t119\n", "34\t112\t401.1\t0\t112\n", "35\t129\t401.1\t0\t129\n", "36\t95\t401.1\t0\t95\n", "37\t136\t401.1\t0\t136\n", "38\t135\t401.1\t0\t135\n", "39\t202\t401.1\t0\t202\n", "40\t188\t401.1\t0\t188\n", "41\t141\t401.1\t0\t141\n", "42\t150\t401.1\t0\t150\n", "43\t140\t401.1\t0\t140\n", "44\t124\t401.1\t0\t124\n", "45\t151\t401.1\t0\t151\n", "46\t151\t401.1\t0\t151\n", "47\t127\t401.1\t0\t127\n", "48\t109\t401.1\t0\t109\n", "49\t118\t401.1\t0\t118\n", "50\t84\t401.1\t0\t84\n", "51\t92\t401.1\t0\t92\n", "52\t121\t401.1\t0\t121\n", "53\t114\t401.1\t0\t114\n", "54\t100\t401.1\t0\t100\n", "55\t88\t401.1\t0\t88\n", "56\t115\t401.1\t0\t115\n", "57\t90\t401.1\t0\t90\n", "58\t106\t401.1\t0\t106\n", "59\t109\t401.1\t0\t109\n", "60\t108\t401.1\t0\t108\n", "61\t134\t401.1\t0\t134\n", "62\t109\t401.1\t0\t109\n", "63\t124\t401.1\t0\t124\n", "64\t100\t401.1\t0\t100\n", "65\t111\t401.1\t0\t111\n", "66\t111\t401.1\t0\t111\n", "67\t106\t401.1\t0\t106\n", "68\t76\t401.1\t0\t76\n", "69\t89\t401.1\t0\t89\n", "70\t107\t401.1\t0\t107\n", "71\t88\t401.1\t0\t88\n", "72\t102\t401.1\t0\t102\n", "73\t123\t401.1\t0\t123\n", "74\t127\t401.1\t0\t127\n", "75\t107\t401.1\t0\t107\n", "76\t137\t401.1\t0\t137\n", "77\t128\t401.1\t0\t128\n", "78\t121\t401.1\t0\t121\n", "79\t120\t401.1\t0\t120\n", "80\t183\t401.1\t0\t183\n", "81\t131\t401.1\t0\t131\n", "82\t202\t401.1\t0\t202\n", "83\t168\t401.1\t0\t168\n", "84\t136\t401.1\t0\t136\n", "85\t137\t401.1\t0\t137\n", "86\t94\t401.1\t0\t94\n", "87\t128\t401.1\t0\t128\n", "88\t187\t401.1\t0\t187\n", "89\t163\t401.1\t0\t163\n", "90\t117\t401.1\t0\t117\n", "91\t88\t401.1\t0\t88\n", "92\t64\t401.1\t0\t64\n", "93\t48\t401.1\t0\t48\n", "94\t78\t401.1\t0\t78\n", "95\t80\t401.1\t0\t80\n", "96\t63\t401.1\t0\t63\n", "97\t78\t401.1\t0\t78\n", "98\t89\t401.1\t0\t89\n", "99\t115\t401.1\t0\t115\n", "100\t128\t401.1\t0\t128\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 47_S58_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/47.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 68.54 s (13 us/read; 4.78 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,455,003\n", "Reads with adapters: 2,604,936 (47.8%)\n", "Reads written (passing filters): 5,363,627 (98.3%)\n", "\n", "Total basepairs processed: 545,500,300 bp\n", "Quality-trimmed: 1,514,696 bp (0.3%)\n", "Total written (filtered): 460,963,375 bp (84.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2423515 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.2%\n", " G: 32.3%\n", " T: 36.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t127146\t85234.4\t0\t127146\n", "4\t70393\t21308.6\t0\t70393\n", "5\t52518\t5327.2\t0\t52518\n", "6\t38020\t1331.8\t0\t38020\n", "7\t34364\t332.9\t0\t34364\n", "8\t34033\t83.2\t0\t34033\n", "9\t33453\t83.2\t0\t33453\n", "10\t31436\t83.2\t0\t31436\n", "11\t31580\t83.2\t0\t31580\n", "12\t30688\t83.2\t0\t30688\n", "13\t32534\t83.2\t0\t32534\n", "14\t33880\t83.2\t0\t33880\n", "15\t34347\t83.2\t0\t34347\n", "16\t36609\t83.2\t0\t36609\n", "17\t39766\t83.2\t0\t39766\n", "18\t45607\t83.2\t0\t45607\n", "19\t40756\t83.2\t0\t40756\n", "20\t32771\t83.2\t0\t32771\n", "21\t32339\t83.2\t0\t32339\n", "22\t29896\t83.2\t0\t29896\n", "23\t33623\t83.2\t0\t33623\n", "24\t38999\t83.2\t0\t38999\n", "25\t39445\t83.2\t0\t39445\n", "26\t44614\t83.2\t0\t44614\n", "27\t49779\t83.2\t0\t49779\n", "28\t44193\t83.2\t0\t44193\n", "29\t41005\t83.2\t0\t41005\n", "30\t41733\t83.2\t0\t41733\n", "31\t45309\t83.2\t0\t45309\n", "32\t44261\t83.2\t0\t44261\n", "33\t41180\t83.2\t0\t41180\n", "34\t40639\t83.2\t0\t40639\n", "35\t46731\t83.2\t0\t46731\n", "36\t54546\t83.2\t0\t54546\n", "37\t58878\t83.2\t0\t58878\n", "38\t45250\t83.2\t0\t45250\n", "39\t35504\t83.2\t0\t35504\n", "40\t33849\t83.2\t0\t33849\n", "41\t34166\t83.2\t0\t34166\n", "42\t34829\t83.2\t0\t34829\n", "43\t31262\t83.2\t0\t31262\n", "44\t24519\t83.2\t0\t24519\n", "45\t30239\t83.2\t0\t30239\n", "46\t35185\t83.2\t0\t35185\n", "47\t31891\t83.2\t0\t31891\n", "48\t30381\t83.2\t0\t30381\n", "49\t24924\t83.2\t0\t24924\n", "50\t24253\t83.2\t0\t24253\n", "51\t21196\t83.2\t0\t21196\n", "52\t21022\t83.2\t0\t21022\n", "53\t22057\t83.2\t0\t22057\n", "54\t22520\t83.2\t0\t22520\n", "55\t24677\t83.2\t0\t24677\n", "56\t24910\t83.2\t0\t24910\n", "57\t21631\t83.2\t0\t21631\n", "58\t22760\t83.2\t0\t22760\n", "59\t20326\t83.2\t0\t20326\n", "60\t16871\t83.2\t0\t16871\n", "61\t15638\t83.2\t0\t15638\n", "62\t13927\t83.2\t0\t13927\n", "63\t15402\t83.2\t0\t15402\n", "64\t18978\t83.2\t0\t18978\n", "65\t16203\t83.2\t0\t16203\n", "66\t15091\t83.2\t0\t15091\n", "67\t15506\t83.2\t0\t15506\n", "68\t12455\t83.2\t0\t12455\n", "69\t10318\t83.2\t0\t10318\n", "70\t10463\t83.2\t0\t10463\n", "71\t9613\t83.2\t0\t9613\n", "72\t8981\t83.2\t0\t8981\n", "73\t6343\t83.2\t0\t6343\n", "74\t5358\t83.2\t0\t5358\n", "75\t4803\t83.2\t0\t4803\n", "76\t4734\t83.2\t0\t4734\n", "77\t5613\t83.2\t0\t5613\n", "78\t6569\t83.2\t0\t6569\n", "79\t5763\t83.2\t0\t5763\n", "80\t5414\t83.2\t0\t5414\n", "81\t5474\t83.2\t0\t5474\n", "82\t5225\t83.2\t0\t5225\n", "83\t4449\t83.2\t0\t4449\n", "84\t4966\t83.2\t0\t4966\n", "85\t5852\t83.2\t0\t5852\n", "86\t6222\t83.2\t0\t6222\n", "87\t5057\t83.2\t0\t5057\n", "88\t4271\t83.2\t0\t4271\n", "89\t3872\t83.2\t0\t3872\n", "90\t4053\t83.2\t0\t4053\n", "91\t3956\t83.2\t0\t3956\n", "92\t3826\t83.2\t0\t3826\n", "93\t3525\t83.2\t0\t3525\n", "94\t3357\t83.2\t0\t3357\n", "95\t2841\t83.2\t0\t2841\n", "96\t2316\t83.2\t0\t2316\n", "97\t1780\t83.2\t0\t1780\n", "98\t1328\t83.2\t0\t1328\n", "99\t1363\t83.2\t0\t1363\n", "100\t1317\t83.2\t0\t1317\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 64242 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 38.4%\n", " C: 47.0%\n", " G: 0.0%\n", " T: 14.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t24349\t85234.4\t0\t24349\n", "4\t11046\t21308.6\t0\t11046\n", "5\t10926\t5327.2\t0\t10926\n", "6\t687\t1331.8\t0\t687\n", "7\t157\t332.9\t0\t157\n", "8\t139\t83.2\t0\t139\n", "9\t138\t83.2\t0\t138\n", "10\t104\t83.2\t0\t104\n", "11\t82\t83.2\t0\t82\n", "12\t87\t83.2\t0\t87\n", "13\t104\t83.2\t0\t104\n", "14\t99\t83.2\t0\t99\n", "15\t106\t83.2\t0\t106\n", "16\t104\t83.2\t0\t104\n", "17\t156\t83.2\t0\t156\n", "18\t240\t83.2\t0\t240\n", "19\t274\t83.2\t0\t274\n", "20\t249\t83.2\t0\t249\n", "21\t170\t83.2\t0\t170\n", "22\t145\t83.2\t0\t145\n", "23\t139\t83.2\t0\t139\n", "24\t143\t83.2\t0\t143\n", "25\t125\t83.2\t0\t125\n", "26\t158\t83.2\t0\t158\n", "27\t214\t83.2\t0\t214\n", "28\t298\t83.2\t0\t298\n", "29\t446\t83.2\t0\t446\n", "30\t624\t83.2\t0\t624\n", "31\t889\t83.2\t0\t889\n", "32\t1071\t83.2\t0\t1071\n", "33\t1185\t83.2\t0\t1185\n", "34\t1546\t83.2\t0\t1546\n", "35\t1736\t83.2\t0\t1736\n", "36\t1033\t83.2\t0\t1033\n", "37\t332\t83.2\t0\t332\n", "38\t120\t83.2\t0\t120\n", "39\t107\t83.2\t0\t107\n", "40\t89\t83.2\t0\t89\n", "41\t141\t83.2\t0\t141\n", "42\t154\t83.2\t0\t154\n", "43\t182\t83.2\t0\t182\n", "44\t191\t83.2\t0\t191\n", "45\t244\t83.2\t0\t244\n", "46\t316\t83.2\t0\t316\n", "47\t405\t83.2\t0\t405\n", "48\t313\t83.2\t0\t313\n", "49\t253\t83.2\t0\t253\n", "50\t235\t83.2\t0\t235\n", "51\t210\t83.2\t0\t210\n", "52\t250\t83.2\t0\t250\n", "53\t153\t83.2\t0\t153\n", "54\t50\t83.2\t0\t50\n", "55\t54\t83.2\t0\t54\n", "56\t55\t83.2\t0\t55\n", "57\t42\t83.2\t0\t42\n", "58\t40\t83.2\t0\t40\n", "59\t27\t83.2\t0\t27\n", "60\t35\t83.2\t0\t35\n", "61\t31\t83.2\t0\t31\n", "62\t53\t83.2\t0\t53\n", "63\t37\t83.2\t0\t37\n", "64\t35\t83.2\t0\t35\n", "65\t46\t83.2\t0\t46\n", "66\t24\t83.2\t0\t24\n", "67\t30\t83.2\t0\t30\n", "68\t42\t83.2\t0\t42\n", "69\t23\t83.2\t0\t23\n", "70\t11\t83.2\t0\t11\n", "71\t25\t83.2\t0\t25\n", "72\t20\t83.2\t0\t20\n", "73\t25\t83.2\t0\t25\n", "74\t21\t83.2\t0\t21\n", "75\t20\t83.2\t0\t20\n", "76\t15\t83.2\t0\t15\n", "77\t28\t83.2\t0\t28\n", "78\t20\t83.2\t0\t20\n", "79\t12\t83.2\t0\t12\n", "80\t11\t83.2\t0\t11\n", "81\t15\t83.2\t0\t15\n", "82\t13\t83.2\t0\t13\n", "83\t21\t83.2\t0\t21\n", "84\t12\t83.2\t0\t12\n", "85\t9\t83.2\t0\t9\n", "86\t18\t83.2\t0\t18\n", "87\t12\t83.2\t0\t12\n", "88\t15\t83.2\t0\t15\n", "89\t26\t83.2\t0\t26\n", "90\t20\t83.2\t0\t20\n", "91\t26\t83.2\t0\t26\n", "92\t33\t83.2\t0\t33\n", "93\t54\t83.2\t0\t54\n", "94\t57\t83.2\t0\t57\n", "95\t65\t83.2\t0\t65\n", "96\t71\t83.2\t0\t71\n", "97\t67\t83.2\t0\t67\n", "98\t77\t83.2\t0\t77\n", "99\t55\t83.2\t0\t55\n", "100\t80\t83.2\t0\t80\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 117179 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 36.2%\n", " C: 22.5%\n", " G: 15.8%\n", " T: 25.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t86986\t85234.4\t0\t86986\n", "4\t19007\t21308.6\t0\t19007\n", "5\t2811\t5327.2\t0\t2811\n", "6\t198\t1331.8\t0\t198\n", "7\t89\t332.9\t0\t89\n", "8\t102\t332.9\t0\t102\n", "9\t82\t332.9\t0\t82\n", "10\t107\t332.9\t0\t107\n", "11\t93\t332.9\t0\t93\n", "12\t117\t332.9\t0\t117\n", "13\t166\t332.9\t0\t166\n", "14\t147\t332.9\t0\t147\n", "15\t168\t332.9\t0\t168\n", "16\t106\t332.9\t0\t106\n", "17\t121\t332.9\t0\t121\n", "18\t119\t332.9\t0\t119\n", "19\t115\t332.9\t0\t115\n", "20\t126\t332.9\t0\t126\n", "21\t108\t332.9\t0\t108\n", "22\t96\t332.9\t0\t96\n", "23\t112\t332.9\t0\t112\n", "24\t82\t332.9\t0\t82\n", "25\t80\t332.9\t0\t80\n", "26\t95\t332.9\t0\t95\n", "27\t93\t332.9\t0\t93\n", "28\t102\t332.9\t0\t102\n", "29\t93\t332.9\t0\t93\n", "30\t84\t332.9\t0\t84\n", "31\t83\t332.9\t0\t83\n", "32\t98\t332.9\t0\t98\n", "33\t87\t332.9\t0\t87\n", "34\t75\t332.9\t0\t75\n", "35\t90\t332.9\t0\t90\n", "36\t88\t332.9\t0\t88\n", "37\t96\t332.9\t0\t96\n", "38\t98\t332.9\t0\t98\n", "39\t105\t332.9\t0\t105\n", "40\t90\t332.9\t0\t90\n", "41\t70\t332.9\t0\t70\n", "42\t84\t332.9\t0\t84\n", "43\t124\t332.9\t0\t124\n", "44\t76\t332.9\t0\t76\n", "45\t110\t332.9\t0\t110\n", "46\t150\t332.9\t0\t150\n", "47\t80\t332.9\t0\t80\n", "48\t71\t332.9\t0\t71\n", "49\t130\t332.9\t0\t130\n", "50\t75\t332.9\t0\t75\n", "51\t52\t332.9\t0\t52\n", "52\t133\t332.9\t0\t133\n", "53\t82\t332.9\t0\t82\n", "54\t107\t332.9\t0\t107\n", "55\t73\t332.9\t0\t73\n", "56\t68\t332.9\t0\t68\n", "57\t108\t332.9\t0\t108\n", "58\t65\t332.9\t0\t65\n", "59\t69\t332.9\t0\t69\n", "60\t185\t332.9\t0\t185\n", "61\t58\t332.9\t0\t58\n", "62\t101\t332.9\t0\t101\n", "63\t73\t332.9\t0\t73\n", "64\t153\t332.9\t0\t153\n", "65\t45\t332.9\t0\t45\n", "66\t46\t332.9\t0\t46\n", "67\t61\t332.9\t0\t61\n", "68\t46\t332.9\t0\t46\n", "69\t49\t332.9\t0\t49\n", "70\t60\t332.9\t0\t60\n", "71\t42\t332.9\t0\t42\n", "72\t69\t332.9\t0\t69\n", "73\t58\t332.9\t0\t58\n", "74\t60\t332.9\t0\t60\n", "75\t73\t332.9\t0\t73\n", "76\t42\t332.9\t0\t42\n", "77\t58\t332.9\t0\t58\n", "78\t69\t332.9\t0\t69\n", "79\t76\t332.9\t0\t76\n", "80\t70\t332.9\t0\t70\n", "81\t75\t332.9\t0\t75\n", "82\t81\t332.9\t0\t81\n", "83\t84\t332.9\t0\t84\n", "84\t72\t332.9\t0\t72\n", "85\t92\t332.9\t0\t92\n", "86\t49\t332.9\t0\t49\n", "87\t72\t332.9\t0\t72\n", "88\t124\t332.9\t0\t124\n", "89\t70\t332.9\t0\t70\n", "90\t75\t332.9\t0\t75\n", "91\t43\t332.9\t0\t43\n", "92\t48\t332.9\t0\t48\n", "93\t43\t332.9\t0\t43\n", "94\t69\t332.9\t0\t69\n", "95\t42\t332.9\t0\t42\n", "96\t55\t332.9\t0\t55\n", "97\t50\t332.9\t0\t50\n", "98\t70\t332.9\t0\t70\n", "99\t120\t332.9\t0\t120\n", "100\t109\t332.9\t0\t109\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 481_S57_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/481.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 103.47 s (14 us/read; 4.44 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,651,791\n", "Reads with adapters: 5,588,060 (73.0%)\n", "Reads written (passing filters): 7,191,139 (94.0%)\n", "\n", "Total basepairs processed: 765,179,100 bp\n", "Quality-trimmed: 2,514,922 bp (0.3%)\n", "Total written (filtered): 532,754,348 bp (69.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5390591 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.7%\n", " G: 42.4%\n", " T: 29.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t126767\t119559.2\t0\t126767\n", "4\t81164\t29889.8\t0\t81164\n", "5\t67055\t7472.5\t0\t67055\n", "6\t56264\t1868.1\t0\t56264\n", "7\t51966\t467.0\t0\t51966\n", "8\t51557\t116.8\t0\t51557\n", "9\t52127\t116.8\t0\t52127\n", "10\t52142\t116.8\t0\t52142\n", "11\t53354\t116.8\t0\t53354\n", "12\t55915\t116.8\t0\t55915\n", "13\t69584\t116.8\t0\t69584\n", "14\t70429\t116.8\t0\t70429\n", "15\t65217\t116.8\t0\t65217\n", "16\t68598\t116.8\t0\t68598\n", "17\t74080\t116.8\t0\t74080\n", "18\t86787\t116.8\t0\t86787\n", "19\t75313\t116.8\t0\t75313\n", "20\t61102\t116.8\t0\t61102\n", "21\t57375\t116.8\t0\t57375\n", "22\t53581\t116.8\t0\t53581\n", "23\t58571\t116.8\t0\t58571\n", "24\t69028\t116.8\t0\t69028\n", "25\t71334\t116.8\t0\t71334\n", "26\t81545\t116.8\t0\t81545\n", "27\t95723\t116.8\t0\t95723\n", "28\t89919\t116.8\t0\t89919\n", "29\t87849\t116.8\t0\t87849\n", "30\t93706\t116.8\t0\t93706\n", "31\t98643\t116.8\t0\t98643\n", "32\t90594\t116.8\t0\t90594\n", "33\t82583\t116.8\t0\t82583\n", "34\t80904\t116.8\t0\t80904\n", "35\t93813\t116.8\t0\t93813\n", "36\t115337\t116.8\t0\t115337\n", "37\t128468\t116.8\t0\t128468\n", "38\t97253\t116.8\t0\t97253\n", "39\t75802\t116.8\t0\t75802\n", "40\t70461\t116.8\t0\t70461\n", "41\t72394\t116.8\t0\t72394\n", "42\t76263\t116.8\t0\t76263\n", "43\t68866\t116.8\t0\t68866\n", "44\t57932\t116.8\t0\t57932\n", "45\t71699\t116.8\t0\t71699\n", "46\t87014\t116.8\t0\t87014\n", "47\t83218\t116.8\t0\t83218\n", "48\t82150\t116.8\t0\t82150\n", "49\t66014\t116.8\t0\t66014\n", "50\t61152\t116.8\t0\t61152\n", "51\t54955\t116.8\t0\t54955\n", "52\t59638\t116.8\t0\t59638\n", "53\t65326\t116.8\t0\t65326\n", "54\t62519\t116.8\t0\t62519\n", "55\t70459\t116.8\t0\t70459\n", "56\t69563\t116.8\t0\t69563\n", "57\t64861\t116.8\t0\t64861\n", "58\t73510\t116.8\t0\t73510\n", "59\t57369\t116.8\t0\t57369\n", "60\t45854\t116.8\t0\t45854\n", "61\t44062\t116.8\t0\t44062\n", "62\t37496\t116.8\t0\t37496\n", "63\t35685\t116.8\t0\t35685\n", "64\t40742\t116.8\t0\t40742\n", "65\t40363\t116.8\t0\t40363\n", "66\t37790\t116.8\t0\t37790\n", "67\t38506\t116.8\t0\t38506\n", "68\t37377\t116.8\t0\t37377\n", "69\t39158\t116.8\t0\t39158\n", "70\t45874\t116.8\t0\t45874\n", "71\t47388\t116.8\t0\t47388\n", "72\t35425\t116.8\t0\t35425\n", "73\t31221\t116.8\t0\t31221\n", "74\t31887\t116.8\t0\t31887\n", "75\t26928\t116.8\t0\t26928\n", "76\t23239\t116.8\t0\t23239\n", "77\t21257\t116.8\t0\t21257\n", "78\t24358\t116.8\t0\t24358\n", "79\t24124\t116.8\t0\t24124\n", "80\t25493\t116.8\t0\t25493\n", "81\t24114\t116.8\t0\t24114\n", "82\t23116\t116.8\t0\t23116\n", "83\t25842\t116.8\t0\t25842\n", "84\t29720\t116.8\t0\t29720\n", "85\t33277\t116.8\t0\t33277\n", "86\t32074\t116.8\t0\t32074\n", "87\t22801\t116.8\t0\t22801\n", "88\t20929\t116.8\t0\t20929\n", "89\t23081\t116.8\t0\t23081\n", "90\t25501\t116.8\t0\t25501\n", "91\t26335\t116.8\t0\t26335\n", "92\t26822\t116.8\t0\t26822\n", "93\t27668\t116.8\t0\t27668\n", "94\t26665\t116.8\t0\t26665\n", "95\t22839\t116.8\t0\t22839\n", "96\t16936\t116.8\t0\t16936\n", "97\t12195\t116.8\t0\t12195\n", "98\t7562\t116.8\t0\t7562\n", "99\t6519\t116.8\t0\t6519\n", "100\t5556\t116.8\t0\t5556\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 110008 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 83.1%\n", " C: 7.4%\n", " G: 0.0%\n", " T: 9.5%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10613\t119559.2\t0\t10613\n", "4\t3014\t29889.8\t0\t3014\n", "5\t1167\t7472.5\t0\t1167\n", "6\t789\t1868.1\t0\t789\n", "7\t431\t467.0\t0\t431\n", "8\t338\t116.8\t0\t338\n", "9\t371\t116.8\t0\t371\n", "10\t350\t116.8\t0\t350\n", "11\t378\t116.8\t0\t378\n", "12\t337\t116.8\t0\t337\n", "13\t383\t116.8\t0\t383\n", "14\t382\t116.8\t0\t382\n", "15\t451\t116.8\t0\t451\n", "16\t537\t116.8\t0\t537\n", "17\t718\t116.8\t0\t718\n", "18\t1306\t116.8\t0\t1306\n", "19\t2234\t116.8\t0\t2234\n", "20\t4495\t116.8\t0\t4495\n", "21\t3133\t116.8\t0\t3133\n", "22\t1819\t116.8\t0\t1819\n", "23\t1082\t116.8\t0\t1082\n", "24\t889\t116.8\t0\t889\n", "25\t970\t116.8\t0\t970\n", "26\t1519\t116.8\t0\t1519\n", "27\t1499\t116.8\t0\t1499\n", "28\t1714\t116.8\t0\t1714\n", "29\t2150\t116.8\t0\t2150\n", "30\t4343\t116.8\t0\t4343\n", "31\t5285\t116.8\t0\t5285\n", "32\t8859\t116.8\t0\t8859\n", "33\t8773\t116.8\t0\t8773\n", "34\t9186\t116.8\t0\t9186\n", "35\t12068\t116.8\t0\t12068\n", "36\t12348\t116.8\t0\t12348\n", "37\t4426\t116.8\t0\t4426\n", "38\t80\t116.8\t0\t80\n", "39\t42\t116.8\t0\t42\n", "40\t34\t116.8\t0\t34\n", "41\t24\t116.8\t0\t24\n", "42\t34\t116.8\t0\t34\n", "43\t30\t116.8\t0\t30\n", "44\t29\t116.8\t0\t29\n", "45\t34\t116.8\t0\t34\n", "46\t31\t116.8\t0\t31\n", "47\t32\t116.8\t0\t32\n", "48\t27\t116.8\t0\t27\n", "49\t28\t116.8\t0\t28\n", "50\t21\t116.8\t0\t21\n", "51\t24\t116.8\t0\t24\n", "52\t26\t116.8\t0\t26\n", "53\t17\t116.8\t0\t17\n", "54\t25\t116.8\t0\t25\n", "55\t19\t116.8\t0\t19\n", "56\t22\t116.8\t0\t22\n", "57\t23\t116.8\t0\t23\n", "58\t22\t116.8\t0\t22\n", "59\t19\t116.8\t0\t19\n", "60\t22\t116.8\t0\t22\n", "61\t20\t116.8\t0\t20\n", "62\t21\t116.8\t0\t21\n", "63\t22\t116.8\t0\t22\n", "64\t14\t116.8\t0\t14\n", "65\t19\t116.8\t0\t19\n", "66\t13\t116.8\t0\t13\n", "67\t13\t116.8\t0\t13\n", "68\t11\t116.8\t0\t11\n", "69\t7\t116.8\t0\t7\n", "70\t7\t116.8\t0\t7\n", "71\t5\t116.8\t0\t5\n", "72\t3\t116.8\t0\t3\n", "73\t2\t116.8\t0\t2\n", "74\t4\t116.8\t0\t4\n", "75\t6\t116.8\t0\t6\n", "76\t7\t116.8\t0\t7\n", "77\t3\t116.8\t0\t3\n", "78\t6\t116.8\t0\t6\n", "79\t8\t116.8\t0\t8\n", "80\t8\t116.8\t0\t8\n", "81\t7\t116.8\t0\t7\n", "82\t8\t116.8\t0\t8\n", "83\t9\t116.8\t0\t9\n", "84\t1\t116.8\t0\t1\n", "85\t9\t116.8\t0\t9\n", "86\t3\t116.8\t0\t3\n", "87\t4\t116.8\t0\t4\n", "88\t5\t116.8\t0\t5\n", "89\t11\t116.8\t0\t11\n", "90\t12\t116.8\t0\t12\n", "91\t22\t116.8\t0\t22\n", "92\t19\t116.8\t0\t19\n", "93\t44\t116.8\t0\t44\n", "94\t93\t116.8\t0\t93\n", "95\t106\t116.8\t0\t106\n", "96\t87\t116.8\t0\t87\n", "97\t104\t116.8\t0\t104\n", "98\t66\t116.8\t0\t66\n", "99\t53\t116.8\t0\t53\n", "100\t124\t116.8\t0\t124\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 87461 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.0%\n", " C: 15.2%\n", " G: 15.4%\n", " T: 24.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t59234\t119559.2\t0\t59234\n", "4\t14867\t29889.8\t0\t14867\n", "5\t2945\t7472.5\t0\t2945\n", "6\t239\t1868.1\t0\t239\n", "7\t122\t467.0\t0\t122\n", "8\t164\t467.0\t0\t164\n", "9\t134\t467.0\t0\t134\n", "10\t123\t467.0\t0\t123\n", "11\t156\t467.0\t0\t156\n", "12\t179\t467.0\t0\t179\n", "13\t212\t467.0\t0\t212\n", "14\t205\t467.0\t0\t205\n", "15\t228\t467.0\t0\t228\n", "16\t159\t467.0\t0\t159\n", "17\t181\t467.0\t0\t181\n", "18\t185\t467.0\t0\t185\n", "19\t145\t467.0\t0\t145\n", "20\t158\t467.0\t0\t158\n", "21\t125\t467.0\t0\t125\n", "22\t157\t467.0\t0\t157\n", "23\t112\t467.0\t0\t112\n", "24\t131\t467.0\t0\t131\n", "25\t137\t467.0\t0\t137\n", "26\t120\t467.0\t0\t120\n", "27\t140\t467.0\t0\t140\n", "28\t122\t467.0\t0\t122\n", "29\t122\t467.0\t0\t122\n", "30\t125\t467.0\t0\t125\n", "31\t119\t467.0\t0\t119\n", "32\t110\t467.0\t0\t110\n", "33\t127\t467.0\t0\t127\n", "34\t131\t467.0\t0\t131\n", "35\t124\t467.0\t0\t124\n", "36\t120\t467.0\t0\t120\n", "37\t116\t467.0\t0\t116\n", "38\t158\t467.0\t0\t158\n", "39\t136\t467.0\t0\t136\n", "40\t129\t467.0\t0\t129\n", "41\t150\t467.0\t0\t150\n", "42\t87\t467.0\t0\t87\n", "43\t151\t467.0\t0\t151\n", "44\t55\t467.0\t0\t55\n", "45\t89\t467.0\t0\t89\n", "46\t118\t467.0\t0\t118\n", "47\t119\t467.0\t0\t119\n", "48\t85\t467.0\t0\t85\n", "49\t105\t467.0\t0\t105\n", "50\t99\t467.0\t0\t99\n", "51\t117\t467.0\t0\t117\n", "52\t98\t467.0\t0\t98\n", "53\t133\t467.0\t0\t133\n", "54\t85\t467.0\t0\t85\n", "55\t97\t467.0\t0\t97\n", "56\t99\t467.0\t0\t99\n", "57\t104\t467.0\t0\t104\n", "58\t158\t467.0\t0\t158\n", "59\t82\t467.0\t0\t82\n", "60\t185\t467.0\t0\t185\n", "61\t155\t467.0\t0\t155\n", "62\t147\t467.0\t0\t147\n", "63\t100\t467.0\t0\t100\n", "64\t126\t467.0\t0\t126\n", "65\t138\t467.0\t0\t138\n", "66\t126\t467.0\t0\t126\n", "67\t90\t467.0\t0\t90\n", "68\t87\t467.0\t0\t87\n", "69\t65\t467.0\t0\t65\n", "70\t57\t467.0\t0\t57\n", "71\t55\t467.0\t0\t55\n", "72\t69\t467.0\t0\t69\n", "73\t65\t467.0\t0\t65\n", "74\t59\t467.0\t0\t59\n", "75\t50\t467.0\t0\t50\n", "76\t48\t467.0\t0\t48\n", "77\t54\t467.0\t0\t54\n", "78\t57\t467.0\t0\t57\n", "79\t39\t467.0\t0\t39\n", "80\t44\t467.0\t0\t44\n", "81\t56\t467.0\t0\t56\n", "82\t75\t467.0\t0\t75\n", "83\t71\t467.0\t0\t71\n", "84\t52\t467.0\t0\t52\n", "85\t68\t467.0\t0\t68\n", "86\t63\t467.0\t0\t63\n", "87\t62\t467.0\t0\t62\n", "88\t125\t467.0\t0\t125\n", "89\t88\t467.0\t0\t88\n", "90\t78\t467.0\t0\t78\n", "91\t70\t467.0\t0\t70\n", "92\t75\t467.0\t0\t75\n", "93\t68\t467.0\t0\t68\n", "94\t43\t467.0\t0\t43\n", "95\t32\t467.0\t0\t32\n", "96\t31\t467.0\t0\t31\n", "97\t85\t467.0\t0\t85\n", "98\t76\t467.0\t0\t76\n", "99\t88\t467.0\t0\t88\n", "100\t111\t467.0\t0\t111\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 482_S25_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/482.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 68.33 s (13 us/read; 4.76 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,416,476\n", "Reads with adapters: 3,300,881 (60.9%)\n", "Reads written (passing filters): 5,356,061 (98.9%)\n", "\n", "Total basepairs processed: 541,647,600 bp\n", "Quality-trimmed: 1,322,616 bp (0.2%)\n", "Total written (filtered): 434,716,349 bp (80.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3221335 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.3%\n", " G: 34.3%\n", " T: 37.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t136748\t84632.4\t0\t136748\n", "4\t82713\t21158.1\t0\t82713\n", "5\t63953\t5289.5\t0\t63953\n", "6\t49459\t1322.4\t0\t49459\n", "7\t44408\t330.6\t0\t44408\n", "8\t45162\t82.6\t0\t45162\n", "9\t44625\t82.6\t0\t44625\n", "10\t41493\t82.6\t0\t41493\n", "11\t43207\t82.6\t0\t43207\n", "12\t42462\t82.6\t0\t42462\n", "13\t43005\t82.6\t0\t43005\n", "14\t44692\t82.6\t0\t44692\n", "15\t45729\t82.6\t0\t45729\n", "16\t49020\t82.6\t0\t49020\n", "17\t55461\t82.6\t0\t55461\n", "18\t65225\t82.6\t0\t65225\n", "19\t59549\t82.6\t0\t59549\n", "20\t50061\t82.6\t0\t50061\n", "21\t46745\t82.6\t0\t46745\n", "22\t41485\t82.6\t0\t41485\n", "23\t46021\t82.6\t0\t46021\n", "24\t54259\t82.6\t0\t54259\n", "25\t54349\t82.6\t0\t54349\n", "26\t61590\t82.6\t0\t61590\n", "27\t69723\t82.6\t0\t69723\n", "28\t63438\t82.6\t0\t63438\n", "29\t59313\t82.6\t0\t59313\n", "30\t64162\t82.6\t0\t64162\n", "31\t69709\t82.6\t0\t69709\n", "32\t62378\t82.6\t0\t62378\n", "33\t57747\t82.6\t0\t57747\n", "34\t52006\t82.6\t0\t52006\n", "35\t60328\t82.6\t0\t60328\n", "36\t70627\t82.6\t0\t70627\n", "37\t70155\t82.6\t0\t70155\n", "38\t59704\t82.6\t0\t59704\n", "39\t49659\t82.6\t0\t49659\n", "40\t46412\t82.6\t0\t46412\n", "41\t46329\t82.6\t0\t46329\n", "42\t48127\t82.6\t0\t48127\n", "43\t42945\t82.6\t0\t42945\n", "44\t35781\t82.6\t0\t35781\n", "45\t48110\t82.6\t0\t48110\n", "46\t60800\t82.6\t0\t60800\n", "47\t55831\t82.6\t0\t55831\n", "48\t59051\t82.6\t0\t59051\n", "49\t46168\t82.6\t0\t46168\n", "50\t38514\t82.6\t0\t38514\n", "51\t34397\t82.6\t0\t34397\n", "52\t32623\t82.6\t0\t32623\n", "53\t33491\t82.6\t0\t33491\n", "54\t39113\t82.6\t0\t39113\n", "55\t40621\t82.6\t0\t40621\n", "56\t30175\t82.6\t0\t30175\n", "57\t28742\t82.6\t0\t28742\n", "58\t33175\t82.6\t0\t33175\n", "59\t26382\t82.6\t0\t26382\n", "60\t20654\t82.6\t0\t20654\n", "61\t19030\t82.6\t0\t19030\n", "62\t15424\t82.6\t0\t15424\n", "63\t15780\t82.6\t0\t15780\n", "64\t17261\t82.6\t0\t17261\n", "65\t14751\t82.6\t0\t14751\n", "66\t12015\t82.6\t0\t12015\n", "67\t12025\t82.6\t0\t12025\n", "68\t11198\t82.6\t0\t11198\n", "69\t10744\t82.6\t0\t10744\n", "70\t11834\t82.6\t0\t11834\n", "71\t11033\t82.6\t0\t11033\n", "72\t8137\t82.6\t0\t8137\n", "73\t6588\t82.6\t0\t6588\n", "74\t5990\t82.6\t0\t5990\n", "75\t5187\t82.6\t0\t5187\n", "76\t4096\t82.6\t0\t4096\n", "77\t4210\t82.6\t0\t4210\n", "78\t5097\t82.6\t0\t5097\n", "79\t4225\t82.6\t0\t4225\n", "80\t3936\t82.6\t0\t3936\n", "81\t3755\t82.6\t0\t3755\n", "82\t3654\t82.6\t0\t3654\n", "83\t3579\t82.6\t0\t3579\n", "84\t4302\t82.6\t0\t4302\n", "85\t4982\t82.6\t0\t4982\n", "86\t4833\t82.6\t0\t4833\n", "87\t3481\t82.6\t0\t3481\n", "88\t3074\t82.6\t0\t3074\n", "89\t3043\t82.6\t0\t3043\n", "90\t3240\t82.6\t0\t3240\n", "91\t2948\t82.6\t0\t2948\n", "92\t2720\t82.6\t0\t2720\n", "93\t2546\t82.6\t0\t2546\n", "94\t2305\t82.6\t0\t2305\n", "95\t1926\t82.6\t0\t1926\n", "96\t1370\t82.6\t0\t1370\n", "97\t1018\t82.6\t0\t1018\n", "98\t726\t82.6\t0\t726\n", "99\t719\t82.6\t0\t719\n", "100\t742\t82.6\t0\t742\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 9855 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 50.7%\n", " C: 16.1%\n", " G: 0.0%\n", " T: 33.1%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t4865\t84632.4\t0\t4865\n", "4\t908\t21158.1\t0\t908\n", "5\t268\t5289.5\t0\t268\n", "6\t116\t1322.4\t0\t116\n", "7\t64\t330.6\t0\t64\n", "8\t46\t82.6\t0\t46\n", "9\t49\t82.6\t0\t49\n", "10\t34\t82.6\t0\t34\n", "11\t51\t82.6\t0\t51\n", "12\t28\t82.6\t0\t28\n", "13\t41\t82.6\t0\t41\n", "14\t35\t82.6\t0\t35\n", "15\t36\t82.6\t0\t36\n", "16\t41\t82.6\t0\t41\n", "17\t44\t82.6\t0\t44\n", "18\t62\t82.6\t0\t62\n", "19\t92\t82.6\t0\t92\n", "20\t103\t82.6\t0\t103\n", "21\t88\t82.6\t0\t88\n", "22\t73\t82.6\t0\t73\n", "23\t41\t82.6\t0\t41\n", "24\t48\t82.6\t0\t48\n", "25\t38\t82.6\t0\t38\n", "26\t51\t82.6\t0\t51\n", "27\t72\t82.6\t0\t72\n", "28\t57\t82.6\t0\t57\n", "29\t101\t82.6\t0\t101\n", "30\t161\t82.6\t0\t161\n", "31\t196\t82.6\t0\t196\n", "32\t240\t82.6\t0\t240\n", "33\t260\t82.6\t0\t260\n", "34\t296\t82.6\t0\t296\n", "35\t359\t82.6\t0\t359\n", "36\t327\t82.6\t0\t327\n", "37\t164\t82.6\t0\t164\n", "38\t57\t82.6\t0\t57\n", "39\t19\t82.6\t0\t19\n", "40\t13\t82.6\t0\t13\n", "41\t10\t82.6\t0\t10\n", "42\t9\t82.6\t0\t9\n", "43\t6\t82.6\t0\t6\n", "44\t8\t82.6\t0\t8\n", "45\t8\t82.6\t0\t8\n", "46\t7\t82.6\t0\t7\n", "47\t9\t82.6\t0\t9\n", "48\t4\t82.6\t0\t4\n", "49\t4\t82.6\t0\t4\n", "50\t7\t82.6\t0\t7\n", "51\t4\t82.6\t0\t4\n", "52\t5\t82.6\t0\t5\n", "53\t3\t82.6\t0\t3\n", "54\t2\t82.6\t0\t2\n", "55\t2\t82.6\t0\t2\n", "57\t7\t82.6\t0\t7\n", "58\t2\t82.6\t0\t2\n", "59\t3\t82.6\t0\t3\n", "60\t2\t82.6\t0\t2\n", "61\t5\t82.6\t0\t5\n", "62\t3\t82.6\t0\t3\n", "63\t2\t82.6\t0\t2\n", "64\t1\t82.6\t0\t1\n", "65\t2\t82.6\t0\t2\n", "66\t2\t82.6\t0\t2\n", "67\t1\t82.6\t0\t1\n", "68\t1\t82.6\t0\t1\n", "69\t1\t82.6\t0\t1\n", "70\t2\t82.6\t0\t2\n", "71\t1\t82.6\t0\t1\n", "72\t1\t82.6\t0\t1\n", "73\t2\t82.6\t0\t2\n", "74\t1\t82.6\t0\t1\n", "77\t1\t82.6\t0\t1\n", "78\t4\t82.6\t0\t4\n", "79\t2\t82.6\t0\t2\n", "80\t1\t82.6\t0\t1\n", "81\t2\t82.6\t0\t2\n", "82\t2\t82.6\t0\t2\n", "83\t2\t82.6\t0\t2\n", "86\t1\t82.6\t0\t1\n", "87\t1\t82.6\t0\t1\n", "90\t1\t82.6\t0\t1\n", "91\t2\t82.6\t0\t2\n", "92\t4\t82.6\t0\t4\n", "93\t4\t82.6\t0\t4\n", "94\t31\t82.6\t0\t31\n", "95\t22\t82.6\t0\t22\n", "96\t15\t82.6\t0\t15\n", "97\t18\t82.6\t0\t18\n", "98\t21\t82.6\t0\t21\n", "99\t28\t82.6\t0\t28\n", "100\t22\t82.6\t0\t22\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 69691 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 52.9%\n", " C: 13.8%\n", " G: 11.7%\n", " T: 21.6%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t48304\t84632.4\t0\t48304\n", "4\t12721\t21158.1\t0\t12721\n", "5\t4318\t5289.5\t0\t4318\n", "6\t95\t1322.4\t0\t95\n", "7\t23\t330.6\t0\t23\n", "8\t25\t330.6\t0\t25\n", "9\t25\t330.6\t0\t25\n", "10\t56\t330.6\t0\t56\n", "11\t27\t330.6\t0\t27\n", "12\t57\t330.6\t0\t57\n", "13\t42\t330.6\t0\t42\n", "14\t27\t330.6\t0\t27\n", "15\t25\t330.6\t0\t25\n", "16\t30\t330.6\t0\t30\n", "17\t12\t330.6\t0\t12\n", "18\t30\t330.6\t0\t30\n", "19\t19\t330.6\t0\t19\n", "20\t19\t330.6\t0\t19\n", "21\t23\t330.6\t0\t23\n", "22\t28\t330.6\t0\t28\n", "23\t32\t330.6\t0\t32\n", "24\t31\t330.6\t0\t31\n", "25\t32\t330.6\t0\t32\n", "26\t16\t330.6\t0\t16\n", "27\t23\t330.6\t0\t23\n", "28\t24\t330.6\t0\t24\n", "29\t28\t330.6\t0\t28\n", "30\t31\t330.6\t0\t31\n", "31\t33\t330.6\t0\t33\n", "32\t51\t330.6\t0\t51\n", "33\t23\t330.6\t0\t23\n", "34\t35\t330.6\t0\t35\n", "35\t32\t330.6\t0\t32\n", "36\t30\t330.6\t0\t30\n", "37\t31\t330.6\t0\t31\n", "38\t27\t330.6\t0\t27\n", "39\t42\t330.6\t0\t42\n", "40\t37\t330.6\t0\t37\n", "41\t32\t330.6\t0\t32\n", "42\t19\t330.6\t0\t19\n", "43\t25\t330.6\t0\t25\n", "44\t34\t330.6\t0\t34\n", "45\t28\t330.6\t0\t28\n", "46\t29\t330.6\t0\t29\n", "47\t29\t330.6\t0\t29\n", "48\t26\t330.6\t0\t26\n", "49\t43\t330.6\t0\t43\n", "50\t26\t330.6\t0\t26\n", "51\t33\t330.6\t0\t33\n", "52\t34\t330.6\t0\t34\n", "53\t38\t330.6\t0\t38\n", "54\t28\t330.6\t0\t28\n", "55\t26\t330.6\t0\t26\n", "56\t21\t330.6\t0\t21\n", "57\t31\t330.6\t0\t31\n", "58\t47\t330.6\t0\t47\n", "59\t32\t330.6\t0\t32\n", "60\t30\t330.6\t0\t30\n", "61\t30\t330.6\t0\t30\n", "62\t40\t330.6\t0\t40\n", "63\t34\t330.6\t0\t34\n", "64\t39\t330.6\t0\t39\n", "65\t30\t330.6\t0\t30\n", "66\t39\t330.6\t0\t39\n", "67\t38\t330.6\t0\t38\n", "68\t33\t330.6\t0\t33\n", "69\t23\t330.6\t0\t23\n", "70\t34\t330.6\t0\t34\n", "71\t42\t330.6\t0\t42\n", "72\t67\t330.6\t0\t67\n", "73\t134\t330.6\t0\t134\n", "74\t107\t330.6\t0\t107\n", "75\t50\t330.6\t0\t50\n", "76\t97\t330.6\t0\t97\n", "77\t134\t330.6\t0\t134\n", "78\t98\t330.6\t0\t98\n", "79\t85\t330.6\t0\t85\n", "80\t87\t330.6\t0\t87\n", "81\t132\t330.6\t0\t132\n", "82\t119\t330.6\t0\t119\n", "83\t125\t330.6\t0\t125\n", "84\t84\t330.6\t0\t84\n", "85\t85\t330.6\t0\t85\n", "86\t51\t330.6\t0\t51\n", "87\t89\t330.6\t0\t89\n", "88\t63\t330.6\t0\t63\n", "89\t41\t330.6\t0\t41\n", "90\t48\t330.6\t0\t48\n", "91\t48\t330.6\t0\t48\n", "92\t32\t330.6\t0\t32\n", "93\t16\t330.6\t0\t16\n", "94\t35\t330.6\t0\t35\n", "95\t32\t330.6\t0\t32\n", "96\t36\t330.6\t0\t36\n", "97\t75\t330.6\t0\t75\n", "98\t78\t330.6\t0\t78\n", "99\t81\t330.6\t0\t81\n", "100\t105\t330.6\t0\t105\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 483_S7_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/483.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 83.52 s (14 us/read; 4.40 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,128,076\n", "Reads with adapters: 5,210,645 (85.0%)\n", "Reads written (passing filters): 5,681,617 (92.7%)\n", "\n", "Total basepairs processed: 612,807,600 bp\n", "Quality-trimmed: 3,067,602 bp (0.5%)\n", "Total written (filtered): 369,481,138 bp (60.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5123761 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.8%\n", " G: 42.2%\n", " T: 27.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t58585\t95751.2\t0\t58585\n", "4\t40406\t23937.8\t0\t40406\n", "5\t34323\t5984.4\t0\t34323\n", "6\t29385\t1496.1\t0\t29385\n", "7\t28224\t374.0\t0\t28224\n", "8\t27539\t93.5\t0\t27539\n", "9\t27528\t93.5\t0\t27528\n", "10\t28358\t93.5\t0\t28358\n", "11\t29116\t93.5\t0\t29116\n", "12\t31480\t93.5\t0\t31480\n", "13\t39866\t93.5\t0\t39866\n", "14\t40332\t93.5\t0\t40332\n", "15\t36512\t93.5\t0\t36512\n", "16\t39756\t93.5\t0\t39756\n", "17\t44624\t93.5\t0\t44624\n", "18\t51936\t93.5\t0\t51936\n", "19\t48592\t93.5\t0\t48592\n", "20\t43959\t93.5\t0\t43959\n", "21\t45219\t93.5\t0\t45219\n", "22\t41159\t93.5\t0\t41159\n", "23\t45624\t93.5\t0\t45624\n", "24\t55536\t93.5\t0\t55536\n", "25\t60334\t93.5\t0\t60334\n", "26\t69825\t93.5\t0\t69825\n", "27\t78403\t93.5\t0\t78403\n", "28\t74340\t93.5\t0\t74340\n", "29\t73091\t93.5\t0\t73091\n", "30\t78168\t93.5\t0\t78168\n", "31\t84561\t93.5\t0\t84561\n", "32\t83664\t93.5\t0\t83664\n", "33\t75116\t93.5\t0\t75116\n", "34\t76247\t93.5\t0\t76247\n", "35\t87629\t93.5\t0\t87629\n", "36\t108081\t93.5\t0\t108081\n", "37\t128354\t93.5\t0\t128354\n", "38\t98566\t93.5\t0\t98566\n", "39\t78315\t93.5\t0\t78315\n", "40\t77589\t93.5\t0\t77589\n", "41\t83498\t93.5\t0\t83498\n", "42\t92352\t93.5\t0\t92352\n", "43\t81220\t93.5\t0\t81220\n", "44\t67839\t93.5\t0\t67839\n", "45\t88381\t93.5\t0\t88381\n", "46\t111201\t93.5\t0\t111201\n", "47\t115167\t93.5\t0\t115167\n", "48\t117396\t93.5\t0\t117396\n", "49\t93921\t93.5\t0\t93921\n", "50\t85328\t93.5\t0\t85328\n", "51\t80038\t93.5\t0\t80038\n", "52\t76421\t93.5\t0\t76421\n", "53\t65646\t93.5\t0\t65646\n", "54\t75599\t93.5\t0\t75599\n", "55\t83333\t93.5\t0\t83333\n", "56\t80674\t93.5\t0\t80674\n", "57\t80371\t93.5\t0\t80371\n", "58\t101077\t93.5\t0\t101077\n", "59\t75623\t93.5\t0\t75623\n", "60\t61635\t93.5\t0\t61635\n", "61\t55902\t93.5\t0\t55902\n", "62\t47669\t93.5\t0\t47669\n", "63\t49302\t93.5\t0\t49302\n", "64\t55368\t93.5\t0\t55368\n", "65\t49490\t93.5\t0\t49490\n", "66\t43458\t93.5\t0\t43458\n", "67\t46169\t93.5\t0\t46169\n", "68\t46320\t93.5\t0\t46320\n", "69\t49263\t93.5\t0\t49263\n", "70\t56027\t93.5\t0\t56027\n", "71\t52668\t93.5\t0\t52668\n", "72\t39138\t93.5\t0\t39138\n", "73\t30390\t93.5\t0\t30390\n", "74\t27014\t93.5\t0\t27014\n", "75\t24046\t93.5\t0\t24046\n", "76\t20466\t93.5\t0\t20466\n", "77\t23348\t93.5\t0\t23348\n", "78\t29354\t93.5\t0\t29354\n", "79\t25134\t93.5\t0\t25134\n", "80\t23492\t93.5\t0\t23492\n", "81\t22943\t93.5\t0\t22943\n", "82\t21155\t93.5\t0\t21155\n", "83\t21431\t93.5\t0\t21431\n", "84\t26124\t93.5\t0\t26124\n", "85\t32054\t93.5\t0\t32054\n", "86\t31742\t93.5\t0\t31742\n", "87\t22996\t93.5\t0\t22996\n", "88\t18664\t93.5\t0\t18664\n", "89\t19526\t93.5\t0\t19526\n", "90\t21727\t93.5\t0\t21727\n", "91\t23376\t93.5\t0\t23376\n", "92\t24273\t93.5\t0\t24273\n", "93\t27313\t93.5\t0\t27313\n", "94\t27256\t93.5\t0\t27256\n", "95\t23601\t93.5\t0\t23601\n", "96\t17579\t93.5\t0\t17579\n", "97\t11296\t93.5\t0\t11296\n", "98\t6748\t93.5\t0\t6748\n", "99\t9223\t93.5\t0\t9223\n", "100\t3654\t93.5\t0\t3654\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 39257 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 71.5%\n", " C: 14.8%\n", " G: 0.0%\n", " T: 13.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t6982\t95751.2\t0\t6982\n", "4\t2785\t23937.8\t0\t2785\n", "5\t1546\t5984.4\t0\t1546\n", "6\t1342\t1496.1\t0\t1342\n", "7\t528\t374.0\t0\t528\n", "8\t403\t93.5\t0\t403\n", "9\t398\t93.5\t0\t398\n", "10\t414\t93.5\t0\t414\n", "11\t392\t93.5\t0\t392\n", "12\t307\t93.5\t0\t307\n", "13\t286\t93.5\t0\t286\n", "14\t298\t93.5\t0\t298\n", "15\t255\t93.5\t0\t255\n", "16\t277\t93.5\t0\t277\n", "17\t342\t93.5\t0\t342\n", "18\t463\t93.5\t0\t463\n", "19\t614\t93.5\t0\t614\n", "20\t609\t93.5\t0\t609\n", "21\t435\t93.5\t0\t435\n", "22\t346\t93.5\t0\t346\n", "23\t304\t93.5\t0\t304\n", "24\t336\t93.5\t0\t336\n", "25\t444\t93.5\t0\t444\n", "26\t683\t93.5\t0\t683\n", "27\t713\t93.5\t0\t713\n", "28\t741\t93.5\t0\t741\n", "29\t923\t93.5\t0\t923\n", "30\t1540\t93.5\t0\t1540\n", "31\t1804\t93.5\t0\t1804\n", "32\t2435\t93.5\t0\t2435\n", "33\t2129\t93.5\t0\t2129\n", "34\t2278\t93.5\t0\t2278\n", "35\t2769\t93.5\t0\t2769\n", "36\t1956\t93.5\t0\t1956\n", "37\t369\t93.5\t0\t369\n", "38\t25\t93.5\t0\t25\n", "39\t13\t93.5\t0\t13\n", "40\t18\t93.5\t0\t18\n", "41\t16\t93.5\t0\t16\n", "42\t12\t93.5\t0\t12\n", "43\t25\t93.5\t0\t25\n", "44\t16\t93.5\t0\t16\n", "45\t18\t93.5\t0\t18\n", "46\t14\t93.5\t0\t14\n", "47\t14\t93.5\t0\t14\n", "48\t14\t93.5\t0\t14\n", "49\t20\t93.5\t0\t20\n", "50\t11\t93.5\t0\t11\n", "51\t16\t93.5\t0\t16\n", "52\t10\t93.5\t0\t10\n", "53\t13\t93.5\t0\t13\n", "54\t15\t93.5\t0\t15\n", "55\t12\t93.5\t0\t12\n", "56\t6\t93.5\t0\t6\n", "57\t11\t93.5\t0\t11\n", "58\t8\t93.5\t0\t8\n", "59\t5\t93.5\t0\t5\n", "60\t5\t93.5\t0\t5\n", "61\t6\t93.5\t0\t6\n", "62\t14\t93.5\t0\t14\n", "63\t8\t93.5\t0\t8\n", "64\t9\t93.5\t0\t9\n", "65\t8\t93.5\t0\t8\n", "66\t19\t93.5\t0\t19\n", "67\t4\t93.5\t0\t4\n", "68\t8\t93.5\t0\t8\n", "69\t6\t93.5\t0\t6\n", "70\t7\t93.5\t0\t7\n", "71\t2\t93.5\t0\t2\n", "72\t4\t93.5\t0\t4\n", "73\t4\t93.5\t0\t4\n", "74\t3\t93.5\t0\t3\n", "75\t2\t93.5\t0\t2\n", "76\t1\t93.5\t0\t1\n", "77\t4\t93.5\t0\t4\n", "81\t2\t93.5\t0\t2\n", "83\t8\t93.5\t0\t8\n", "84\t4\t93.5\t0\t4\n", "86\t4\t93.5\t0\t4\n", "87\t3\t93.5\t0\t3\n", "89\t3\t93.5\t0\t3\n", "90\t4\t93.5\t0\t4\n", "91\t3\t93.5\t0\t3\n", "92\t15\t93.5\t0\t15\n", "93\t24\t93.5\t0\t24\n", "94\t56\t93.5\t0\t56\n", "95\t63\t93.5\t0\t63\n", "96\t39\t93.5\t0\t39\n", "97\t44\t93.5\t0\t44\n", "98\t41\t93.5\t0\t41\n", "99\t36\t93.5\t0\t36\n", "100\t36\t93.5\t0\t36\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 47627 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 49.4%\n", " C: 14.5%\n", " G: 19.4%\n", " T: 16.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t24048\t95751.2\t0\t24048\n", "4\t4684\t23937.8\t0\t4684\n", "5\t962\t5984.4\t0\t962\n", "6\t331\t1496.1\t0\t331\n", "7\t309\t374.0\t0\t309\n", "8\t341\t374.0\t0\t341\n", "9\t373\t374.0\t0\t373\n", "10\t373\t374.0\t0\t373\n", "11\t363\t374.0\t0\t363\n", "12\t381\t374.0\t0\t381\n", "13\t547\t374.0\t0\t547\n", "14\t526\t374.0\t0\t526\n", "15\t470\t374.0\t0\t470\n", "16\t499\t374.0\t0\t499\n", "17\t449\t374.0\t0\t449\n", "18\t418\t374.0\t0\t418\n", "19\t492\t374.0\t0\t492\n", "20\t463\t374.0\t0\t463\n", "21\t394\t374.0\t0\t394\n", "22\t372\t374.0\t0\t372\n", "23\t418\t374.0\t0\t418\n", "24\t277\t374.0\t0\t277\n", "25\t348\t374.0\t0\t348\n", "26\t356\t374.0\t0\t356\n", "27\t333\t374.0\t0\t333\n", "28\t349\t374.0\t0\t349\n", "29\t331\t374.0\t0\t331\n", "30\t300\t374.0\t0\t300\n", "31\t262\t374.0\t0\t262\n", "32\t375\t374.0\t0\t375\n", "33\t348\t374.0\t0\t348\n", "34\t375\t374.0\t0\t375\n", "35\t338\t374.0\t0\t338\n", "36\t329\t374.0\t0\t329\n", "37\t278\t374.0\t0\t278\n", "38\t295\t374.0\t0\t295\n", "39\t311\t374.0\t0\t311\n", "40\t311\t374.0\t0\t311\n", "41\t243\t374.0\t0\t243\n", "42\t210\t374.0\t0\t210\n", "43\t321\t374.0\t0\t321\n", "44\t50\t374.0\t0\t50\n", "45\t169\t374.0\t0\t169\n", "46\t197\t374.0\t0\t197\n", "47\t183\t374.0\t0\t183\n", "48\t109\t374.0\t0\t109\n", "49\t152\t374.0\t0\t152\n", "50\t143\t374.0\t0\t143\n", "51\t129\t374.0\t0\t129\n", "52\t150\t374.0\t0\t150\n", "53\t149\t374.0\t0\t149\n", "54\t91\t374.0\t0\t91\n", "55\t172\t374.0\t0\t172\n", "56\t121\t374.0\t0\t121\n", "57\t127\t374.0\t0\t127\n", "58\t108\t374.0\t0\t108\n", "59\t38\t374.0\t0\t38\n", "60\t114\t374.0\t0\t114\n", "61\t86\t374.0\t0\t86\n", "62\t47\t374.0\t0\t47\n", "63\t68\t374.0\t0\t68\n", "64\t117\t374.0\t0\t117\n", "65\t36\t374.0\t0\t36\n", "66\t89\t374.0\t0\t89\n", "67\t78\t374.0\t0\t78\n", "68\t117\t374.0\t0\t117\n", "69\t13\t374.0\t0\t13\n", "70\t32\t374.0\t0\t32\n", "71\t55\t374.0\t0\t55\n", "72\t54\t374.0\t0\t54\n", "73\t78\t374.0\t0\t78\n", "74\t62\t374.0\t0\t62\n", "75\t49\t374.0\t0\t49\n", "76\t32\t374.0\t0\t32\n", "77\t35\t374.0\t0\t35\n", "78\t23\t374.0\t0\t23\n", "79\t26\t374.0\t0\t26\n", "80\t40\t374.0\t0\t40\n", "81\t43\t374.0\t0\t43\n", "82\t57\t374.0\t0\t57\n", "83\t59\t374.0\t0\t59\n", "84\t49\t374.0\t0\t49\n", "85\t43\t374.0\t0\t43\n", "86\t28\t374.0\t0\t28\n", "87\t43\t374.0\t0\t43\n", "88\t59\t374.0\t0\t59\n", "89\t45\t374.0\t0\t45\n", "90\t37\t374.0\t0\t37\n", "91\t25\t374.0\t0\t25\n", "92\t40\t374.0\t0\t40\n", "93\t28\t374.0\t0\t28\n", "94\t35\t374.0\t0\t35\n", "95\t24\t374.0\t0\t24\n", "96\t29\t374.0\t0\t29\n", "97\t44\t374.0\t0\t44\n", "98\t39\t374.0\t0\t39\n", "99\t28\t374.0\t0\t28\n", "100\t30\t374.0\t0\t30\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 484_S43_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/484.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 66.73 s (13 us/read; 4.67 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,194,506\n", "Reads with adapters: 3,016,458 (58.1%)\n", "Reads written (passing filters): 5,100,265 (98.2%)\n", "\n", "Total basepairs processed: 519,450,600 bp\n", "Quality-trimmed: 1,234,618 bp (0.2%)\n", "Total written (filtered): 416,865,621 bp (80.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2882637 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.0%\n", " G: 41.4%\n", " T: 28.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t109787\t81164.2\t0\t109787\n", "4\t63045\t20291.0\t0\t63045\n", "5\t49317\t5072.8\t0\t49317\n", "6\t39748\t1268.2\t0\t39748\n", "7\t36971\t317.0\t0\t36971\n", "8\t37593\t79.3\t0\t37593\n", "9\t36593\t79.3\t0\t36593\n", "10\t36190\t79.3\t0\t36190\n", "11\t35677\t79.3\t0\t35677\n", "12\t36031\t79.3\t0\t36031\n", "13\t39063\t79.3\t0\t39063\n", "14\t40214\t79.3\t0\t40214\n", "15\t40145\t79.3\t0\t40145\n", "16\t42060\t79.3\t0\t42060\n", "17\t45127\t79.3\t0\t45127\n", "18\t52518\t79.3\t0\t52518\n", "19\t48661\t79.3\t0\t48661\n", "20\t40837\t79.3\t0\t40837\n", "21\t40284\t79.3\t0\t40284\n", "22\t36382\t79.3\t0\t36382\n", "23\t39549\t79.3\t0\t39549\n", "24\t46326\t79.3\t0\t46326\n", "25\t47368\t79.3\t0\t47368\n", "26\t54726\t79.3\t0\t54726\n", "27\t60344\t79.3\t0\t60344\n", "28\t55389\t79.3\t0\t55389\n", "29\t51866\t79.3\t0\t51866\n", "30\t52393\t79.3\t0\t52393\n", "31\t56641\t79.3\t0\t56641\n", "32\t56479\t79.3\t0\t56479\n", "33\t51556\t79.3\t0\t51556\n", "34\t51497\t79.3\t0\t51497\n", "35\t56607\t79.3\t0\t56607\n", "36\t69213\t79.3\t0\t69213\n", "37\t75327\t79.3\t0\t75327\n", "38\t57079\t79.3\t0\t57079\n", "39\t40891\t79.3\t0\t40891\n", "40\t40628\t79.3\t0\t40628\n", "41\t45783\t79.3\t0\t45783\n", "42\t51108\t79.3\t0\t51108\n", "43\t42963\t79.3\t0\t42963\n", "44\t32216\t79.3\t0\t32216\n", "45\t39731\t79.3\t0\t39731\n", "46\t46498\t79.3\t0\t46498\n", "47\t43734\t79.3\t0\t43734\n", "48\t41734\t79.3\t0\t41734\n", "49\t32625\t79.3\t0\t32625\n", "50\t30668\t79.3\t0\t30668\n", "51\t30766\t79.3\t0\t30766\n", "52\t31481\t79.3\t0\t31481\n", "53\t27933\t79.3\t0\t27933\n", "54\t30674\t79.3\t0\t30674\n", "55\t31144\t79.3\t0\t31144\n", "56\t28566\t79.3\t0\t28566\n", "57\t29606\t79.3\t0\t29606\n", "58\t34828\t79.3\t0\t34828\n", "59\t25338\t79.3\t0\t25338\n", "60\t20045\t79.3\t0\t20045\n", "61\t17970\t79.3\t0\t17970\n", "62\t15187\t79.3\t0\t15187\n", "63\t14238\t79.3\t0\t14238\n", "64\t16105\t79.3\t0\t16105\n", "65\t14985\t79.3\t0\t14985\n", "66\t13075\t79.3\t0\t13075\n", "67\t12789\t79.3\t0\t12789\n", "68\t13126\t79.3\t0\t13126\n", "69\t13423\t79.3\t0\t13423\n", "70\t14054\t79.3\t0\t14054\n", "71\t13400\t79.3\t0\t13400\n", "72\t10512\t79.3\t0\t10512\n", "73\t8966\t79.3\t0\t8966\n", "74\t9150\t79.3\t0\t9150\n", "75\t7787\t79.3\t0\t7787\n", "76\t6338\t79.3\t0\t6338\n", "77\t6107\t79.3\t0\t6107\n", "78\t7042\t79.3\t0\t7042\n", "79\t6553\t79.3\t0\t6553\n", "80\t6480\t79.3\t0\t6480\n", "81\t6062\t79.3\t0\t6062\n", "82\t5490\t79.3\t0\t5490\n", "83\t5816\t79.3\t0\t5816\n", "84\t6316\t79.3\t0\t6316\n", "85\t7365\t79.3\t0\t7365\n", "86\t6751\t79.3\t0\t6751\n", "87\t4503\t79.3\t0\t4503\n", "88\t4194\t79.3\t0\t4194\n", "89\t4347\t79.3\t0\t4347\n", "90\t4599\t79.3\t0\t4599\n", "91\t4702\t79.3\t0\t4702\n", "92\t4915\t79.3\t0\t4915\n", "93\t5176\t79.3\t0\t5176\n", "94\t4887\t79.3\t0\t4887\n", "95\t4234\t79.3\t0\t4234\n", "96\t2979\t79.3\t0\t2979\n", "97\t2080\t79.3\t0\t2080\n", "98\t1265\t79.3\t0\t1265\n", "99\t1214\t79.3\t0\t1214\n", "100\t892\t79.3\t0\t892\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 35769 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 54.4%\n", " C: 26.6%\n", " G: 0.0%\n", " T: 18.8%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t15255\t81164.2\t0\t15255\n", "4\t4078\t20291.0\t0\t4078\n", "5\t2132\t5072.8\t0\t2132\n", "6\t1586\t1268.2\t0\t1586\n", "7\t537\t317.0\t0\t537\n", "8\t368\t79.3\t0\t368\n", "9\t346\t79.3\t0\t346\n", "10\t301\t79.3\t0\t301\n", "11\t324\t79.3\t0\t324\n", "12\t250\t79.3\t0\t250\n", "13\t230\t79.3\t0\t230\n", "14\t237\t79.3\t0\t237\n", "15\t228\t79.3\t0\t228\n", "16\t221\t79.3\t0\t221\n", "17\t222\t79.3\t0\t222\n", "18\t281\t79.3\t0\t281\n", "19\t322\t79.3\t0\t322\n", "20\t364\t79.3\t0\t364\n", "21\t294\t79.3\t0\t294\n", "22\t243\t79.3\t0\t243\n", "23\t177\t79.3\t0\t177\n", "24\t200\t79.3\t0\t200\n", "25\t237\t79.3\t0\t237\n", "26\t339\t79.3\t0\t339\n", "27\t292\t79.3\t0\t292\n", "28\t344\t79.3\t0\t344\n", "29\t319\t79.3\t0\t319\n", "30\t476\t79.3\t0\t476\n", "31\t506\t79.3\t0\t506\n", "32\t721\t79.3\t0\t721\n", "33\t634\t79.3\t0\t634\n", "34\t617\t79.3\t0\t617\n", "35\t792\t79.3\t0\t792\n", "36\t729\t79.3\t0\t729\n", "37\t259\t79.3\t0\t259\n", "38\t33\t79.3\t0\t33\n", "39\t32\t79.3\t0\t32\n", "40\t26\t79.3\t0\t26\n", "41\t33\t79.3\t0\t33\n", "42\t25\t79.3\t0\t25\n", "43\t29\t79.3\t0\t29\n", "44\t21\t79.3\t0\t21\n", "45\t24\t79.3\t0\t24\n", "46\t21\t79.3\t0\t21\n", "47\t28\t79.3\t0\t28\n", "48\t23\t79.3\t0\t23\n", "49\t28\t79.3\t0\t28\n", "50\t32\t79.3\t0\t32\n", "51\t25\t79.3\t0\t25\n", "52\t20\t79.3\t0\t20\n", "53\t21\t79.3\t0\t21\n", "54\t20\t79.3\t0\t20\n", "55\t23\t79.3\t0\t23\n", "56\t15\t79.3\t0\t15\n", "57\t23\t79.3\t0\t23\n", "58\t18\t79.3\t0\t18\n", "59\t24\t79.3\t0\t24\n", "60\t20\t79.3\t0\t20\n", "61\t19\t79.3\t0\t19\n", "62\t13\t79.3\t0\t13\n", "63\t6\t79.3\t0\t6\n", "64\t22\t79.3\t0\t22\n", "65\t22\t79.3\t0\t22\n", "66\t4\t79.3\t0\t4\n", "67\t12\t79.3\t0\t12\n", "68\t12\t79.3\t0\t12\n", "69\t10\t79.3\t0\t10\n", "70\t13\t79.3\t0\t13\n", "71\t7\t79.3\t0\t7\n", "72\t11\t79.3\t0\t11\n", "73\t4\t79.3\t0\t4\n", "74\t4\t79.3\t0\t4\n", "75\t4\t79.3\t0\t4\n", "76\t6\t79.3\t0\t6\n", "77\t10\t79.3\t0\t10\n", "78\t7\t79.3\t0\t7\n", "79\t8\t79.3\t0\t8\n", "80\t9\t79.3\t0\t9\n", "81\t9\t79.3\t0\t9\n", "82\t5\t79.3\t0\t5\n", "83\t6\t79.3\t0\t6\n", "84\t9\t79.3\t0\t9\n", "85\t12\t79.3\t0\t12\n", "86\t15\t79.3\t0\t15\n", "87\t11\t79.3\t0\t11\n", "88\t11\t79.3\t0\t11\n", "89\t12\t79.3\t0\t12\n", "90\t7\t79.3\t0\t7\n", "91\t6\t79.3\t0\t6\n", "92\t15\t79.3\t0\t15\n", "93\t21\t79.3\t0\t21\n", "94\t40\t79.3\t0\t40\n", "95\t86\t79.3\t0\t86\n", "96\t50\t79.3\t0\t50\n", "97\t45\t79.3\t0\t45\n", "98\t60\t79.3\t0\t60\n", "99\t42\t79.3\t0\t42\n", "100\t79\t79.3\t0\t79\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 98052 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.7%\n", " C: 19.8%\n", " G: 17.5%\n", " T: 19.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t65478\t81164.2\t0\t65478\n", "4\t13491\t20291.0\t0\t13491\n", "5\t2340\t5072.8\t0\t2340\n", "6\t500\t1268.2\t0\t500\n", "7\t401\t317.0\t0\t401\n", "8\t452\t317.0\t0\t452\n", "9\t389\t317.0\t0\t389\n", "10\t369\t317.0\t0\t369\n", "11\t386\t317.0\t0\t386\n", "12\t367\t317.0\t0\t367\n", "13\t432\t317.0\t0\t432\n", "14\t458\t317.0\t0\t458\n", "15\t455\t317.0\t0\t455\n", "16\t399\t317.0\t0\t399\n", "17\t410\t317.0\t0\t410\n", "18\t397\t317.0\t0\t397\n", "19\t372\t317.0\t0\t372\n", "20\t396\t317.0\t0\t396\n", "21\t364\t317.0\t0\t364\n", "22\t352\t317.0\t0\t352\n", "23\t318\t317.0\t0\t318\n", "24\t331\t317.0\t0\t331\n", "25\t287\t317.0\t0\t287\n", "26\t284\t317.0\t0\t284\n", "27\t273\t317.0\t0\t273\n", "28\t270\t317.0\t0\t270\n", "29\t276\t317.0\t0\t276\n", "30\t282\t317.0\t0\t282\n", "31\t256\t317.0\t0\t256\n", "32\t263\t317.0\t0\t263\n", "33\t209\t317.0\t0\t209\n", "34\t252\t317.0\t0\t252\n", "35\t237\t317.0\t0\t237\n", "36\t208\t317.0\t0\t208\n", "37\t195\t317.0\t0\t195\n", "38\t200\t317.0\t0\t200\n", "39\t198\t317.0\t0\t198\n", "40\t199\t317.0\t0\t199\n", "41\t185\t317.0\t0\t185\n", "42\t162\t317.0\t0\t162\n", "43\t248\t317.0\t0\t248\n", "44\t83\t317.0\t0\t83\n", "45\t166\t317.0\t0\t166\n", "46\t156\t317.0\t0\t156\n", "47\t135\t317.0\t0\t135\n", "48\t134\t317.0\t0\t134\n", "49\t107\t317.0\t0\t107\n", "50\t124\t317.0\t0\t124\n", "51\t111\t317.0\t0\t111\n", "52\t120\t317.0\t0\t120\n", "53\t107\t317.0\t0\t107\n", "54\t101\t317.0\t0\t101\n", "55\t127\t317.0\t0\t127\n", "56\t97\t317.0\t0\t97\n", "57\t97\t317.0\t0\t97\n", "58\t105\t317.0\t0\t105\n", "59\t80\t317.0\t0\t80\n", "60\t87\t317.0\t0\t87\n", "61\t83\t317.0\t0\t83\n", "62\t80\t317.0\t0\t80\n", "63\t60\t317.0\t0\t60\n", "64\t82\t317.0\t0\t82\n", "65\t68\t317.0\t0\t68\n", "66\t72\t317.0\t0\t72\n", "67\t95\t317.0\t0\t95\n", "68\t95\t317.0\t0\t95\n", "69\t64\t317.0\t0\t64\n", "70\t48\t317.0\t0\t48\n", "71\t65\t317.0\t0\t65\n", "72\t79\t317.0\t0\t79\n", "73\t76\t317.0\t0\t76\n", "74\t78\t317.0\t0\t78\n", "75\t82\t317.0\t0\t82\n", "76\t67\t317.0\t0\t67\n", "77\t71\t317.0\t0\t71\n", "78\t79\t317.0\t0\t79\n", "79\t49\t317.0\t0\t49\n", "80\t61\t317.0\t0\t61\n", "81\t61\t317.0\t0\t61\n", "82\t84\t317.0\t0\t84\n", "83\t76\t317.0\t0\t76\n", "84\t71\t317.0\t0\t71\n", "85\t84\t317.0\t0\t84\n", "86\t50\t317.0\t0\t50\n", "87\t73\t317.0\t0\t73\n", "88\t87\t317.0\t0\t87\n", "89\t57\t317.0\t0\t57\n", "90\t53\t317.0\t0\t53\n", "91\t38\t317.0\t0\t38\n", "92\t62\t317.0\t0\t62\n", "93\t26\t317.0\t0\t26\n", "94\t48\t317.0\t0\t48\n", "95\t40\t317.0\t0\t40\n", "96\t45\t317.0\t0\t45\n", "97\t57\t317.0\t0\t57\n", "98\t86\t317.0\t0\t86\n", "99\t109\t317.0\t0\t109\n", "100\t113\t317.0\t0\t113\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 485_S21_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/485.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 95.27 s (13 us/read; 4.50 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,146,672\n", "Reads with adapters: 3,632,747 (50.8%)\n", "Reads written (passing filters): 7,025,728 (98.3%)\n", "\n", "Total basepairs processed: 714,667,200 bp\n", "Quality-trimmed: 1,491,106 bp (0.2%)\n", "Total written (filtered): 598,885,192 bp (83.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3456755 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.3%\n", " G: 37.6%\n", " T: 32.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t177599\t111666.8\t0\t177599\n", "4\t101530\t27916.7\t0\t101530\n", "5\t77495\t6979.2\t0\t77495\n", "6\t60466\t1744.8\t0\t60466\n", "7\t53856\t436.2\t0\t53856\n", "8\t51805\t109.0\t0\t51805\n", "9\t50826\t109.0\t0\t50826\n", "10\t48808\t109.0\t0\t48808\n", "11\t48629\t109.0\t0\t48629\n", "12\t49381\t109.0\t0\t49381\n", "13\t50749\t109.0\t0\t50749\n", "14\t51816\t109.0\t0\t51816\n", "15\t51189\t109.0\t0\t51189\n", "16\t53130\t109.0\t0\t53130\n", "17\t58053\t109.0\t0\t58053\n", "18\t67577\t109.0\t0\t67577\n", "19\t62000\t109.0\t0\t62000\n", "20\t51390\t109.0\t0\t51390\n", "21\t49433\t109.0\t0\t49433\n", "22\t44412\t109.0\t0\t44412\n", "23\t48417\t109.0\t0\t48417\n", "24\t56897\t109.0\t0\t56897\n", "25\t58283\t109.0\t0\t58283\n", "26\t65709\t109.0\t0\t65709\n", "27\t72297\t109.0\t0\t72297\n", "28\t64951\t109.0\t0\t64951\n", "29\t59652\t109.0\t0\t59652\n", "30\t62342\t109.0\t0\t62342\n", "31\t69062\t109.0\t0\t69062\n", "32\t61345\t109.0\t0\t61345\n", "33\t57535\t109.0\t0\t57535\n", "34\t53058\t109.0\t0\t53058\n", "35\t60712\t109.0\t0\t60712\n", "36\t73799\t109.0\t0\t73799\n", "37\t74734\t109.0\t0\t74734\n", "38\t60492\t109.0\t0\t60492\n", "39\t47139\t109.0\t0\t47139\n", "40\t44921\t109.0\t0\t44921\n", "41\t49477\t109.0\t0\t49477\n", "42\t54110\t109.0\t0\t54110\n", "43\t46928\t109.0\t0\t46928\n", "44\t35866\t109.0\t0\t35866\n", "45\t44553\t109.0\t0\t44553\n", "46\t52418\t109.0\t0\t52418\n", "47\t50442\t109.0\t0\t50442\n", "48\t49402\t109.0\t0\t49402\n", "49\t38871\t109.0\t0\t38871\n", "50\t36370\t109.0\t0\t36370\n", "51\t31402\t109.0\t0\t31402\n", "52\t33673\t109.0\t0\t33673\n", "53\t36829\t109.0\t0\t36829\n", "54\t34500\t109.0\t0\t34500\n", "55\t36751\t109.0\t0\t36751\n", "56\t31359\t109.0\t0\t31359\n", "57\t31621\t109.0\t0\t31621\n", "58\t28786\t109.0\t0\t28786\n", "59\t23179\t109.0\t0\t23179\n", "60\t19597\t109.0\t0\t19597\n", "61\t18675\t109.0\t0\t18675\n", "62\t15642\t109.0\t0\t15642\n", "63\t15075\t109.0\t0\t15075\n", "64\t16363\t109.0\t0\t16363\n", "65\t15774\t109.0\t0\t15774\n", "66\t13722\t109.0\t0\t13722\n", "67\t13254\t109.0\t0\t13254\n", "68\t12951\t109.0\t0\t12951\n", "69\t12846\t109.0\t0\t12846\n", "70\t13311\t109.0\t0\t13311\n", "71\t12791\t109.0\t0\t12791\n", "72\t9950\t109.0\t0\t9950\n", "73\t8853\t109.0\t0\t8853\n", "74\t8602\t109.0\t0\t8602\n", "75\t7682\t109.0\t0\t7682\n", "76\t6425\t109.0\t0\t6425\n", "77\t6128\t109.0\t0\t6128\n", "78\t6809\t109.0\t0\t6809\n", "79\t6573\t109.0\t0\t6573\n", "80\t6510\t109.0\t0\t6510\n", "81\t6346\t109.0\t0\t6346\n", "82\t6177\t109.0\t0\t6177\n", "83\t6597\t109.0\t0\t6597\n", "84\t7699\t109.0\t0\t7699\n", "85\t8679\t109.0\t0\t8679\n", "86\t8675\t109.0\t0\t8675\n", "87\t6587\t109.0\t0\t6587\n", "88\t6209\t109.0\t0\t6209\n", "89\t6350\t109.0\t0\t6350\n", "90\t6705\t109.0\t0\t6705\n", "91\t6319\t109.0\t0\t6319\n", "92\t6362\t109.0\t0\t6362\n", "93\t6581\t109.0\t0\t6581\n", "94\t6372\t109.0\t0\t6372\n", "95\t5361\t109.0\t0\t5361\n", "96\t3971\t109.0\t0\t3971\n", "97\t2496\t109.0\t0\t2496\n", "98\t1594\t109.0\t0\t1594\n", "99\t1101\t109.0\t0\t1101\n", "100\t1015\t109.0\t0\t1015\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 33689 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 48.7%\n", " C: 24.4%\n", " G: 0.0%\n", " T: 26.6%\n", " none/other: 0.3%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t17004\t111666.8\t0\t17004\n", "4\t3825\t27916.7\t0\t3825\n", "5\t1507\t6979.2\t0\t1507\n", "6\t1128\t1744.8\t0\t1128\n", "7\t210\t436.2\t0\t210\n", "8\t267\t109.0\t0\t267\n", "9\t110\t109.0\t0\t110\n", "10\t116\t109.0\t0\t116\n", "11\t114\t109.0\t0\t114\n", "12\t122\t109.0\t0\t122\n", "13\t107\t109.0\t0\t107\n", "14\t92\t109.0\t0\t92\n", "15\t81\t109.0\t0\t81\n", "16\t92\t109.0\t0\t92\n", "17\t91\t109.0\t0\t91\n", "18\t99\t109.0\t0\t99\n", "19\t118\t109.0\t0\t118\n", "20\t154\t109.0\t0\t154\n", "21\t107\t109.0\t0\t107\n", "22\t93\t109.0\t0\t93\n", "23\t114\t109.0\t0\t114\n", "24\t121\t109.0\t0\t121\n", "25\t125\t109.0\t0\t125\n", "26\t215\t109.0\t0\t215\n", "27\t149\t109.0\t0\t149\n", "28\t161\t109.0\t0\t161\n", "29\t214\t109.0\t0\t214\n", "30\t345\t109.0\t0\t345\n", "31\t432\t109.0\t0\t432\n", "32\t668\t109.0\t0\t668\n", "33\t587\t109.0\t0\t587\n", "34\t558\t109.0\t0\t558\n", "35\t785\t109.0\t0\t785\n", "36\t739\t109.0\t0\t739\n", "37\t253\t109.0\t0\t253\n", "38\t51\t109.0\t0\t51\n", "39\t48\t109.0\t0\t48\n", "40\t37\t109.0\t0\t37\n", "41\t57\t109.0\t0\t57\n", "42\t48\t109.0\t0\t48\n", "43\t49\t109.0\t0\t49\n", "44\t41\t109.0\t0\t41\n", "45\t41\t109.0\t0\t41\n", "46\t40\t109.0\t0\t40\n", "47\t55\t109.0\t0\t55\n", "48\t44\t109.0\t0\t44\n", "49\t54\t109.0\t0\t54\n", "50\t37\t109.0\t0\t37\n", "51\t27\t109.0\t0\t27\n", "52\t36\t109.0\t0\t36\n", "53\t24\t109.0\t0\t24\n", "54\t23\t109.0\t0\t23\n", "55\t24\t109.0\t0\t24\n", "56\t29\t109.0\t0\t29\n", "57\t26\t109.0\t0\t26\n", "58\t18\t109.0\t0\t18\n", "59\t20\t109.0\t0\t20\n", "60\t22\t109.0\t0\t22\n", "61\t21\t109.0\t0\t21\n", "62\t23\t109.0\t0\t23\n", "63\t28\t109.0\t0\t28\n", "64\t35\t109.0\t0\t35\n", "65\t22\t109.0\t0\t22\n", "66\t18\t109.0\t0\t18\n", "67\t15\t109.0\t0\t15\n", "68\t25\t109.0\t0\t25\n", "69\t22\t109.0\t0\t22\n", "70\t12\t109.0\t0\t12\n", "71\t13\t109.0\t0\t13\n", "72\t10\t109.0\t0\t10\n", "73\t10\t109.0\t0\t10\n", "74\t11\t109.0\t0\t11\n", "75\t11\t109.0\t0\t11\n", "76\t8\t109.0\t0\t8\n", "77\t12\t109.0\t0\t12\n", "78\t11\t109.0\t0\t11\n", "79\t11\t109.0\t0\t11\n", "80\t12\t109.0\t0\t12\n", "81\t12\t109.0\t0\t12\n", "82\t15\t109.0\t0\t15\n", "83\t14\t109.0\t0\t14\n", "84\t15\t109.0\t0\t15\n", "85\t12\t109.0\t0\t12\n", "86\t16\t109.0\t0\t16\n", "87\t15\t109.0\t0\t15\n", "88\t11\t109.0\t0\t11\n", "89\t15\t109.0\t0\t15\n", "90\t27\t109.0\t0\t27\n", "91\t33\t109.0\t0\t33\n", "92\t52\t109.0\t0\t52\n", "93\t87\t109.0\t0\t87\n", "94\t181\t109.0\t0\t181\n", "95\t197\t109.0\t0\t197\n", "96\t175\t109.0\t0\t175\n", "97\t194\t109.0\t0\t194\n", "98\t144\t109.0\t0\t144\n", "99\t126\t109.0\t0\t126\n", "100\t264\t109.0\t0\t264\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 142303 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.2%\n", " C: 21.7%\n", " G: 16.4%\n", " T: 20.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t105846\t111666.8\t0\t105846\n", "4\t21157\t27916.7\t0\t21157\n", "5\t4315\t6979.2\t0\t4315\n", "6\t367\t1744.8\t0\t367\n", "7\t179\t436.2\t0\t179\n", "8\t153\t436.2\t0\t153\n", "9\t146\t436.2\t0\t146\n", "10\t151\t436.2\t0\t151\n", "11\t166\t436.2\t0\t166\n", "12\t166\t436.2\t0\t166\n", "13\t177\t436.2\t0\t177\n", "14\t149\t436.2\t0\t149\n", "15\t154\t436.2\t0\t154\n", "16\t163\t436.2\t0\t163\n", "17\t162\t436.2\t0\t162\n", "18\t165\t436.2\t0\t165\n", "19\t175\t436.2\t0\t175\n", "20\t126\t436.2\t0\t126\n", "21\t138\t436.2\t0\t138\n", "22\t126\t436.2\t0\t126\n", "23\t99\t436.2\t0\t99\n", "24\t112\t436.2\t0\t112\n", "25\t123\t436.2\t0\t123\n", "26\t118\t436.2\t0\t118\n", "27\t122\t436.2\t0\t122\n", "28\t133\t436.2\t0\t133\n", "29\t110\t436.2\t0\t110\n", "30\t142\t436.2\t0\t142\n", "31\t136\t436.2\t0\t136\n", "32\t164\t436.2\t0\t164\n", "33\t116\t436.2\t0\t116\n", "34\t107\t436.2\t0\t107\n", "35\t117\t436.2\t0\t117\n", "36\t100\t436.2\t0\t100\n", "37\t125\t436.2\t0\t125\n", "38\t107\t436.2\t0\t107\n", "39\t141\t436.2\t0\t141\n", "40\t120\t436.2\t0\t120\n", "41\t100\t436.2\t0\t100\n", "42\t94\t436.2\t0\t94\n", "43\t111\t436.2\t0\t111\n", "44\t78\t436.2\t0\t78\n", "45\t87\t436.2\t0\t87\n", "46\t99\t436.2\t0\t99\n", "47\t98\t436.2\t0\t98\n", "48\t107\t436.2\t0\t107\n", "49\t95\t436.2\t0\t95\n", "50\t104\t436.2\t0\t104\n", "51\t81\t436.2\t0\t81\n", "52\t75\t436.2\t0\t75\n", "53\t97\t436.2\t0\t97\n", "54\t89\t436.2\t0\t89\n", "55\t89\t436.2\t0\t89\n", "56\t100\t436.2\t0\t100\n", "57\t95\t436.2\t0\t95\n", "58\t77\t436.2\t0\t77\n", "59\t70\t436.2\t0\t70\n", "60\t100\t436.2\t0\t100\n", "61\t72\t436.2\t0\t72\n", "62\t83\t436.2\t0\t83\n", "63\t72\t436.2\t0\t72\n", "64\t85\t436.2\t0\t85\n", "65\t90\t436.2\t0\t90\n", "66\t65\t436.2\t0\t65\n", "67\t77\t436.2\t0\t77\n", "68\t85\t436.2\t0\t85\n", "69\t63\t436.2\t0\t63\n", "70\t74\t436.2\t0\t74\n", "71\t70\t436.2\t0\t70\n", "72\t69\t436.2\t0\t69\n", "73\t86\t436.2\t0\t86\n", "74\t115\t436.2\t0\t115\n", "75\t74\t436.2\t0\t74\n", "76\t142\t436.2\t0\t142\n", "77\t120\t436.2\t0\t120\n", "78\t110\t436.2\t0\t110\n", "79\t116\t436.2\t0\t116\n", "80\t136\t436.2\t0\t136\n", "81\t129\t436.2\t0\t129\n", "82\t174\t436.2\t0\t174\n", "83\t172\t436.2\t0\t172\n", "84\t125\t436.2\t0\t125\n", "85\t118\t436.2\t0\t118\n", "86\t104\t436.2\t0\t104\n", "87\t113\t436.2\t0\t113\n", "88\t131\t436.2\t0\t131\n", "89\t91\t436.2\t0\t91\n", "90\t107\t436.2\t0\t107\n", "91\t75\t436.2\t0\t75\n", "92\t70\t436.2\t0\t70\n", "93\t61\t436.2\t0\t61\n", "94\t92\t436.2\t0\t92\n", "95\t79\t436.2\t0\t79\n", "96\t81\t436.2\t0\t81\n", "97\t96\t436.2\t0\t96\n", "98\t129\t436.2\t0\t129\n", "99\t154\t436.2\t0\t154\n", "100\t179\t436.2\t0\t179\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 487_S6_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/487.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 98.18 s (13 us/read; 4.53 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,411,766\n", "Reads with adapters: 4,389,164 (59.2%)\n", "Reads written (passing filters): 7,171,226 (96.8%)\n", "\n", "Total basepairs processed: 741,176,600 bp\n", "Quality-trimmed: 2,145,269 bp (0.3%)\n", "Total written (filtered): 565,640,395 bp (76.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4217630 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 32.5%\n", " G: 39.4%\n", " T: 28.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t148178\t115808.8\t0\t148178\n", "4\t80086\t28952.2\t0\t80086\n", "5\t59109\t7238.1\t0\t59109\n", "6\t45936\t1809.5\t0\t45936\n", "7\t42715\t452.4\t0\t42715\n", "8\t42842\t113.1\t0\t42842\n", "9\t42274\t113.1\t0\t42274\n", "10\t41443\t113.1\t0\t41443\n", "11\t41807\t113.1\t0\t41807\n", "12\t41961\t113.1\t0\t41961\n", "13\t43307\t113.1\t0\t43307\n", "14\t45183\t113.1\t0\t45183\n", "15\t45826\t113.1\t0\t45826\n", "16\t48737\t113.1\t0\t48737\n", "17\t52512\t113.1\t0\t52512\n", "18\t58764\t113.1\t0\t58764\n", "19\t55615\t113.1\t0\t55615\n", "20\t47318\t113.1\t0\t47318\n", "21\t44805\t113.1\t0\t44805\n", "22\t42197\t113.1\t0\t42197\n", "23\t45457\t113.1\t0\t45457\n", "24\t51312\t113.1\t0\t51312\n", "25\t54232\t113.1\t0\t54232\n", "26\t61078\t113.1\t0\t61078\n", "27\t67749\t113.1\t0\t67749\n", "28\t63717\t113.1\t0\t63717\n", "29\t59920\t113.1\t0\t59920\n", "30\t61425\t113.1\t0\t61425\n", "31\t65629\t113.1\t0\t65629\n", "32\t64688\t113.1\t0\t64688\n", "33\t60757\t113.1\t0\t60757\n", "34\t60350\t113.1\t0\t60350\n", "35\t67938\t113.1\t0\t67938\n", "36\t75976\t113.1\t0\t75976\n", "37\t78670\t113.1\t0\t78670\n", "38\t67669\t113.1\t0\t67669\n", "39\t60211\t113.1\t0\t60211\n", "40\t57912\t113.1\t0\t57912\n", "41\t63099\t113.1\t0\t63099\n", "42\t70688\t113.1\t0\t70688\n", "43\t63127\t113.1\t0\t63127\n", "44\t53774\t113.1\t0\t53774\n", "45\t63897\t113.1\t0\t63897\n", "46\t74596\t113.1\t0\t74596\n", "47\t71404\t113.1\t0\t71404\n", "48\t69122\t113.1\t0\t69122\n", "49\t56096\t113.1\t0\t56096\n", "50\t55442\t113.1\t0\t55442\n", "51\t52807\t113.1\t0\t52807\n", "52\t59654\t113.1\t0\t59654\n", "53\t66165\t113.1\t0\t66165\n", "54\t63143\t113.1\t0\t63143\n", "55\t62326\t113.1\t0\t62326\n", "56\t54240\t113.1\t0\t54240\n", "57\t49201\t113.1\t0\t49201\n", "58\t52878\t113.1\t0\t52878\n", "59\t50169\t113.1\t0\t50169\n", "60\t43874\t113.1\t0\t43874\n", "61\t41997\t113.1\t0\t41997\n", "62\t35982\t113.1\t0\t35982\n", "63\t34838\t113.1\t0\t34838\n", "64\t38817\t113.1\t0\t38817\n", "65\t38849\t113.1\t0\t38849\n", "66\t35865\t113.1\t0\t35865\n", "67\t35296\t113.1\t0\t35296\n", "68\t34563\t113.1\t0\t34563\n", "69\t35540\t113.1\t0\t35540\n", "70\t36716\t113.1\t0\t36716\n", "71\t34885\t113.1\t0\t34885\n", "72\t29099\t113.1\t0\t29099\n", "73\t26497\t113.1\t0\t26497\n", "74\t26040\t113.1\t0\t26040\n", "75\t22894\t113.1\t0\t22894\n", "76\t19410\t113.1\t0\t19410\n", "77\t18306\t113.1\t0\t18306\n", "78\t20005\t113.1\t0\t20005\n", "79\t19336\t113.1\t0\t19336\n", "80\t18735\t113.1\t0\t18735\n", "81\t17036\t113.1\t0\t17036\n", "82\t15838\t113.1\t0\t15838\n", "83\t16507\t113.1\t0\t16507\n", "84\t17711\t113.1\t0\t17711\n", "85\t19421\t113.1\t0\t19421\n", "86\t17982\t113.1\t0\t17982\n", "87\t13284\t113.1\t0\t13284\n", "88\t12275\t113.1\t0\t12275\n", "89\t12167\t113.1\t0\t12167\n", "90\t12790\t113.1\t0\t12790\n", "91\t13251\t113.1\t0\t13251\n", "92\t12893\t113.1\t0\t12893\n", "93\t12441\t113.1\t0\t12441\n", "94\t9702\t113.1\t0\t9702\n", "95\t6868\t113.1\t0\t6868\n", "96\t4678\t113.1\t0\t4678\n", "97\t2684\t113.1\t0\t2684\n", "98\t1722\t113.1\t0\t1722\n", "99\t2074\t113.1\t0\t2074\n", "100\t1629\t113.1\t0\t1629\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 31644 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.8%\n", " C: 24.4%\n", " G: 0.0%\n", " T: 29.8%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t17158\t115808.8\t0\t17158\n", "4\t4129\t28952.2\t0\t4129\n", "5\t1483\t7238.1\t0\t1483\n", "6\t743\t1809.5\t0\t743\n", "7\t234\t452.4\t0\t234\n", "8\t196\t113.1\t0\t196\n", "9\t156\t113.1\t0\t156\n", "10\t147\t113.1\t0\t147\n", "11\t190\t113.1\t0\t190\n", "12\t140\t113.1\t0\t140\n", "13\t152\t113.1\t0\t152\n", "14\t149\t113.1\t0\t149\n", "15\t153\t113.1\t0\t153\n", "16\t155\t113.1\t0\t155\n", "17\t144\t113.1\t0\t144\n", "18\t136\t113.1\t0\t136\n", "19\t172\t113.1\t0\t172\n", "20\t205\t113.1\t0\t205\n", "21\t172\t113.1\t0\t172\n", "22\t153\t113.1\t0\t153\n", "23\t127\t113.1\t0\t127\n", "24\t156\t113.1\t0\t156\n", "25\t111\t113.1\t0\t111\n", "26\t190\t113.1\t0\t190\n", "27\t173\t113.1\t0\t173\n", "28\t138\t113.1\t0\t138\n", "29\t152\t113.1\t0\t152\n", "30\t206\t113.1\t0\t206\n", "31\t206\t113.1\t0\t206\n", "32\t339\t113.1\t0\t339\n", "33\t322\t113.1\t0\t322\n", "34\t332\t113.1\t0\t332\n", "35\t453\t113.1\t0\t453\n", "36\t450\t113.1\t0\t450\n", "37\t203\t113.1\t0\t203\n", "38\t42\t113.1\t0\t42\n", "39\t77\t113.1\t0\t77\n", "40\t45\t113.1\t0\t45\n", "41\t47\t113.1\t0\t47\n", "42\t44\t113.1\t0\t44\n", "43\t36\t113.1\t0\t36\n", "44\t45\t113.1\t0\t45\n", "45\t50\t113.1\t0\t50\n", "46\t55\t113.1\t0\t55\n", "47\t51\t113.1\t0\t51\n", "48\t47\t113.1\t0\t47\n", "49\t62\t113.1\t0\t62\n", "50\t59\t113.1\t0\t59\n", "51\t55\t113.1\t0\t55\n", "52\t40\t113.1\t0\t40\n", "53\t33\t113.1\t0\t33\n", "54\t40\t113.1\t0\t40\n", "55\t42\t113.1\t0\t42\n", "56\t33\t113.1\t0\t33\n", "57\t46\t113.1\t0\t46\n", "58\t40\t113.1\t0\t40\n", "59\t37\t113.1\t0\t37\n", "60\t31\t113.1\t0\t31\n", "61\t24\t113.1\t0\t24\n", "62\t37\t113.1\t0\t37\n", "63\t28\t113.1\t0\t28\n", "64\t24\t113.1\t0\t24\n", "65\t33\t113.1\t0\t33\n", "66\t32\t113.1\t0\t32\n", "67\t24\t113.1\t0\t24\n", "68\t24\t113.1\t0\t24\n", "69\t29\t113.1\t0\t29\n", "70\t23\t113.1\t0\t23\n", "71\t22\t113.1\t0\t22\n", "72\t16\t113.1\t0\t16\n", "73\t25\t113.1\t0\t25\n", "74\t12\t113.1\t0\t12\n", "75\t23\t113.1\t0\t23\n", "76\t16\t113.1\t0\t16\n", "77\t14\t113.1\t0\t14\n", "78\t9\t113.1\t0\t9\n", "79\t11\t113.1\t0\t11\n", "80\t7\t113.1\t0\t7\n", "81\t18\t113.1\t0\t18\n", "82\t10\t113.1\t0\t10\n", "83\t12\t113.1\t0\t12\n", "84\t9\t113.1\t0\t9\n", "85\t15\t113.1\t0\t15\n", "86\t5\t113.1\t0\t5\n", "87\t7\t113.1\t0\t7\n", "88\t5\t113.1\t0\t5\n", "89\t16\t113.1\t0\t16\n", "90\t7\t113.1\t0\t7\n", "91\t13\t113.1\t0\t13\n", "92\t21\t113.1\t0\t21\n", "93\t23\t113.1\t0\t23\n", "94\t33\t113.1\t0\t33\n", "95\t30\t113.1\t0\t30\n", "96\t55\t113.1\t0\t55\n", "97\t42\t113.1\t0\t42\n", "98\t42\t113.1\t0\t42\n", "99\t25\t113.1\t0\t25\n", "100\t41\t113.1\t0\t41\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 139890 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.1%\n", " C: 21.2%\n", " G: 17.1%\n", " T: 21.6%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t100659\t115808.8\t0\t100659\n", "4\t20987\t28952.2\t0\t20987\n", "5\t3675\t7238.1\t0\t3675\n", "6\t406\t1809.5\t0\t406\n", "7\t226\t452.4\t0\t226\n", "8\t236\t452.4\t0\t236\n", "9\t198\t452.4\t0\t198\n", "10\t270\t452.4\t0\t270\n", "11\t221\t452.4\t0\t221\n", "12\t251\t452.4\t0\t251\n", "13\t239\t452.4\t0\t239\n", "14\t201\t452.4\t0\t201\n", "15\t219\t452.4\t0\t219\n", "16\t258\t452.4\t0\t258\n", "17\t216\t452.4\t0\t216\n", "18\t219\t452.4\t0\t219\n", "19\t271\t452.4\t0\t271\n", "20\t191\t452.4\t0\t191\n", "21\t224\t452.4\t0\t224\n", "22\t192\t452.4\t0\t192\n", "23\t184\t452.4\t0\t184\n", "24\t209\t452.4\t0\t209\n", "25\t202\t452.4\t0\t202\n", "26\t163\t452.4\t0\t163\n", "27\t171\t452.4\t0\t171\n", "28\t165\t452.4\t0\t165\n", "29\t187\t452.4\t0\t187\n", "30\t189\t452.4\t0\t189\n", "31\t181\t452.4\t0\t181\n", "32\t179\t452.4\t0\t179\n", "33\t201\t452.4\t0\t201\n", "34\t224\t452.4\t0\t224\n", "35\t220\t452.4\t0\t220\n", "36\t200\t452.4\t0\t200\n", "37\t194\t452.4\t0\t194\n", "38\t197\t452.4\t0\t197\n", "39\t231\t452.4\t0\t231\n", "40\t228\t452.4\t0\t228\n", "41\t196\t452.4\t0\t196\n", "42\t147\t452.4\t0\t147\n", "43\t247\t452.4\t0\t247\n", "44\t145\t452.4\t0\t145\n", "45\t144\t452.4\t0\t144\n", "46\t166\t452.4\t0\t166\n", "47\t176\t452.4\t0\t176\n", "48\t134\t452.4\t0\t134\n", "49\t129\t452.4\t0\t129\n", "50\t160\t452.4\t0\t160\n", "51\t106\t452.4\t0\t106\n", "52\t143\t452.4\t0\t143\n", "53\t114\t452.4\t0\t114\n", "54\t132\t452.4\t0\t132\n", "55\t126\t452.4\t0\t126\n", "56\t120\t452.4\t0\t120\n", "57\t103\t452.4\t0\t103\n", "58\t111\t452.4\t0\t111\n", "59\t121\t452.4\t0\t121\n", "60\t112\t452.4\t0\t112\n", "61\t97\t452.4\t0\t97\n", "62\t102\t452.4\t0\t102\n", "63\t93\t452.4\t0\t93\n", "64\t121\t452.4\t0\t121\n", "65\t104\t452.4\t0\t104\n", "66\t91\t452.4\t0\t91\n", "67\t86\t452.4\t0\t86\n", "68\t129\t452.4\t0\t129\n", "69\t70\t452.4\t0\t70\n", "70\t56\t452.4\t0\t56\n", "71\t88\t452.4\t0\t88\n", "72\t121\t452.4\t0\t121\n", "73\t93\t452.4\t0\t93\n", "74\t131\t452.4\t0\t131\n", "75\t74\t452.4\t0\t74\n", "76\t111\t452.4\t0\t111\n", "77\t129\t452.4\t0\t129\n", "78\t124\t452.4\t0\t124\n", "79\t109\t452.4\t0\t109\n", "80\t137\t452.4\t0\t137\n", "81\t127\t452.4\t0\t127\n", "82\t187\t452.4\t0\t187\n", "83\t149\t452.4\t0\t149\n", "84\t132\t452.4\t0\t132\n", "85\t117\t452.4\t0\t117\n", "86\t92\t452.4\t0\t92\n", "87\t102\t452.4\t0\t102\n", "88\t139\t452.4\t0\t139\n", "89\t95\t452.4\t0\t95\n", "90\t108\t452.4\t0\t108\n", "91\t74\t452.4\t0\t74\n", "92\t93\t452.4\t0\t93\n", "93\t74\t452.4\t0\t74\n", "94\t63\t452.4\t0\t63\n", "95\t46\t452.4\t0\t46\n", "96\t43\t452.4\t0\t43\n", "97\t83\t452.4\t0\t83\n", "98\t92\t452.4\t0\t92\n", "99\t122\t452.4\t0\t122\n", "100\t170\t452.4\t0\t170\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 488_S26_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/488.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 88.25 s (13 us/read; 4.71 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,926,901\n", "Reads with adapters: 4,056,774 (58.6%)\n", "Reads written (passing filters): 6,865,968 (99.1%)\n", "\n", "Total basepairs processed: 692,690,100 bp\n", "Quality-trimmed: 1,723,420 bp (0.2%)\n", "Total written (filtered): 568,115,347 bp (82.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3955843 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.0%\n", " G: 32.2%\n", " T: 39.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t188522\t108232.8\t0\t188522\n", "4\t114610\t27058.2\t0\t114610\n", "5\t88775\t6764.6\t0\t88775\n", "6\t68729\t1691.1\t0\t68729\n", "7\t63241\t422.8\t0\t63241\n", "8\t64430\t105.7\t0\t64430\n", "9\t63235\t105.7\t0\t63235\n", "10\t58281\t105.7\t0\t58281\n", "11\t58137\t105.7\t0\t58137\n", "12\t57724\t105.7\t0\t57724\n", "13\t58427\t105.7\t0\t58427\n", "14\t60951\t105.7\t0\t60951\n", "15\t62199\t105.7\t0\t62199\n", "16\t64624\t105.7\t0\t64624\n", "17\t73541\t105.7\t0\t73541\n", "18\t85276\t105.7\t0\t85276\n", "19\t80771\t105.7\t0\t80771\n", "20\t66718\t105.7\t0\t66718\n", "21\t62018\t105.7\t0\t62018\n", "22\t54219\t105.7\t0\t54219\n", "23\t60214\t105.7\t0\t60214\n", "24\t69363\t105.7\t0\t69363\n", "25\t68959\t105.7\t0\t68959\n", "26\t76645\t105.7\t0\t76645\n", "27\t85872\t105.7\t0\t85872\n", "28\t77481\t105.7\t0\t77481\n", "29\t73959\t105.7\t0\t73959\n", "30\t77179\t105.7\t0\t77179\n", "31\t82512\t105.7\t0\t82512\n", "32\t75531\t105.7\t0\t75531\n", "33\t68853\t105.7\t0\t68853\n", "34\t63674\t105.7\t0\t63674\n", "35\t71390\t105.7\t0\t71390\n", "36\t81545\t105.7\t0\t81545\n", "37\t79563\t105.7\t0\t79563\n", "38\t67548\t105.7\t0\t67548\n", "39\t57001\t105.7\t0\t57001\n", "40\t53951\t105.7\t0\t53951\n", "41\t53174\t105.7\t0\t53174\n", "42\t56221\t105.7\t0\t56221\n", "43\t51045\t105.7\t0\t51045\n", "44\t41379\t105.7\t0\t41379\n", "45\t53248\t105.7\t0\t53248\n", "46\t64651\t105.7\t0\t64651\n", "47\t64357\t105.7\t0\t64357\n", "48\t64720\t105.7\t0\t64720\n", "49\t49441\t105.7\t0\t49441\n", "50\t41024\t105.7\t0\t41024\n", "51\t41750\t105.7\t0\t41750\n", "52\t41177\t105.7\t0\t41177\n", "53\t37071\t105.7\t0\t37071\n", "54\t40618\t105.7\t0\t40618\n", "55\t34749\t105.7\t0\t34749\n", "56\t32821\t105.7\t0\t32821\n", "57\t30432\t105.7\t0\t30432\n", "58\t34094\t105.7\t0\t34094\n", "59\t29451\t105.7\t0\t29451\n", "60\t24748\t105.7\t0\t24748\n", "61\t22687\t105.7\t0\t22687\n", "62\t19174\t105.7\t0\t19174\n", "63\t19757\t105.7\t0\t19757\n", "64\t22314\t105.7\t0\t22314\n", "65\t17602\t105.7\t0\t17602\n", "66\t15450\t105.7\t0\t15450\n", "67\t16580\t105.7\t0\t16580\n", "68\t13627\t105.7\t0\t13627\n", "69\t11913\t105.7\t0\t11913\n", "70\t13251\t105.7\t0\t13251\n", "71\t11664\t105.7\t0\t11664\n", "72\t9201\t105.7\t0\t9201\n", "73\t6336\t105.7\t0\t6336\n", "74\t5272\t105.7\t0\t5272\n", "75\t4667\t105.7\t0\t4667\n", "76\t4137\t105.7\t0\t4137\n", "77\t4715\t105.7\t0\t4715\n", "78\t5589\t105.7\t0\t5589\n", "79\t4359\t105.7\t0\t4359\n", "80\t3952\t105.7\t0\t3952\n", "81\t4110\t105.7\t0\t4110\n", "82\t3712\t105.7\t0\t3712\n", "83\t3444\t105.7\t0\t3444\n", "84\t4053\t105.7\t0\t4053\n", "85\t4810\t105.7\t0\t4810\n", "86\t5081\t105.7\t0\t5081\n", "87\t3749\t105.7\t0\t3749\n", "88\t3034\t105.7\t0\t3034\n", "89\t2794\t105.7\t0\t2794\n", "90\t2893\t105.7\t0\t2893\n", "91\t2726\t105.7\t0\t2726\n", "92\t2475\t105.7\t0\t2475\n", "93\t2275\t105.7\t0\t2275\n", "94\t1943\t105.7\t0\t1943\n", "95\t1683\t105.7\t0\t1683\n", "96\t1113\t105.7\t0\t1113\n", "97\t745\t105.7\t0\t745\n", "98\t450\t105.7\t0\t450\n", "99\t362\t105.7\t0\t362\n", "100\t305\t105.7\t0\t305\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 11239 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 48.8%\n", " C: 16.1%\n", " G: 0.0%\n", " T: 35.0%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t6190\t108232.8\t0\t6190\n", "4\t1258\t27058.2\t0\t1258\n", "5\t445\t6764.6\t0\t445\n", "6\t286\t1691.1\t0\t286\n", "7\t68\t422.8\t0\t68\n", "8\t52\t105.7\t0\t52\n", "9\t55\t105.7\t0\t55\n", "10\t32\t105.7\t0\t32\n", "11\t35\t105.7\t0\t35\n", "12\t43\t105.7\t0\t43\n", "13\t38\t105.7\t0\t38\n", "14\t39\t105.7\t0\t39\n", "15\t43\t105.7\t0\t43\n", "16\t38\t105.7\t0\t38\n", "17\t49\t105.7\t0\t49\n", "18\t48\t105.7\t0\t48\n", "19\t59\t105.7\t0\t59\n", "20\t64\t105.7\t0\t64\n", "21\t55\t105.7\t0\t55\n", "22\t28\t105.7\t0\t28\n", "23\t44\t105.7\t0\t44\n", "24\t47\t105.7\t0\t47\n", "25\t35\t105.7\t0\t35\n", "26\t63\t105.7\t0\t63\n", "27\t46\t105.7\t0\t46\n", "28\t65\t105.7\t0\t65\n", "29\t90\t105.7\t0\t90\n", "30\t119\t105.7\t0\t119\n", "31\t147\t105.7\t0\t147\n", "32\t203\t105.7\t0\t203\n", "33\t237\t105.7\t0\t237\n", "34\t264\t105.7\t0\t264\n", "35\t354\t105.7\t0\t354\n", "36\t209\t105.7\t0\t209\n", "37\t87\t105.7\t0\t87\n", "38\t20\t105.7\t0\t20\n", "39\t13\t105.7\t0\t13\n", "40\t8\t105.7\t0\t8\n", "41\t7\t105.7\t0\t7\n", "42\t8\t105.7\t0\t8\n", "43\t18\t105.7\t0\t18\n", "44\t13\t105.7\t0\t13\n", "45\t12\t105.7\t0\t12\n", "46\t19\t105.7\t0\t19\n", "47\t13\t105.7\t0\t13\n", "48\t9\t105.7\t0\t9\n", "49\t6\t105.7\t0\t6\n", "50\t8\t105.7\t0\t8\n", "51\t5\t105.7\t0\t5\n", "52\t4\t105.7\t0\t4\n", "53\t10\t105.7\t0\t10\n", "54\t2\t105.7\t0\t2\n", "55\t4\t105.7\t0\t4\n", "56\t9\t105.7\t0\t9\n", "57\t4\t105.7\t0\t4\n", "58\t1\t105.7\t0\t1\n", "59\t2\t105.7\t0\t2\n", "60\t1\t105.7\t0\t1\n", "61\t2\t105.7\t0\t2\n", "62\t4\t105.7\t0\t4\n", "63\t3\t105.7\t0\t3\n", "64\t1\t105.7\t0\t1\n", "66\t5\t105.7\t0\t5\n", "68\t3\t105.7\t0\t3\n", "69\t1\t105.7\t0\t1\n", "70\t1\t105.7\t0\t1\n", "71\t1\t105.7\t0\t1\n", "72\t1\t105.7\t0\t1\n", "76\t1\t105.7\t0\t1\n", "77\t1\t105.7\t0\t1\n", "80\t1\t105.7\t0\t1\n", "81\t1\t105.7\t0\t1\n", "82\t1\t105.7\t0\t1\n", "83\t1\t105.7\t0\t1\n", "84\t3\t105.7\t0\t3\n", "85\t1\t105.7\t0\t1\n", "89\t1\t105.7\t0\t1\n", "90\t3\t105.7\t0\t3\n", "91\t2\t105.7\t0\t2\n", "92\t10\t105.7\t0\t10\n", "93\t10\t105.7\t0\t10\n", "94\t13\t105.7\t0\t13\n", "95\t13\t105.7\t0\t13\n", "96\t6\t105.7\t0\t6\n", "97\t2\t105.7\t0\t2\n", "98\t4\t105.7\t0\t4\n", "99\t5\t105.7\t0\t5\n", "100\t7\t105.7\t0\t7\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 89692 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 52.0%\n", " C: 13.6%\n", " G: 12.9%\n", " T: 21.5%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t62862\t108232.8\t0\t62862\n", "4\t16607\t27058.2\t0\t16607\n", "5\t4690\t6764.6\t0\t4690\n", "6\t127\t1691.1\t0\t127\n", "7\t43\t422.8\t0\t43\n", "8\t32\t422.8\t0\t32\n", "9\t48\t422.8\t0\t48\n", "10\t61\t422.8\t0\t61\n", "11\t50\t422.8\t0\t50\n", "12\t48\t422.8\t0\t48\n", "13\t35\t422.8\t0\t35\n", "14\t31\t422.8\t0\t31\n", "15\t27\t422.8\t0\t27\n", "16\t21\t422.8\t0\t21\n", "17\t17\t422.8\t0\t17\n", "18\t25\t422.8\t0\t25\n", "19\t36\t422.8\t0\t36\n", "20\t23\t422.8\t0\t23\n", "21\t26\t422.8\t0\t26\n", "22\t27\t422.8\t0\t27\n", "23\t27\t422.8\t0\t27\n", "24\t19\t422.8\t0\t19\n", "25\t24\t422.8\t0\t24\n", "26\t20\t422.8\t0\t20\n", "27\t26\t422.8\t0\t26\n", "28\t28\t422.8\t0\t28\n", "29\t34\t422.8\t0\t34\n", "30\t32\t422.8\t0\t32\n", "31\t31\t422.8\t0\t31\n", "32\t33\t422.8\t0\t33\n", "33\t23\t422.8\t0\t23\n", "34\t26\t422.8\t0\t26\n", "35\t25\t422.8\t0\t25\n", "36\t32\t422.8\t0\t32\n", "37\t21\t422.8\t0\t21\n", "38\t25\t422.8\t0\t25\n", "39\t40\t422.8\t0\t40\n", "40\t33\t422.8\t0\t33\n", "41\t33\t422.8\t0\t33\n", "42\t37\t422.8\t0\t37\n", "43\t62\t422.8\t0\t62\n", "44\t37\t422.8\t0\t37\n", "45\t54\t422.8\t0\t54\n", "46\t50\t422.8\t0\t50\n", "47\t36\t422.8\t0\t36\n", "48\t43\t422.8\t0\t43\n", "49\t37\t422.8\t0\t37\n", "50\t22\t422.8\t0\t22\n", "51\t26\t422.8\t0\t26\n", "52\t45\t422.8\t0\t45\n", "53\t38\t422.8\t0\t38\n", "54\t33\t422.8\t0\t33\n", "55\t34\t422.8\t0\t34\n", "56\t37\t422.8\t0\t37\n", "57\t45\t422.8\t0\t45\n", "58\t39\t422.8\t0\t39\n", "59\t43\t422.8\t0\t43\n", "60\t49\t422.8\t0\t49\n", "61\t45\t422.8\t0\t45\n", "62\t44\t422.8\t0\t44\n", "63\t45\t422.8\t0\t45\n", "64\t51\t422.8\t0\t51\n", "65\t58\t422.8\t0\t58\n", "66\t44\t422.8\t0\t44\n", "67\t61\t422.8\t0\t61\n", "68\t24\t422.8\t0\t24\n", "69\t28\t422.8\t0\t28\n", "70\t38\t422.8\t0\t38\n", "71\t51\t422.8\t0\t51\n", "72\t75\t422.8\t0\t75\n", "73\t127\t422.8\t0\t127\n", "74\t135\t422.8\t0\t135\n", "75\t100\t422.8\t0\t100\n", "76\t119\t422.8\t0\t119\n", "77\t180\t422.8\t0\t180\n", "78\t104\t422.8\t0\t104\n", "79\t123\t422.8\t0\t123\n", "80\t117\t422.8\t0\t117\n", "81\t159\t422.8\t0\t159\n", "82\t230\t422.8\t0\t230\n", "83\t140\t422.8\t0\t140\n", "84\t115\t422.8\t0\t115\n", "85\t107\t422.8\t0\t107\n", "86\t68\t422.8\t0\t68\n", "87\t110\t422.8\t0\t110\n", "88\t93\t422.8\t0\t93\n", "89\t79\t422.8\t0\t79\n", "90\t73\t422.8\t0\t73\n", "91\t45\t422.8\t0\t45\n", "92\t34\t422.8\t0\t34\n", "93\t33\t422.8\t0\t33\n", "94\t54\t422.8\t0\t54\n", "95\t49\t422.8\t0\t49\n", "96\t50\t422.8\t0\t50\n", "97\t103\t422.8\t0\t103\n", "98\t108\t422.8\t0\t108\n", "99\t145\t422.8\t0\t145\n", "100\t193\t422.8\t0\t193\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 489_S35_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/489.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 93.00 s (13 us/read; 4.77 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,390,384\n", "Reads with adapters: 4,105,717 (55.6%)\n", "Reads written (passing filters): 7,259,955 (98.2%)\n", "\n", "Total basepairs processed: 739,038,400 bp\n", "Quality-trimmed: 1,686,169 bp (0.2%)\n", "Total written (filtered): 601,450,218 bp (81.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3922422 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.4%\n", " G: 42.9%\n", " T: 25.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t166763\t115474.8\t0\t166763\n", "4\t89653\t28868.7\t0\t89653\n", "5\t69086\t7217.2\t0\t69086\n", "6\t56971\t1804.3\t0\t56971\n", "7\t53745\t451.1\t0\t53745\n", "8\t53074\t112.8\t0\t53074\n", "9\t52854\t112.8\t0\t52854\n", "10\t52003\t112.8\t0\t52003\n", "11\t52839\t112.8\t0\t52839\n", "12\t54815\t112.8\t0\t54815\n", "13\t64595\t112.8\t0\t64595\n", "14\t64878\t112.8\t0\t64878\n", "15\t58304\t112.8\t0\t58304\n", "16\t59931\t112.8\t0\t59931\n", "17\t63580\t112.8\t0\t63580\n", "18\t73236\t112.8\t0\t73236\n", "19\t70635\t112.8\t0\t70635\n", "20\t58324\t112.8\t0\t58324\n", "21\t55356\t112.8\t0\t55356\n", "22\t49537\t112.8\t0\t49537\n", "23\t53343\t112.8\t0\t53343\n", "24\t62666\t112.8\t0\t62666\n", "25\t67454\t112.8\t0\t67454\n", "26\t73646\t112.8\t0\t73646\n", "27\t72181\t112.8\t0\t72181\n", "28\t67907\t112.8\t0\t67907\n", "29\t64376\t112.8\t0\t64376\n", "30\t65143\t112.8\t0\t65143\n", "31\t70355\t112.8\t0\t70355\n", "32\t69289\t112.8\t0\t69289\n", "33\t65047\t112.8\t0\t65047\n", "34\t64206\t112.8\t0\t64206\n", "35\t71561\t112.8\t0\t71561\n", "36\t81258\t112.8\t0\t81258\n", "37\t83939\t112.8\t0\t83939\n", "38\t66363\t112.8\t0\t66363\n", "39\t58246\t112.8\t0\t58246\n", "40\t55953\t112.8\t0\t55953\n", "41\t63657\t112.8\t0\t63657\n", "42\t72552\t112.8\t0\t72552\n", "43\t60719\t112.8\t0\t60719\n", "44\t46360\t112.8\t0\t46360\n", "45\t55328\t112.8\t0\t55328\n", "46\t63680\t112.8\t0\t63680\n", "47\t59784\t112.8\t0\t59784\n", "48\t57084\t112.8\t0\t57084\n", "49\t47403\t112.8\t0\t47403\n", "50\t45927\t112.8\t0\t45927\n", "51\t38897\t112.8\t0\t38897\n", "52\t38528\t112.8\t0\t38528\n", "53\t34842\t112.8\t0\t34842\n", "54\t41157\t112.8\t0\t41157\n", "55\t46708\t112.8\t0\t46708\n", "56\t44220\t112.8\t0\t44220\n", "57\t40240\t112.8\t0\t40240\n", "58\t42360\t112.8\t0\t42360\n", "59\t32477\t112.8\t0\t32477\n", "60\t27140\t112.8\t0\t27140\n", "61\t25032\t112.8\t0\t25032\n", "62\t21250\t112.8\t0\t21250\n", "63\t19612\t112.8\t0\t19612\n", "64\t21867\t112.8\t0\t21867\n", "65\t20772\t112.8\t0\t20772\n", "66\t17972\t112.8\t0\t17972\n", "67\t17926\t112.8\t0\t17926\n", "68\t17669\t112.8\t0\t17669\n", "69\t18516\t112.8\t0\t18516\n", "70\t19598\t112.8\t0\t19598\n", "71\t18428\t112.8\t0\t18428\n", "72\t14038\t112.8\t0\t14038\n", "73\t12117\t112.8\t0\t12117\n", "74\t11670\t112.8\t0\t11670\n", "75\t10415\t112.8\t0\t10415\n", "76\t8475\t112.8\t0\t8475\n", "77\t8035\t112.8\t0\t8035\n", "78\t9260\t112.8\t0\t9260\n", "79\t8633\t112.8\t0\t8633\n", "80\t8167\t112.8\t0\t8167\n", "81\t7880\t112.8\t0\t7880\n", "82\t7270\t112.8\t0\t7270\n", "83\t7753\t112.8\t0\t7753\n", "84\t8834\t112.8\t0\t8834\n", "85\t9783\t112.8\t0\t9783\n", "86\t8979\t112.8\t0\t8979\n", "87\t6554\t112.8\t0\t6554\n", "88\t6002\t112.8\t0\t6002\n", "89\t6187\t112.8\t0\t6187\n", "90\t6467\t112.8\t0\t6467\n", "91\t6701\t112.8\t0\t6701\n", "92\t7033\t112.8\t0\t7033\n", "93\t7413\t112.8\t0\t7413\n", "94\t7188\t112.8\t0\t7188\n", "95\t5969\t112.8\t0\t5969\n", "96\t4211\t112.8\t0\t4211\n", "97\t2747\t112.8\t0\t2747\n", "98\t1509\t112.8\t0\t1509\n", "99\t1470\t112.8\t0\t1470\n", "100\t845\t112.8\t0\t845\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 48702 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.2%\n", " C: 30.3%\n", " G: 0.0%\n", " T: 25.4%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t26109\t115474.8\t0\t26109\n", "4\t6621\t28868.7\t0\t6621\n", "5\t2292\t7217.2\t0\t2292\n", "6\t1702\t1804.3\t0\t1702\n", "7\t349\t451.1\t0\t349\n", "8\t239\t112.8\t0\t239\n", "9\t198\t112.8\t0\t198\n", "10\t187\t112.8\t0\t187\n", "11\t229\t112.8\t0\t229\n", "12\t180\t112.8\t0\t180\n", "13\t167\t112.8\t0\t167\n", "14\t179\t112.8\t0\t179\n", "15\t171\t112.8\t0\t171\n", "16\t170\t112.8\t0\t170\n", "17\t193\t112.8\t0\t193\n", "18\t206\t112.8\t0\t206\n", "19\t239\t112.8\t0\t239\n", "20\t253\t112.8\t0\t253\n", "21\t246\t112.8\t0\t246\n", "22\t186\t112.8\t0\t186\n", "23\t168\t112.8\t0\t168\n", "24\t173\t112.8\t0\t173\n", "25\t191\t112.8\t0\t191\n", "26\t281\t112.8\t0\t281\n", "27\t292\t112.8\t0\t292\n", "28\t257\t112.8\t0\t257\n", "29\t248\t112.8\t0\t248\n", "30\t416\t112.8\t0\t416\n", "31\t477\t112.8\t0\t477\n", "32\t648\t112.8\t0\t648\n", "33\t649\t112.8\t0\t649\n", "34\t639\t112.8\t0\t639\n", "35\t792\t112.8\t0\t792\n", "36\t718\t112.8\t0\t718\n", "37\t254\t112.8\t0\t254\n", "38\t70\t112.8\t0\t70\n", "39\t49\t112.8\t0\t49\n", "40\t67\t112.8\t0\t67\n", "41\t56\t112.8\t0\t56\n", "42\t37\t112.8\t0\t37\n", "43\t55\t112.8\t0\t55\n", "44\t52\t112.8\t0\t52\n", "45\t47\t112.8\t0\t47\n", "46\t53\t112.8\t0\t53\n", "47\t43\t112.8\t0\t43\n", "48\t46\t112.8\t0\t46\n", "49\t33\t112.8\t0\t33\n", "50\t48\t112.8\t0\t48\n", "51\t48\t112.8\t0\t48\n", "52\t53\t112.8\t0\t53\n", "53\t53\t112.8\t0\t53\n", "54\t39\t112.8\t0\t39\n", "55\t33\t112.8\t0\t33\n", "56\t37\t112.8\t0\t37\n", "57\t34\t112.8\t0\t34\n", "58\t37\t112.8\t0\t37\n", "59\t37\t112.8\t0\t37\n", "60\t24\t112.8\t0\t24\n", "61\t23\t112.8\t0\t23\n", "62\t27\t112.8\t0\t27\n", "63\t33\t112.8\t0\t33\n", "64\t35\t112.8\t0\t35\n", "65\t31\t112.8\t0\t31\n", "66\t25\t112.8\t0\t25\n", "67\t24\t112.8\t0\t24\n", "68\t22\t112.8\t0\t22\n", "69\t18\t112.8\t0\t18\n", "70\t26\t112.8\t0\t26\n", "71\t9\t112.8\t0\t9\n", "72\t14\t112.8\t0\t14\n", "73\t9\t112.8\t0\t9\n", "74\t8\t112.8\t0\t8\n", "75\t11\t112.8\t0\t11\n", "76\t13\t112.8\t0\t13\n", "77\t14\t112.8\t0\t14\n", "78\t9\t112.8\t0\t9\n", "79\t14\t112.8\t0\t14\n", "80\t21\t112.8\t0\t21\n", "81\t8\t112.8\t0\t8\n", "82\t15\t112.8\t0\t15\n", "83\t9\t112.8\t0\t9\n", "84\t17\t112.8\t0\t17\n", "85\t17\t112.8\t0\t17\n", "86\t17\t112.8\t0\t17\n", "87\t16\t112.8\t0\t16\n", "88\t10\t112.8\t0\t10\n", "89\t26\t112.8\t0\t26\n", "90\t17\t112.8\t0\t17\n", "91\t18\t112.8\t0\t18\n", "92\t35\t112.8\t0\t35\n", "93\t77\t112.8\t0\t77\n", "94\t87\t112.8\t0\t87\n", "95\t111\t112.8\t0\t111\n", "96\t85\t112.8\t0\t85\n", "97\t113\t112.8\t0\t113\n", "98\t87\t112.8\t0\t87\n", "99\t71\t112.8\t0\t71\n", "100\t110\t112.8\t0\t110\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 134593 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.3%\n", " C: 21.3%\n", " G: 19.8%\n", " T: 18.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t96719\t115474.8\t0\t96719\n", "4\t18206\t28868.7\t0\t18206\n", "5\t3277\t7217.2\t0\t3277\n", "6\t525\t1804.3\t0\t525\n", "7\t292\t451.1\t0\t292\n", "8\t350\t451.1\t0\t350\n", "9\t240\t451.1\t0\t240\n", "10\t333\t451.1\t0\t333\n", "11\t314\t451.1\t0\t314\n", "12\t344\t451.1\t0\t344\n", "13\t336\t451.1\t0\t336\n", "14\t337\t451.1\t0\t337\n", "15\t353\t451.1\t0\t353\n", "16\t322\t451.1\t0\t322\n", "17\t331\t451.1\t0\t331\n", "18\t291\t451.1\t0\t291\n", "19\t285\t451.1\t0\t285\n", "20\t278\t451.1\t0\t278\n", "21\t238\t451.1\t0\t238\n", "22\t256\t451.1\t0\t256\n", "23\t235\t451.1\t0\t235\n", "24\t240\t451.1\t0\t240\n", "25\t250\t451.1\t0\t250\n", "26\t237\t451.1\t0\t237\n", "27\t240\t451.1\t0\t240\n", "28\t212\t451.1\t0\t212\n", "29\t244\t451.1\t0\t244\n", "30\t211\t451.1\t0\t211\n", "31\t209\t451.1\t0\t209\n", "32\t233\t451.1\t0\t233\n", "33\t196\t451.1\t0\t196\n", "34\t186\t451.1\t0\t186\n", "35\t206\t451.1\t0\t206\n", "36\t202\t451.1\t0\t202\n", "37\t186\t451.1\t0\t186\n", "38\t176\t451.1\t0\t176\n", "39\t189\t451.1\t0\t189\n", "40\t211\t451.1\t0\t211\n", "41\t205\t451.1\t0\t205\n", "42\t148\t451.1\t0\t148\n", "43\t198\t451.1\t0\t198\n", "44\t88\t451.1\t0\t88\n", "45\t151\t451.1\t0\t151\n", "46\t152\t451.1\t0\t152\n", "47\t148\t451.1\t0\t148\n", "48\t148\t451.1\t0\t148\n", "49\t116\t451.1\t0\t116\n", "50\t115\t451.1\t0\t115\n", "51\t143\t451.1\t0\t143\n", "52\t151\t451.1\t0\t151\n", "53\t135\t451.1\t0\t135\n", "54\t126\t451.1\t0\t126\n", "55\t117\t451.1\t0\t117\n", "56\t125\t451.1\t0\t125\n", "57\t115\t451.1\t0\t115\n", "58\t121\t451.1\t0\t121\n", "59\t103\t451.1\t0\t103\n", "60\t92\t451.1\t0\t92\n", "61\t129\t451.1\t0\t129\n", "62\t118\t451.1\t0\t118\n", "63\t91\t451.1\t0\t91\n", "64\t101\t451.1\t0\t101\n", "65\t120\t451.1\t0\t120\n", "66\t120\t451.1\t0\t120\n", "67\t100\t451.1\t0\t100\n", "68\t109\t451.1\t0\t109\n", "69\t108\t451.1\t0\t108\n", "70\t102\t451.1\t0\t102\n", "71\t111\t451.1\t0\t111\n", "72\t122\t451.1\t0\t122\n", "73\t108\t451.1\t0\t108\n", "74\t97\t451.1\t0\t97\n", "75\t98\t451.1\t0\t98\n", "76\t107\t451.1\t0\t107\n", "77\t92\t451.1\t0\t92\n", "78\t112\t451.1\t0\t112\n", "79\t115\t451.1\t0\t115\n", "80\t115\t451.1\t0\t115\n", "81\t103\t451.1\t0\t103\n", "82\t147\t451.1\t0\t147\n", "83\t124\t451.1\t0\t124\n", "84\t112\t451.1\t0\t112\n", "85\t124\t451.1\t0\t124\n", "86\t120\t451.1\t0\t120\n", "87\t149\t451.1\t0\t149\n", "88\t137\t451.1\t0\t137\n", "89\t114\t451.1\t0\t114\n", "90\t116\t451.1\t0\t116\n", "91\t93\t451.1\t0\t93\n", "92\t80\t451.1\t0\t80\n", "93\t77\t451.1\t0\t77\n", "94\t112\t451.1\t0\t112\n", "95\t79\t451.1\t0\t79\n", "96\t77\t451.1\t0\t77\n", "97\t86\t451.1\t0\t86\n", "98\t80\t451.1\t0\t80\n", "99\t147\t451.1\t0\t147\n", "100\t154\t451.1\t0\t154\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 490_S19_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/490.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 78.58 s (13 us/read; 4.55 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,956,648\n", "Reads with adapters: 3,468,790 (58.2%)\n", "Reads written (passing filters): 5,790,529 (97.2%)\n", "\n", "Total basepairs processed: 595,664,800 bp\n", "Quality-trimmed: 1,540,181 bp (0.3%)\n", "Total written (filtered): 466,052,180 bp (78.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3319680 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.3%\n", " G: 39.1%\n", " T: 29.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t122602\t93072.6\t0\t122602\n", "4\t70316\t23268.2\t0\t70316\n", "5\t52469\t5817.0\t0\t52469\n", "6\t42332\t1454.3\t0\t42332\n", "7\t37325\t363.6\t0\t37325\n", "8\t37148\t90.9\t0\t37148\n", "9\t36552\t90.9\t0\t36552\n", "10\t35134\t90.9\t0\t35134\n", "11\t35643\t90.9\t0\t35643\n", "12\t35918\t90.9\t0\t35918\n", "13\t36941\t90.9\t0\t36941\n", "14\t38351\t90.9\t0\t38351\n", "15\t38705\t90.9\t0\t38705\n", "16\t39898\t90.9\t0\t39898\n", "17\t44588\t90.9\t0\t44588\n", "18\t51928\t90.9\t0\t51928\n", "19\t48803\t90.9\t0\t48803\n", "20\t39970\t90.9\t0\t39970\n", "21\t39965\t90.9\t0\t39965\n", "22\t36156\t90.9\t0\t36156\n", "23\t39341\t90.9\t0\t39341\n", "24\t46450\t90.9\t0\t46450\n", "25\t46988\t90.9\t0\t46988\n", "26\t54144\t90.9\t0\t54144\n", "27\t60965\t90.9\t0\t60965\n", "28\t55267\t90.9\t0\t55267\n", "29\t52970\t90.9\t0\t52970\n", "30\t54432\t90.9\t0\t54432\n", "31\t60519\t90.9\t0\t60519\n", "32\t59062\t90.9\t0\t59062\n", "33\t53888\t90.9\t0\t53888\n", "34\t49347\t90.9\t0\t49347\n", "35\t57574\t90.9\t0\t57574\n", "36\t67654\t90.9\t0\t67654\n", "37\t71376\t90.9\t0\t71376\n", "38\t58972\t90.9\t0\t58972\n", "39\t49878\t90.9\t0\t49878\n", "40\t46181\t90.9\t0\t46181\n", "41\t50835\t90.9\t0\t50835\n", "42\t57778\t90.9\t0\t57778\n", "43\t50227\t90.9\t0\t50227\n", "44\t39023\t90.9\t0\t39023\n", "45\t50778\t90.9\t0\t50778\n", "46\t61490\t90.9\t0\t61490\n", "47\t60726\t90.9\t0\t60726\n", "48\t60071\t90.9\t0\t60071\n", "49\t46021\t90.9\t0\t46021\n", "50\t44164\t90.9\t0\t44164\n", "51\t41569\t90.9\t0\t41569\n", "52\t45675\t90.9\t0\t45675\n", "53\t43654\t90.9\t0\t43654\n", "54\t41033\t90.9\t0\t41033\n", "55\t39188\t90.9\t0\t39188\n", "56\t34051\t90.9\t0\t34051\n", "57\t37887\t90.9\t0\t37887\n", "58\t47087\t90.9\t0\t47087\n", "59\t37014\t90.9\t0\t37014\n", "60\t28468\t90.9\t0\t28468\n", "61\t26351\t90.9\t0\t26351\n", "62\t22083\t90.9\t0\t22083\n", "63\t20959\t90.9\t0\t20959\n", "64\t24128\t90.9\t0\t24128\n", "65\t23251\t90.9\t0\t23251\n", "66\t20383\t90.9\t0\t20383\n", "67\t19927\t90.9\t0\t19927\n", "68\t19230\t90.9\t0\t19230\n", "69\t19765\t90.9\t0\t19765\n", "70\t20692\t90.9\t0\t20692\n", "71\t19804\t90.9\t0\t19804\n", "72\t15528\t90.9\t0\t15528\n", "73\t13925\t90.9\t0\t13925\n", "74\t14220\t90.9\t0\t14220\n", "75\t12155\t90.9\t0\t12155\n", "76\t9831\t90.9\t0\t9831\n", "77\t8982\t90.9\t0\t8982\n", "78\t10474\t90.9\t0\t10474\n", "79\t9903\t90.9\t0\t9903\n", "80\t9989\t90.9\t0\t9989\n", "81\t9328\t90.9\t0\t9328\n", "82\t8767\t90.9\t0\t8767\n", "83\t9203\t90.9\t0\t9203\n", "84\t10668\t90.9\t0\t10668\n", "85\t12334\t90.9\t0\t12334\n", "86\t11489\t90.9\t0\t11489\n", "87\t7964\t90.9\t0\t7964\n", "88\t7035\t90.9\t0\t7035\n", "89\t7923\t90.9\t0\t7923\n", "90\t8427\t90.9\t0\t8427\n", "91\t9213\t90.9\t0\t9213\n", "92\t9197\t90.9\t0\t9197\n", "93\t10294\t90.9\t0\t10294\n", "94\t9536\t90.9\t0\t9536\n", "95\t8219\t90.9\t0\t8219\n", "96\t6026\t90.9\t0\t6026\n", "97\t3816\t90.9\t0\t3816\n", "98\t2266\t90.9\t0\t2266\n", "99\t2481\t90.9\t0\t2481\n", "100\t1423\t90.9\t0\t1423\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 38285 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 63.3%\n", " C: 17.5%\n", " G: 0.0%\n", " T: 19.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t13088\t93072.6\t0\t13088\n", "4\t3014\t23268.2\t0\t3014\n", "5\t1104\t5817.0\t0\t1104\n", "6\t612\t1454.3\t0\t612\n", "7\t187\t363.6\t0\t187\n", "8\t142\t90.9\t0\t142\n", "9\t145\t90.9\t0\t145\n", "10\t130\t90.9\t0\t130\n", "11\t138\t90.9\t0\t138\n", "12\t130\t90.9\t0\t130\n", "13\t119\t90.9\t0\t119\n", "14\t124\t90.9\t0\t124\n", "15\t129\t90.9\t0\t129\n", "16\t131\t90.9\t0\t131\n", "17\t185\t90.9\t0\t185\n", "18\t237\t90.9\t0\t237\n", "19\t373\t90.9\t0\t373\n", "20\t643\t90.9\t0\t643\n", "21\t377\t90.9\t0\t377\n", "22\t230\t90.9\t0\t230\n", "23\t178\t90.9\t0\t178\n", "24\t176\t90.9\t0\t176\n", "25\t214\t90.9\t0\t214\n", "26\t354\t90.9\t0\t354\n", "27\t375\t90.9\t0\t375\n", "28\t442\t90.9\t0\t442\n", "29\t575\t90.9\t0\t575\n", "30\t951\t90.9\t0\t951\n", "31\t1091\t90.9\t0\t1091\n", "32\t1629\t90.9\t0\t1629\n", "33\t1635\t90.9\t0\t1635\n", "34\t1762\t90.9\t0\t1762\n", "35\t2473\t90.9\t0\t2473\n", "36\t2594\t90.9\t0\t2594\n", "37\t1003\t90.9\t0\t1003\n", "38\t70\t90.9\t0\t70\n", "39\t48\t90.9\t0\t48\n", "40\t43\t90.9\t0\t43\n", "41\t38\t90.9\t0\t38\n", "42\t42\t90.9\t0\t42\n", "43\t41\t90.9\t0\t41\n", "44\t28\t90.9\t0\t28\n", "45\t24\t90.9\t0\t24\n", "46\t37\t90.9\t0\t37\n", "47\t43\t90.9\t0\t43\n", "48\t24\t90.9\t0\t24\n", "49\t33\t90.9\t0\t33\n", "50\t26\t90.9\t0\t26\n", "51\t23\t90.9\t0\t23\n", "52\t37\t90.9\t0\t37\n", "53\t23\t90.9\t0\t23\n", "54\t27\t90.9\t0\t27\n", "55\t27\t90.9\t0\t27\n", "56\t22\t90.9\t0\t22\n", "57\t16\t90.9\t0\t16\n", "58\t22\t90.9\t0\t22\n", "59\t15\t90.9\t0\t15\n", "60\t24\t90.9\t0\t24\n", "61\t13\t90.9\t0\t13\n", "62\t16\t90.9\t0\t16\n", "63\t17\t90.9\t0\t17\n", "64\t22\t90.9\t0\t22\n", "65\t19\t90.9\t0\t19\n", "66\t22\t90.9\t0\t22\n", "67\t15\t90.9\t0\t15\n", "68\t17\t90.9\t0\t17\n", "69\t19\t90.9\t0\t19\n", "70\t6\t90.9\t0\t6\n", "71\t7\t90.9\t0\t7\n", "72\t6\t90.9\t0\t6\n", "73\t19\t90.9\t0\t19\n", "74\t10\t90.9\t0\t10\n", "75\t10\t90.9\t0\t10\n", "76\t5\t90.9\t0\t5\n", "77\t12\t90.9\t0\t12\n", "78\t10\t90.9\t0\t10\n", "79\t9\t90.9\t0\t9\n", "80\t8\t90.9\t0\t8\n", "81\t7\t90.9\t0\t7\n", "82\t6\t90.9\t0\t6\n", "83\t5\t90.9\t0\t5\n", "84\t10\t90.9\t0\t10\n", "85\t18\t90.9\t0\t18\n", "86\t6\t90.9\t0\t6\n", "87\t15\t90.9\t0\t15\n", "88\t6\t90.9\t0\t6\n", "89\t4\t90.9\t0\t4\n", "90\t10\t90.9\t0\t10\n", "91\t13\t90.9\t0\t13\n", "92\t28\t90.9\t0\t28\n", "93\t48\t90.9\t0\t48\n", "94\t77\t90.9\t0\t77\n", "95\t50\t90.9\t0\t50\n", "96\t68\t90.9\t0\t68\n", "97\t68\t90.9\t0\t68\n", "98\t40\t90.9\t0\t40\n", "99\t44\t90.9\t0\t44\n", "100\t77\t90.9\t0\t77\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 110825 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.9%\n", " C: 21.5%\n", " G: 15.8%\n", " T: 21.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t79917\t93072.6\t0\t79917\n", "4\t16414\t23268.2\t0\t16414\n", "5\t3264\t5817.0\t0\t3264\n", "6\t336\t1454.3\t0\t336\n", "7\t153\t363.6\t0\t153\n", "8\t189\t363.6\t0\t189\n", "9\t160\t363.6\t0\t160\n", "10\t172\t363.6\t0\t172\n", "11\t171\t363.6\t0\t171\n", "12\t190\t363.6\t0\t190\n", "13\t187\t363.6\t0\t187\n", "14\t167\t363.6\t0\t167\n", "15\t189\t363.6\t0\t189\n", "16\t174\t363.6\t0\t174\n", "17\t179\t363.6\t0\t179\n", "18\t144\t363.6\t0\t144\n", "19\t168\t363.6\t0\t168\n", "20\t185\t363.6\t0\t185\n", "21\t157\t363.6\t0\t157\n", "22\t167\t363.6\t0\t167\n", "23\t151\t363.6\t0\t151\n", "24\t142\t363.6\t0\t142\n", "25\t149\t363.6\t0\t149\n", "26\t138\t363.6\t0\t138\n", "27\t134\t363.6\t0\t134\n", "28\t169\t363.6\t0\t169\n", "29\t150\t363.6\t0\t150\n", "30\t161\t363.6\t0\t161\n", "31\t141\t363.6\t0\t141\n", "32\t146\t363.6\t0\t146\n", "33\t131\t363.6\t0\t131\n", "34\t138\t363.6\t0\t138\n", "35\t147\t363.6\t0\t147\n", "36\t150\t363.6\t0\t150\n", "37\t145\t363.6\t0\t145\n", "38\t120\t363.6\t0\t120\n", "39\t180\t363.6\t0\t180\n", "40\t183\t363.6\t0\t183\n", "41\t163\t363.6\t0\t163\n", "42\t120\t363.6\t0\t120\n", "43\t190\t363.6\t0\t190\n", "44\t86\t363.6\t0\t86\n", "45\t110\t363.6\t0\t110\n", "46\t129\t363.6\t0\t129\n", "47\t122\t363.6\t0\t122\n", "48\t108\t363.6\t0\t108\n", "49\t108\t363.6\t0\t108\n", "50\t95\t363.6\t0\t95\n", "51\t100\t363.6\t0\t100\n", "52\t106\t363.6\t0\t106\n", "53\t99\t363.6\t0\t99\n", "54\t95\t363.6\t0\t95\n", "55\t87\t363.6\t0\t87\n", "56\t112\t363.6\t0\t112\n", "57\t71\t363.6\t0\t71\n", "58\t81\t363.6\t0\t81\n", "59\t75\t363.6\t0\t75\n", "60\t79\t363.6\t0\t79\n", "61\t92\t363.6\t0\t92\n", "62\t91\t363.6\t0\t91\n", "63\t59\t363.6\t0\t59\n", "64\t75\t363.6\t0\t75\n", "65\t84\t363.6\t0\t84\n", "66\t63\t363.6\t0\t63\n", "67\t88\t363.6\t0\t88\n", "68\t81\t363.6\t0\t81\n", "69\t58\t363.6\t0\t58\n", "70\t78\t363.6\t0\t78\n", "71\t79\t363.6\t0\t79\n", "72\t80\t363.6\t0\t80\n", "73\t76\t363.6\t0\t76\n", "74\t84\t363.6\t0\t84\n", "75\t77\t363.6\t0\t77\n", "76\t91\t363.6\t0\t91\n", "77\t122\t363.6\t0\t122\n", "78\t90\t363.6\t0\t90\n", "79\t93\t363.6\t0\t93\n", "80\t121\t363.6\t0\t121\n", "81\t100\t363.6\t0\t100\n", "82\t146\t363.6\t0\t146\n", "83\t136\t363.6\t0\t136\n", "84\t92\t363.6\t0\t92\n", "85\t84\t363.6\t0\t84\n", "86\t68\t363.6\t0\t68\n", "87\t98\t363.6\t0\t98\n", "88\t105\t363.6\t0\t105\n", "89\t64\t363.6\t0\t64\n", "90\t92\t363.6\t0\t92\n", "91\t50\t363.6\t0\t50\n", "92\t45\t363.6\t0\t45\n", "93\t45\t363.6\t0\t45\n", "94\t72\t363.6\t0\t72\n", "95\t56\t363.6\t0\t56\n", "96\t63\t363.6\t0\t63\n", "97\t77\t363.6\t0\t77\n", "98\t69\t363.6\t0\t69\n", "99\t83\t363.6\t0\t83\n", "100\t104\t363.6\t0\t104\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 491_S50_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/491.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 84.74 s (13 us/read; 4.61 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,516,171\n", "Reads with adapters: 3,840,780 (58.9%)\n", "Reads written (passing filters): 6,417,993 (98.5%)\n", "\n", "Total basepairs processed: 651,617,100 bp\n", "Quality-trimmed: 1,542,262 bp (0.2%)\n", "Total written (filtered): 525,677,433 bp (80.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3740375 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 25.3%\n", " G: 33.0%\n", " T: 41.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t167873\t101815.2\t0\t167873\n", "4\t101294\t25453.8\t0\t101294\n", "5\t78459\t6363.4\t0\t78459\n", "6\t61457\t1590.9\t0\t61457\n", "7\t53972\t397.7\t0\t53972\n", "8\t50967\t99.4\t0\t50967\n", "9\t50308\t99.4\t0\t50308\n", "10\t47557\t99.4\t0\t47557\n", "11\t46915\t99.4\t0\t46915\n", "12\t46007\t99.4\t0\t46007\n", "13\t47405\t99.4\t0\t47405\n", "14\t49715\t99.4\t0\t49715\n", "15\t50682\t99.4\t0\t50682\n", "16\t52562\t99.4\t0\t52562\n", "17\t59371\t99.4\t0\t59371\n", "18\t68111\t99.4\t0\t68111\n", "19\t64302\t99.4\t0\t64302\n", "20\t55409\t99.4\t0\t55409\n", "21\t53737\t99.4\t0\t53737\n", "22\t48117\t99.4\t0\t48117\n", "23\t53251\t99.4\t0\t53251\n", "24\t63109\t99.4\t0\t63109\n", "25\t63762\t99.4\t0\t63762\n", "26\t72606\t99.4\t0\t72606\n", "27\t82843\t99.4\t0\t82843\n", "28\t76721\t99.4\t0\t76721\n", "29\t72125\t99.4\t0\t72125\n", "30\t74724\t99.4\t0\t74724\n", "31\t77347\t99.4\t0\t77347\n", "32\t74417\t99.4\t0\t74417\n", "33\t64764\t99.4\t0\t64764\n", "34\t62564\t99.4\t0\t62564\n", "35\t69617\t99.4\t0\t69617\n", "36\t84864\t99.4\t0\t84864\n", "37\t93515\t99.4\t0\t93515\n", "38\t73591\t99.4\t0\t73591\n", "39\t56401\t99.4\t0\t56401\n", "40\t51829\t99.4\t0\t51829\n", "41\t51057\t99.4\t0\t51057\n", "42\t54911\t99.4\t0\t54911\n", "43\t49124\t99.4\t0\t49124\n", "44\t41649\t99.4\t0\t41649\n", "45\t52096\t99.4\t0\t52096\n", "46\t62189\t99.4\t0\t62189\n", "47\t59775\t99.4\t0\t59775\n", "48\t63581\t99.4\t0\t63581\n", "49\t51467\t99.4\t0\t51467\n", "50\t44129\t99.4\t0\t44129\n", "51\t35352\t99.4\t0\t35352\n", "52\t32381\t99.4\t0\t32381\n", "53\t35239\t99.4\t0\t35239\n", "54\t43248\t99.4\t0\t43248\n", "55\t44321\t99.4\t0\t44321\n", "56\t35451\t99.4\t0\t35451\n", "57\t31962\t99.4\t0\t31962\n", "58\t40743\t99.4\t0\t40743\n", "59\t31013\t99.4\t0\t31013\n", "60\t25126\t99.4\t0\t25126\n", "61\t22743\t99.4\t0\t22743\n", "62\t18070\t99.4\t0\t18070\n", "63\t18101\t99.4\t0\t18101\n", "64\t19213\t99.4\t0\t19213\n", "65\t17479\t99.4\t0\t17479\n", "66\t14633\t99.4\t0\t14633\n", "67\t14221\t99.4\t0\t14221\n", "68\t13351\t99.4\t0\t13351\n", "69\t12971\t99.4\t0\t12971\n", "70\t14169\t99.4\t0\t14169\n", "71\t13339\t99.4\t0\t13339\n", "72\t10511\t99.4\t0\t10511\n", "73\t8833\t99.4\t0\t8833\n", "74\t8264\t99.4\t0\t8264\n", "75\t7188\t99.4\t0\t7188\n", "76\t5856\t99.4\t0\t5856\n", "77\t5646\t99.4\t0\t5646\n", "78\t6446\t99.4\t0\t6446\n", "79\t5905\t99.4\t0\t5905\n", "80\t5837\t99.4\t0\t5837\n", "81\t5562\t99.4\t0\t5562\n", "82\t5287\t99.4\t0\t5287\n", "83\t5714\t99.4\t0\t5714\n", "84\t6655\t99.4\t0\t6655\n", "85\t7763\t99.4\t0\t7763\n", "86\t7820\t99.4\t0\t7820\n", "87\t5889\t99.4\t0\t5889\n", "88\t5049\t99.4\t0\t5049\n", "89\t5308\t99.4\t0\t5308\n", "90\t5351\t99.4\t0\t5351\n", "91\t5071\t99.4\t0\t5071\n", "92\t4502\t99.4\t0\t4502\n", "93\t4600\t99.4\t0\t4600\n", "94\t4223\t99.4\t0\t4223\n", "95\t3616\t99.4\t0\t3616\n", "96\t2710\t99.4\t0\t2710\n", "97\t1873\t99.4\t0\t1873\n", "98\t1229\t99.4\t0\t1229\n", "99\t1193\t99.4\t0\t1193\n", "100\t1100\t99.4\t0\t1100\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 16637 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 62.0%\n", " C: 12.4%\n", " G: 0.0%\n", " T: 25.4%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t5638\t101815.2\t0\t5638\n", "4\t1398\t25453.8\t0\t1398\n", "5\t807\t6363.4\t0\t807\n", "6\t718\t1590.9\t0\t718\n", "7\t77\t397.7\t0\t77\n", "8\t56\t99.4\t0\t56\n", "9\t47\t99.4\t0\t47\n", "10\t44\t99.4\t0\t44\n", "11\t47\t99.4\t0\t47\n", "12\t46\t99.4\t0\t46\n", "13\t49\t99.4\t0\t49\n", "14\t44\t99.4\t0\t44\n", "15\t40\t99.4\t0\t40\n", "16\t43\t99.4\t0\t43\n", "17\t54\t99.4\t0\t54\n", "18\t57\t99.4\t0\t57\n", "19\t70\t99.4\t0\t70\n", "20\t97\t99.4\t0\t97\n", "21\t70\t99.4\t0\t70\n", "22\t71\t99.4\t0\t71\n", "23\t60\t99.4\t0\t60\n", "24\t63\t99.4\t0\t63\n", "25\t79\t99.4\t0\t79\n", "26\t121\t99.4\t0\t121\n", "27\t128\t99.4\t0\t128\n", "28\t130\t99.4\t0\t130\n", "29\t221\t99.4\t0\t221\n", "30\t357\t99.4\t0\t357\n", "31\t463\t99.4\t0\t463\n", "32\t681\t99.4\t0\t681\n", "33\t702\t99.4\t0\t702\n", "34\t782\t99.4\t0\t782\n", "35\t1017\t99.4\t0\t1017\n", "36\t1042\t99.4\t0\t1042\n", "37\t507\t99.4\t0\t507\n", "38\t114\t99.4\t0\t114\n", "39\t22\t99.4\t0\t22\n", "40\t13\t99.4\t0\t13\n", "41\t9\t99.4\t0\t9\n", "42\t15\t99.4\t0\t15\n", "43\t7\t99.4\t0\t7\n", "44\t6\t99.4\t0\t6\n", "45\t10\t99.4\t0\t10\n", "46\t13\t99.4\t0\t13\n", "47\t5\t99.4\t0\t5\n", "48\t7\t99.4\t0\t7\n", "49\t12\t99.4\t0\t12\n", "50\t8\t99.4\t0\t8\n", "51\t8\t99.4\t0\t8\n", "52\t6\t99.4\t0\t6\n", "53\t4\t99.4\t0\t4\n", "54\t5\t99.4\t0\t5\n", "55\t6\t99.4\t0\t6\n", "56\t7\t99.4\t0\t7\n", "57\t11\t99.4\t0\t11\n", "58\t3\t99.4\t0\t3\n", "59\t4\t99.4\t0\t4\n", "60\t3\t99.4\t0\t3\n", "61\t9\t99.4\t0\t9\n", "62\t7\t99.4\t0\t7\n", "63\t3\t99.4\t0\t3\n", "64\t2\t99.4\t0\t2\n", "65\t4\t99.4\t0\t4\n", "66\t1\t99.4\t0\t1\n", "67\t2\t99.4\t0\t2\n", "68\t1\t99.4\t0\t1\n", "70\t1\t99.4\t0\t1\n", "71\t1\t99.4\t0\t1\n", "72\t2\t99.4\t0\t2\n", "73\t1\t99.4\t0\t1\n", "74\t3\t99.4\t0\t3\n", "75\t1\t99.4\t0\t1\n", "76\t4\t99.4\t0\t4\n", "77\t1\t99.4\t0\t1\n", "78\t2\t99.4\t0\t2\n", "79\t4\t99.4\t0\t4\n", "80\t1\t99.4\t0\t1\n", "81\t3\t99.4\t0\t3\n", "82\t1\t99.4\t0\t1\n", "83\t1\t99.4\t0\t1\n", "84\t4\t99.4\t0\t4\n", "85\t1\t99.4\t0\t1\n", "86\t1\t99.4\t0\t1\n", "87\t4\t99.4\t0\t4\n", "88\t2\t99.4\t0\t2\n", "89\t2\t99.4\t0\t2\n", "90\t2\t99.4\t0\t2\n", "92\t10\t99.4\t0\t10\n", "93\t32\t99.4\t0\t32\n", "94\t72\t99.4\t0\t72\n", "95\t77\t99.4\t0\t77\n", "96\t47\t99.4\t0\t47\n", "97\t48\t99.4\t0\t48\n", "98\t27\t99.4\t0\t27\n", "99\t42\t99.4\t0\t42\n", "100\t87\t99.4\t0\t87\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 83768 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 47.5%\n", " C: 16.9%\n", " G: 10.5%\n", " T: 25.1%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t60992\t101815.2\t0\t60992\n", "4\t14913\t25453.8\t0\t14913\n", "5\t3070\t6363.4\t0\t3070\n", "6\t125\t1590.9\t0\t125\n", "7\t54\t397.7\t0\t54\n", "8\t60\t397.7\t0\t60\n", "9\t61\t397.7\t0\t61\n", "10\t69\t397.7\t0\t69\n", "11\t54\t397.7\t0\t54\n", "12\t75\t397.7\t0\t75\n", "13\t64\t397.7\t0\t64\n", "14\t37\t397.7\t0\t37\n", "15\t49\t397.7\t0\t49\n", "16\t32\t397.7\t0\t32\n", "17\t38\t397.7\t0\t38\n", "18\t39\t397.7\t0\t39\n", "19\t37\t397.7\t0\t37\n", "20\t51\t397.7\t0\t51\n", "21\t46\t397.7\t0\t46\n", "22\t43\t397.7\t0\t43\n", "23\t37\t397.7\t0\t37\n", "24\t31\t397.7\t0\t31\n", "25\t31\t397.7\t0\t31\n", "26\t27\t397.7\t0\t27\n", "27\t42\t397.7\t0\t42\n", "28\t40\t397.7\t0\t40\n", "29\t26\t397.7\t0\t26\n", "30\t46\t397.7\t0\t46\n", "31\t36\t397.7\t0\t36\n", "32\t37\t397.7\t0\t37\n", "33\t36\t397.7\t0\t36\n", "34\t48\t397.7\t0\t48\n", "35\t29\t397.7\t0\t29\n", "36\t36\t397.7\t0\t36\n", "37\t19\t397.7\t0\t19\n", "38\t45\t397.7\t0\t45\n", "39\t55\t397.7\t0\t55\n", "40\t36\t397.7\t0\t36\n", "41\t47\t397.7\t0\t47\n", "42\t32\t397.7\t0\t32\n", "43\t33\t397.7\t0\t33\n", "44\t36\t397.7\t0\t36\n", "45\t39\t397.7\t0\t39\n", "46\t48\t397.7\t0\t48\n", "47\t36\t397.7\t0\t36\n", "48\t50\t397.7\t0\t50\n", "49\t51\t397.7\t0\t51\n", "50\t39\t397.7\t0\t39\n", "51\t32\t397.7\t0\t32\n", "52\t46\t397.7\t0\t46\n", "53\t41\t397.7\t0\t41\n", "54\t30\t397.7\t0\t30\n", "55\t21\t397.7\t0\t21\n", "56\t21\t397.7\t0\t21\n", "57\t23\t397.7\t0\t23\n", "58\t31\t397.7\t0\t31\n", "59\t16\t397.7\t0\t16\n", "60\t31\t397.7\t0\t31\n", "61\t39\t397.7\t0\t39\n", "62\t32\t397.7\t0\t32\n", "63\t36\t397.7\t0\t36\n", "64\t36\t397.7\t0\t36\n", "65\t30\t397.7\t0\t30\n", "66\t38\t397.7\t0\t38\n", "67\t36\t397.7\t0\t36\n", "68\t23\t397.7\t0\t23\n", "69\t17\t397.7\t0\t17\n", "70\t29\t397.7\t0\t29\n", "71\t39\t397.7\t0\t39\n", "72\t53\t397.7\t0\t53\n", "73\t72\t397.7\t0\t72\n", "74\t112\t397.7\t0\t112\n", "75\t99\t397.7\t0\t99\n", "76\t88\t397.7\t0\t88\n", "77\t139\t397.7\t0\t139\n", "78\t58\t397.7\t0\t58\n", "79\t75\t397.7\t0\t75\n", "80\t77\t397.7\t0\t77\n", "81\t113\t397.7\t0\t113\n", "82\t124\t397.7\t0\t124\n", "83\t83\t397.7\t0\t83\n", "84\t97\t397.7\t0\t97\n", "85\t51\t397.7\t0\t51\n", "86\t56\t397.7\t0\t56\n", "87\t71\t397.7\t0\t71\n", "88\t66\t397.7\t0\t66\n", "89\t38\t397.7\t0\t38\n", "90\t32\t397.7\t0\t32\n", "91\t23\t397.7\t0\t23\n", "92\t34\t397.7\t0\t34\n", "93\t27\t397.7\t0\t27\n", "94\t44\t397.7\t0\t44\n", "95\t39\t397.7\t0\t39\n", "96\t37\t397.7\t0\t37\n", "97\t75\t397.7\t0\t75\n", "98\t91\t397.7\t0\t91\n", "99\t125\t397.7\t0\t125\n", "100\t145\t397.7\t0\t145\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 492_S40_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/492.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 104.98 s (13 us/read; 4.56 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,972,788\n", "Reads with adapters: 5,462,135 (68.5%)\n", "Reads written (passing filters): 7,797,298 (97.8%)\n", "\n", "Total basepairs processed: 797,278,800 bp\n", "Quality-trimmed: 2,506,567 bp (0.3%)\n", "Total written (filtered): 593,775,944 bp (74.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5335144 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.9%\n", " G: 35.5%\n", " T: 35.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t166190\t124574.8\t0\t166190\n", "4\t99526\t31143.7\t0\t99526\n", "5\t80151\t7785.9\t0\t80151\n", "6\t64176\t1946.5\t0\t64176\n", "7\t59081\t486.6\t0\t59081\n", "8\t60943\t121.7\t0\t60943\n", "9\t59551\t121.7\t0\t59551\n", "10\t55705\t121.7\t0\t55705\n", "11\t56765\t121.7\t0\t56765\n", "12\t56946\t121.7\t0\t56946\n", "13\t59321\t121.7\t0\t59321\n", "14\t61286\t121.7\t0\t61286\n", "15\t62400\t121.7\t0\t62400\n", "16\t66547\t121.7\t0\t66547\n", "17\t75252\t121.7\t0\t75252\n", "18\t87480\t121.7\t0\t87480\n", "19\t79400\t121.7\t0\t79400\n", "20\t67145\t121.7\t0\t67145\n", "21\t63151\t121.7\t0\t63151\n", "22\t57886\t121.7\t0\t57886\n", "23\t64971\t121.7\t0\t64971\n", "24\t75442\t121.7\t0\t75442\n", "25\t77369\t121.7\t0\t77369\n", "26\t88359\t121.7\t0\t88359\n", "27\t101760\t121.7\t0\t101760\n", "28\t93357\t121.7\t0\t93357\n", "29\t88910\t121.7\t0\t88910\n", "30\t94881\t121.7\t0\t94881\n", "31\t102142\t121.7\t0\t102142\n", "32\t96645\t121.7\t0\t96645\n", "33\t89575\t121.7\t0\t89575\n", "34\t84974\t121.7\t0\t84974\n", "35\t99480\t121.7\t0\t99480\n", "36\t121499\t121.7\t0\t121499\n", "37\t119523\t121.7\t0\t119523\n", "38\t103625\t121.7\t0\t103625\n", "39\t80188\t121.7\t0\t80188\n", "40\t78027\t121.7\t0\t78027\n", "41\t80723\t121.7\t0\t80723\n", "42\t89143\t121.7\t0\t89143\n", "43\t79479\t121.7\t0\t79479\n", "44\t66281\t121.7\t0\t66281\n", "45\t86154\t121.7\t0\t86154\n", "46\t104062\t121.7\t0\t104062\n", "47\t99365\t121.7\t0\t99365\n", "48\t98170\t121.7\t0\t98170\n", "49\t74731\t121.7\t0\t74731\n", "50\t69129\t121.7\t0\t69129\n", "51\t65545\t121.7\t0\t65545\n", "52\t62300\t121.7\t0\t62300\n", "53\t71860\t121.7\t0\t71860\n", "54\t83639\t121.7\t0\t83639\n", "55\t70510\t121.7\t0\t70510\n", "56\t66072\t121.7\t0\t66072\n", "57\t63781\t121.7\t0\t63781\n", "58\t70301\t121.7\t0\t70301\n", "59\t62349\t121.7\t0\t62349\n", "60\t49930\t121.7\t0\t49930\n", "61\t46898\t121.7\t0\t46898\n", "62\t38830\t121.7\t0\t38830\n", "63\t40796\t121.7\t0\t40796\n", "64\t46223\t121.7\t0\t46223\n", "65\t40143\t121.7\t0\t40143\n", "66\t33112\t121.7\t0\t33112\n", "67\t33657\t121.7\t0\t33657\n", "68\t32317\t121.7\t0\t32317\n", "69\t33573\t121.7\t0\t33573\n", "70\t37725\t121.7\t0\t37725\n", "71\t34238\t121.7\t0\t34238\n", "72\t24939\t121.7\t0\t24939\n", "73\t19214\t121.7\t0\t19214\n", "74\t17539\t121.7\t0\t17539\n", "75\t15581\t121.7\t0\t15581\n", "76\t12512\t121.7\t0\t12512\n", "77\t13660\t121.7\t0\t13660\n", "78\t16664\t121.7\t0\t16664\n", "79\t13514\t121.7\t0\t13514\n", "80\t12101\t121.7\t0\t12101\n", "81\t11783\t121.7\t0\t11783\n", "82\t10928\t121.7\t0\t10928\n", "83\t10895\t121.7\t0\t10895\n", "84\t13042\t121.7\t0\t13042\n", "85\t15514\t121.7\t0\t15514\n", "86\t14751\t121.7\t0\t14751\n", "87\t9929\t121.7\t0\t9929\n", "88\t8080\t121.7\t0\t8080\n", "89\t8256\t121.7\t0\t8256\n", "90\t8790\t121.7\t0\t8790\n", "91\t8257\t121.7\t0\t8257\n", "92\t7556\t121.7\t0\t7556\n", "93\t7174\t121.7\t0\t7174\n", "94\t6605\t121.7\t0\t6605\n", "95\t5371\t121.7\t0\t5371\n", "96\t3986\t121.7\t0\t3986\n", "97\t2730\t121.7\t0\t2730\n", "98\t1816\t121.7\t0\t1816\n", "99\t1894\t121.7\t0\t1894\n", "100\t1398\t121.7\t0\t1398\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 21913 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 65.4%\n", " C: 12.6%\n", " G: 0.0%\n", " T: 21.9%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t7716\t124574.8\t0\t7716\n", "4\t1885\t31143.7\t0\t1885\n", "5\t493\t7785.9\t0\t493\n", "6\t298\t1946.5\t0\t298\n", "7\t163\t486.6\t0\t163\n", "8\t126\t121.7\t0\t126\n", "9\t110\t121.7\t0\t110\n", "10\t106\t121.7\t0\t106\n", "11\t100\t121.7\t0\t100\n", "12\t118\t121.7\t0\t118\n", "13\t79\t121.7\t0\t79\n", "14\t89\t121.7\t0\t89\n", "15\t89\t121.7\t0\t89\n", "16\t96\t121.7\t0\t96\n", "17\t99\t121.7\t0\t99\n", "18\t123\t121.7\t0\t123\n", "19\t170\t121.7\t0\t170\n", "20\t184\t121.7\t0\t184\n", "21\t142\t121.7\t0\t142\n", "22\t132\t121.7\t0\t132\n", "23\t122\t121.7\t0\t122\n", "24\t114\t121.7\t0\t114\n", "25\t121\t121.7\t0\t121\n", "26\t200\t121.7\t0\t200\n", "27\t206\t121.7\t0\t206\n", "28\t232\t121.7\t0\t232\n", "29\t275\t121.7\t0\t275\n", "30\t418\t121.7\t0\t418\n", "31\t504\t121.7\t0\t504\n", "32\t798\t121.7\t0\t798\n", "33\t940\t121.7\t0\t940\n", "34\t1046\t121.7\t0\t1046\n", "35\t1248\t121.7\t0\t1248\n", "36\t1280\t121.7\t0\t1280\n", "37\t902\t121.7\t0\t902\n", "38\t402\t121.7\t0\t402\n", "39\t33\t121.7\t0\t33\n", "40\t18\t121.7\t0\t18\n", "41\t23\t121.7\t0\t23\n", "42\t13\t121.7\t0\t13\n", "43\t22\t121.7\t0\t22\n", "44\t15\t121.7\t0\t15\n", "45\t19\t121.7\t0\t19\n", "46\t17\t121.7\t0\t17\n", "47\t9\t121.7\t0\t9\n", "48\t26\t121.7\t0\t26\n", "49\t14\t121.7\t0\t14\n", "50\t11\t121.7\t0\t11\n", "51\t17\t121.7\t0\t17\n", "52\t12\t121.7\t0\t12\n", "53\t10\t121.7\t0\t10\n", "54\t19\t121.7\t0\t19\n", "55\t6\t121.7\t0\t6\n", "56\t7\t121.7\t0\t7\n", "57\t8\t121.7\t0\t8\n", "58\t11\t121.7\t0\t11\n", "59\t8\t121.7\t0\t8\n", "60\t6\t121.7\t0\t6\n", "61\t11\t121.7\t0\t11\n", "62\t10\t121.7\t0\t10\n", "63\t8\t121.7\t0\t8\n", "64\t5\t121.7\t0\t5\n", "65\t12\t121.7\t0\t12\n", "66\t7\t121.7\t0\t7\n", "67\t1\t121.7\t0\t1\n", "68\t9\t121.7\t0\t9\n", "69\t8\t121.7\t0\t8\n", "70\t6\t121.7\t0\t6\n", "71\t4\t121.7\t0\t4\n", "72\t5\t121.7\t0\t5\n", "73\t3\t121.7\t0\t3\n", "74\t2\t121.7\t0\t2\n", "75\t2\t121.7\t0\t2\n", "77\t2\t121.7\t0\t2\n", "78\t5\t121.7\t0\t5\n", "79\t1\t121.7\t0\t1\n", "80\t5\t121.7\t0\t5\n", "81\t5\t121.7\t0\t5\n", "82\t3\t121.7\t0\t3\n", "84\t2\t121.7\t0\t2\n", "85\t3\t121.7\t0\t3\n", "86\t2\t121.7\t0\t2\n", "87\t4\t121.7\t0\t4\n", "88\t5\t121.7\t0\t5\n", "89\t3\t121.7\t0\t3\n", "90\t5\t121.7\t0\t5\n", "91\t11\t121.7\t0\t11\n", "92\t7\t121.7\t0\t7\n", "93\t22\t121.7\t0\t22\n", "94\t47\t121.7\t0\t47\n", "95\t46\t121.7\t0\t46\n", "96\t47\t121.7\t0\t47\n", "97\t32\t121.7\t0\t32\n", "98\t26\t121.7\t0\t26\n", "99\t32\t121.7\t0\t32\n", "100\t55\t121.7\t0\t55\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 105078 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.9%\n", " C: 14.8%\n", " G: 12.3%\n", " T: 26.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t71808\t124574.8\t0\t71808\n", "4\t19403\t31143.7\t0\t19403\n", "5\t3436\t7785.9\t0\t3436\n", "6\t234\t1946.5\t0\t234\n", "7\t112\t486.6\t0\t112\n", "8\t152\t486.6\t0\t152\n", "9\t110\t486.6\t0\t110\n", "10\t110\t486.6\t0\t110\n", "11\t112\t486.6\t0\t112\n", "12\t129\t486.6\t0\t129\n", "13\t133\t486.6\t0\t133\n", "14\t115\t486.6\t0\t115\n", "15\t129\t486.6\t0\t129\n", "16\t118\t486.6\t0\t118\n", "17\t110\t486.6\t0\t110\n", "18\t130\t486.6\t0\t130\n", "19\t108\t486.6\t0\t108\n", "20\t98\t486.6\t0\t98\n", "21\t85\t486.6\t0\t85\n", "22\t117\t486.6\t0\t117\n", "23\t93\t486.6\t0\t93\n", "24\t89\t486.6\t0\t89\n", "25\t76\t486.6\t0\t76\n", "26\t98\t486.6\t0\t98\n", "27\t105\t486.6\t0\t105\n", "28\t106\t486.6\t0\t106\n", "29\t90\t486.6\t0\t90\n", "30\t110\t486.6\t0\t110\n", "31\t102\t486.6\t0\t102\n", "32\t129\t486.6\t0\t129\n", "33\t118\t486.6\t0\t118\n", "34\t98\t486.6\t0\t98\n", "35\t121\t486.6\t0\t121\n", "36\t102\t486.6\t0\t102\n", "37\t89\t486.6\t0\t89\n", "38\t96\t486.6\t0\t96\n", "39\t123\t486.6\t0\t123\n", "40\t146\t486.6\t0\t146\n", "41\t138\t486.6\t0\t138\n", "42\t112\t486.6\t0\t112\n", "43\t114\t486.6\t0\t114\n", "44\t82\t486.6\t0\t82\n", "45\t120\t486.6\t0\t120\n", "46\t135\t486.6\t0\t135\n", "47\t125\t486.6\t0\t125\n", "48\t94\t486.6\t0\t94\n", "49\t87\t486.6\t0\t87\n", "50\t72\t486.6\t0\t72\n", "51\t67\t486.6\t0\t67\n", "52\t106\t486.6\t0\t106\n", "53\t116\t486.6\t0\t116\n", "54\t84\t486.6\t0\t84\n", "55\t92\t486.6\t0\t92\n", "56\t89\t486.6\t0\t89\n", "57\t116\t486.6\t0\t116\n", "58\t103\t486.6\t0\t103\n", "59\t71\t486.6\t0\t71\n", "60\t109\t486.6\t0\t109\n", "61\t109\t486.6\t0\t109\n", "62\t101\t486.6\t0\t101\n", "63\t119\t486.6\t0\t119\n", "64\t107\t486.6\t0\t107\n", "65\t72\t486.6\t0\t72\n", "66\t72\t486.6\t0\t72\n", "67\t69\t486.6\t0\t69\n", "68\t76\t486.6\t0\t76\n", "69\t47\t486.6\t0\t47\n", "70\t61\t486.6\t0\t61\n", "71\t61\t486.6\t0\t61\n", "72\t111\t486.6\t0\t111\n", "73\t159\t486.6\t0\t159\n", "74\t179\t486.6\t0\t179\n", "75\t94\t486.6\t0\t94\n", "76\t124\t486.6\t0\t124\n", "77\t175\t486.6\t0\t175\n", "78\t116\t486.6\t0\t116\n", "79\t145\t486.6\t0\t145\n", "80\t170\t486.6\t0\t170\n", "81\t166\t486.6\t0\t166\n", "82\t278\t486.6\t0\t278\n", "83\t197\t486.6\t0\t197\n", "84\t124\t486.6\t0\t124\n", "85\t135\t486.6\t0\t135\n", "86\t79\t486.6\t0\t79\n", "87\t166\t486.6\t0\t166\n", "88\t151\t486.6\t0\t151\n", "89\t95\t486.6\t0\t95\n", "90\t67\t486.6\t0\t67\n", "91\t58\t486.6\t0\t58\n", "92\t48\t486.6\t0\t48\n", "93\t36\t486.6\t0\t36\n", "94\t45\t486.6\t0\t45\n", "95\t58\t486.6\t0\t58\n", "96\t67\t486.6\t0\t67\n", "97\t96\t486.6\t0\t96\n", "98\t107\t486.6\t0\t107\n", "99\t129\t486.6\t0\t129\n", "100\t137\t486.6\t0\t137\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 506_S47_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/506.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 82.38 s (14 us/read; 4.28 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,879,831\n", "Reads with adapters: 4,182,759 (71.1%)\n", "Reads written (passing filters): 5,742,555 (97.7%)\n", "\n", "Total basepairs processed: 587,983,100 bp\n", "Quality-trimmed: 2,010,954 bp (0.3%)\n", "Total written (filtered): 428,971,125 bp (73.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4113710 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 25.3%\n", " G: 40.7%\n", " T: 34.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t115158\t91872.4\t0\t115158\n", "4\t72029\t22968.1\t0\t72029\n", "5\t60734\t5742.0\t0\t60734\n", "6\t44503\t1435.5\t0\t44503\n", "7\t42113\t358.9\t0\t42113\n", "8\t45062\t89.7\t0\t45062\n", "9\t44351\t89.7\t0\t44351\n", "10\t39276\t89.7\t0\t39276\n", "11\t39053\t89.7\t0\t39053\n", "12\t36964\t89.7\t0\t36964\n", "13\t37774\t89.7\t0\t37774\n", "14\t39558\t89.7\t0\t39558\n", "15\t41242\t89.7\t0\t41242\n", "16\t44377\t89.7\t0\t44377\n", "17\t51763\t89.7\t0\t51763\n", "18\t64787\t89.7\t0\t64787\n", "19\t62299\t89.7\t0\t62299\n", "20\t53789\t89.7\t0\t53789\n", "21\t50338\t89.7\t0\t50338\n", "22\t44514\t89.7\t0\t44514\n", "23\t48636\t89.7\t0\t48636\n", "24\t58778\t89.7\t0\t58778\n", "25\t59901\t89.7\t0\t59901\n", "26\t68165\t89.7\t0\t68165\n", "27\t80513\t89.7\t0\t80513\n", "28\t76076\t89.7\t0\t76076\n", "29\t76214\t89.7\t0\t76214\n", "30\t81953\t89.7\t0\t81953\n", "31\t85299\t89.7\t0\t85299\n", "32\t78551\t89.7\t0\t78551\n", "33\t70546\t89.7\t0\t70546\n", "34\t65257\t89.7\t0\t65257\n", "35\t73821\t89.7\t0\t73821\n", "36\t91620\t89.7\t0\t91620\n", "37\t95798\t89.7\t0\t95798\n", "38\t80380\t89.7\t0\t80380\n", "39\t64704\t89.7\t0\t64704\n", "40\t59771\t89.7\t0\t59771\n", "41\t58576\t89.7\t0\t58576\n", "42\t64247\t89.7\t0\t64247\n", "43\t56219\t89.7\t0\t56219\n", "44\t47515\t89.7\t0\t47515\n", "45\t64675\t89.7\t0\t64675\n", "46\t82683\t89.7\t0\t82683\n", "47\t85401\t89.7\t0\t85401\n", "48\t93228\t89.7\t0\t93228\n", "49\t76000\t89.7\t0\t76000\n", "50\t62799\t89.7\t0\t62799\n", "51\t52902\t89.7\t0\t52902\n", "52\t54177\t89.7\t0\t54177\n", "53\t61468\t89.7\t0\t61468\n", "54\t60668\t89.7\t0\t60668\n", "55\t60947\t89.7\t0\t60947\n", "56\t46165\t89.7\t0\t46165\n", "57\t45444\t89.7\t0\t45444\n", "58\t60417\t89.7\t0\t60417\n", "59\t48974\t89.7\t0\t48974\n", "60\t39593\t89.7\t0\t39593\n", "61\t36081\t89.7\t0\t36081\n", "62\t29344\t89.7\t0\t29344\n", "63\t31691\t89.7\t0\t31691\n", "64\t36430\t89.7\t0\t36430\n", "65\t29651\t89.7\t0\t29651\n", "66\t24782\t89.7\t0\t24782\n", "67\t25659\t89.7\t0\t25659\n", "68\t23303\t89.7\t0\t23303\n", "69\t24507\t89.7\t0\t24507\n", "70\t28997\t89.7\t0\t28997\n", "71\t25880\t89.7\t0\t25880\n", "72\t19482\t89.7\t0\t19482\n", "73\t13675\t89.7\t0\t13675\n", "74\t12084\t89.7\t0\t12084\n", "75\t10750\t89.7\t0\t10750\n", "76\t9120\t89.7\t0\t9120\n", "77\t10290\t89.7\t0\t10290\n", "78\t12918\t89.7\t0\t12918\n", "79\t10154\t89.7\t0\t10154\n", "80\t9291\t89.7\t0\t9291\n", "81\t9200\t89.7\t0\t9200\n", "82\t8286\t89.7\t0\t8286\n", "83\t7970\t89.7\t0\t7970\n", "84\t9915\t89.7\t0\t9915\n", "85\t12496\t89.7\t0\t12496\n", "86\t12164\t89.7\t0\t12164\n", "87\t8573\t89.7\t0\t8573\n", "88\t6682\t89.7\t0\t6682\n", "89\t6899\t89.7\t0\t6899\n", "90\t7081\t89.7\t0\t7081\n", "91\t6262\t89.7\t0\t6262\n", "92\t5591\t89.7\t0\t5591\n", "93\t4995\t89.7\t0\t4995\n", "94\t4441\t89.7\t0\t4441\n", "95\t3756\t89.7\t0\t3756\n", "96\t2550\t89.7\t0\t2550\n", "97\t1850\t89.7\t0\t1850\n", "98\t1153\t89.7\t0\t1153\n", "99\t1115\t89.7\t0\t1115\n", "100\t877\t89.7\t0\t877\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 9922 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 71.4%\n", " C: 9.4%\n", " G: 0.0%\n", " T: 18.9%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t2646\t91872.4\t0\t2646\n", "4\t687\t22968.1\t0\t687\n", "5\t217\t5742.0\t0\t217\n", "6\t164\t1435.5\t0\t164\n", "7\t79\t358.9\t0\t79\n", "8\t47\t89.7\t0\t47\n", "9\t35\t89.7\t0\t35\n", "10\t38\t89.7\t0\t38\n", "11\t47\t89.7\t0\t47\n", "12\t40\t89.7\t0\t40\n", "13\t47\t89.7\t0\t47\n", "14\t41\t89.7\t0\t41\n", "15\t40\t89.7\t0\t40\n", "16\t36\t89.7\t0\t36\n", "17\t45\t89.7\t0\t45\n", "18\t63\t89.7\t0\t63\n", "19\t83\t89.7\t0\t83\n", "20\t104\t89.7\t0\t104\n", "21\t73\t89.7\t0\t73\n", "22\t63\t89.7\t0\t63\n", "23\t51\t89.7\t0\t51\n", "24\t65\t89.7\t0\t65\n", "25\t86\t89.7\t0\t86\n", "26\t80\t89.7\t0\t80\n", "27\t103\t89.7\t0\t103\n", "28\t130\t89.7\t0\t130\n", "29\t194\t89.7\t0\t194\n", "30\t353\t89.7\t0\t353\n", "31\t395\t89.7\t0\t395\n", "32\t546\t89.7\t0\t546\n", "33\t573\t89.7\t0\t573\n", "34\t699\t89.7\t0\t699\n", "35\t891\t89.7\t0\t891\n", "36\t700\t89.7\t0\t700\n", "37\t188\t89.7\t0\t188\n", "38\t12\t89.7\t0\t12\n", "39\t6\t89.7\t0\t6\n", "40\t6\t89.7\t0\t6\n", "41\t7\t89.7\t0\t7\n", "42\t5\t89.7\t0\t5\n", "43\t6\t89.7\t0\t6\n", "44\t1\t89.7\t0\t1\n", "45\t4\t89.7\t0\t4\n", "46\t4\t89.7\t0\t4\n", "47\t3\t89.7\t0\t3\n", "48\t3\t89.7\t0\t3\n", "49\t3\t89.7\t0\t3\n", "50\t1\t89.7\t0\t1\n", "51\t3\t89.7\t0\t3\n", "53\t1\t89.7\t0\t1\n", "54\t2\t89.7\t0\t2\n", "55\t1\t89.7\t0\t1\n", "56\t1\t89.7\t0\t1\n", "57\t2\t89.7\t0\t2\n", "58\t2\t89.7\t0\t2\n", "60\t2\t89.7\t0\t2\n", "62\t1\t89.7\t0\t1\n", "63\t2\t89.7\t0\t2\n", "64\t1\t89.7\t0\t1\n", "66\t1\t89.7\t0\t1\n", "68\t2\t89.7\t0\t2\n", "70\t2\t89.7\t0\t2\n", "75\t1\t89.7\t0\t1\n", "82\t1\t89.7\t0\t1\n", "84\t1\t89.7\t0\t1\n", "86\t3\t89.7\t0\t3\n", "89\t1\t89.7\t0\t1\n", "91\t1\t89.7\t0\t1\n", "92\t2\t89.7\t0\t2\n", "93\t19\t89.7\t0\t19\n", "94\t47\t89.7\t0\t47\n", "95\t31\t89.7\t0\t31\n", "96\t13\t89.7\t0\t13\n", "97\t16\t89.7\t0\t16\n", "98\t10\t89.7\t0\t10\n", "99\t12\t89.7\t0\t12\n", "100\t31\t89.7\t0\t31\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 59127 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 54.8%\n", " C: 9.5%\n", " G: 8.6%\n", " T: 27.0%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t38622\t91872.4\t0\t38622\n", "4\t13424\t22968.1\t0\t13424\n", "5\t4140\t5742.0\t0\t4140\n", "6\t55\t1435.5\t0\t55\n", "7\t29\t358.9\t0\t29\n", "8\t23\t358.9\t0\t23\n", "9\t13\t358.9\t0\t13\n", "10\t28\t358.9\t0\t28\n", "11\t21\t358.9\t0\t21\n", "12\t21\t358.9\t0\t21\n", "13\t24\t358.9\t0\t24\n", "14\t21\t358.9\t0\t21\n", "15\t19\t358.9\t0\t19\n", "16\t22\t358.9\t0\t22\n", "17\t26\t358.9\t0\t26\n", "18\t27\t358.9\t0\t27\n", "19\t20\t358.9\t0\t20\n", "20\t31\t358.9\t0\t31\n", "21\t16\t358.9\t0\t16\n", "22\t23\t358.9\t0\t23\n", "23\t15\t358.9\t0\t15\n", "24\t19\t358.9\t0\t19\n", "25\t16\t358.9\t0\t16\n", "26\t15\t358.9\t0\t15\n", "27\t32\t358.9\t0\t32\n", "28\t24\t358.9\t0\t24\n", "29\t16\t358.9\t0\t16\n", "30\t15\t358.9\t0\t15\n", "31\t17\t358.9\t0\t17\n", "32\t23\t358.9\t0\t23\n", "33\t20\t358.9\t0\t20\n", "34\t21\t358.9\t0\t21\n", "35\t15\t358.9\t0\t15\n", "36\t16\t358.9\t0\t16\n", "37\t16\t358.9\t0\t16\n", "38\t17\t358.9\t0\t17\n", "39\t20\t358.9\t0\t20\n", "40\t28\t358.9\t0\t28\n", "41\t19\t358.9\t0\t19\n", "42\t20\t358.9\t0\t20\n", "43\t25\t358.9\t0\t25\n", "44\t10\t358.9\t0\t10\n", "45\t29\t358.9\t0\t29\n", "46\t26\t358.9\t0\t26\n", "47\t22\t358.9\t0\t22\n", "48\t16\t358.9\t0\t16\n", "49\t35\t358.9\t0\t35\n", "50\t22\t358.9\t0\t22\n", "51\t23\t358.9\t0\t23\n", "52\t26\t358.9\t0\t26\n", "53\t24\t358.9\t0\t24\n", "54\t13\t358.9\t0\t13\n", "55\t17\t358.9\t0\t17\n", "56\t15\t358.9\t0\t15\n", "57\t19\t358.9\t0\t19\n", "58\t12\t358.9\t0\t12\n", "59\t8\t358.9\t0\t8\n", "60\t11\t358.9\t0\t11\n", "61\t23\t358.9\t0\t23\n", "62\t12\t358.9\t0\t12\n", "63\t17\t358.9\t0\t17\n", "64\t20\t358.9\t0\t20\n", "65\t19\t358.9\t0\t19\n", "66\t10\t358.9\t0\t10\n", "67\t12\t358.9\t0\t12\n", "68\t20\t358.9\t0\t20\n", "69\t25\t358.9\t0\t25\n", "70\t17\t358.9\t0\t17\n", "71\t26\t358.9\t0\t26\n", "72\t37\t358.9\t0\t37\n", "73\t71\t358.9\t0\t71\n", "74\t61\t358.9\t0\t61\n", "75\t26\t358.9\t0\t26\n", "76\t53\t358.9\t0\t53\n", "77\t48\t358.9\t0\t48\n", "78\t53\t358.9\t0\t53\n", "79\t53\t358.9\t0\t53\n", "80\t45\t358.9\t0\t45\n", "81\t49\t358.9\t0\t49\n", "82\t64\t358.9\t0\t64\n", "83\t68\t358.9\t0\t68\n", "84\t53\t358.9\t0\t53\n", "85\t50\t358.9\t0\t50\n", "86\t46\t358.9\t0\t46\n", "87\t48\t358.9\t0\t48\n", "88\t46\t358.9\t0\t46\n", "89\t43\t358.9\t0\t43\n", "90\t37\t358.9\t0\t37\n", "91\t29\t358.9\t0\t29\n", "92\t23\t358.9\t0\t23\n", "93\t27\t358.9\t0\t27\n", "94\t31\t358.9\t0\t31\n", "95\t40\t358.9\t0\t40\n", "96\t44\t358.9\t0\t44\n", "97\t60\t358.9\t0\t60\n", "98\t87\t358.9\t0\t87\n", "99\t124\t358.9\t0\t124\n", "100\t168\t358.9\t0\t168\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 513_S56_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/513.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 90.04 s (14 us/read; 4.26 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,387,260\n", "Reads with adapters: 4,721,914 (73.9%)\n", "Reads written (passing filters): 6,258,815 (98.0%)\n", "\n", "Total basepairs processed: 638,726,000 bp\n", "Quality-trimmed: 2,028,898 bp (0.3%)\n", "Total written (filtered): 461,512,434 bp (72.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4625868 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.6%\n", " G: 40.9%\n", " T: 27.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t109324\t99800.9\t0\t109324\n", "4\t68858\t24950.2\t0\t68858\n", "5\t58557\t6237.6\t0\t58557\n", "6\t49708\t1559.4\t0\t49708\n", "7\t47263\t389.8\t0\t47263\n", "8\t48668\t97.5\t0\t48668\n", "9\t47538\t97.5\t0\t47538\n", "10\t45762\t97.5\t0\t45762\n", "11\t46399\t97.5\t0\t46399\n", "12\t47846\t97.5\t0\t47846\n", "13\t51843\t97.5\t0\t51843\n", "14\t53697\t97.5\t0\t53697\n", "15\t53691\t97.5\t0\t53691\n", "16\t56181\t97.5\t0\t56181\n", "17\t61834\t97.5\t0\t61834\n", "18\t72105\t97.5\t0\t72105\n", "19\t68314\t97.5\t0\t68314\n", "20\t58427\t97.5\t0\t58427\n", "21\t58408\t97.5\t0\t58408\n", "22\t52434\t97.5\t0\t52434\n", "23\t58008\t97.5\t0\t58008\n", "24\t69002\t97.5\t0\t69002\n", "25\t71457\t97.5\t0\t71457\n", "26\t81336\t97.5\t0\t81336\n", "27\t91140\t97.5\t0\t91140\n", "28\t84663\t97.5\t0\t84663\n", "29\t80833\t97.5\t0\t80833\n", "30\t83283\t97.5\t0\t83283\n", "31\t89437\t97.5\t0\t89437\n", "32\t87763\t97.5\t0\t87763\n", "33\t79769\t97.5\t0\t79769\n", "34\t78532\t97.5\t0\t78532\n", "35\t89991\t97.5\t0\t89991\n", "36\t107620\t97.5\t0\t107620\n", "37\t116213\t97.5\t0\t116213\n", "38\t93054\t97.5\t0\t93054\n", "39\t74281\t97.5\t0\t74281\n", "40\t71583\t97.5\t0\t71583\n", "41\t75698\t97.5\t0\t75698\n", "42\t84371\t97.5\t0\t84371\n", "43\t74712\t97.5\t0\t74712\n", "44\t61927\t97.5\t0\t61927\n", "45\t78764\t97.5\t0\t78764\n", "46\t93293\t97.5\t0\t93293\n", "47\t85424\t97.5\t0\t85424\n", "48\t84055\t97.5\t0\t84055\n", "49\t70588\t97.5\t0\t70588\n", "50\t67753\t97.5\t0\t67753\n", "51\t63501\t97.5\t0\t63501\n", "52\t62434\t97.5\t0\t62434\n", "53\t62308\t97.5\t0\t62308\n", "54\t59798\t97.5\t0\t59798\n", "55\t69578\t97.5\t0\t69578\n", "56\t71090\t97.5\t0\t71090\n", "57\t61567\t97.5\t0\t61567\n", "58\t68550\t97.5\t0\t68550\n", "59\t53284\t97.5\t0\t53284\n", "60\t41731\t97.5\t0\t41731\n", "61\t39352\t97.5\t0\t39352\n", "62\t32754\t97.5\t0\t32754\n", "63\t31201\t97.5\t0\t31201\n", "64\t34673\t97.5\t0\t34673\n", "65\t33266\t97.5\t0\t33266\n", "66\t28046\t97.5\t0\t28046\n", "67\t27147\t97.5\t0\t27147\n", "68\t25599\t97.5\t0\t25599\n", "69\t25851\t97.5\t0\t25851\n", "70\t26774\t97.5\t0\t26774\n", "71\t25386\t97.5\t0\t25386\n", "72\t19676\t97.5\t0\t19676\n", "73\t17100\t97.5\t0\t17100\n", "74\t16244\t97.5\t0\t16244\n", "75\t13789\t97.5\t0\t13789\n", "76\t11335\t97.5\t0\t11335\n", "77\t10246\t97.5\t0\t10246\n", "78\t11889\t97.5\t0\t11889\n", "79\t10906\t97.5\t0\t10906\n", "80\t10275\t97.5\t0\t10275\n", "81\t9624\t97.5\t0\t9624\n", "82\t8957\t97.5\t0\t8957\n", "83\t9323\t97.5\t0\t9323\n", "84\t10293\t97.5\t0\t10293\n", "85\t11324\t97.5\t0\t11324\n", "86\t10122\t97.5\t0\t10122\n", "87\t6861\t97.5\t0\t6861\n", "88\t6004\t97.5\t0\t6004\n", "89\t6127\t97.5\t0\t6127\n", "90\t6263\t97.5\t0\t6263\n", "91\t5926\t97.5\t0\t5926\n", "92\t5606\t97.5\t0\t5606\n", "93\t5581\t97.5\t0\t5581\n", "94\t5042\t97.5\t0\t5042\n", "95\t4104\t97.5\t0\t4104\n", "96\t2996\t97.5\t0\t2996\n", "97\t1899\t97.5\t0\t1899\n", "98\t1265\t97.5\t0\t1265\n", "99\t1014\t97.5\t0\t1014\n", "100\t780\t97.5\t0\t780\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 17479 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 56.1%\n", " C: 19.7%\n", " G: 0.0%\n", " T: 24.1%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t7609\t99800.9\t0\t7609\n", "4\t1820\t24950.2\t0\t1820\n", "5\t563\t6237.6\t0\t563\n", "6\t365\t1559.4\t0\t365\n", "7\t114\t389.8\t0\t114\n", "8\t91\t97.5\t0\t91\n", "9\t70\t97.5\t0\t70\n", "10\t65\t97.5\t0\t65\n", "11\t77\t97.5\t0\t77\n", "12\t66\t97.5\t0\t66\n", "13\t65\t97.5\t0\t65\n", "14\t61\t97.5\t0\t61\n", "15\t56\t97.5\t0\t56\n", "16\t75\t97.5\t0\t75\n", "17\t82\t97.5\t0\t82\n", "18\t64\t97.5\t0\t64\n", "19\t104\t97.5\t0\t104\n", "20\t136\t97.5\t0\t136\n", "21\t101\t97.5\t0\t101\n", "22\t80\t97.5\t0\t80\n", "23\t71\t97.5\t0\t71\n", "24\t66\t97.5\t0\t66\n", "25\t83\t97.5\t0\t83\n", "26\t128\t97.5\t0\t128\n", "27\t118\t97.5\t0\t118\n", "28\t135\t97.5\t0\t135\n", "29\t182\t97.5\t0\t182\n", "30\t289\t97.5\t0\t289\n", "31\t370\t97.5\t0\t370\n", "32\t568\t97.5\t0\t568\n", "33\t507\t97.5\t0\t507\n", "34\t568\t97.5\t0\t568\n", "35\t686\t97.5\t0\t686\n", "36\t642\t97.5\t0\t642\n", "37\t249\t97.5\t0\t249\n", "38\t27\t97.5\t0\t27\n", "39\t29\t97.5\t0\t29\n", "40\t27\t97.5\t0\t27\n", "41\t41\t97.5\t0\t41\n", "42\t23\t97.5\t0\t23\n", "43\t25\t97.5\t0\t25\n", "44\t26\t97.5\t0\t26\n", "45\t27\t97.5\t0\t27\n", "46\t27\t97.5\t0\t27\n", "47\t30\t97.5\t0\t30\n", "48\t29\t97.5\t0\t29\n", "49\t29\t97.5\t0\t29\n", "50\t37\t97.5\t0\t37\n", "51\t23\t97.5\t0\t23\n", "52\t15\t97.5\t0\t15\n", "53\t24\t97.5\t0\t24\n", "54\t17\t97.5\t0\t17\n", "55\t9\t97.5\t0\t9\n", "56\t13\t97.5\t0\t13\n", "57\t16\t97.5\t0\t16\n", "58\t20\t97.5\t0\t20\n", "59\t14\t97.5\t0\t14\n", "60\t20\t97.5\t0\t20\n", "61\t20\t97.5\t0\t20\n", "62\t17\t97.5\t0\t17\n", "63\t16\t97.5\t0\t16\n", "64\t16\t97.5\t0\t16\n", "65\t12\t97.5\t0\t12\n", "66\t8\t97.5\t0\t8\n", "67\t6\t97.5\t0\t6\n", "68\t12\t97.5\t0\t12\n", "69\t11\t97.5\t0\t11\n", "70\t15\t97.5\t0\t15\n", "71\t7\t97.5\t0\t7\n", "72\t3\t97.5\t0\t3\n", "73\t6\t97.5\t0\t6\n", "74\t4\t97.5\t0\t4\n", "75\t7\t97.5\t0\t7\n", "76\t5\t97.5\t0\t5\n", "77\t5\t97.5\t0\t5\n", "78\t2\t97.5\t0\t2\n", "79\t8\t97.5\t0\t8\n", "80\t6\t97.5\t0\t6\n", "81\t5\t97.5\t0\t5\n", "82\t5\t97.5\t0\t5\n", "83\t6\t97.5\t0\t6\n", "84\t6\t97.5\t0\t6\n", "85\t9\t97.5\t0\t9\n", "86\t9\t97.5\t0\t9\n", "87\t6\t97.5\t0\t6\n", "88\t6\t97.5\t0\t6\n", "89\t8\t97.5\t0\t8\n", "90\t8\t97.5\t0\t8\n", "91\t10\t97.5\t0\t10\n", "92\t13\t97.5\t0\t13\n", "93\t25\t97.5\t0\t25\n", "94\t54\t97.5\t0\t54\n", "95\t56\t97.5\t0\t56\n", "96\t44\t97.5\t0\t44\n", "97\t45\t97.5\t0\t45\n", "98\t34\t97.5\t0\t34\n", "99\t31\t97.5\t0\t31\n", "100\t39\t97.5\t0\t39\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 78567 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.4%\n", " C: 16.9%\n", " G: 16.0%\n", " T: 24.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t56194\t99800.9\t0\t56194\n", "4\t13821\t24950.2\t0\t13821\n", "5\t2006\t6237.6\t0\t2006\n", "6\t227\t1559.4\t0\t227\n", "7\t98\t389.8\t0\t98\n", "8\t64\t389.8\t0\t64\n", "9\t99\t389.8\t0\t99\n", "10\t94\t389.8\t0\t94\n", "11\t83\t389.8\t0\t83\n", "12\t104\t389.8\t0\t104\n", "13\t109\t389.8\t0\t109\n", "14\t109\t389.8\t0\t109\n", "15\t131\t389.8\t0\t131\n", "16\t115\t389.8\t0\t115\n", "17\t101\t389.8\t0\t101\n", "18\t106\t389.8\t0\t106\n", "19\t100\t389.8\t0\t100\n", "20\t105\t389.8\t0\t105\n", "21\t90\t389.8\t0\t90\n", "22\t80\t389.8\t0\t80\n", "23\t86\t389.8\t0\t86\n", "24\t93\t389.8\t0\t93\n", "25\t94\t389.8\t0\t94\n", "26\t69\t389.8\t0\t69\n", "27\t72\t389.8\t0\t72\n", "28\t98\t389.8\t0\t98\n", "29\t71\t389.8\t0\t71\n", "30\t96\t389.8\t0\t96\n", "31\t75\t389.8\t0\t75\n", "32\t85\t389.8\t0\t85\n", "33\t65\t389.8\t0\t65\n", "34\t69\t389.8\t0\t69\n", "35\t66\t389.8\t0\t66\n", "36\t66\t389.8\t0\t66\n", "37\t58\t389.8\t0\t58\n", "38\t95\t389.8\t0\t95\n", "39\t72\t389.8\t0\t72\n", "40\t77\t389.8\t0\t77\n", "41\t91\t389.8\t0\t91\n", "42\t74\t389.8\t0\t74\n", "43\t75\t389.8\t0\t75\n", "44\t40\t389.8\t0\t40\n", "45\t66\t389.8\t0\t66\n", "46\t78\t389.8\t0\t78\n", "47\t76\t389.8\t0\t76\n", "48\t64\t389.8\t0\t64\n", "49\t61\t389.8\t0\t61\n", "50\t56\t389.8\t0\t56\n", "51\t38\t389.8\t0\t38\n", "52\t44\t389.8\t0\t44\n", "53\t53\t389.8\t0\t53\n", "54\t48\t389.8\t0\t48\n", "55\t40\t389.8\t0\t40\n", "56\t29\t389.8\t0\t29\n", "57\t47\t389.8\t0\t47\n", "58\t38\t389.8\t0\t38\n", "59\t37\t389.8\t0\t37\n", "60\t36\t389.8\t0\t36\n", "61\t47\t389.8\t0\t47\n", "62\t47\t389.8\t0\t47\n", "63\t38\t389.8\t0\t38\n", "64\t31\t389.8\t0\t31\n", "65\t31\t389.8\t0\t31\n", "66\t59\t389.8\t0\t59\n", "67\t44\t389.8\t0\t44\n", "68\t36\t389.8\t0\t36\n", "69\t39\t389.8\t0\t39\n", "70\t26\t389.8\t0\t26\n", "71\t37\t389.8\t0\t37\n", "72\t36\t389.8\t0\t36\n", "73\t43\t389.8\t0\t43\n", "74\t41\t389.8\t0\t41\n", "75\t52\t389.8\t0\t52\n", "76\t49\t389.8\t0\t49\n", "77\t78\t389.8\t0\t78\n", "78\t48\t389.8\t0\t48\n", "79\t58\t389.8\t0\t58\n", "80\t83\t389.8\t0\t83\n", "81\t72\t389.8\t0\t72\n", "82\t88\t389.8\t0\t88\n", "83\t86\t389.8\t0\t86\n", "84\t80\t389.8\t0\t80\n", "85\t58\t389.8\t0\t58\n", "86\t47\t389.8\t0\t47\n", "87\t68\t389.8\t0\t68\n", "88\t95\t389.8\t0\t95\n", "89\t63\t389.8\t0\t63\n", "90\t61\t389.8\t0\t61\n", "91\t60\t389.8\t0\t60\n", "92\t52\t389.8\t0\t52\n", "93\t47\t389.8\t0\t47\n", "94\t44\t389.8\t0\t44\n", "95\t40\t389.8\t0\t40\n", "96\t44\t389.8\t0\t44\n", "97\t64\t389.8\t0\t64\n", "98\t65\t389.8\t0\t65\n", "99\t78\t389.8\t0\t78\n", "100\t98\t389.8\t0\t98\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 521_S65_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/521.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 156.14 s (13 us/read; 4.52 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 11,767,309\n", "Reads with adapters: 7,969,674 (67.7%)\n", "Reads written (passing filters): 11,458,532 (97.4%)\n", "\n", "Total basepairs processed: 1,176,730,900 bp\n", "Quality-trimmed: 4,015,139 bp (0.3%)\n", "Total written (filtered): 875,931,362 bp (74.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 7723371 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 21.4%\n", " G: 48.1%\n", " T: 30.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t232091\t183864.2\t0\t232091\n", "4\t104801\t45966.1\t0\t104801\n", "5\t82949\t11491.5\t0\t82949\n", "6\t69701\t2872.9\t0\t69701\n", "7\t65315\t718.2\t0\t65315\n", "8\t62819\t179.6\t0\t62819\n", "9\t63463\t179.6\t0\t63463\n", "10\t66537\t179.6\t0\t66537\n", "11\t73031\t179.6\t0\t73031\n", "12\t85243\t179.6\t0\t85243\n", "13\t150423\t179.6\t0\t150423\n", "14\t145067\t179.6\t0\t145067\n", "15\t103021\t179.6\t0\t103021\n", "16\t105748\t179.6\t0\t105748\n", "17\t106972\t179.6\t0\t106972\n", "18\t127167\t179.6\t0\t127167\n", "19\t94585\t179.6\t0\t94585\n", "20\t75015\t179.6\t0\t75015\n", "21\t72543\t179.6\t0\t72543\n", "22\t67674\t179.6\t0\t67674\n", "23\t73611\t179.6\t0\t73611\n", "24\t89431\t179.6\t0\t89431\n", "25\t93343\t179.6\t0\t93343\n", "26\t114037\t179.6\t0\t114037\n", "27\t140411\t179.6\t0\t140411\n", "28\t156653\t179.6\t0\t156653\n", "29\t177553\t179.6\t0\t177553\n", "30\t198465\t179.6\t0\t198465\n", "31\t195590\t179.6\t0\t195590\n", "32\t169603\t179.6\t0\t169603\n", "33\t132980\t179.6\t0\t132980\n", "34\t123388\t179.6\t0\t123388\n", "35\t141300\t179.6\t0\t141300\n", "36\t175036\t179.6\t0\t175036\n", "37\t197023\t179.6\t0\t197023\n", "38\t162336\t179.6\t0\t162336\n", "39\t133314\t179.6\t0\t133314\n", "40\t123259\t179.6\t0\t123259\n", "41\t109720\t179.6\t0\t109720\n", "42\t113801\t179.6\t0\t113801\n", "43\t99368\t179.6\t0\t99368\n", "44\t83032\t179.6\t0\t83032\n", "45\t115421\t179.6\t0\t115421\n", "46\t146468\t179.6\t0\t146468\n", "47\t149764\t179.6\t0\t149764\n", "48\t154391\t179.6\t0\t154391\n", "49\t118497\t179.6\t0\t118497\n", "50\t101107\t179.6\t0\t101107\n", "51\t89131\t179.6\t0\t89131\n", "52\t95704\t179.6\t0\t95704\n", "53\t107189\t179.6\t0\t107189\n", "54\t109162\t179.6\t0\t109162\n", "55\t106957\t179.6\t0\t106957\n", "56\t97252\t179.6\t0\t97252\n", "57\t97968\t179.6\t0\t97968\n", "58\t116542\t179.6\t0\t116542\n", "59\t75066\t179.6\t0\t75066\n", "60\t61190\t179.6\t0\t61190\n", "61\t58514\t179.6\t0\t58514\n", "62\t47110\t179.6\t0\t47110\n", "63\t46588\t179.6\t0\t46588\n", "64\t52205\t179.6\t0\t52205\n", "65\t49725\t179.6\t0\t49725\n", "66\t46524\t179.6\t0\t46524\n", "67\t47014\t179.6\t0\t47014\n", "68\t42293\t179.6\t0\t42293\n", "69\t40544\t179.6\t0\t40544\n", "70\t44024\t179.6\t0\t44024\n", "71\t43937\t179.6\t0\t43937\n", "72\t33710\t179.6\t0\t33710\n", "73\t30668\t179.6\t0\t30668\n", "74\t31146\t179.6\t0\t31146\n", "75\t25215\t179.6\t0\t25215\n", "76\t21821\t179.6\t0\t21821\n", "77\t19773\t179.6\t0\t19773\n", "78\t21159\t179.6\t0\t21159\n", "79\t20896\t179.6\t0\t20896\n", "80\t22366\t179.6\t0\t22366\n", "81\t20504\t179.6\t0\t20504\n", "82\t19001\t179.6\t0\t19001\n", "83\t20126\t179.6\t0\t20126\n", "84\t21234\t179.6\t0\t21234\n", "85\t23111\t179.6\t0\t23111\n", "86\t21712\t179.6\t0\t21712\n", "87\t16227\t179.6\t0\t16227\n", "88\t15113\t179.6\t0\t15113\n", "89\t15496\t179.6\t0\t15496\n", "90\t15244\t179.6\t0\t15244\n", "91\t14983\t179.6\t0\t14983\n", "92\t14125\t179.6\t0\t14125\n", "93\t13884\t179.6\t0\t13884\n", "94\t12489\t179.6\t0\t12489\n", "95\t10414\t179.6\t0\t10414\n", "96\t7834\t179.6\t0\t7834\n", "97\t5900\t179.6\t0\t5900\n", "98\t4233\t179.6\t0\t4233\n", "99\t4258\t179.6\t0\t4258\n", "100\t3023\t179.6\t0\t3023\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 97328 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 71.2%\n", " C: 17.9%\n", " G: 0.0%\n", " T: 10.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t16617\t183864.2\t0\t16617\n", "4\t5613\t45966.1\t0\t5613\n", "5\t4487\t11491.5\t0\t4487\n", "6\t3029\t2872.9\t0\t3029\n", "7\t903\t718.2\t0\t903\n", "8\t776\t179.6\t0\t776\n", "9\t727\t179.6\t0\t727\n", "10\t647\t179.6\t0\t647\n", "11\t736\t179.6\t0\t736\n", "12\t602\t179.6\t0\t602\n", "13\t586\t179.6\t0\t586\n", "14\t569\t179.6\t0\t569\n", "15\t619\t179.6\t0\t619\n", "16\t596\t179.6\t0\t596\n", "17\t631\t179.6\t0\t631\n", "18\t1017\t179.6\t0\t1017\n", "19\t1250\t179.6\t0\t1250\n", "20\t2189\t179.6\t0\t2189\n", "21\t1493\t179.6\t0\t1493\n", "22\t956\t179.6\t0\t956\n", "23\t697\t179.6\t0\t697\n", "24\t806\t179.6\t0\t806\n", "25\t861\t179.6\t0\t861\n", "26\t1508\t179.6\t0\t1508\n", "27\t1510\t179.6\t0\t1510\n", "28\t1489\t179.6\t0\t1489\n", "29\t1599\t179.6\t0\t1599\n", "30\t2685\t179.6\t0\t2685\n", "31\t3095\t179.6\t0\t3095\n", "32\t5220\t179.6\t0\t5220\n", "33\t5803\t179.6\t0\t5803\n", "34\t6202\t179.6\t0\t6202\n", "35\t8201\t179.6\t0\t8201\n", "36\t8148\t179.6\t0\t8148\n", "37\t3818\t179.6\t0\t3818\n", "38\t183\t179.6\t0\t183\n", "39\t99\t179.6\t0\t99\n", "40\t26\t179.6\t0\t26\n", "41\t10\t179.6\t0\t10\n", "42\t17\t179.6\t0\t17\n", "43\t10\t179.6\t0\t10\n", "44\t14\t179.6\t0\t14\n", "45\t17\t179.6\t0\t17\n", "46\t23\t179.6\t0\t23\n", "47\t13\t179.6\t0\t13\n", "48\t9\t179.6\t0\t9\n", "49\t12\t179.6\t0\t12\n", "50\t14\t179.6\t0\t14\n", "51\t24\t179.6\t0\t24\n", "52\t29\t179.6\t0\t29\n", "53\t19\t179.6\t0\t19\n", "54\t12\t179.6\t0\t12\n", "55\t14\t179.6\t0\t14\n", "56\t11\t179.6\t0\t11\n", "57\t7\t179.6\t0\t7\n", "58\t20\t179.6\t0\t20\n", "59\t16\t179.6\t0\t16\n", "60\t9\t179.6\t0\t9\n", "61\t6\t179.6\t0\t6\n", "62\t13\t179.6\t0\t13\n", "63\t7\t179.6\t0\t7\n", "64\t10\t179.6\t0\t10\n", "65\t13\t179.6\t0\t13\n", "66\t5\t179.6\t0\t5\n", "67\t6\t179.6\t0\t6\n", "68\t7\t179.6\t0\t7\n", "69\t3\t179.6\t0\t3\n", "70\t2\t179.6\t0\t2\n", "71\t1\t179.6\t0\t1\n", "72\t9\t179.6\t0\t9\n", "73\t3\t179.6\t0\t3\n", "75\t5\t179.6\t0\t5\n", "78\t2\t179.6\t0\t2\n", "79\t1\t179.6\t0\t1\n", "80\t1\t179.6\t0\t1\n", "81\t4\t179.6\t0\t4\n", "82\t5\t179.6\t0\t5\n", "83\t5\t179.6\t0\t5\n", "85\t3\t179.6\t0\t3\n", "86\t2\t179.6\t0\t2\n", "87\t3\t179.6\t0\t3\n", "88\t2\t179.6\t0\t2\n", "89\t6\t179.6\t0\t6\n", "90\t5\t179.6\t0\t5\n", "91\t4\t179.6\t0\t4\n", "92\t17\t179.6\t0\t17\n", "93\t34\t179.6\t0\t34\n", "94\t103\t179.6\t0\t103\n", "95\t185\t179.6\t0\t185\n", "96\t122\t179.6\t0\t122\n", "97\t140\t179.6\t0\t140\n", "98\t136\t179.6\t0\t136\n", "99\t76\t179.6\t0\t76\n", "100\t89\t179.6\t0\t89\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 148975 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.9%\n", " C: 15.9%\n", " G: 10.9%\n", " T: 32.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t98341\t183864.2\t0\t98341\n", "4\t31725\t45966.1\t0\t31725\n", "5\t2463\t11491.5\t0\t2463\n", "6\t394\t2872.9\t0\t394\n", "7\t296\t718.2\t0\t296\n", "8\t333\t718.2\t0\t333\n", "9\t307\t718.2\t0\t307\n", "10\t319\t718.2\t0\t319\n", "11\t340\t718.2\t0\t340\n", "12\t478\t718.2\t0\t478\n", "13\t504\t718.2\t0\t504\n", "14\t496\t718.2\t0\t496\n", "15\t450\t718.2\t0\t450\n", "16\t374\t718.2\t0\t374\n", "17\t358\t718.2\t0\t358\n", "18\t311\t718.2\t0\t311\n", "19\t314\t718.2\t0\t314\n", "20\t304\t718.2\t0\t304\n", "21\t277\t718.2\t0\t277\n", "22\t265\t718.2\t0\t265\n", "23\t187\t718.2\t0\t187\n", "24\t176\t718.2\t0\t176\n", "25\t206\t718.2\t0\t206\n", "26\t210\t718.2\t0\t210\n", "27\t245\t718.2\t0\t245\n", "28\t195\t718.2\t0\t195\n", "29\t217\t718.2\t0\t217\n", "30\t212\t718.2\t0\t212\n", "31\t189\t718.2\t0\t189\n", "32\t237\t718.2\t0\t237\n", "33\t196\t718.2\t0\t196\n", "34\t246\t718.2\t0\t246\n", "35\t237\t718.2\t0\t237\n", "36\t193\t718.2\t0\t193\n", "37\t234\t718.2\t0\t234\n", "38\t164\t718.2\t0\t164\n", "39\t213\t718.2\t0\t213\n", "40\t217\t718.2\t0\t217\n", "41\t212\t718.2\t0\t212\n", "42\t132\t718.2\t0\t132\n", "43\t198\t718.2\t0\t198\n", "44\t76\t718.2\t0\t76\n", "45\t138\t718.2\t0\t138\n", "46\t160\t718.2\t0\t160\n", "47\t128\t718.2\t0\t128\n", "48\t124\t718.2\t0\t124\n", "49\t113\t718.2\t0\t113\n", "50\t121\t718.2\t0\t121\n", "51\t99\t718.2\t0\t99\n", "52\t141\t718.2\t0\t141\n", "53\t169\t718.2\t0\t169\n", "54\t154\t718.2\t0\t154\n", "55\t162\t718.2\t0\t162\n", "56\t200\t718.2\t0\t200\n", "57\t139\t718.2\t0\t139\n", "58\t173\t718.2\t0\t173\n", "59\t125\t718.2\t0\t125\n", "60\t209\t718.2\t0\t209\n", "61\t164\t718.2\t0\t164\n", "62\t156\t718.2\t0\t156\n", "63\t109\t718.2\t0\t109\n", "64\t138\t718.2\t0\t138\n", "65\t98\t718.2\t0\t98\n", "66\t134\t718.2\t0\t134\n", "67\t103\t718.2\t0\t103\n", "68\t99\t718.2\t0\t99\n", "69\t32\t718.2\t0\t32\n", "70\t38\t718.2\t0\t38\n", "71\t70\t718.2\t0\t70\n", "72\t92\t718.2\t0\t92\n", "73\t82\t718.2\t0\t82\n", "74\t82\t718.2\t0\t82\n", "75\t32\t718.2\t0\t32\n", "76\t67\t718.2\t0\t67\n", "77\t104\t718.2\t0\t104\n", "78\t62\t718.2\t0\t62\n", "79\t63\t718.2\t0\t63\n", "80\t84\t718.2\t0\t84\n", "81\t102\t718.2\t0\t102\n", "82\t101\t718.2\t0\t101\n", "83\t89\t718.2\t0\t89\n", "84\t72\t718.2\t0\t72\n", "85\t62\t718.2\t0\t62\n", "86\t50\t718.2\t0\t50\n", "87\t89\t718.2\t0\t89\n", "88\t115\t718.2\t0\t115\n", "89\t75\t718.2\t0\t75\n", "90\t73\t718.2\t0\t73\n", "91\t50\t718.2\t0\t50\n", "92\t41\t718.2\t0\t41\n", "93\t44\t718.2\t0\t44\n", "94\t61\t718.2\t0\t61\n", "95\t33\t718.2\t0\t33\n", "96\t69\t718.2\t0\t69\n", "97\t173\t718.2\t0\t173\n", "98\t130\t718.2\t0\t130\n", "99\t171\t718.2\t0\t171\n", "100\t170\t718.2\t0\t170\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 522_S1_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/522.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 76.07 s (13 us/read; 4.63 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,875,819\n", "Reads with adapters: 3,519,936 (59.9%)\n", "Reads written (passing filters): 5,760,534 (98.0%)\n", "\n", "Total basepairs processed: 587,581,900 bp\n", "Quality-trimmed: 1,567,520 bp (0.3%)\n", "Total written (filtered): 458,522,561 bp (78.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3391460 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 26.4%\n", " G: 37.5%\n", " T: 36.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t125908\t91809.7\t0\t125908\n", "4\t68035\t22952.4\t0\t68035\n", "5\t51168\t5738.1\t0\t51168\n", "6\t41319\t1434.5\t0\t41319\n", "7\t35285\t358.6\t0\t35285\n", "8\t35139\t89.7\t0\t35139\n", "9\t34808\t89.7\t0\t34808\n", "10\t32719\t89.7\t0\t32719\n", "11\t33299\t89.7\t0\t33299\n", "12\t33066\t89.7\t0\t33066\n", "13\t35969\t89.7\t0\t35969\n", "14\t36916\t89.7\t0\t36916\n", "15\t37732\t89.7\t0\t37732\n", "16\t39648\t89.7\t0\t39648\n", "17\t42166\t89.7\t0\t42166\n", "18\t49424\t89.7\t0\t49424\n", "19\t46996\t89.7\t0\t46996\n", "20\t40347\t89.7\t0\t40347\n", "21\t39227\t89.7\t0\t39227\n", "22\t36220\t89.7\t0\t36220\n", "23\t41117\t89.7\t0\t41117\n", "24\t49068\t89.7\t0\t49068\n", "25\t50449\t89.7\t0\t50449\n", "26\t57372\t89.7\t0\t57372\n", "27\t67368\t89.7\t0\t67368\n", "28\t64347\t89.7\t0\t64347\n", "29\t61748\t89.7\t0\t61748\n", "30\t65287\t89.7\t0\t65287\n", "31\t69782\t89.7\t0\t69782\n", "32\t66623\t89.7\t0\t66623\n", "33\t57817\t89.7\t0\t57817\n", "34\t54537\t89.7\t0\t54537\n", "35\t62892\t89.7\t0\t62892\n", "36\t79251\t89.7\t0\t79251\n", "37\t89286\t89.7\t0\t89286\n", "38\t71901\t89.7\t0\t71901\n", "39\t53810\t89.7\t0\t53810\n", "40\t50433\t89.7\t0\t50433\n", "41\t50532\t89.7\t0\t50532\n", "42\t56109\t89.7\t0\t56109\n", "43\t48619\t89.7\t0\t48619\n", "44\t40928\t89.7\t0\t40928\n", "45\t53751\t89.7\t0\t53751\n", "46\t64745\t89.7\t0\t64745\n", "47\t59712\t89.7\t0\t59712\n", "48\t60972\t89.7\t0\t60972\n", "49\t48840\t89.7\t0\t48840\n", "50\t45200\t89.7\t0\t45200\n", "51\t41621\t89.7\t0\t41621\n", "52\t43911\t89.7\t0\t43911\n", "53\t45148\t89.7\t0\t45148\n", "54\t49426\t89.7\t0\t49426\n", "55\t44824\t89.7\t0\t44824\n", "56\t40289\t89.7\t0\t40289\n", "57\t36212\t89.7\t0\t36212\n", "58\t41833\t89.7\t0\t41833\n", "59\t34661\t89.7\t0\t34661\n", "60\t28790\t89.7\t0\t28790\n", "61\t27622\t89.7\t0\t27622\n", "62\t22545\t89.7\t0\t22545\n", "63\t22429\t89.7\t0\t22429\n", "64\t24839\t89.7\t0\t24839\n", "65\t24141\t89.7\t0\t24141\n", "66\t21295\t89.7\t0\t21295\n", "67\t20224\t89.7\t0\t20224\n", "68\t18876\t89.7\t0\t18876\n", "69\t19134\t89.7\t0\t19134\n", "70\t20057\t89.7\t0\t20057\n", "71\t18677\t89.7\t0\t18677\n", "72\t15487\t89.7\t0\t15487\n", "73\t13836\t89.7\t0\t13836\n", "74\t13508\t89.7\t0\t13508\n", "75\t11400\t89.7\t0\t11400\n", "76\t9504\t89.7\t0\t9504\n", "77\t8437\t89.7\t0\t8437\n", "78\t9469\t89.7\t0\t9469\n", "79\t8983\t89.7\t0\t8983\n", "80\t9231\t89.7\t0\t9231\n", "81\t8080\t89.7\t0\t8080\n", "82\t7563\t89.7\t0\t7563\n", "83\t8119\t89.7\t0\t8119\n", "84\t8908\t89.7\t0\t8908\n", "85\t9827\t89.7\t0\t9827\n", "86\t8779\t89.7\t0\t8779\n", "87\t5978\t89.7\t0\t5978\n", "88\t5253\t89.7\t0\t5253\n", "89\t5535\t89.7\t0\t5535\n", "90\t5746\t89.7\t0\t5746\n", "91\t5393\t89.7\t0\t5393\n", "92\t5224\t89.7\t0\t5224\n", "93\t5200\t89.7\t0\t5200\n", "94\t4766\t89.7\t0\t4766\n", "95\t4056\t89.7\t0\t4056\n", "96\t2905\t89.7\t0\t2905\n", "97\t2074\t89.7\t0\t2074\n", "98\t1302\t89.7\t0\t1302\n", "99\t1467\t89.7\t0\t1467\n", "100\t989\t89.7\t0\t989\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 19825 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 59.0%\n", " C: 16.3%\n", " G: 0.0%\n", " T: 24.6%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t8403\t91809.7\t0\t8403\n", "4\t1912\t22952.4\t0\t1912\n", "5\t789\t5738.1\t0\t789\n", "6\t618\t1434.5\t0\t618\n", "7\t262\t358.6\t0\t262\n", "8\t206\t89.7\t0\t206\n", "9\t155\t89.7\t0\t155\n", "10\t167\t89.7\t0\t167\n", "11\t168\t89.7\t0\t168\n", "12\t128\t89.7\t0\t128\n", "13\t120\t89.7\t0\t120\n", "14\t134\t89.7\t0\t134\n", "15\t112\t89.7\t0\t112\n", "16\t114\t89.7\t0\t114\n", "17\t106\t89.7\t0\t106\n", "18\t115\t89.7\t0\t115\n", "19\t143\t89.7\t0\t143\n", "20\t184\t89.7\t0\t184\n", "21\t141\t89.7\t0\t141\n", "22\t118\t89.7\t0\t118\n", "23\t115\t89.7\t0\t115\n", "24\t104\t89.7\t0\t104\n", "25\t105\t89.7\t0\t105\n", "26\t167\t89.7\t0\t167\n", "27\t177\t89.7\t0\t177\n", "28\t178\t89.7\t0\t178\n", "29\t184\t89.7\t0\t184\n", "30\t293\t89.7\t0\t293\n", "31\t389\t89.7\t0\t389\n", "32\t574\t89.7\t0\t574\n", "33\t530\t89.7\t0\t530\n", "34\t512\t89.7\t0\t512\n", "35\t691\t89.7\t0\t691\n", "36\t743\t89.7\t0\t743\n", "37\t284\t89.7\t0\t284\n", "38\t31\t89.7\t0\t31\n", "39\t30\t89.7\t0\t30\n", "40\t17\t89.7\t0\t17\n", "41\t21\t89.7\t0\t21\n", "42\t19\t89.7\t0\t19\n", "43\t21\t89.7\t0\t21\n", "44\t10\t89.7\t0\t10\n", "45\t19\t89.7\t0\t19\n", "46\t15\t89.7\t0\t15\n", "47\t12\t89.7\t0\t12\n", "48\t12\t89.7\t0\t12\n", "49\t13\t89.7\t0\t13\n", "50\t8\t89.7\t0\t8\n", "51\t15\t89.7\t0\t15\n", "52\t14\t89.7\t0\t14\n", "53\t10\t89.7\t0\t10\n", "54\t8\t89.7\t0\t8\n", "55\t8\t89.7\t0\t8\n", "56\t12\t89.7\t0\t12\n", "57\t11\t89.7\t0\t11\n", "58\t5\t89.7\t0\t5\n", "59\t6\t89.7\t0\t6\n", "60\t8\t89.7\t0\t8\n", "61\t4\t89.7\t0\t4\n", "62\t8\t89.7\t0\t8\n", "63\t7\t89.7\t0\t7\n", "64\t14\t89.7\t0\t14\n", "65\t7\t89.7\t0\t7\n", "66\t10\t89.7\t0\t10\n", "67\t8\t89.7\t0\t8\n", "68\t5\t89.7\t0\t5\n", "69\t2\t89.7\t0\t2\n", "70\t2\t89.7\t0\t2\n", "71\t4\t89.7\t0\t4\n", "72\t4\t89.7\t0\t4\n", "73\t2\t89.7\t0\t2\n", "74\t2\t89.7\t0\t2\n", "75\t3\t89.7\t0\t3\n", "76\t1\t89.7\t0\t1\n", "77\t2\t89.7\t0\t2\n", "78\t5\t89.7\t0\t5\n", "79\t1\t89.7\t0\t1\n", "80\t2\t89.7\t0\t2\n", "81\t1\t89.7\t0\t1\n", "82\t2\t89.7\t0\t2\n", "83\t1\t89.7\t0\t1\n", "85\t3\t89.7\t0\t3\n", "86\t5\t89.7\t0\t5\n", "87\t8\t89.7\t0\t8\n", "88\t5\t89.7\t0\t5\n", "89\t3\t89.7\t0\t3\n", "90\t1\t89.7\t0\t1\n", "91\t1\t89.7\t0\t1\n", "92\t9\t89.7\t0\t9\n", "93\t19\t89.7\t0\t19\n", "94\t35\t89.7\t0\t35\n", "95\t40\t89.7\t0\t40\n", "96\t35\t89.7\t0\t35\n", "97\t20\t89.7\t0\t20\n", "98\t22\t89.7\t0\t22\n", "99\t18\t89.7\t0\t18\n", "100\t38\t89.7\t0\t38\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 108651 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 42.4%\n", " C: 18.9%\n", " G: 12.1%\n", " T: 26.6%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t74583\t91809.7\t0\t74583\n", "4\t17500\t22952.4\t0\t17500\n", "5\t2672\t5738.1\t0\t2672\n", "6\t333\t1434.5\t0\t333\n", "7\t231\t358.6\t0\t231\n", "8\t253\t358.6\t0\t253\n", "9\t239\t358.6\t0\t239\n", "10\t239\t358.6\t0\t239\n", "11\t292\t358.6\t0\t292\n", "12\t292\t358.6\t0\t292\n", "13\t287\t358.6\t0\t287\n", "14\t252\t358.6\t0\t252\n", "15\t273\t358.6\t0\t273\n", "16\t279\t358.6\t0\t279\n", "17\t283\t358.6\t0\t283\n", "18\t241\t358.6\t0\t241\n", "19\t228\t358.6\t0\t228\n", "20\t202\t358.6\t0\t202\n", "21\t232\t358.6\t0\t232\n", "22\t196\t358.6\t0\t196\n", "23\t206\t358.6\t0\t206\n", "24\t204\t358.6\t0\t204\n", "25\t195\t358.6\t0\t195\n", "26\t185\t358.6\t0\t185\n", "27\t226\t358.6\t0\t226\n", "28\t189\t358.6\t0\t189\n", "29\t204\t358.6\t0\t204\n", "30\t203\t358.6\t0\t203\n", "31\t188\t358.6\t0\t188\n", "32\t201\t358.6\t0\t201\n", "33\t204\t358.6\t0\t204\n", "34\t253\t358.6\t0\t253\n", "35\t218\t358.6\t0\t218\n", "36\t204\t358.6\t0\t204\n", "37\t188\t358.6\t0\t188\n", "38\t178\t358.6\t0\t178\n", "39\t250\t358.6\t0\t250\n", "40\t173\t358.6\t0\t173\n", "41\t208\t358.6\t0\t208\n", "42\t153\t358.6\t0\t153\n", "43\t214\t358.6\t0\t214\n", "44\t75\t358.6\t0\t75\n", "45\t164\t358.6\t0\t164\n", "46\t168\t358.6\t0\t168\n", "47\t166\t358.6\t0\t166\n", "48\t129\t358.6\t0\t129\n", "49\t121\t358.6\t0\t121\n", "50\t139\t358.6\t0\t139\n", "51\t137\t358.6\t0\t137\n", "52\t122\t358.6\t0\t122\n", "53\t117\t358.6\t0\t117\n", "54\t121\t358.6\t0\t121\n", "55\t109\t358.6\t0\t109\n", "56\t74\t358.6\t0\t74\n", "57\t93\t358.6\t0\t93\n", "58\t102\t358.6\t0\t102\n", "59\t61\t358.6\t0\t61\n", "60\t91\t358.6\t0\t91\n", "61\t98\t358.6\t0\t98\n", "62\t81\t358.6\t0\t81\n", "63\t89\t358.6\t0\t89\n", "64\t79\t358.6\t0\t79\n", "65\t72\t358.6\t0\t72\n", "66\t102\t358.6\t0\t102\n", "67\t67\t358.6\t0\t67\n", "68\t103\t358.6\t0\t103\n", "69\t53\t358.6\t0\t53\n", "70\t45\t358.6\t0\t45\n", "71\t64\t358.6\t0\t64\n", "72\t92\t358.6\t0\t92\n", "73\t87\t358.6\t0\t87\n", "74\t95\t358.6\t0\t95\n", "75\t62\t358.6\t0\t62\n", "76\t101\t358.6\t0\t101\n", "77\t77\t358.6\t0\t77\n", "78\t61\t358.6\t0\t61\n", "79\t81\t358.6\t0\t81\n", "80\t100\t358.6\t0\t100\n", "81\t117\t358.6\t0\t117\n", "82\t130\t358.6\t0\t130\n", "83\t127\t358.6\t0\t127\n", "84\t99\t358.6\t0\t99\n", "85\t93\t358.6\t0\t93\n", "86\t62\t358.6\t0\t62\n", "87\t85\t358.6\t0\t85\n", "88\t72\t358.6\t0\t72\n", "89\t72\t358.6\t0\t72\n", "90\t49\t358.6\t0\t49\n", "91\t42\t358.6\t0\t42\n", "92\t44\t358.6\t0\t44\n", "93\t35\t358.6\t0\t35\n", "94\t52\t358.6\t0\t52\n", "95\t55\t358.6\t0\t55\n", "96\t50\t358.6\t0\t50\n", "97\t94\t358.6\t0\t94\n", "98\t106\t358.6\t0\t106\n", "99\t164\t358.6\t0\t164\n", "100\t154\t358.6\t0\t154\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 523_S4_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/523.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 94.41 s (13 us/read; 4.50 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,083,612\n", "Reads with adapters: 4,144,605 (58.5%)\n", "Reads written (passing filters): 6,915,805 (97.6%)\n", "\n", "Total basepairs processed: 708,361,200 bp\n", "Quality-trimmed: 1,880,345 bp (0.3%)\n", "Total written (filtered): 557,600,334 bp (78.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3978639 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.8%\n", " G: 36.7%\n", " T: 35.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t145682\t110681.4\t0\t145682\n", "4\t88574\t27670.4\t0\t88574\n", "5\t66350\t6917.6\t0\t66350\n", "6\t52722\t1729.4\t0\t52722\n", "7\t45851\t432.3\t0\t45851\n", "8\t44051\t108.1\t0\t44051\n", "9\t43087\t108.1\t0\t43087\n", "10\t40585\t108.1\t0\t40585\n", "11\t41695\t108.1\t0\t41695\n", "12\t42199\t108.1\t0\t42199\n", "13\t44748\t108.1\t0\t44748\n", "14\t46741\t108.1\t0\t46741\n", "15\t48003\t108.1\t0\t48003\n", "16\t51164\t108.1\t0\t51164\n", "17\t55314\t108.1\t0\t55314\n", "18\t63997\t108.1\t0\t63997\n", "19\t59771\t108.1\t0\t59771\n", "20\t51035\t108.1\t0\t51035\n", "21\t50043\t108.1\t0\t50043\n", "22\t45629\t108.1\t0\t45629\n", "23\t49512\t108.1\t0\t49512\n", "24\t59536\t108.1\t0\t59536\n", "25\t63207\t108.1\t0\t63207\n", "26\t72006\t108.1\t0\t72006\n", "27\t79693\t108.1\t0\t79693\n", "28\t74077\t108.1\t0\t74077\n", "29\t68345\t108.1\t0\t68345\n", "30\t69668\t108.1\t0\t69668\n", "31\t75548\t108.1\t0\t75548\n", "32\t71387\t108.1\t0\t71387\n", "33\t67013\t108.1\t0\t67013\n", "34\t68748\t108.1\t0\t68748\n", "35\t77433\t108.1\t0\t77433\n", "36\t92981\t108.1\t0\t92981\n", "37\t104596\t108.1\t0\t104596\n", "38\t78229\t108.1\t0\t78229\n", "39\t62602\t108.1\t0\t62602\n", "40\t59350\t108.1\t0\t59350\n", "41\t64164\t108.1\t0\t64164\n", "42\t70440\t108.1\t0\t70440\n", "43\t58491\t108.1\t0\t58491\n", "44\t45623\t108.1\t0\t45623\n", "45\t54724\t108.1\t0\t54724\n", "46\t63054\t108.1\t0\t63054\n", "47\t60346\t108.1\t0\t60346\n", "48\t59618\t108.1\t0\t59618\n", "49\t48835\t108.1\t0\t48835\n", "50\t47566\t108.1\t0\t47566\n", "51\t43708\t108.1\t0\t43708\n", "52\t44230\t108.1\t0\t44230\n", "53\t41709\t108.1\t0\t41709\n", "54\t45880\t108.1\t0\t45880\n", "55\t47804\t108.1\t0\t47804\n", "56\t45042\t108.1\t0\t45042\n", "57\t43659\t108.1\t0\t43659\n", "58\t51035\t108.1\t0\t51035\n", "59\t43279\t108.1\t0\t43279\n", "60\t36350\t108.1\t0\t36350\n", "61\t31029\t108.1\t0\t31029\n", "62\t24911\t108.1\t0\t24911\n", "63\t23590\t108.1\t0\t23590\n", "64\t25946\t108.1\t0\t25946\n", "65\t25160\t108.1\t0\t25160\n", "66\t22314\t108.1\t0\t22314\n", "67\t21920\t108.1\t0\t21920\n", "68\t21794\t108.1\t0\t21794\n", "69\t22294\t108.1\t0\t22294\n", "70\t23470\t108.1\t0\t23470\n", "71\t22183\t108.1\t0\t22183\n", "72\t18181\t108.1\t0\t18181\n", "73\t16123\t108.1\t0\t16123\n", "74\t15866\t108.1\t0\t15866\n", "75\t13683\t108.1\t0\t13683\n", "76\t11291\t108.1\t0\t11291\n", "77\t10985\t108.1\t0\t10985\n", "78\t12146\t108.1\t0\t12146\n", "79\t11562\t108.1\t0\t11562\n", "80\t11607\t108.1\t0\t11607\n", "81\t10528\t108.1\t0\t10528\n", "82\t9665\t108.1\t0\t9665\n", "83\t10133\t108.1\t0\t10133\n", "84\t11606\t108.1\t0\t11606\n", "85\t12581\t108.1\t0\t12581\n", "86\t11682\t108.1\t0\t11682\n", "87\t8271\t108.1\t0\t8271\n", "88\t7495\t108.1\t0\t7495\n", "89\t7800\t108.1\t0\t7800\n", "90\t8276\t108.1\t0\t8276\n", "91\t8245\t108.1\t0\t8245\n", "92\t7999\t108.1\t0\t7999\n", "93\t8681\t108.1\t0\t8681\n", "94\t8586\t108.1\t0\t8586\n", "95\t7523\t108.1\t0\t7523\n", "96\t5628\t108.1\t0\t5628\n", "97\t3963\t108.1\t0\t3963\n", "98\t2791\t108.1\t0\t2791\n", "99\t2454\t108.1\t0\t2454\n", "100\t1948\t108.1\t0\t1948\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 55674 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 61.8%\n", " C: 23.4%\n", " G: 0.0%\n", " T: 14.8%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t16158\t110681.4\t0\t16158\n", "4\t4738\t27670.4\t0\t4738\n", "5\t3165\t6917.6\t0\t3165\n", "6\t1968\t1729.4\t0\t1968\n", "7\t711\t432.3\t0\t711\n", "8\t553\t108.1\t0\t553\n", "9\t440\t108.1\t0\t440\n", "10\t404\t108.1\t0\t404\n", "11\t490\t108.1\t0\t490\n", "12\t399\t108.1\t0\t399\n", "13\t348\t108.1\t0\t348\n", "14\t371\t108.1\t0\t371\n", "15\t339\t108.1\t0\t339\n", "16\t327\t108.1\t0\t327\n", "17\t312\t108.1\t0\t312\n", "18\t399\t108.1\t0\t399\n", "19\t379\t108.1\t0\t379\n", "20\t433\t108.1\t0\t433\n", "21\t313\t108.1\t0\t313\n", "22\t308\t108.1\t0\t308\n", "23\t305\t108.1\t0\t305\n", "24\t283\t108.1\t0\t283\n", "25\t331\t108.1\t0\t331\n", "26\t631\t108.1\t0\t631\n", "27\t643\t108.1\t0\t643\n", "28\t672\t108.1\t0\t672\n", "29\t858\t108.1\t0\t858\n", "30\t1572\t108.1\t0\t1572\n", "31\t1729\t108.1\t0\t1729\n", "32\t2701\t108.1\t0\t2701\n", "33\t2524\t108.1\t0\t2524\n", "34\t2502\t108.1\t0\t2502\n", "35\t2957\t108.1\t0\t2957\n", "36\t2670\t108.1\t0\t2670\n", "37\t982\t108.1\t0\t982\n", "38\t71\t108.1\t0\t71\n", "39\t31\t108.1\t0\t31\n", "40\t32\t108.1\t0\t32\n", "41\t29\t108.1\t0\t29\n", "42\t38\t108.1\t0\t38\n", "43\t25\t108.1\t0\t25\n", "44\t25\t108.1\t0\t25\n", "45\t29\t108.1\t0\t29\n", "46\t34\t108.1\t0\t34\n", "47\t22\t108.1\t0\t22\n", "48\t29\t108.1\t0\t29\n", "49\t42\t108.1\t0\t42\n", "50\t42\t108.1\t0\t42\n", "51\t39\t108.1\t0\t39\n", "52\t43\t108.1\t0\t43\n", "53\t36\t108.1\t0\t36\n", "54\t32\t108.1\t0\t32\n", "55\t26\t108.1\t0\t26\n", "56\t37\t108.1\t0\t37\n", "57\t26\t108.1\t0\t26\n", "58\t34\t108.1\t0\t34\n", "59\t28\t108.1\t0\t28\n", "60\t23\t108.1\t0\t23\n", "61\t25\t108.1\t0\t25\n", "62\t23\t108.1\t0\t23\n", "63\t25\t108.1\t0\t25\n", "64\t20\t108.1\t0\t20\n", "65\t25\t108.1\t0\t25\n", "66\t20\t108.1\t0\t20\n", "67\t11\t108.1\t0\t11\n", "68\t18\t108.1\t0\t18\n", "69\t14\t108.1\t0\t14\n", "70\t15\t108.1\t0\t15\n", "71\t12\t108.1\t0\t12\n", "72\t12\t108.1\t0\t12\n", "73\t4\t108.1\t0\t4\n", "74\t6\t108.1\t0\t6\n", "75\t5\t108.1\t0\t5\n", "76\t8\t108.1\t0\t8\n", "77\t4\t108.1\t0\t4\n", "78\t7\t108.1\t0\t7\n", "79\t4\t108.1\t0\t4\n", "80\t5\t108.1\t0\t5\n", "81\t10\t108.1\t0\t10\n", "82\t17\t108.1\t0\t17\n", "83\t16\t108.1\t0\t16\n", "84\t5\t108.1\t0\t5\n", "85\t9\t108.1\t0\t9\n", "86\t8\t108.1\t0\t8\n", "87\t6\t108.1\t0\t6\n", "88\t8\t108.1\t0\t8\n", "89\t5\t108.1\t0\t5\n", "90\t5\t108.1\t0\t5\n", "91\t10\t108.1\t0\t10\n", "92\t22\t108.1\t0\t22\n", "93\t61\t108.1\t0\t61\n", "94\t88\t108.1\t0\t88\n", "95\t135\t108.1\t0\t135\n", "96\t68\t108.1\t0\t68\n", "97\t60\t108.1\t0\t60\n", "98\t50\t108.1\t0\t50\n", "99\t63\t108.1\t0\t63\n", "100\t77\t108.1\t0\t77\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 110292 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 46.9%\n", " C: 18.2%\n", " G: 13.0%\n", " T: 21.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t72751\t110681.4\t0\t72751\n", "4\t14530\t27670.4\t0\t14530\n", "5\t2626\t6917.6\t0\t2626\n", "6\t400\t1729.4\t0\t400\n", "7\t353\t432.3\t0\t353\n", "8\t361\t432.3\t0\t361\n", "9\t338\t432.3\t0\t338\n", "10\t410\t432.3\t0\t410\n", "11\t391\t432.3\t0\t391\n", "12\t473\t432.3\t0\t473\n", "13\t669\t432.3\t0\t669\n", "14\t709\t432.3\t0\t709\n", "15\t630\t432.3\t0\t630\n", "16\t629\t432.3\t0\t629\n", "17\t686\t432.3\t0\t686\n", "18\t670\t432.3\t0\t670\n", "19\t549\t432.3\t0\t549\n", "20\t645\t432.3\t0\t645\n", "21\t530\t432.3\t0\t530\n", "22\t506\t432.3\t0\t506\n", "23\t431\t432.3\t0\t431\n", "24\t387\t432.3\t0\t387\n", "25\t366\t432.3\t0\t366\n", "26\t306\t432.3\t0\t306\n", "27\t381\t432.3\t0\t381\n", "28\t338\t432.3\t0\t338\n", "29\t284\t432.3\t0\t284\n", "30\t276\t432.3\t0\t276\n", "31\t255\t432.3\t0\t255\n", "32\t223\t432.3\t0\t223\n", "33\t246\t432.3\t0\t246\n", "34\t240\t432.3\t0\t240\n", "35\t234\t432.3\t0\t234\n", "36\t223\t432.3\t0\t223\n", "37\t253\t432.3\t0\t253\n", "38\t210\t432.3\t0\t210\n", "39\t227\t432.3\t0\t227\n", "40\t213\t432.3\t0\t213\n", "41\t209\t432.3\t0\t209\n", "42\t214\t432.3\t0\t214\n", "43\t278\t432.3\t0\t278\n", "44\t66\t432.3\t0\t66\n", "45\t180\t432.3\t0\t180\n", "46\t195\t432.3\t0\t195\n", "47\t175\t432.3\t0\t175\n", "48\t164\t432.3\t0\t164\n", "49\t165\t432.3\t0\t165\n", "50\t147\t432.3\t0\t147\n", "51\t142\t432.3\t0\t142\n", "52\t146\t432.3\t0\t146\n", "53\t171\t432.3\t0\t171\n", "54\t149\t432.3\t0\t149\n", "55\t204\t432.3\t0\t204\n", "56\t185\t432.3\t0\t185\n", "57\t119\t432.3\t0\t119\n", "58\t129\t432.3\t0\t129\n", "59\t103\t432.3\t0\t103\n", "60\t144\t432.3\t0\t144\n", "61\t108\t432.3\t0\t108\n", "62\t104\t432.3\t0\t104\n", "63\t78\t432.3\t0\t78\n", "64\t87\t432.3\t0\t87\n", "65\t87\t432.3\t0\t87\n", "66\t87\t432.3\t0\t87\n", "67\t117\t432.3\t0\t117\n", "68\t123\t432.3\t0\t123\n", "69\t44\t432.3\t0\t44\n", "70\t34\t432.3\t0\t34\n", "71\t75\t432.3\t0\t75\n", "72\t92\t432.3\t0\t92\n", "73\t104\t432.3\t0\t104\n", "74\t107\t432.3\t0\t107\n", "75\t80\t432.3\t0\t80\n", "76\t83\t432.3\t0\t83\n", "77\t93\t432.3\t0\t93\n", "78\t62\t432.3\t0\t62\n", "79\t61\t432.3\t0\t61\n", "80\t69\t432.3\t0\t69\n", "81\t76\t432.3\t0\t76\n", "82\t86\t432.3\t0\t86\n", "83\t80\t432.3\t0\t80\n", "84\t71\t432.3\t0\t71\n", "85\t56\t432.3\t0\t56\n", "86\t53\t432.3\t0\t53\n", "87\t82\t432.3\t0\t82\n", "88\t62\t432.3\t0\t62\n", "89\t63\t432.3\t0\t63\n", "90\t47\t432.3\t0\t47\n", "91\t47\t432.3\t0\t47\n", "92\t26\t432.3\t0\t26\n", "93\t32\t432.3\t0\t32\n", "94\t31\t432.3\t0\t31\n", "95\t56\t432.3\t0\t56\n", "96\t76\t432.3\t0\t76\n", "97\t106\t432.3\t0\t106\n", "98\t95\t432.3\t0\t95\n", "99\t111\t432.3\t0\t111\n", "100\t107\t432.3\t0\t107\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 524_S11_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/524.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 82.82 s (13 us/read; 4.47 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,169,181\n", "Reads with adapters: 3,363,867 (54.5%)\n", "Reads written (passing filters): 6,095,565 (98.8%)\n", "\n", "Total basepairs processed: 616,918,100 bp\n", "Quality-trimmed: 1,272,513 bp (0.2%)\n", "Total written (filtered): 509,745,756 bp (82.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3248325 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.9%\n", " G: 34.0%\n", " T: 38.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t160833\t96393.5\t0\t160833\n", "4\t94887\t24098.4\t0\t94887\n", "5\t72655\t6024.6\t0\t72655\n", "6\t56411\t1506.1\t0\t56411\n", "7\t49605\t376.5\t0\t49605\n", "8\t47957\t94.1\t0\t47957\n", "9\t47093\t94.1\t0\t47093\n", "10\t43624\t94.1\t0\t43624\n", "11\t45001\t94.1\t0\t45001\n", "12\t44161\t94.1\t0\t44161\n", "13\t45039\t94.1\t0\t45039\n", "14\t46049\t94.1\t0\t46049\n", "15\t46211\t94.1\t0\t46211\n", "16\t47689\t94.1\t0\t47689\n", "17\t53921\t94.1\t0\t53921\n", "18\t62549\t94.1\t0\t62549\n", "19\t57983\t94.1\t0\t57983\n", "20\t47287\t94.1\t0\t47287\n", "21\t46780\t94.1\t0\t46780\n", "22\t41331\t94.1\t0\t41331\n", "23\t47170\t94.1\t0\t47170\n", "24\t55263\t94.1\t0\t55263\n", "25\t55506\t94.1\t0\t55506\n", "26\t62083\t94.1\t0\t62083\n", "27\t68389\t94.1\t0\t68389\n", "28\t61930\t94.1\t0\t61930\n", "29\t58630\t94.1\t0\t58630\n", "30\t61668\t94.1\t0\t61668\n", "31\t66977\t94.1\t0\t66977\n", "32\t59008\t94.1\t0\t59008\n", "33\t53562\t94.1\t0\t53562\n", "34\t51199\t94.1\t0\t51199\n", "35\t58935\t94.1\t0\t58935\n", "36\t69270\t94.1\t0\t69270\n", "37\t69509\t94.1\t0\t69509\n", "38\t56810\t94.1\t0\t56810\n", "39\t47230\t94.1\t0\t47230\n", "40\t42555\t94.1\t0\t42555\n", "41\t44060\t94.1\t0\t44060\n", "42\t48499\t94.1\t0\t48499\n", "43\t43013\t94.1\t0\t43013\n", "44\t33283\t94.1\t0\t33283\n", "45\t43976\t94.1\t0\t43976\n", "46\t51983\t94.1\t0\t51983\n", "47\t50127\t94.1\t0\t50127\n", "48\t50140\t94.1\t0\t50140\n", "49\t39865\t94.1\t0\t39865\n", "50\t36661\t94.1\t0\t36661\n", "51\t30401\t94.1\t0\t30401\n", "52\t31220\t94.1\t0\t31220\n", "53\t36364\t94.1\t0\t36364\n", "54\t42524\t94.1\t0\t42524\n", "55\t36443\t94.1\t0\t36443\n", "56\t34692\t94.1\t0\t34692\n", "57\t32173\t94.1\t0\t32173\n", "58\t31132\t94.1\t0\t31132\n", "59\t22899\t94.1\t0\t22899\n", "60\t20110\t94.1\t0\t20110\n", "61\t19812\t94.1\t0\t19812\n", "62\t15658\t94.1\t0\t15658\n", "63\t14835\t94.1\t0\t14835\n", "64\t16709\t94.1\t0\t16709\n", "65\t16286\t94.1\t0\t16286\n", "66\t13781\t94.1\t0\t13781\n", "67\t13116\t94.1\t0\t13116\n", "68\t12296\t94.1\t0\t12296\n", "69\t12242\t94.1\t0\t12242\n", "70\t12488\t94.1\t0\t12488\n", "71\t11717\t94.1\t0\t11717\n", "72\t9465\t94.1\t0\t9465\n", "73\t8248\t94.1\t0\t8248\n", "74\t8278\t94.1\t0\t8278\n", "75\t6757\t94.1\t0\t6757\n", "76\t5529\t94.1\t0\t5529\n", "77\t4857\t94.1\t0\t4857\n", "78\t5569\t94.1\t0\t5569\n", "79\t5124\t94.1\t0\t5124\n", "80\t5140\t94.1\t0\t5140\n", "81\t4807\t94.1\t0\t4807\n", "82\t4571\t94.1\t0\t4571\n", "83\t5065\t94.1\t0\t5065\n", "84\t5701\t94.1\t0\t5701\n", "85\t6251\t94.1\t0\t6251\n", "86\t5897\t94.1\t0\t5897\n", "87\t4090\t94.1\t0\t4090\n", "88\t3794\t94.1\t0\t3794\n", "89\t4007\t94.1\t0\t4007\n", "90\t3970\t94.1\t0\t3970\n", "91\t3642\t94.1\t0\t3642\n", "92\t3302\t94.1\t0\t3302\n", "93\t3186\t94.1\t0\t3186\n", "94\t2911\t94.1\t0\t2911\n", "95\t2416\t94.1\t0\t2416\n", "96\t1758\t94.1\t0\t1758\n", "97\t1069\t94.1\t0\t1069\n", "98\t686\t94.1\t0\t686\n", "99\t554\t94.1\t0\t554\n", "100\t416\t94.1\t0\t416\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 14500 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 48.1%\n", " C: 17.8%\n", " G: 0.0%\n", " T: 33.4%\n", " none/other: 0.7%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t8094\t96393.5\t0\t8094\n", "4\t1769\t24098.4\t0\t1769\n", "5\t469\t6024.6\t0\t469\n", "6\t196\t1506.1\t0\t196\n", "7\t95\t376.5\t0\t95\n", "8\t86\t94.1\t0\t86\n", "9\t73\t94.1\t0\t73\n", "10\t48\t94.1\t0\t48\n", "11\t69\t94.1\t0\t69\n", "12\t57\t94.1\t0\t57\n", "13\t51\t94.1\t0\t51\n", "14\t73\t94.1\t0\t73\n", "15\t55\t94.1\t0\t55\n", "16\t54\t94.1\t0\t54\n", "17\t56\t94.1\t0\t56\n", "18\t53\t94.1\t0\t53\n", "19\t61\t94.1\t0\t61\n", "20\t65\t94.1\t0\t65\n", "21\t51\t94.1\t0\t51\n", "22\t54\t94.1\t0\t54\n", "23\t36\t94.1\t0\t36\n", "24\t52\t94.1\t0\t52\n", "25\t46\t94.1\t0\t46\n", "26\t76\t94.1\t0\t76\n", "27\t69\t94.1\t0\t69\n", "28\t72\t94.1\t0\t72\n", "29\t84\t94.1\t0\t84\n", "30\t127\t94.1\t0\t127\n", "31\t154\t94.1\t0\t154\n", "32\t234\t94.1\t0\t234\n", "33\t218\t94.1\t0\t218\n", "34\t207\t94.1\t0\t207\n", "35\t290\t94.1\t0\t290\n", "36\t290\t94.1\t0\t290\n", "37\t119\t94.1\t0\t119\n", "38\t33\t94.1\t0\t33\n", "39\t20\t94.1\t0\t20\n", "40\t10\t94.1\t0\t10\n", "41\t20\t94.1\t0\t20\n", "42\t13\t94.1\t0\t13\n", "43\t20\t94.1\t0\t20\n", "44\t18\t94.1\t0\t18\n", "45\t15\t94.1\t0\t15\n", "46\t15\t94.1\t0\t15\n", "47\t16\t94.1\t0\t16\n", "48\t18\t94.1\t0\t18\n", "49\t21\t94.1\t0\t21\n", "50\t17\t94.1\t0\t17\n", "51\t17\t94.1\t0\t17\n", "52\t19\t94.1\t0\t19\n", "53\t14\t94.1\t0\t14\n", "54\t11\t94.1\t0\t11\n", "55\t13\t94.1\t0\t13\n", "56\t11\t94.1\t0\t11\n", "57\t10\t94.1\t0\t10\n", "58\t7\t94.1\t0\t7\n", "59\t8\t94.1\t0\t8\n", "60\t6\t94.1\t0\t6\n", "61\t10\t94.1\t0\t10\n", "62\t13\t94.1\t0\t13\n", "63\t10\t94.1\t0\t10\n", "64\t8\t94.1\t0\t8\n", "65\t7\t94.1\t0\t7\n", "66\t8\t94.1\t0\t8\n", "67\t3\t94.1\t0\t3\n", "68\t6\t94.1\t0\t6\n", "69\t4\t94.1\t0\t4\n", "70\t6\t94.1\t0\t6\n", "71\t7\t94.1\t0\t7\n", "72\t4\t94.1\t0\t4\n", "73\t5\t94.1\t0\t5\n", "74\t4\t94.1\t0\t4\n", "75\t2\t94.1\t0\t2\n", "76\t3\t94.1\t0\t3\n", "77\t3\t94.1\t0\t3\n", "78\t2\t94.1\t0\t2\n", "80\t3\t94.1\t0\t3\n", "82\t1\t94.1\t0\t1\n", "83\t6\t94.1\t0\t6\n", "84\t9\t94.1\t0\t9\n", "85\t2\t94.1\t0\t2\n", "86\t5\t94.1\t0\t5\n", "87\t4\t94.1\t0\t4\n", "88\t3\t94.1\t0\t3\n", "89\t2\t94.1\t0\t2\n", "90\t5\t94.1\t0\t5\n", "91\t4\t94.1\t0\t4\n", "92\t16\t94.1\t0\t16\n", "93\t27\t94.1\t0\t27\n", "94\t46\t94.1\t0\t46\n", "95\t72\t94.1\t0\t72\n", "96\t32\t94.1\t0\t32\n", "97\t29\t94.1\t0\t29\n", "98\t28\t94.1\t0\t28\n", "99\t39\t94.1\t0\t39\n", "100\t107\t94.1\t0\t107\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 101042 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 46.3%\n", " C: 19.2%\n", " G: 12.9%\n", " T: 21.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t72164\t96393.5\t0\t72164\n", "4\t16455\t24098.4\t0\t16455\n", "5\t4205\t6024.6\t0\t4205\n", "6\t254\t1506.1\t0\t254\n", "7\t122\t376.5\t0\t122\n", "8\t142\t376.5\t0\t142\n", "9\t123\t376.5\t0\t123\n", "10\t166\t376.5\t0\t166\n", "11\t164\t376.5\t0\t164\n", "12\t163\t376.5\t0\t163\n", "13\t138\t376.5\t0\t138\n", "14\t128\t376.5\t0\t128\n", "15\t132\t376.5\t0\t132\n", "16\t135\t376.5\t0\t135\n", "17\t106\t376.5\t0\t106\n", "18\t118\t376.5\t0\t118\n", "19\t128\t376.5\t0\t128\n", "20\t105\t376.5\t0\t105\n", "21\t101\t376.5\t0\t101\n", "22\t104\t376.5\t0\t104\n", "23\t83\t376.5\t0\t83\n", "24\t83\t376.5\t0\t83\n", "25\t87\t376.5\t0\t87\n", "26\t103\t376.5\t0\t103\n", "27\t104\t376.5\t0\t104\n", "28\t94\t376.5\t0\t94\n", "29\t74\t376.5\t0\t74\n", "30\t102\t376.5\t0\t102\n", "31\t98\t376.5\t0\t98\n", "32\t116\t376.5\t0\t116\n", "33\t93\t376.5\t0\t93\n", "34\t92\t376.5\t0\t92\n", "35\t80\t376.5\t0\t80\n", "36\t76\t376.5\t0\t76\n", "37\t83\t376.5\t0\t83\n", "38\t73\t376.5\t0\t73\n", "39\t99\t376.5\t0\t99\n", "40\t101\t376.5\t0\t101\n", "41\t95\t376.5\t0\t95\n", "42\t75\t376.5\t0\t75\n", "43\t108\t376.5\t0\t108\n", "44\t44\t376.5\t0\t44\n", "45\t91\t376.5\t0\t91\n", "46\t88\t376.5\t0\t88\n", "47\t81\t376.5\t0\t81\n", "48\t63\t376.5\t0\t63\n", "49\t60\t376.5\t0\t60\n", "50\t48\t376.5\t0\t48\n", "51\t68\t376.5\t0\t68\n", "52\t64\t376.5\t0\t64\n", "53\t80\t376.5\t0\t80\n", "54\t73\t376.5\t0\t73\n", "55\t44\t376.5\t0\t44\n", "56\t46\t376.5\t0\t46\n", "57\t50\t376.5\t0\t50\n", "58\t44\t376.5\t0\t44\n", "59\t48\t376.5\t0\t48\n", "60\t59\t376.5\t0\t59\n", "61\t71\t376.5\t0\t71\n", "62\t58\t376.5\t0\t58\n", "63\t62\t376.5\t0\t62\n", "64\t61\t376.5\t0\t61\n", "65\t40\t376.5\t0\t40\n", "66\t62\t376.5\t0\t62\n", "67\t43\t376.5\t0\t43\n", "68\t44\t376.5\t0\t44\n", "69\t35\t376.5\t0\t35\n", "70\t42\t376.5\t0\t42\n", "71\t45\t376.5\t0\t45\n", "72\t68\t376.5\t0\t68\n", "73\t93\t376.5\t0\t93\n", "74\t92\t376.5\t0\t92\n", "75\t59\t376.5\t0\t59\n", "76\t70\t376.5\t0\t70\n", "77\t98\t376.5\t0\t98\n", "78\t81\t376.5\t0\t81\n", "79\t84\t376.5\t0\t84\n", "80\t106\t376.5\t0\t106\n", "81\t124\t376.5\t0\t124\n", "82\t157\t376.5\t0\t157\n", "83\t109\t376.5\t0\t109\n", "84\t91\t376.5\t0\t91\n", "85\t87\t376.5\t0\t87\n", "86\t56\t376.5\t0\t56\n", "87\t85\t376.5\t0\t85\n", "88\t57\t376.5\t0\t57\n", "89\t59\t376.5\t0\t59\n", "90\t57\t376.5\t0\t57\n", "91\t62\t376.5\t0\t62\n", "92\t36\t376.5\t0\t36\n", "93\t48\t376.5\t0\t48\n", "94\t59\t376.5\t0\t59\n", "95\t27\t376.5\t0\t27\n", "96\t52\t376.5\t0\t52\n", "97\t91\t376.5\t0\t91\n", "98\t93\t376.5\t0\t93\n", "99\t112\t376.5\t0\t112\n", "100\t143\t376.5\t0\t143\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 525_S18_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/525.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 69.69 s (13 us/read; 4.69 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,450,396\n", "Reads with adapters: 3,199,335 (58.7%)\n", "Reads written (passing filters): 5,336,335 (97.9%)\n", "\n", "Total basepairs processed: 545,039,600 bp\n", "Quality-trimmed: 1,445,137 bp (0.3%)\n", "Total written (filtered): 432,782,936 bp (79.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3074431 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 32.3%\n", " G: 40.8%\n", " T: 26.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t114518\t85162.4\t0\t114518\n", "4\t66066\t21290.6\t0\t66066\n", "5\t50736\t5322.7\t0\t50736\n", "6\t41500\t1330.7\t0\t41500\n", "7\t38951\t332.7\t0\t38951\n", "8\t39058\t83.2\t0\t39058\n", "9\t38364\t83.2\t0\t38364\n", "10\t37754\t83.2\t0\t37754\n", "11\t37657\t83.2\t0\t37657\n", "12\t38674\t83.2\t0\t38674\n", "13\t42791\t83.2\t0\t42791\n", "14\t43381\t83.2\t0\t43381\n", "15\t41630\t83.2\t0\t41630\n", "16\t43223\t83.2\t0\t43223\n", "17\t47809\t83.2\t0\t47809\n", "18\t55211\t83.2\t0\t55211\n", "19\t51175\t83.2\t0\t51175\n", "20\t42516\t83.2\t0\t42516\n", "21\t41389\t83.2\t0\t41389\n", "22\t37237\t83.2\t0\t37237\n", "23\t40199\t83.2\t0\t40199\n", "24\t46447\t83.2\t0\t46447\n", "25\t48051\t83.2\t0\t48051\n", "26\t55164\t83.2\t0\t55164\n", "27\t60656\t83.2\t0\t60656\n", "28\t53746\t83.2\t0\t53746\n", "29\t50333\t83.2\t0\t50333\n", "30\t50130\t83.2\t0\t50130\n", "31\t55624\t83.2\t0\t55624\n", "32\t55131\t83.2\t0\t55131\n", "33\t50801\t83.2\t0\t50801\n", "34\t49206\t83.2\t0\t49206\n", "35\t56044\t83.2\t0\t56044\n", "36\t63834\t83.2\t0\t63834\n", "37\t62472\t83.2\t0\t62472\n", "38\t52410\t83.2\t0\t52410\n", "39\t46895\t83.2\t0\t46895\n", "40\t45156\t83.2\t0\t45156\n", "41\t51132\t83.2\t0\t51132\n", "42\t57602\t83.2\t0\t57602\n", "43\t49155\t83.2\t0\t49155\n", "44\t37850\t83.2\t0\t37850\n", "45\t48161\t83.2\t0\t48161\n", "46\t58176\t83.2\t0\t58176\n", "47\t50603\t83.2\t0\t50603\n", "48\t50250\t83.2\t0\t50250\n", "49\t40714\t83.2\t0\t40714\n", "50\t41323\t83.2\t0\t41323\n", "51\t35738\t83.2\t0\t35738\n", "52\t34721\t83.2\t0\t34721\n", "53\t31563\t83.2\t0\t31563\n", "54\t35874\t83.2\t0\t35874\n", "55\t40285\t83.2\t0\t40285\n", "56\t33976\t83.2\t0\t33976\n", "57\t30374\t83.2\t0\t30374\n", "58\t34212\t83.2\t0\t34212\n", "59\t28440\t83.2\t0\t28440\n", "60\t23275\t83.2\t0\t23275\n", "61\t21755\t83.2\t0\t21755\n", "62\t17896\t83.2\t0\t17896\n", "63\t16559\t83.2\t0\t16559\n", "64\t19211\t83.2\t0\t19211\n", "65\t18883\t83.2\t0\t18883\n", "66\t15603\t83.2\t0\t15603\n", "67\t15517\t83.2\t0\t15517\n", "68\t15270\t83.2\t0\t15270\n", "69\t15625\t83.2\t0\t15625\n", "70\t16291\t83.2\t0\t16291\n", "71\t15362\t83.2\t0\t15362\n", "72\t11503\t83.2\t0\t11503\n", "73\t9997\t83.2\t0\t9997\n", "74\t9862\t83.2\t0\t9862\n", "75\t8764\t83.2\t0\t8764\n", "76\t6858\t83.2\t0\t6858\n", "77\t6532\t83.2\t0\t6532\n", "78\t7933\t83.2\t0\t7933\n", "79\t7153\t83.2\t0\t7153\n", "80\t7127\t83.2\t0\t7127\n", "81\t6589\t83.2\t0\t6589\n", "82\t6167\t83.2\t0\t6167\n", "83\t6370\t83.2\t0\t6370\n", "84\t7312\t83.2\t0\t7312\n", "85\t8367\t83.2\t0\t8367\n", "86\t7900\t83.2\t0\t7900\n", "87\t5648\t83.2\t0\t5648\n", "88\t4975\t83.2\t0\t4975\n", "89\t5530\t83.2\t0\t5530\n", "90\t5788\t83.2\t0\t5788\n", "91\t5859\t83.2\t0\t5859\n", "92\t6255\t83.2\t0\t6255\n", "93\t6785\t83.2\t0\t6785\n", "94\t6483\t83.2\t0\t6483\n", "95\t5553\t83.2\t0\t5553\n", "96\t3958\t83.2\t0\t3958\n", "97\t2487\t83.2\t0\t2487\n", "98\t1380\t83.2\t0\t1380\n", "99\t1175\t83.2\t0\t1175\n", "100\t786\t83.2\t0\t786\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27900 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.1%\n", " C: 31.0%\n", " G: 0.0%\n", " T: 23.8%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t14513\t85162.4\t0\t14513\n", "4\t3376\t21290.6\t0\t3376\n", "5\t1299\t5322.7\t0\t1299\n", "6\t805\t1330.7\t0\t805\n", "7\t170\t332.7\t0\t170\n", "8\t125\t83.2\t0\t125\n", "9\t113\t83.2\t0\t113\n", "10\t113\t83.2\t0\t113\n", "11\t115\t83.2\t0\t115\n", "12\t110\t83.2\t0\t110\n", "13\t82\t83.2\t0\t82\n", "14\t121\t83.2\t0\t121\n", "15\t96\t83.2\t0\t96\n", "16\t101\t83.2\t0\t101\n", "17\t101\t83.2\t0\t101\n", "18\t122\t83.2\t0\t122\n", "19\t147\t83.2\t0\t147\n", "20\t173\t83.2\t0\t173\n", "21\t141\t83.2\t0\t141\n", "22\t134\t83.2\t0\t134\n", "23\t105\t83.2\t0\t105\n", "24\t111\t83.2\t0\t111\n", "25\t100\t83.2\t0\t100\n", "26\t181\t83.2\t0\t181\n", "27\t168\t83.2\t0\t168\n", "28\t140\t83.2\t0\t140\n", "29\t188\t83.2\t0\t188\n", "30\t283\t83.2\t0\t283\n", "31\t322\t83.2\t0\t322\n", "32\t459\t83.2\t0\t459\n", "33\t423\t83.2\t0\t423\n", "34\t423\t83.2\t0\t423\n", "35\t561\t83.2\t0\t561\n", "36\t504\t83.2\t0\t504\n", "37\t185\t83.2\t0\t185\n", "38\t46\t83.2\t0\t46\n", "39\t50\t83.2\t0\t50\n", "40\t53\t83.2\t0\t53\n", "41\t30\t83.2\t0\t30\n", "42\t42\t83.2\t0\t42\n", "43\t38\t83.2\t0\t38\n", "44\t31\t83.2\t0\t31\n", "45\t30\t83.2\t0\t30\n", "46\t42\t83.2\t0\t42\n", "47\t37\t83.2\t0\t37\n", "48\t36\t83.2\t0\t36\n", "49\t49\t83.2\t0\t49\n", "50\t37\t83.2\t0\t37\n", "51\t39\t83.2\t0\t39\n", "52\t29\t83.2\t0\t29\n", "53\t35\t83.2\t0\t35\n", "54\t21\t83.2\t0\t21\n", "55\t21\t83.2\t0\t21\n", "56\t30\t83.2\t0\t30\n", "57\t35\t83.2\t0\t35\n", "58\t28\t83.2\t0\t28\n", "59\t24\t83.2\t0\t24\n", "60\t12\t83.2\t0\t12\n", "61\t25\t83.2\t0\t25\n", "62\t31\t83.2\t0\t31\n", "63\t19\t83.2\t0\t19\n", "64\t18\t83.2\t0\t18\n", "65\t26\t83.2\t0\t26\n", "66\t14\t83.2\t0\t14\n", "67\t16\t83.2\t0\t16\n", "68\t14\t83.2\t0\t14\n", "69\t14\t83.2\t0\t14\n", "70\t10\t83.2\t0\t10\n", "71\t16\t83.2\t0\t16\n", "72\t15\t83.2\t0\t15\n", "73\t13\t83.2\t0\t13\n", "74\t7\t83.2\t0\t7\n", "75\t11\t83.2\t0\t11\n", "76\t5\t83.2\t0\t5\n", "77\t10\t83.2\t0\t10\n", "78\t8\t83.2\t0\t8\n", "79\t8\t83.2\t0\t8\n", "80\t13\t83.2\t0\t13\n", "81\t13\t83.2\t0\t13\n", "82\t10\t83.2\t0\t10\n", "83\t8\t83.2\t0\t8\n", "84\t14\t83.2\t0\t14\n", "85\t12\t83.2\t0\t12\n", "86\t13\t83.2\t0\t13\n", "87\t10\t83.2\t0\t10\n", "88\t5\t83.2\t0\t5\n", "89\t12\t83.2\t0\t12\n", "90\t8\t83.2\t0\t8\n", "91\t16\t83.2\t0\t16\n", "92\t20\t83.2\t0\t20\n", "93\t52\t83.2\t0\t52\n", "94\t83\t83.2\t0\t83\n", "95\t90\t83.2\t0\t90\n", "96\t84\t83.2\t0\t84\n", "97\t88\t83.2\t0\t88\n", "98\t58\t83.2\t0\t58\n", "99\t44\t83.2\t0\t44\n", "100\t62\t83.2\t0\t62\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 97004 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 41.5%\n", " C: 21.4%\n", " G: 18.7%\n", " T: 18.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t69769\t85162.4\t0\t69769\n", "4\t13628\t21290.6\t0\t13628\n", "5\t2590\t5322.7\t0\t2590\n", "6\t375\t1330.7\t0\t375\n", "7\t200\t332.7\t0\t200\n", "8\t217\t332.7\t0\t217\n", "9\t208\t332.7\t0\t208\n", "10\t233\t332.7\t0\t233\n", "11\t204\t332.7\t0\t204\n", "12\t214\t332.7\t0\t214\n", "13\t205\t332.7\t0\t205\n", "14\t212\t332.7\t0\t212\n", "15\t222\t332.7\t0\t222\n", "16\t213\t332.7\t0\t213\n", "17\t186\t332.7\t0\t186\n", "18\t171\t332.7\t0\t171\n", "19\t194\t332.7\t0\t194\n", "20\t192\t332.7\t0\t192\n", "21\t205\t332.7\t0\t205\n", "22\t176\t332.7\t0\t176\n", "23\t154\t332.7\t0\t154\n", "24\t148\t332.7\t0\t148\n", "25\t189\t332.7\t0\t189\n", "26\t160\t332.7\t0\t160\n", "27\t166\t332.7\t0\t166\n", "28\t159\t332.7\t0\t159\n", "29\t167\t332.7\t0\t167\n", "30\t144\t332.7\t0\t144\n", "31\t146\t332.7\t0\t146\n", "32\t143\t332.7\t0\t143\n", "33\t128\t332.7\t0\t128\n", "34\t139\t332.7\t0\t139\n", "35\t162\t332.7\t0\t162\n", "36\t128\t332.7\t0\t128\n", "37\t140\t332.7\t0\t140\n", "38\t128\t332.7\t0\t128\n", "39\t151\t332.7\t0\t151\n", "40\t160\t332.7\t0\t160\n", "41\t116\t332.7\t0\t116\n", "42\t114\t332.7\t0\t114\n", "43\t124\t332.7\t0\t124\n", "44\t74\t332.7\t0\t74\n", "45\t104\t332.7\t0\t104\n", "46\t110\t332.7\t0\t110\n", "47\t109\t332.7\t0\t109\n", "48\t113\t332.7\t0\t113\n", "49\t94\t332.7\t0\t94\n", "50\t97\t332.7\t0\t97\n", "51\t93\t332.7\t0\t93\n", "52\t94\t332.7\t0\t94\n", "53\t83\t332.7\t0\t83\n", "54\t67\t332.7\t0\t67\n", "55\t64\t332.7\t0\t64\n", "56\t63\t332.7\t0\t63\n", "57\t49\t332.7\t0\t49\n", "58\t63\t332.7\t0\t63\n", "59\t34\t332.7\t0\t34\n", "60\t67\t332.7\t0\t67\n", "61\t84\t332.7\t0\t84\n", "62\t63\t332.7\t0\t63\n", "63\t70\t332.7\t0\t70\n", "64\t73\t332.7\t0\t73\n", "65\t51\t332.7\t0\t51\n", "66\t55\t332.7\t0\t55\n", "67\t65\t332.7\t0\t65\n", "68\t73\t332.7\t0\t73\n", "69\t62\t332.7\t0\t62\n", "70\t50\t332.7\t0\t50\n", "71\t52\t332.7\t0\t52\n", "72\t66\t332.7\t0\t66\n", "73\t67\t332.7\t0\t67\n", "74\t67\t332.7\t0\t67\n", "75\t75\t332.7\t0\t75\n", "76\t96\t332.7\t0\t96\n", "77\t91\t332.7\t0\t91\n", "78\t97\t332.7\t0\t97\n", "79\t86\t332.7\t0\t86\n", "80\t89\t332.7\t0\t89\n", "81\t97\t332.7\t0\t97\n", "82\t104\t332.7\t0\t104\n", "83\t106\t332.7\t0\t106\n", "84\t98\t332.7\t0\t98\n", "85\t97\t332.7\t0\t97\n", "86\t85\t332.7\t0\t85\n", "87\t82\t332.7\t0\t82\n", "88\t88\t332.7\t0\t88\n", "89\t80\t332.7\t0\t80\n", "90\t65\t332.7\t0\t65\n", "91\t54\t332.7\t0\t54\n", "92\t48\t332.7\t0\t48\n", "93\t53\t332.7\t0\t53\n", "94\t47\t332.7\t0\t47\n", "95\t51\t332.7\t0\t51\n", "96\t57\t332.7\t0\t57\n", "97\t48\t332.7\t0\t48\n", "98\t79\t332.7\t0\t79\n", "99\t88\t332.7\t0\t88\n", "100\t87\t332.7\t0\t87\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 526_S15_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/526.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 67.56 s (13 us/read; 4.73 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,331,939\n", "Reads with adapters: 2,546,898 (47.8%)\n", "Reads written (passing filters): 5,230,794 (98.1%)\n", "\n", "Total basepairs processed: 533,193,900 bp\n", "Quality-trimmed: 1,274,103 bp (0.2%)\n", "Total written (filtered): 446,056,394 bp (83.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2406228 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.7%\n", " G: 38.1%\n", " T: 31.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t122149\t83311.5\t0\t122149\n", "4\t65932\t20827.9\t0\t65932\n", "5\t45472\t5207.0\t0\t45472\n", "6\t36779\t1301.7\t0\t36779\n", "7\t31366\t325.4\t0\t31366\n", "8\t31725\t81.4\t0\t31725\n", "9\t30599\t81.4\t0\t30599\n", "10\t29616\t81.4\t0\t29616\n", "11\t29806\t81.4\t0\t29806\n", "12\t29495\t81.4\t0\t29495\n", "13\t30758\t81.4\t0\t30758\n", "14\t31890\t81.4\t0\t31890\n", "15\t31638\t81.4\t0\t31638\n", "16\t32676\t81.4\t0\t32676\n", "17\t35953\t81.4\t0\t35953\n", "18\t40880\t81.4\t0\t40880\n", "19\t39149\t81.4\t0\t39149\n", "20\t32012\t81.4\t0\t32012\n", "21\t30645\t81.4\t0\t30645\n", "22\t27813\t81.4\t0\t27813\n", "23\t30104\t81.4\t0\t30104\n", "24\t35382\t81.4\t0\t35382\n", "25\t35794\t81.4\t0\t35794\n", "26\t40506\t81.4\t0\t40506\n", "27\t44696\t81.4\t0\t44696\n", "28\t40680\t81.4\t0\t40680\n", "29\t38471\t81.4\t0\t38471\n", "30\t39721\t81.4\t0\t39721\n", "31\t43522\t81.4\t0\t43522\n", "32\t42160\t81.4\t0\t42160\n", "33\t38822\t81.4\t0\t38822\n", "34\t37591\t81.4\t0\t37591\n", "35\t42482\t81.4\t0\t42482\n", "36\t49251\t81.4\t0\t49251\n", "37\t50908\t81.4\t0\t50908\n", "38\t41703\t81.4\t0\t41703\n", "39\t35123\t81.4\t0\t35123\n", "40\t33125\t81.4\t0\t33125\n", "41\t34946\t81.4\t0\t34946\n", "42\t37963\t81.4\t0\t37963\n", "43\t33741\t81.4\t0\t33741\n", "44\t27199\t81.4\t0\t27199\n", "45\t34457\t81.4\t0\t34457\n", "46\t40694\t81.4\t0\t40694\n", "47\t36801\t81.4\t0\t36801\n", "48\t38555\t81.4\t0\t38555\n", "49\t31295\t81.4\t0\t31295\n", "50\t31952\t81.4\t0\t31952\n", "51\t27653\t81.4\t0\t27653\n", "52\t27743\t81.4\t0\t27743\n", "53\t21757\t81.4\t0\t21757\n", "54\t21416\t81.4\t0\t21416\n", "55\t24682\t81.4\t0\t24682\n", "56\t23807\t81.4\t0\t23807\n", "57\t23950\t81.4\t0\t23950\n", "58\t28127\t81.4\t0\t28127\n", "59\t24167\t81.4\t0\t24167\n", "60\t20191\t81.4\t0\t20191\n", "61\t17849\t81.4\t0\t17849\n", "62\t14353\t81.4\t0\t14353\n", "63\t14273\t81.4\t0\t14273\n", "64\t16708\t81.4\t0\t16708\n", "65\t14851\t81.4\t0\t14851\n", "66\t12247\t81.4\t0\t12247\n", "67\t12994\t81.4\t0\t12994\n", "68\t12563\t81.4\t0\t12563\n", "69\t12908\t81.4\t0\t12908\n", "70\t14777\t81.4\t0\t14777\n", "71\t13449\t81.4\t0\t13449\n", "72\t9938\t81.4\t0\t9938\n", "73\t7609\t81.4\t0\t7609\n", "74\t7115\t81.4\t0\t7115\n", "75\t6732\t81.4\t0\t6732\n", "76\t5640\t81.4\t0\t5640\n", "77\t6175\t81.4\t0\t6175\n", "78\t7539\t81.4\t0\t7539\n", "79\t6371\t81.4\t0\t6371\n", "80\t5703\t81.4\t0\t5703\n", "81\t5826\t81.4\t0\t5826\n", "82\t5497\t81.4\t0\t5497\n", "83\t5506\t81.4\t0\t5506\n", "84\t6127\t81.4\t0\t6127\n", "85\t7243\t81.4\t0\t7243\n", "86\t7023\t81.4\t0\t7023\n", "87\t5297\t81.4\t0\t5297\n", "88\t4835\t81.4\t0\t4835\n", "89\t5056\t81.4\t0\t5056\n", "90\t5209\t81.4\t0\t5209\n", "91\t5252\t81.4\t0\t5252\n", "92\t5102\t81.4\t0\t5102\n", "93\t5037\t81.4\t0\t5037\n", "94\t4545\t81.4\t0\t4545\n", "95\t3592\t81.4\t0\t3592\n", "96\t2613\t81.4\t0\t2613\n", "97\t1820\t81.4\t0\t1820\n", "98\t1154\t81.4\t0\t1154\n", "99\t1342\t81.4\t0\t1342\n", "100\t868\t81.4\t0\t868\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28227 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.2%\n", " C: 30.6%\n", " G: 0.0%\n", " T: 25.1%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t15543\t83311.5\t0\t15543\n", "4\t4169\t20827.9\t0\t4169\n", "5\t1854\t5207.0\t0\t1854\n", "6\t653\t1301.7\t0\t653\n", "7\t143\t325.4\t0\t143\n", "8\t118\t81.4\t0\t118\n", "9\t95\t81.4\t0\t95\n", "10\t93\t81.4\t0\t93\n", "11\t92\t81.4\t0\t92\n", "12\t85\t81.4\t0\t85\n", "13\t82\t81.4\t0\t82\n", "14\t93\t81.4\t0\t93\n", "15\t85\t81.4\t0\t85\n", "16\t84\t81.4\t0\t84\n", "17\t81\t81.4\t0\t81\n", "18\t132\t81.4\t0\t132\n", "19\t160\t81.4\t0\t160\n", "20\t209\t81.4\t0\t209\n", "21\t142\t81.4\t0\t142\n", "22\t116\t81.4\t0\t116\n", "23\t91\t81.4\t0\t91\n", "24\t99\t81.4\t0\t99\n", "25\t89\t81.4\t0\t89\n", "26\t131\t81.4\t0\t131\n", "27\t119\t81.4\t0\t119\n", "28\t109\t81.4\t0\t109\n", "29\t165\t81.4\t0\t165\n", "30\t232\t81.4\t0\t232\n", "31\t249\t81.4\t0\t249\n", "32\t308\t81.4\t0\t308\n", "33\t285\t81.4\t0\t285\n", "34\t282\t81.4\t0\t282\n", "35\t356\t81.4\t0\t356\n", "36\t264\t81.4\t0\t264\n", "37\t142\t81.4\t0\t142\n", "38\t40\t81.4\t0\t40\n", "39\t48\t81.4\t0\t48\n", "40\t32\t81.4\t0\t32\n", "41\t22\t81.4\t0\t22\n", "42\t26\t81.4\t0\t26\n", "43\t28\t81.4\t0\t28\n", "44\t30\t81.4\t0\t30\n", "45\t28\t81.4\t0\t28\n", "46\t34\t81.4\t0\t34\n", "47\t29\t81.4\t0\t29\n", "48\t15\t81.4\t0\t15\n", "49\t36\t81.4\t0\t36\n", "50\t33\t81.4\t0\t33\n", "51\t26\t81.4\t0\t26\n", "52\t21\t81.4\t0\t21\n", "53\t18\t81.4\t0\t18\n", "54\t21\t81.4\t0\t21\n", "55\t14\t81.4\t0\t14\n", "56\t23\t81.4\t0\t23\n", "57\t23\t81.4\t0\t23\n", "58\t21\t81.4\t0\t21\n", "59\t26\t81.4\t0\t26\n", "60\t14\t81.4\t0\t14\n", "61\t22\t81.4\t0\t22\n", "62\t18\t81.4\t0\t18\n", "63\t17\t81.4\t0\t17\n", "64\t13\t81.4\t0\t13\n", "65\t22\t81.4\t0\t22\n", "66\t19\t81.4\t0\t19\n", "67\t14\t81.4\t0\t14\n", "68\t7\t81.4\t0\t7\n", "69\t9\t81.4\t0\t9\n", "70\t8\t81.4\t0\t8\n", "71\t11\t81.4\t0\t11\n", "72\t10\t81.4\t0\t10\n", "73\t10\t81.4\t0\t10\n", "74\t12\t81.4\t0\t12\n", "75\t9\t81.4\t0\t9\n", "76\t7\t81.4\t0\t7\n", "77\t4\t81.4\t0\t4\n", "78\t9\t81.4\t0\t9\n", "79\t9\t81.4\t0\t9\n", "80\t11\t81.4\t0\t11\n", "81\t7\t81.4\t0\t7\n", "82\t2\t81.4\t0\t2\n", "83\t7\t81.4\t0\t7\n", "84\t9\t81.4\t0\t9\n", "85\t6\t81.4\t0\t6\n", "86\t14\t81.4\t0\t14\n", "87\t5\t81.4\t0\t5\n", "88\t10\t81.4\t0\t10\n", "89\t9\t81.4\t0\t9\n", "90\t5\t81.4\t0\t5\n", "91\t8\t81.4\t0\t8\n", "92\t19\t81.4\t0\t19\n", "93\t23\t81.4\t0\t23\n", "94\t35\t81.4\t0\t35\n", "95\t40\t81.4\t0\t40\n", "96\t50\t81.4\t0\t50\n", "97\t42\t81.4\t0\t42\n", "98\t30\t81.4\t0\t30\n", "99\t32\t81.4\t0\t32\n", "100\t75\t81.4\t0\t75\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 112443 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.0%\n", " C: 22.9%\n", " G: 16.4%\n", " T: 21.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t84254\t83311.5\t0\t84254\n", "4\t16356\t20827.9\t0\t16356\n", "5\t2871\t5207.0\t0\t2871\n", "6\t293\t1301.7\t0\t293\n", "7\t113\t325.4\t0\t113\n", "8\t121\t325.4\t0\t121\n", "9\t121\t325.4\t0\t121\n", "10\t117\t325.4\t0\t117\n", "11\t131\t325.4\t0\t131\n", "12\t135\t325.4\t0\t135\n", "13\t141\t325.4\t0\t141\n", "14\t134\t325.4\t0\t134\n", "15\t159\t325.4\t0\t159\n", "16\t149\t325.4\t0\t149\n", "17\t143\t325.4\t0\t143\n", "18\t137\t325.4\t0\t137\n", "19\t136\t325.4\t0\t136\n", "20\t118\t325.4\t0\t118\n", "21\t107\t325.4\t0\t107\n", "22\t110\t325.4\t0\t110\n", "23\t107\t325.4\t0\t107\n", "24\t105\t325.4\t0\t105\n", "25\t87\t325.4\t0\t87\n", "26\t88\t325.4\t0\t88\n", "27\t119\t325.4\t0\t119\n", "28\t115\t325.4\t0\t115\n", "29\t102\t325.4\t0\t102\n", "30\t117\t325.4\t0\t117\n", "31\t89\t325.4\t0\t89\n", "32\t115\t325.4\t0\t115\n", "33\t102\t325.4\t0\t102\n", "34\t109\t325.4\t0\t109\n", "35\t76\t325.4\t0\t76\n", "36\t103\t325.4\t0\t103\n", "37\t108\t325.4\t0\t108\n", "38\t101\t325.4\t0\t101\n", "39\t125\t325.4\t0\t125\n", "40\t110\t325.4\t0\t110\n", "41\t103\t325.4\t0\t103\n", "42\t92\t325.4\t0\t92\n", "43\t118\t325.4\t0\t118\n", "44\t73\t325.4\t0\t73\n", "45\t98\t325.4\t0\t98\n", "46\t113\t325.4\t0\t113\n", "47\t83\t325.4\t0\t83\n", "48\t79\t325.4\t0\t79\n", "49\t88\t325.4\t0\t88\n", "50\t110\t325.4\t0\t110\n", "51\t74\t325.4\t0\t74\n", "52\t84\t325.4\t0\t84\n", "53\t106\t325.4\t0\t106\n", "54\t69\t325.4\t0\t69\n", "55\t60\t325.4\t0\t60\n", "56\t68\t325.4\t0\t68\n", "57\t82\t325.4\t0\t82\n", "58\t71\t325.4\t0\t71\n", "59\t58\t325.4\t0\t58\n", "60\t89\t325.4\t0\t89\n", "61\t82\t325.4\t0\t82\n", "62\t64\t325.4\t0\t64\n", "63\t78\t325.4\t0\t78\n", "64\t67\t325.4\t0\t67\n", "65\t56\t325.4\t0\t56\n", "66\t72\t325.4\t0\t72\n", "67\t65\t325.4\t0\t65\n", "68\t65\t325.4\t0\t65\n", "69\t60\t325.4\t0\t60\n", "70\t45\t325.4\t0\t45\n", "71\t71\t325.4\t0\t71\n", "72\t62\t325.4\t0\t62\n", "73\t91\t325.4\t0\t91\n", "74\t84\t325.4\t0\t84\n", "75\t79\t325.4\t0\t79\n", "76\t79\t325.4\t0\t79\n", "77\t94\t325.4\t0\t94\n", "78\t98\t325.4\t0\t98\n", "79\t97\t325.4\t0\t97\n", "80\t91\t325.4\t0\t91\n", "81\t98\t325.4\t0\t98\n", "82\t124\t325.4\t0\t124\n", "83\t88\t325.4\t0\t88\n", "84\t96\t325.4\t0\t96\n", "85\t85\t325.4\t0\t85\n", "86\t69\t325.4\t0\t69\n", "87\t87\t325.4\t0\t87\n", "88\t87\t325.4\t0\t87\n", "89\t93\t325.4\t0\t93\n", "90\t83\t325.4\t0\t83\n", "91\t62\t325.4\t0\t62\n", "92\t53\t325.4\t0\t53\n", "93\t32\t325.4\t0\t32\n", "94\t53\t325.4\t0\t53\n", "95\t47\t325.4\t0\t47\n", "96\t44\t325.4\t0\t44\n", "97\t54\t325.4\t0\t54\n", "98\t81\t325.4\t0\t81\n", "99\t77\t325.4\t0\t77\n", "100\t88\t325.4\t0\t88\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 527_S39_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/527.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 110.51 s (14 us/read; 4.36 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,035,172\n", "Reads with adapters: 5,923,113 (73.7%)\n", "Reads written (passing filters): 7,826,889 (97.4%)\n", "\n", "Total basepairs processed: 803,517,200 bp\n", "Quality-trimmed: 2,528,000 bp (0.3%)\n", "Total written (filtered): 590,892,584 bp (73.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5796947 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.2%\n", " G: 37.4%\n", " T: 31.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t148656\t125549.6\t0\t148656\n", "4\t102438\t31387.4\t0\t102438\n", "5\t89015\t7846.8\t0\t89015\n", "6\t73705\t1961.7\t0\t73705\n", "7\t70794\t490.4\t0\t70794\n", "8\t70628\t122.6\t0\t70628\n", "9\t70636\t122.6\t0\t70636\n", "10\t68054\t122.6\t0\t68054\n", "11\t68686\t122.6\t0\t68686\n", "12\t69635\t122.6\t0\t69635\n", "13\t71670\t122.6\t0\t71670\n", "14\t73841\t122.6\t0\t73841\n", "15\t75216\t122.6\t0\t75216\n", "16\t79530\t122.6\t0\t79530\n", "17\t90989\t122.6\t0\t90989\n", "18\t106221\t122.6\t0\t106221\n", "19\t97860\t122.6\t0\t97860\n", "20\t82659\t122.6\t0\t82659\n", "21\t81424\t122.6\t0\t81424\n", "22\t72714\t122.6\t0\t72714\n", "23\t80267\t122.6\t0\t80267\n", "24\t94450\t122.6\t0\t94450\n", "25\t97457\t122.6\t0\t97457\n", "26\t112269\t122.6\t0\t112269\n", "27\t124772\t122.6\t0\t124772\n", "28\t114233\t122.6\t0\t114233\n", "29\t106544\t122.6\t0\t106544\n", "30\t110239\t122.6\t0\t110239\n", "31\t119141\t122.6\t0\t119141\n", "32\t115176\t122.6\t0\t115176\n", "33\t103846\t122.6\t0\t103846\n", "34\t101342\t122.6\t0\t101342\n", "35\t116792\t122.6\t0\t116792\n", "36\t139422\t122.6\t0\t139422\n", "37\t144916\t122.6\t0\t144916\n", "38\t113821\t122.6\t0\t113821\n", "39\t90717\t122.6\t0\t90717\n", "40\t84540\t122.6\t0\t84540\n", "41\t88632\t122.6\t0\t88632\n", "42\t96409\t122.6\t0\t96409\n", "43\t84372\t122.6\t0\t84372\n", "44\t68119\t122.6\t0\t68119\n", "45\t89170\t122.6\t0\t89170\n", "46\t110029\t122.6\t0\t110029\n", "47\t98579\t122.6\t0\t98579\n", "48\t96369\t122.6\t0\t96369\n", "49\t77491\t122.6\t0\t77491\n", "50\t74043\t122.6\t0\t74043\n", "51\t67243\t122.6\t0\t67243\n", "52\t65204\t122.6\t0\t65204\n", "53\t63380\t122.6\t0\t63380\n", "54\t66519\t122.6\t0\t66519\n", "55\t73382\t122.6\t0\t73382\n", "56\t67818\t122.6\t0\t67818\n", "57\t57941\t122.6\t0\t57941\n", "58\t70357\t122.6\t0\t70357\n", "59\t52090\t122.6\t0\t52090\n", "60\t39514\t122.6\t0\t39514\n", "61\t39219\t122.6\t0\t39219\n", "62\t31314\t122.6\t0\t31314\n", "63\t30132\t122.6\t0\t30132\n", "64\t33603\t122.6\t0\t33603\n", "65\t32650\t122.6\t0\t32650\n", "66\t28646\t122.6\t0\t28646\n", "67\t27323\t122.6\t0\t27323\n", "68\t25364\t122.6\t0\t25364\n", "69\t25296\t122.6\t0\t25296\n", "70\t26411\t122.6\t0\t26411\n", "71\t24353\t122.6\t0\t24353\n", "72\t19708\t122.6\t0\t19708\n", "73\t18226\t122.6\t0\t18226\n", "74\t18311\t122.6\t0\t18311\n", "75\t15379\t122.6\t0\t15379\n", "76\t12832\t122.6\t0\t12832\n", "77\t11121\t122.6\t0\t11121\n", "78\t12787\t122.6\t0\t12787\n", "79\t12301\t122.6\t0\t12301\n", "80\t13115\t122.6\t0\t13115\n", "81\t11900\t122.6\t0\t11900\n", "82\t11364\t122.6\t0\t11364\n", "83\t13343\t122.6\t0\t13343\n", "84\t15760\t122.6\t0\t15760\n", "85\t18171\t122.6\t0\t18171\n", "86\t16613\t122.6\t0\t16613\n", "87\t10672\t122.6\t0\t10672\n", "88\t9448\t122.6\t0\t9448\n", "89\t11271\t122.6\t0\t11271\n", "90\t12018\t122.6\t0\t12018\n", "91\t11304\t122.6\t0\t11304\n", "92\t10578\t122.6\t0\t10578\n", "93\t11255\t122.6\t0\t11255\n", "94\t10975\t122.6\t0\t10975\n", "95\t9020\t122.6\t0\t9020\n", "96\t6051\t122.6\t0\t6051\n", "97\t3842\t122.6\t0\t3842\n", "98\t1959\t122.6\t0\t1959\n", "99\t1395\t122.6\t0\t1395\n", "100\t941\t122.6\t0\t941\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 24983 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 61.8%\n", " C: 15.7%\n", " G: 0.0%\n", " T: 22.3%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9482\t125549.6\t0\t9482\n", "4\t2425\t31387.4\t0\t2425\n", "5\t797\t7846.8\t0\t797\n", "6\t539\t1961.7\t0\t539\n", "7\t313\t490.4\t0\t313\n", "8\t210\t122.6\t0\t210\n", "9\t182\t122.6\t0\t182\n", "10\t184\t122.6\t0\t184\n", "11\t206\t122.6\t0\t206\n", "12\t172\t122.6\t0\t172\n", "13\t161\t122.6\t0\t161\n", "14\t167\t122.6\t0\t167\n", "15\t155\t122.6\t0\t155\n", "16\t129\t122.6\t0\t129\n", "17\t135\t122.6\t0\t135\n", "18\t114\t122.6\t0\t114\n", "19\t152\t122.6\t0\t152\n", "20\t180\t122.6\t0\t180\n", "21\t167\t122.6\t0\t167\n", "22\t150\t122.6\t0\t150\n", "23\t118\t122.6\t0\t118\n", "24\t132\t122.6\t0\t132\n", "25\t139\t122.6\t0\t139\n", "26\t291\t122.6\t0\t291\n", "27\t259\t122.6\t0\t259\n", "28\t277\t122.6\t0\t277\n", "29\t337\t122.6\t0\t337\n", "30\t588\t122.6\t0\t588\n", "31\t665\t122.6\t0\t665\n", "32\t972\t122.6\t0\t972\n", "33\t808\t122.6\t0\t808\n", "34\t827\t122.6\t0\t827\n", "35\t999\t122.6\t0\t999\n", "36\t1039\t122.6\t0\t1039\n", "37\t301\t122.6\t0\t301\n", "38\t27\t122.6\t0\t27\n", "39\t32\t122.6\t0\t32\n", "40\t28\t122.6\t0\t28\n", "41\t23\t122.6\t0\t23\n", "42\t20\t122.6\t0\t20\n", "43\t22\t122.6\t0\t22\n", "44\t21\t122.6\t0\t21\n", "45\t21\t122.6\t0\t21\n", "46\t26\t122.6\t0\t26\n", "47\t20\t122.6\t0\t20\n", "48\t28\t122.6\t0\t28\n", "49\t22\t122.6\t0\t22\n", "50\t18\t122.6\t0\t18\n", "51\t24\t122.6\t0\t24\n", "52\t21\t122.6\t0\t21\n", "53\t17\t122.6\t0\t17\n", "54\t11\t122.6\t0\t11\n", "55\t14\t122.6\t0\t14\n", "56\t7\t122.6\t0\t7\n", "57\t12\t122.6\t0\t12\n", "58\t13\t122.6\t0\t13\n", "59\t6\t122.6\t0\t6\n", "60\t14\t122.6\t0\t14\n", "61\t10\t122.6\t0\t10\n", "62\t10\t122.6\t0\t10\n", "63\t10\t122.6\t0\t10\n", "64\t9\t122.6\t0\t9\n", "65\t9\t122.6\t0\t9\n", "66\t10\t122.6\t0\t10\n", "67\t10\t122.6\t0\t10\n", "68\t9\t122.6\t0\t9\n", "69\t8\t122.6\t0\t8\n", "70\t8\t122.6\t0\t8\n", "71\t10\t122.6\t0\t10\n", "72\t2\t122.6\t0\t2\n", "73\t7\t122.6\t0\t7\n", "74\t1\t122.6\t0\t1\n", "75\t6\t122.6\t0\t6\n", "76\t3\t122.6\t0\t3\n", "77\t5\t122.6\t0\t5\n", "78\t2\t122.6\t0\t2\n", "79\t4\t122.6\t0\t4\n", "80\t1\t122.6\t0\t1\n", "81\t2\t122.6\t0\t2\n", "82\t3\t122.6\t0\t3\n", "84\t3\t122.6\t0\t3\n", "85\t8\t122.6\t0\t8\n", "86\t2\t122.6\t0\t2\n", "87\t2\t122.6\t0\t2\n", "88\t4\t122.6\t0\t4\n", "89\t4\t122.6\t0\t4\n", "90\t5\t122.6\t0\t5\n", "91\t5\t122.6\t0\t5\n", "92\t19\t122.6\t0\t19\n", "93\t43\t122.6\t0\t43\n", "94\t86\t122.6\t0\t86\n", "95\t94\t122.6\t0\t94\n", "96\t72\t122.6\t0\t72\n", "97\t73\t122.6\t0\t73\n", "98\t59\t122.6\t0\t59\n", "99\t55\t122.6\t0\t55\n", "100\t91\t122.6\t0\t91\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 101183 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 46.3%\n", " C: 17.7%\n", " G: 16.6%\n", " T: 19.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t61886\t125549.6\t0\t61886\n", "4\t14434\t31387.4\t0\t14434\n", "5\t2883\t7846.8\t0\t2883\n", "6\t625\t1961.7\t0\t625\n", "7\t480\t490.4\t0\t480\n", "8\t502\t490.4\t0\t502\n", "9\t457\t490.4\t0\t457\n", "10\t497\t490.4\t0\t497\n", "11\t544\t490.4\t0\t544\n", "12\t500\t490.4\t0\t500\n", "13\t495\t490.4\t0\t495\n", "14\t515\t490.4\t0\t515\n", "15\t527\t490.4\t0\t527\n", "16\t498\t490.4\t0\t498\n", "17\t447\t490.4\t0\t447\n", "18\t474\t490.4\t0\t474\n", "19\t435\t490.4\t0\t435\n", "20\t340\t490.4\t0\t340\n", "21\t429\t490.4\t0\t429\n", "22\t393\t490.4\t0\t393\n", "23\t339\t490.4\t0\t339\n", "24\t338\t490.4\t0\t338\n", "25\t325\t490.4\t0\t325\n", "26\t290\t490.4\t0\t290\n", "27\t327\t490.4\t0\t327\n", "28\t327\t490.4\t0\t327\n", "29\t326\t490.4\t0\t326\n", "30\t332\t490.4\t0\t332\n", "31\t288\t490.4\t0\t288\n", "32\t321\t490.4\t0\t321\n", "33\t325\t490.4\t0\t325\n", "34\t312\t490.4\t0\t312\n", "35\t306\t490.4\t0\t306\n", "36\t256\t490.4\t0\t256\n", "37\t289\t490.4\t0\t289\n", "38\t248\t490.4\t0\t248\n", "39\t272\t490.4\t0\t272\n", "40\t294\t490.4\t0\t294\n", "41\t270\t490.4\t0\t270\n", "42\t190\t490.4\t0\t190\n", "43\t340\t490.4\t0\t340\n", "44\t97\t490.4\t0\t97\n", "45\t213\t490.4\t0\t213\n", "46\t194\t490.4\t0\t194\n", "47\t206\t490.4\t0\t206\n", "48\t169\t490.4\t0\t169\n", "49\t228\t490.4\t0\t228\n", "50\t189\t490.4\t0\t189\n", "51\t140\t490.4\t0\t140\n", "52\t172\t490.4\t0\t172\n", "53\t191\t490.4\t0\t191\n", "54\t124\t490.4\t0\t124\n", "55\t119\t490.4\t0\t119\n", "56\t136\t490.4\t0\t136\n", "57\t119\t490.4\t0\t119\n", "58\t134\t490.4\t0\t134\n", "59\t105\t490.4\t0\t105\n", "60\t119\t490.4\t0\t119\n", "61\t143\t490.4\t0\t143\n", "62\t130\t490.4\t0\t130\n", "63\t92\t490.4\t0\t92\n", "64\t98\t490.4\t0\t98\n", "65\t115\t490.4\t0\t115\n", "66\t93\t490.4\t0\t93\n", "67\t93\t490.4\t0\t93\n", "68\t79\t490.4\t0\t79\n", "69\t58\t490.4\t0\t58\n", "70\t55\t490.4\t0\t55\n", "71\t91\t490.4\t0\t91\n", "72\t126\t490.4\t0\t126\n", "73\t116\t490.4\t0\t116\n", "74\t170\t490.4\t0\t170\n", "75\t67\t490.4\t0\t67\n", "76\t114\t490.4\t0\t114\n", "77\t161\t490.4\t0\t161\n", "78\t134\t490.4\t0\t134\n", "79\t168\t490.4\t0\t168\n", "80\t198\t490.4\t0\t198\n", "81\t208\t490.4\t0\t208\n", "82\t288\t490.4\t0\t288\n", "83\t213\t490.4\t0\t213\n", "84\t154\t490.4\t0\t154\n", "85\t119\t490.4\t0\t119\n", "86\t90\t490.4\t0\t90\n", "87\t146\t490.4\t0\t146\n", "88\t104\t490.4\t0\t104\n", "89\t107\t490.4\t0\t107\n", "90\t85\t490.4\t0\t85\n", "91\t74\t490.4\t0\t74\n", "92\t88\t490.4\t0\t88\n", "93\t88\t490.4\t0\t88\n", "94\t96\t490.4\t0\t96\n", "95\t75\t490.4\t0\t75\n", "96\t95\t490.4\t0\t95\n", "97\t119\t490.4\t0\t119\n", "98\t127\t490.4\t0\t127\n", "99\t122\t490.4\t0\t122\n", "100\t153\t490.4\t0\t153\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 528_S27_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/528.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 117.92 s (13 us/read; 4.47 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,784,739\n", "Reads with adapters: 5,825,927 (66.3%)\n", "Reads written (passing filters): 8,623,428 (98.2%)\n", "\n", "Total basepairs processed: 878,473,900 bp\n", "Quality-trimmed: 2,509,948 bp (0.3%)\n", "Total written (filtered): 671,009,626 bp (76.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 5688361 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 29.7%\n", " G: 36.2%\n", " T: 34.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t182075\t137261.5\t0\t182075\n", "4\t116591\t34315.4\t0\t116591\n", "5\t94631\t8578.8\t0\t94631\n", "6\t75587\t2144.7\t0\t75587\n", "7\t69099\t536.2\t0\t69099\n", "8\t67300\t134.0\t0\t67300\n", "9\t67005\t134.0\t0\t67005\n", "10\t64973\t134.0\t0\t64973\n", "11\t64654\t134.0\t0\t64654\n", "12\t64989\t134.0\t0\t64989\n", "13\t66783\t134.0\t0\t66783\n", "14\t68513\t134.0\t0\t68513\n", "15\t69498\t134.0\t0\t69498\n", "16\t72911\t134.0\t0\t72911\n", "17\t82927\t134.0\t0\t82927\n", "18\t96961\t134.0\t0\t96961\n", "19\t92351\t134.0\t0\t92351\n", "20\t76703\t134.0\t0\t76703\n", "21\t74749\t134.0\t0\t74749\n", "22\t67156\t134.0\t0\t67156\n", "23\t74531\t134.0\t0\t74531\n", "24\t88929\t134.0\t0\t88929\n", "25\t91103\t134.0\t0\t91103\n", "26\t104673\t134.0\t0\t104673\n", "27\t116320\t134.0\t0\t116320\n", "28\t105186\t134.0\t0\t105186\n", "29\t100317\t134.0\t0\t100317\n", "30\t104864\t134.0\t0\t104864\n", "31\t117296\t134.0\t0\t117296\n", "32\t105835\t134.0\t0\t105835\n", "33\t97247\t134.0\t0\t97247\n", "34\t92807\t134.0\t0\t92807\n", "35\t107877\t134.0\t0\t107877\n", "36\t126019\t134.0\t0\t126019\n", "37\t125277\t134.0\t0\t125277\n", "38\t104161\t134.0\t0\t104161\n", "39\t89055\t134.0\t0\t89055\n", "40\t84131\t134.0\t0\t84131\n", "41\t89489\t134.0\t0\t89489\n", "42\t97813\t134.0\t0\t97813\n", "43\t87195\t134.0\t0\t87195\n", "44\t68896\t134.0\t0\t68896\n", "45\t89522\t134.0\t0\t89522\n", "46\t109551\t134.0\t0\t109551\n", "47\t109253\t134.0\t0\t109253\n", "48\t107541\t134.0\t0\t107541\n", "49\t80437\t134.0\t0\t80437\n", "50\t75596\t134.0\t0\t75596\n", "51\t75339\t134.0\t0\t75339\n", "52\t75737\t134.0\t0\t75737\n", "53\t65313\t134.0\t0\t65313\n", "54\t72763\t134.0\t0\t72763\n", "55\t74017\t134.0\t0\t74017\n", "56\t71036\t134.0\t0\t71036\n", "57\t70779\t134.0\t0\t70779\n", "58\t71575\t134.0\t0\t71575\n", "59\t56553\t134.0\t0\t56553\n", "60\t47769\t134.0\t0\t47769\n", "61\t43758\t134.0\t0\t43758\n", "62\t33895\t134.0\t0\t33895\n", "63\t31634\t134.0\t0\t31634\n", "64\t35328\t134.0\t0\t35328\n", "65\t34853\t134.0\t0\t34853\n", "66\t31051\t134.0\t0\t31051\n", "67\t28819\t134.0\t0\t28819\n", "68\t27232\t134.0\t0\t27232\n", "69\t26608\t134.0\t0\t26608\n", "70\t26931\t134.0\t0\t26931\n", "71\t25148\t134.0\t0\t25148\n", "72\t19979\t134.0\t0\t19979\n", "73\t17937\t134.0\t0\t17937\n", "74\t17918\t134.0\t0\t17918\n", "75\t14589\t134.0\t0\t14589\n", "76\t12200\t134.0\t0\t12200\n", "77\t10416\t134.0\t0\t10416\n", "78\t11431\t134.0\t0\t11431\n", "79\t10779\t134.0\t0\t10779\n", "80\t10649\t134.0\t0\t10649\n", "81\t9972\t134.0\t0\t9972\n", "82\t9519\t134.0\t0\t9519\n", "83\t10367\t134.0\t0\t10367\n", "84\t11433\t134.0\t0\t11433\n", "85\t12583\t134.0\t0\t12583\n", "86\t11796\t134.0\t0\t11796\n", "87\t8747\t134.0\t0\t8747\n", "88\t8242\t134.0\t0\t8242\n", "89\t8630\t134.0\t0\t8630\n", "90\t8735\t134.0\t0\t8735\n", "91\t8468\t134.0\t0\t8468\n", "92\t8024\t134.0\t0\t8024\n", "93\t8352\t134.0\t0\t8352\n", "94\t7621\t134.0\t0\t7621\n", "95\t6407\t134.0\t0\t6407\n", "96\t4535\t134.0\t0\t4535\n", "97\t2864\t134.0\t0\t2864\n", "98\t1665\t134.0\t0\t1665\n", "99\t1136\t134.0\t0\t1136\n", "100\t852\t134.0\t0\t852\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 21514 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 55.7%\n", " C: 15.8%\n", " G: 0.0%\n", " T: 28.1%\n", " none/other: 0.3%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9309\t137261.5\t0\t9309\n", "4\t2078\t34315.4\t0\t2078\n", "5\t900\t8578.8\t0\t900\n", "6\t712\t2144.7\t0\t712\n", "7\t148\t536.2\t0\t148\n", "8\t96\t134.0\t0\t96\n", "9\t81\t134.0\t0\t81\n", "10\t79\t134.0\t0\t79\n", "11\t81\t134.0\t0\t81\n", "12\t75\t134.0\t0\t75\n", "13\t77\t134.0\t0\t77\n", "14\t66\t134.0\t0\t66\n", "15\t77\t134.0\t0\t77\n", "16\t74\t134.0\t0\t74\n", "17\t74\t134.0\t0\t74\n", "18\t75\t134.0\t0\t75\n", "19\t105\t134.0\t0\t105\n", "20\t114\t134.0\t0\t114\n", "21\t119\t134.0\t0\t119\n", "22\t88\t134.0\t0\t88\n", "23\t89\t134.0\t0\t89\n", "24\t76\t134.0\t0\t76\n", "25\t85\t134.0\t0\t85\n", "26\t133\t134.0\t0\t133\n", "27\t138\t134.0\t0\t138\n", "28\t131\t134.0\t0\t131\n", "29\t180\t134.0\t0\t180\n", "30\t312\t134.0\t0\t312\n", "31\t350\t134.0\t0\t350\n", "32\t698\t134.0\t0\t698\n", "33\t577\t134.0\t0\t577\n", "34\t651\t134.0\t0\t651\n", "35\t835\t134.0\t0\t835\n", "36\t810\t134.0\t0\t810\n", "37\t332\t134.0\t0\t332\n", "38\t31\t134.0\t0\t31\n", "39\t33\t134.0\t0\t33\n", "40\t28\t134.0\t0\t28\n", "41\t29\t134.0\t0\t29\n", "42\t23\t134.0\t0\t23\n", "43\t27\t134.0\t0\t27\n", "44\t25\t134.0\t0\t25\n", "45\t25\t134.0\t0\t25\n", "46\t22\t134.0\t0\t22\n", "47\t26\t134.0\t0\t26\n", "48\t25\t134.0\t0\t25\n", "49\t22\t134.0\t0\t22\n", "50\t30\t134.0\t0\t30\n", "51\t35\t134.0\t0\t35\n", "52\t22\t134.0\t0\t22\n", "53\t31\t134.0\t0\t31\n", "54\t18\t134.0\t0\t18\n", "55\t18\t134.0\t0\t18\n", "56\t21\t134.0\t0\t21\n", "57\t19\t134.0\t0\t19\n", "58\t21\t134.0\t0\t21\n", "59\t15\t134.0\t0\t15\n", "60\t17\t134.0\t0\t17\n", "61\t11\t134.0\t0\t11\n", "62\t24\t134.0\t0\t24\n", "63\t14\t134.0\t0\t14\n", "64\t18\t134.0\t0\t18\n", "65\t25\t134.0\t0\t25\n", "66\t9\t134.0\t0\t9\n", "67\t10\t134.0\t0\t10\n", "68\t18\t134.0\t0\t18\n", "69\t13\t134.0\t0\t13\n", "70\t3\t134.0\t0\t3\n", "71\t10\t134.0\t0\t10\n", "72\t6\t134.0\t0\t6\n", "73\t8\t134.0\t0\t8\n", "74\t2\t134.0\t0\t2\n", "75\t7\t134.0\t0\t7\n", "76\t8\t134.0\t0\t8\n", "77\t2\t134.0\t0\t2\n", "78\t1\t134.0\t0\t1\n", "79\t3\t134.0\t0\t3\n", "80\t5\t134.0\t0\t5\n", "81\t5\t134.0\t0\t5\n", "82\t5\t134.0\t0\t5\n", "83\t5\t134.0\t0\t5\n", "84\t10\t134.0\t0\t10\n", "85\t9\t134.0\t0\t9\n", "86\t6\t134.0\t0\t6\n", "87\t4\t134.0\t0\t4\n", "88\t7\t134.0\t0\t7\n", "89\t4\t134.0\t0\t4\n", "90\t11\t134.0\t0\t11\n", "91\t8\t134.0\t0\t8\n", "92\t20\t134.0\t0\t20\n", "93\t53\t134.0\t0\t53\n", "94\t141\t134.0\t0\t141\n", "95\t117\t134.0\t0\t117\n", "96\t108\t134.0\t0\t108\n", "97\t98\t134.0\t0\t98\n", "98\t75\t134.0\t0\t75\n", "99\t77\t134.0\t0\t77\n", "100\t166\t134.0\t0\t166\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 116052 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.4%\n", " C: 17.9%\n", " G: 14.2%\n", " T: 22.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t82666\t137261.5\t0\t82666\n", "4\t18724\t34315.4\t0\t18724\n", "5\t4372\t8578.8\t0\t4372\n", "6\t336\t2144.7\t0\t336\n", "7\t192\t536.2\t0\t192\n", "8\t180\t536.2\t0\t180\n", "9\t189\t536.2\t0\t189\n", "10\t205\t536.2\t0\t205\n", "11\t184\t536.2\t0\t184\n", "12\t198\t536.2\t0\t198\n", "13\t182\t536.2\t0\t182\n", "14\t167\t536.2\t0\t167\n", "15\t164\t536.2\t0\t164\n", "16\t196\t536.2\t0\t196\n", "17\t156\t536.2\t0\t156\n", "18\t169\t536.2\t0\t169\n", "19\t167\t536.2\t0\t167\n", "20\t147\t536.2\t0\t147\n", "21\t168\t536.2\t0\t168\n", "22\t141\t536.2\t0\t141\n", "23\t148\t536.2\t0\t148\n", "24\t151\t536.2\t0\t151\n", "25\t144\t536.2\t0\t144\n", "26\t139\t536.2\t0\t139\n", "27\t143\t536.2\t0\t143\n", "28\t143\t536.2\t0\t143\n", "29\t142\t536.2\t0\t142\n", "30\t137\t536.2\t0\t137\n", "31\t112\t536.2\t0\t112\n", "32\t149\t536.2\t0\t149\n", "33\t145\t536.2\t0\t145\n", "34\t124\t536.2\t0\t124\n", "35\t124\t536.2\t0\t124\n", "36\t123\t536.2\t0\t123\n", "37\t109\t536.2\t0\t109\n", "38\t108\t536.2\t0\t108\n", "39\t116\t536.2\t0\t116\n", "40\t121\t536.2\t0\t121\n", "41\t98\t536.2\t0\t98\n", "42\t90\t536.2\t0\t90\n", "43\t108\t536.2\t0\t108\n", "44\t57\t536.2\t0\t57\n", "45\t86\t536.2\t0\t86\n", "46\t108\t536.2\t0\t108\n", "47\t97\t536.2\t0\t97\n", "48\t100\t536.2\t0\t100\n", "49\t100\t536.2\t0\t100\n", "50\t77\t536.2\t0\t77\n", "51\t92\t536.2\t0\t92\n", "52\t60\t536.2\t0\t60\n", "53\t84\t536.2\t0\t84\n", "54\t70\t536.2\t0\t70\n", "55\t63\t536.2\t0\t63\n", "56\t69\t536.2\t0\t69\n", "57\t57\t536.2\t0\t57\n", "58\t58\t536.2\t0\t58\n", "59\t57\t536.2\t0\t57\n", "60\t62\t536.2\t0\t62\n", "61\t70\t536.2\t0\t70\n", "62\t70\t536.2\t0\t70\n", "63\t59\t536.2\t0\t59\n", "64\t58\t536.2\t0\t58\n", "65\t53\t536.2\t0\t53\n", "66\t74\t536.2\t0\t74\n", "67\t73\t536.2\t0\t73\n", "68\t52\t536.2\t0\t52\n", "69\t49\t536.2\t0\t49\n", "70\t66\t536.2\t0\t66\n", "71\t61\t536.2\t0\t61\n", "72\t65\t536.2\t0\t65\n", "73\t67\t536.2\t0\t67\n", "74\t80\t536.2\t0\t80\n", "75\t73\t536.2\t0\t73\n", "76\t87\t536.2\t0\t87\n", "77\t103\t536.2\t0\t103\n", "78\t78\t536.2\t0\t78\n", "79\t85\t536.2\t0\t85\n", "80\t102\t536.2\t0\t102\n", "81\t107\t536.2\t0\t107\n", "82\t142\t536.2\t0\t142\n", "83\t138\t536.2\t0\t138\n", "84\t97\t536.2\t0\t97\n", "85\t98\t536.2\t0\t98\n", "86\t75\t536.2\t0\t75\n", "87\t84\t536.2\t0\t84\n", "88\t93\t536.2\t0\t93\n", "89\t90\t536.2\t0\t90\n", "90\t67\t536.2\t0\t67\n", "91\t58\t536.2\t0\t58\n", "92\t50\t536.2\t0\t50\n", "93\t62\t536.2\t0\t62\n", "94\t65\t536.2\t0\t65\n", "95\t51\t536.2\t0\t51\n", "96\t55\t536.2\t0\t55\n", "97\t100\t536.2\t0\t100\n", "98\t72\t536.2\t0\t72\n", "99\t111\t536.2\t0\t111\n", "100\t138\t536.2\t0\t138\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 529_S53_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/529.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 92.20 s (13 us/read; 4.54 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,972,407\n", "Reads with adapters: 3,960,516 (56.8%)\n", "Reads written (passing filters): 6,863,657 (98.4%)\n", "\n", "Total basepairs processed: 697,240,700 bp\n", "Quality-trimmed: 1,595,969 bp (0.2%)\n", "Total written (filtered): 569,087,128 bp (81.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3857162 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 26.3%\n", " G: 34.5%\n", " T: 39.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t191413\t108943.9\t0\t191413\n", "4\t113200\t27236.0\t0\t113200\n", "5\t87385\t6809.0\t0\t87385\n", "6\t66250\t1702.2\t0\t66250\n", "7\t57554\t425.6\t0\t57554\n", "8\t55838\t106.4\t0\t55838\n", "9\t54978\t106.4\t0\t54978\n", "10\t50179\t106.4\t0\t50179\n", "11\t51686\t106.4\t0\t51686\n", "12\t50701\t106.4\t0\t50701\n", "13\t51597\t106.4\t0\t51597\n", "14\t53158\t106.4\t0\t53158\n", "15\t54029\t106.4\t0\t54029\n", "16\t56293\t106.4\t0\t56293\n", "17\t64095\t106.4\t0\t64095\n", "18\t73378\t106.4\t0\t73378\n", "19\t69783\t106.4\t0\t69783\n", "20\t59369\t106.4\t0\t59369\n", "21\t56968\t106.4\t0\t56968\n", "22\t49993\t106.4\t0\t49993\n", "23\t55967\t106.4\t0\t55967\n", "24\t66710\t106.4\t0\t66710\n", "25\t67069\t106.4\t0\t67069\n", "26\t74225\t106.4\t0\t74225\n", "27\t83370\t106.4\t0\t83370\n", "28\t76562\t106.4\t0\t76562\n", "29\t72063\t106.4\t0\t72063\n", "30\t74833\t106.4\t0\t74833\n", "31\t77848\t106.4\t0\t77848\n", "32\t72195\t106.4\t0\t72195\n", "33\t61561\t106.4\t0\t61561\n", "34\t59695\t106.4\t0\t59695\n", "35\t67521\t106.4\t0\t67521\n", "36\t81105\t106.4\t0\t81105\n", "37\t85839\t106.4\t0\t85839\n", "38\t69411\t106.4\t0\t69411\n", "39\t52745\t106.4\t0\t52745\n", "40\t48458\t106.4\t0\t48458\n", "41\t48388\t106.4\t0\t48388\n", "42\t52496\t106.4\t0\t52496\n", "43\t46298\t106.4\t0\t46298\n", "44\t39483\t106.4\t0\t39483\n", "45\t50833\t106.4\t0\t50833\n", "46\t63811\t106.4\t0\t63811\n", "47\t62711\t106.4\t0\t62711\n", "48\t67036\t106.4\t0\t67036\n", "49\t55621\t106.4\t0\t55621\n", "50\t45246\t106.4\t0\t45246\n", "51\t39431\t106.4\t0\t39431\n", "52\t37679\t106.4\t0\t37679\n", "53\t38682\t106.4\t0\t38682\n", "54\t42207\t106.4\t0\t42207\n", "55\t43265\t106.4\t0\t43265\n", "56\t39192\t106.4\t0\t39192\n", "57\t34608\t106.4\t0\t34608\n", "58\t35621\t106.4\t0\t35621\n", "59\t25938\t106.4\t0\t25938\n", "60\t22452\t106.4\t0\t22452\n", "61\t21913\t106.4\t0\t21913\n", "62\t17816\t106.4\t0\t17816\n", "63\t18613\t106.4\t0\t18613\n", "64\t19348\t106.4\t0\t19348\n", "65\t18073\t106.4\t0\t18073\n", "66\t16193\t106.4\t0\t16193\n", "67\t15114\t106.4\t0\t15114\n", "68\t13635\t106.4\t0\t13635\n", "69\t13190\t106.4\t0\t13190\n", "70\t13693\t106.4\t0\t13693\n", "71\t13184\t106.4\t0\t13184\n", "72\t10794\t106.4\t0\t10794\n", "73\t9564\t106.4\t0\t9564\n", "74\t9414\t106.4\t0\t9414\n", "75\t7648\t106.4\t0\t7648\n", "76\t6498\t106.4\t0\t6498\n", "77\t5627\t106.4\t0\t5627\n", "78\t6186\t106.4\t0\t6186\n", "79\t5830\t106.4\t0\t5830\n", "80\t6253\t106.4\t0\t6253\n", "81\t5577\t106.4\t0\t5577\n", "82\t5540\t106.4\t0\t5540\n", "83\t6339\t106.4\t0\t6339\n", "84\t7680\t106.4\t0\t7680\n", "85\t9482\t106.4\t0\t9482\n", "86\t9111\t106.4\t0\t9111\n", "87\t6453\t106.4\t0\t6453\n", "88\t5598\t106.4\t0\t5598\n", "89\t6257\t106.4\t0\t6257\n", "90\t6414\t106.4\t0\t6414\n", "91\t5985\t106.4\t0\t5985\n", "92\t5334\t106.4\t0\t5334\n", "93\t5519\t106.4\t0\t5519\n", "94\t5043\t106.4\t0\t5043\n", "95\t4535\t106.4\t0\t4535\n", "96\t3107\t106.4\t0\t3107\n", "97\t1970\t106.4\t0\t1970\n", "98\t1151\t106.4\t0\t1151\n", "99\t857\t106.4\t0\t857\n", "100\t602\t106.4\t0\t602\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 15229 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 62.4%\n", " C: 11.3%\n", " G: 0.0%\n", " T: 25.9%\n", " none/other: 0.5%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t5544\t108943.9\t0\t5544\n", "4\t1324\t27236.0\t0\t1324\n", "5\t290\t6809.0\t0\t290\n", "6\t128\t1702.2\t0\t128\n", "7\t81\t425.6\t0\t81\n", "8\t55\t106.4\t0\t55\n", "9\t49\t106.4\t0\t49\n", "10\t28\t106.4\t0\t28\n", "11\t38\t106.4\t0\t38\n", "12\t32\t106.4\t0\t32\n", "13\t60\t106.4\t0\t60\n", "14\t36\t106.4\t0\t36\n", "15\t39\t106.4\t0\t39\n", "16\t37\t106.4\t0\t37\n", "17\t37\t106.4\t0\t37\n", "18\t46\t106.4\t0\t46\n", "19\t58\t106.4\t0\t58\n", "20\t78\t106.4\t0\t78\n", "21\t67\t106.4\t0\t67\n", "22\t75\t106.4\t0\t75\n", "23\t47\t106.4\t0\t47\n", "24\t59\t106.4\t0\t59\n", "25\t63\t106.4\t0\t63\n", "26\t105\t106.4\t0\t105\n", "27\t145\t106.4\t0\t145\n", "28\t169\t106.4\t0\t169\n", "29\t200\t106.4\t0\t200\n", "30\t383\t106.4\t0\t383\n", "31\t498\t106.4\t0\t498\n", "32\t798\t106.4\t0\t798\n", "33\t823\t106.4\t0\t823\n", "34\t818\t106.4\t0\t818\n", "35\t1096\t106.4\t0\t1096\n", "36\t1101\t106.4\t0\t1101\n", "37\t369\t106.4\t0\t369\n", "38\t30\t106.4\t0\t30\n", "39\t16\t106.4\t0\t16\n", "40\t8\t106.4\t0\t8\n", "41\t6\t106.4\t0\t6\n", "42\t7\t106.4\t0\t7\n", "43\t7\t106.4\t0\t7\n", "44\t7\t106.4\t0\t7\n", "45\t9\t106.4\t0\t9\n", "46\t6\t106.4\t0\t6\n", "47\t3\t106.4\t0\t3\n", "48\t4\t106.4\t0\t4\n", "49\t3\t106.4\t0\t3\n", "50\t2\t106.4\t0\t2\n", "51\t4\t106.4\t0\t4\n", "52\t2\t106.4\t0\t2\n", "53\t1\t106.4\t0\t1\n", "54\t2\t106.4\t0\t2\n", "55\t7\t106.4\t0\t7\n", "56\t5\t106.4\t0\t5\n", "57\t5\t106.4\t0\t5\n", "58\t2\t106.4\t0\t2\n", "60\t1\t106.4\t0\t1\n", "61\t4\t106.4\t0\t4\n", "62\t3\t106.4\t0\t3\n", "63\t3\t106.4\t0\t3\n", "65\t1\t106.4\t0\t1\n", "66\t1\t106.4\t0\t1\n", "67\t1\t106.4\t0\t1\n", "69\t1\t106.4\t0\t1\n", "70\t2\t106.4\t0\t2\n", "71\t1\t106.4\t0\t1\n", "72\t2\t106.4\t0\t2\n", "76\t1\t106.4\t0\t1\n", "80\t1\t106.4\t0\t1\n", "82\t1\t106.4\t0\t1\n", "83\t2\t106.4\t0\t2\n", "90\t1\t106.4\t0\t1\n", "91\t1\t106.4\t0\t1\n", "92\t5\t106.4\t0\t5\n", "93\t24\t106.4\t0\t24\n", "94\t43\t106.4\t0\t43\n", "95\t44\t106.4\t0\t44\n", "96\t15\t106.4\t0\t15\n", "97\t34\t106.4\t0\t34\n", "98\t16\t106.4\t0\t16\n", "99\t40\t106.4\t0\t40\n", "100\t69\t106.4\t0\t69\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 88125 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 51.3%\n", " C: 14.4%\n", " G: 10.8%\n", " T: 23.4%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t62936\t108943.9\t0\t62936\n", "4\t16252\t27236.0\t0\t16252\n", "5\t3747\t6809.0\t0\t3747\n", "6\t112\t1702.2\t0\t112\n", "7\t36\t425.6\t0\t36\n", "8\t56\t425.6\t0\t56\n", "9\t40\t425.6\t0\t40\n", "10\t60\t425.6\t0\t60\n", "11\t46\t425.6\t0\t46\n", "12\t84\t425.6\t0\t84\n", "13\t50\t425.6\t0\t50\n", "14\t33\t425.6\t0\t33\n", "15\t21\t425.6\t0\t21\n", "16\t16\t425.6\t0\t16\n", "17\t18\t425.6\t0\t18\n", "18\t26\t425.6\t0\t26\n", "19\t27\t425.6\t0\t27\n", "20\t19\t425.6\t0\t19\n", "21\t29\t425.6\t0\t29\n", "22\t23\t425.6\t0\t23\n", "23\t18\t425.6\t0\t18\n", "24\t20\t425.6\t0\t20\n", "25\t33\t425.6\t0\t33\n", "26\t20\t425.6\t0\t20\n", "27\t29\t425.6\t0\t29\n", "28\t27\t425.6\t0\t27\n", "29\t18\t425.6\t0\t18\n", "30\t39\t425.6\t0\t39\n", "31\t37\t425.6\t0\t37\n", "32\t30\t425.6\t0\t30\n", "33\t32\t425.6\t0\t32\n", "34\t23\t425.6\t0\t23\n", "35\t30\t425.6\t0\t30\n", "36\t34\t425.6\t0\t34\n", "37\t38\t425.6\t0\t38\n", "38\t44\t425.6\t0\t44\n", "39\t33\t425.6\t0\t33\n", "40\t55\t425.6\t0\t55\n", "41\t47\t425.6\t0\t47\n", "42\t55\t425.6\t0\t55\n", "43\t54\t425.6\t0\t54\n", "44\t44\t425.6\t0\t44\n", "45\t31\t425.6\t0\t31\n", "46\t31\t425.6\t0\t31\n", "47\t38\t425.6\t0\t38\n", "48\t35\t425.6\t0\t35\n", "49\t21\t425.6\t0\t21\n", "50\t41\t425.6\t0\t41\n", "51\t35\t425.6\t0\t35\n", "52\t31\t425.6\t0\t31\n", "53\t29\t425.6\t0\t29\n", "54\t46\t425.6\t0\t46\n", "55\t30\t425.6\t0\t30\n", "56\t30\t425.6\t0\t30\n", "57\t36\t425.6\t0\t36\n", "58\t26\t425.6\t0\t26\n", "59\t17\t425.6\t0\t17\n", "60\t40\t425.6\t0\t40\n", "61\t56\t425.6\t0\t56\n", "62\t44\t425.6\t0\t44\n", "63\t51\t425.6\t0\t51\n", "64\t49\t425.6\t0\t49\n", "65\t67\t425.6\t0\t67\n", "66\t58\t425.6\t0\t58\n", "67\t50\t425.6\t0\t50\n", "68\t27\t425.6\t0\t27\n", "69\t32\t425.6\t0\t32\n", "70\t44\t425.6\t0\t44\n", "71\t53\t425.6\t0\t53\n", "72\t78\t425.6\t0\t78\n", "73\t138\t425.6\t0\t138\n", "74\t111\t425.6\t0\t111\n", "75\t79\t425.6\t0\t79\n", "76\t70\t425.6\t0\t70\n", "77\t143\t425.6\t0\t143\n", "78\t94\t425.6\t0\t94\n", "79\t114\t425.6\t0\t114\n", "80\t127\t425.6\t0\t127\n", "81\t127\t425.6\t0\t127\n", "82\t162\t425.6\t0\t162\n", "83\t140\t425.6\t0\t140\n", "84\t107\t425.6\t0\t107\n", "85\t84\t425.6\t0\t84\n", "86\t84\t425.6\t0\t84\n", "87\t109\t425.6\t0\t109\n", "88\t65\t425.6\t0\t65\n", "89\t51\t425.6\t0\t51\n", "90\t50\t425.6\t0\t50\n", "91\t47\t425.6\t0\t47\n", "92\t46\t425.6\t0\t46\n", "93\t29\t425.6\t0\t29\n", "94\t42\t425.6\t0\t42\n", "95\t45\t425.6\t0\t45\n", "96\t62\t425.6\t0\t62\n", "97\t79\t425.6\t0\t79\n", "98\t116\t425.6\t0\t116\n", "99\t114\t425.6\t0\t114\n", "100\t173\t425.6\t0\t173\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 531_S44_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/531.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 66.43 s (13 us/read; 4.59 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,086,934\n", "Reads with adapters: 3,057,282 (60.1%)\n", "Reads written (passing filters): 4,945,903 (97.2%)\n", "\n", "Total basepairs processed: 508,693,400 bp\n", "Quality-trimmed: 1,395,910 bp (0.3%)\n", "Total written (filtered): 394,640,336 bp (77.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2941507 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.7%\n", " G: 41.6%\n", " T: 26.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t102953\t79483.3\t0\t102953\n", "4\t57572\t19870.8\t0\t57572\n", "5\t44374\t4967.7\t0\t44374\n", "6\t36651\t1241.9\t0\t36651\n", "7\t33612\t310.5\t0\t33612\n", "8\t34214\t77.6\t0\t34214\n", "9\t33019\t77.6\t0\t33019\n", "10\t33046\t77.6\t0\t33046\n", "11\t32925\t77.6\t0\t32925\n", "12\t33571\t77.6\t0\t33571\n", "13\t35812\t77.6\t0\t35812\n", "14\t37085\t77.6\t0\t37085\n", "15\t35716\t77.6\t0\t35716\n", "16\t37234\t77.6\t0\t37234\n", "17\t41120\t77.6\t0\t41120\n", "18\t47215\t77.6\t0\t47215\n", "19\t43740\t77.6\t0\t43740\n", "20\t36592\t77.6\t0\t36592\n", "21\t35619\t77.6\t0\t35619\n", "22\t32776\t77.6\t0\t32776\n", "23\t35247\t77.6\t0\t35247\n", "24\t41443\t77.6\t0\t41443\n", "25\t43362\t77.6\t0\t43362\n", "26\t49240\t77.6\t0\t49240\n", "27\t54591\t77.6\t0\t54591\n", "28\t49009\t77.6\t0\t49009\n", "29\t45967\t77.6\t0\t45967\n", "30\t47351\t77.6\t0\t47351\n", "31\t52887\t77.6\t0\t52887\n", "32\t50924\t77.6\t0\t50924\n", "33\t47961\t77.6\t0\t47961\n", "34\t46212\t77.6\t0\t46212\n", "35\t52297\t77.6\t0\t52297\n", "36\t60893\t77.6\t0\t60893\n", "37\t63834\t77.6\t0\t63834\n", "38\t51834\t77.6\t0\t51834\n", "39\t43259\t77.6\t0\t43259\n", "40\t41770\t77.6\t0\t41770\n", "41\t46586\t77.6\t0\t46586\n", "42\t51931\t77.6\t0\t51931\n", "43\t44790\t77.6\t0\t44790\n", "44\t35539\t77.6\t0\t35539\n", "45\t44537\t77.6\t0\t44537\n", "46\t52661\t77.6\t0\t52661\n", "47\t47848\t77.6\t0\t47848\n", "48\t47971\t77.6\t0\t47971\n", "49\t39189\t77.6\t0\t39189\n", "50\t37721\t77.6\t0\t37721\n", "51\t31883\t77.6\t0\t31883\n", "52\t31956\t77.6\t0\t31956\n", "53\t36858\t77.6\t0\t36858\n", "54\t43104\t77.6\t0\t43104\n", "55\t37688\t77.6\t0\t37688\n", "56\t34973\t77.6\t0\t34973\n", "57\t32893\t77.6\t0\t32893\n", "58\t38159\t77.6\t0\t38159\n", "59\t31874\t77.6\t0\t31874\n", "60\t26016\t77.6\t0\t26016\n", "61\t24229\t77.6\t0\t24229\n", "62\t20066\t77.6\t0\t20066\n", "63\t19375\t77.6\t0\t19375\n", "64\t22297\t77.6\t0\t22297\n", "65\t20897\t77.6\t0\t20897\n", "66\t17614\t77.6\t0\t17614\n", "67\t17848\t77.6\t0\t17848\n", "68\t17617\t77.6\t0\t17617\n", "69\t18386\t77.6\t0\t18386\n", "70\t20115\t77.6\t0\t20115\n", "71\t19883\t77.6\t0\t19883\n", "72\t14646\t77.6\t0\t14646\n", "73\t12272\t77.6\t0\t12272\n", "74\t11803\t77.6\t0\t11803\n", "75\t10649\t77.6\t0\t10649\n", "76\t8458\t77.6\t0\t8458\n", "77\t8727\t77.6\t0\t8727\n", "78\t10292\t77.6\t0\t10292\n", "79\t9328\t77.6\t0\t9328\n", "80\t8861\t77.6\t0\t8861\n", "81\t8504\t77.6\t0\t8504\n", "82\t7922\t77.6\t0\t7922\n", "83\t8058\t77.6\t0\t8058\n", "84\t9256\t77.6\t0\t9256\n", "85\t10547\t77.6\t0\t10547\n", "86\t10417\t77.6\t0\t10417\n", "87\t7439\t77.6\t0\t7439\n", "88\t6494\t77.6\t0\t6494\n", "89\t6794\t77.6\t0\t6794\n", "90\t7117\t77.6\t0\t7117\n", "91\t7248\t77.6\t0\t7248\n", "92\t7314\t77.6\t0\t7314\n", "93\t7784\t77.6\t0\t7784\n", "94\t7450\t77.6\t0\t7450\n", "95\t6295\t77.6\t0\t6295\n", "96\t4496\t77.6\t0\t4496\n", "97\t2843\t77.6\t0\t2843\n", "98\t1731\t77.6\t0\t1731\n", "99\t2090\t77.6\t0\t2090\n", "100\t1241\t77.6\t0\t1241\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28453 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 46.9%\n", " C: 33.4%\n", " G: 0.0%\n", " T: 19.6%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t14466\t79483.3\t0\t14466\n", "4\t3801\t19870.8\t0\t3801\n", "5\t1643\t4967.7\t0\t1643\n", "6\t1006\t1241.9\t0\t1006\n", "7\t222\t310.5\t0\t222\n", "8\t146\t77.6\t0\t146\n", "9\t118\t77.6\t0\t118\n", "10\t154\t77.6\t0\t154\n", "11\t141\t77.6\t0\t141\n", "12\t109\t77.6\t0\t109\n", "13\t118\t77.6\t0\t118\n", "14\t147\t77.6\t0\t147\n", "15\t99\t77.6\t0\t99\n", "16\t105\t77.6\t0\t105\n", "17\t136\t77.6\t0\t136\n", "18\t181\t77.6\t0\t181\n", "19\t164\t77.6\t0\t164\n", "20\t203\t77.6\t0\t203\n", "21\t162\t77.6\t0\t162\n", "22\t152\t77.6\t0\t152\n", "23\t105\t77.6\t0\t105\n", "24\t119\t77.6\t0\t119\n", "25\t143\t77.6\t0\t143\n", "26\t210\t77.6\t0\t210\n", "27\t171\t77.6\t0\t171\n", "28\t145\t77.6\t0\t145\n", "29\t213\t77.6\t0\t213\n", "30\t252\t77.6\t0\t252\n", "31\t326\t77.6\t0\t326\n", "32\t484\t77.6\t0\t484\n", "33\t376\t77.6\t0\t376\n", "34\t378\t77.6\t0\t378\n", "35\t433\t77.6\t0\t433\n", "36\t412\t77.6\t0\t412\n", "37\t155\t77.6\t0\t155\n", "38\t28\t77.6\t0\t28\n", "39\t31\t77.6\t0\t31\n", "40\t31\t77.6\t0\t31\n", "41\t30\t77.6\t0\t30\n", "42\t26\t77.6\t0\t26\n", "43\t27\t77.6\t0\t27\n", "44\t23\t77.6\t0\t23\n", "45\t33\t77.6\t0\t33\n", "46\t23\t77.6\t0\t23\n", "47\t21\t77.6\t0\t21\n", "48\t32\t77.6\t0\t32\n", "49\t19\t77.6\t0\t19\n", "50\t28\t77.6\t0\t28\n", "51\t26\t77.6\t0\t26\n", "52\t28\t77.6\t0\t28\n", "53\t24\t77.6\t0\t24\n", "54\t18\t77.6\t0\t18\n", "55\t19\t77.6\t0\t19\n", "56\t19\t77.6\t0\t19\n", "57\t16\t77.6\t0\t16\n", "58\t23\t77.6\t0\t23\n", "59\t15\t77.6\t0\t15\n", "60\t13\t77.6\t0\t13\n", "61\t15\t77.6\t0\t15\n", "62\t16\t77.6\t0\t16\n", "63\t7\t77.6\t0\t7\n", "64\t15\t77.6\t0\t15\n", "65\t13\t77.6\t0\t13\n", "66\t10\t77.6\t0\t10\n", "67\t11\t77.6\t0\t11\n", "68\t21\t77.6\t0\t21\n", "69\t8\t77.6\t0\t8\n", "70\t11\t77.6\t0\t11\n", "71\t9\t77.6\t0\t9\n", "72\t11\t77.6\t0\t11\n", "73\t8\t77.6\t0\t8\n", "74\t8\t77.6\t0\t8\n", "75\t5\t77.6\t0\t5\n", "76\t7\t77.6\t0\t7\n", "77\t7\t77.6\t0\t7\n", "78\t6\t77.6\t0\t6\n", "79\t9\t77.6\t0\t9\n", "80\t5\t77.6\t0\t5\n", "81\t8\t77.6\t0\t8\n", "82\t10\t77.6\t0\t10\n", "83\t4\t77.6\t0\t4\n", "84\t2\t77.6\t0\t2\n", "85\t11\t77.6\t0\t11\n", "86\t3\t77.6\t0\t3\n", "87\t8\t77.6\t0\t8\n", "88\t5\t77.6\t0\t5\n", "89\t9\t77.6\t0\t9\n", "90\t12\t77.6\t0\t12\n", "91\t15\t77.6\t0\t15\n", "92\t25\t77.6\t0\t25\n", "93\t20\t77.6\t0\t20\n", "94\t49\t77.6\t0\t49\n", "95\t58\t77.6\t0\t58\n", "96\t62\t77.6\t0\t62\n", "97\t63\t77.6\t0\t63\n", "98\t38\t77.6\t0\t38\n", "99\t41\t77.6\t0\t41\n", "100\t60\t77.6\t0\t60\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 87322 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.0%\n", " C: 21.6%\n", " G: 17.8%\n", " T: 20.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t63780\t79483.3\t0\t63780\n", "4\t12684\t19870.8\t0\t12684\n", "5\t2088\t4967.7\t0\t2088\n", "6\t258\t1241.9\t0\t258\n", "7\t168\t310.5\t0\t168\n", "8\t143\t310.5\t0\t143\n", "9\t152\t310.5\t0\t152\n", "10\t164\t310.5\t0\t164\n", "11\t178\t310.5\t0\t178\n", "12\t162\t310.5\t0\t162\n", "13\t185\t310.5\t0\t185\n", "14\t179\t310.5\t0\t179\n", "15\t144\t310.5\t0\t144\n", "16\t174\t310.5\t0\t174\n", "17\t172\t310.5\t0\t172\n", "18\t181\t310.5\t0\t181\n", "19\t165\t310.5\t0\t165\n", "20\t146\t310.5\t0\t146\n", "21\t129\t310.5\t0\t129\n", "22\t163\t310.5\t0\t163\n", "23\t140\t310.5\t0\t140\n", "24\t118\t310.5\t0\t118\n", "25\t133\t310.5\t0\t133\n", "26\t124\t310.5\t0\t124\n", "27\t148\t310.5\t0\t148\n", "28\t124\t310.5\t0\t124\n", "29\t116\t310.5\t0\t116\n", "30\t116\t310.5\t0\t116\n", "31\t115\t310.5\t0\t115\n", "32\t121\t310.5\t0\t121\n", "33\t108\t310.5\t0\t108\n", "34\t104\t310.5\t0\t104\n", "35\t104\t310.5\t0\t104\n", "36\t91\t310.5\t0\t91\n", "37\t98\t310.5\t0\t98\n", "38\t103\t310.5\t0\t103\n", "39\t98\t310.5\t0\t98\n", "40\t104\t310.5\t0\t104\n", "41\t85\t310.5\t0\t85\n", "42\t74\t310.5\t0\t74\n", "43\t115\t310.5\t0\t115\n", "44\t58\t310.5\t0\t58\n", "45\t87\t310.5\t0\t87\n", "46\t101\t310.5\t0\t101\n", "47\t85\t310.5\t0\t85\n", "48\t76\t310.5\t0\t76\n", "49\t83\t310.5\t0\t83\n", "50\t79\t310.5\t0\t79\n", "51\t55\t310.5\t0\t55\n", "52\t90\t310.5\t0\t90\n", "53\t68\t310.5\t0\t68\n", "54\t63\t310.5\t0\t63\n", "55\t61\t310.5\t0\t61\n", "56\t74\t310.5\t0\t74\n", "57\t65\t310.5\t0\t65\n", "58\t56\t310.5\t0\t56\n", "59\t51\t310.5\t0\t51\n", "60\t66\t310.5\t0\t66\n", "61\t57\t310.5\t0\t57\n", "62\t52\t310.5\t0\t52\n", "63\t42\t310.5\t0\t42\n", "64\t49\t310.5\t0\t49\n", "65\t73\t310.5\t0\t73\n", "66\t61\t310.5\t0\t61\n", "67\t52\t310.5\t0\t52\n", "68\t65\t310.5\t0\t65\n", "69\t44\t310.5\t0\t44\n", "70\t38\t310.5\t0\t38\n", "71\t56\t310.5\t0\t56\n", "72\t65\t310.5\t0\t65\n", "73\t62\t310.5\t0\t62\n", "74\t73\t310.5\t0\t73\n", "75\t52\t310.5\t0\t52\n", "76\t74\t310.5\t0\t74\n", "77\t77\t310.5\t0\t77\n", "78\t59\t310.5\t0\t59\n", "79\t42\t310.5\t0\t42\n", "80\t72\t310.5\t0\t72\n", "81\t71\t310.5\t0\t71\n", "82\t70\t310.5\t0\t70\n", "83\t65\t310.5\t0\t65\n", "84\t78\t310.5\t0\t78\n", "85\t44\t310.5\t0\t44\n", "86\t66\t310.5\t0\t66\n", "87\t67\t310.5\t0\t67\n", "88\t72\t310.5\t0\t72\n", "89\t70\t310.5\t0\t70\n", "90\t59\t310.5\t0\t59\n", "91\t43\t310.5\t0\t43\n", "92\t43\t310.5\t0\t43\n", "93\t35\t310.5\t0\t35\n", "94\t60\t310.5\t0\t60\n", "95\t36\t310.5\t0\t36\n", "96\t36\t310.5\t0\t36\n", "97\t49\t310.5\t0\t49\n", "98\t70\t310.5\t0\t70\n", "99\t69\t310.5\t0\t69\n", "100\t82\t310.5\t0\t82\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 532_S33_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/532.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 65.91 s (13 us/read; 4.67 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,128,341\n", "Reads with adapters: 2,682,427 (52.3%)\n", "Reads written (passing filters): 5,065,262 (98.8%)\n", "\n", "Total basepairs processed: 512,834,100 bp\n", "Quality-trimmed: 1,002,935 bp (0.2%)\n", "Total written (filtered): 432,403,124 bp (84.3%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2579501 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.5%\n", " G: 34.2%\n", " T: 38.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t139982\t80130.3\t0\t139982\n", "4\t83903\t20032.6\t0\t83903\n", "5\t66443\t5008.1\t0\t66443\n", "6\t50762\t1252.0\t0\t50762\n", "7\t43295\t313.0\t0\t43295\n", "8\t41972\t78.3\t0\t41972\n", "9\t40104\t78.3\t0\t40104\n", "10\t37972\t78.3\t0\t37972\n", "11\t37659\t78.3\t0\t37659\n", "12\t37659\t78.3\t0\t37659\n", "13\t39054\t78.3\t0\t39054\n", "14\t40057\t78.3\t0\t40057\n", "15\t39243\t78.3\t0\t39243\n", "16\t41129\t78.3\t0\t41129\n", "17\t46356\t78.3\t0\t46356\n", "18\t53385\t78.3\t0\t53385\n", "19\t48788\t78.3\t0\t48788\n", "20\t40497\t78.3\t0\t40497\n", "21\t40521\t78.3\t0\t40521\n", "22\t35312\t78.3\t0\t35312\n", "23\t39195\t78.3\t0\t39195\n", "24\t46099\t78.3\t0\t46099\n", "25\t45518\t78.3\t0\t45518\n", "26\t52551\t78.3\t0\t52551\n", "27\t58609\t78.3\t0\t58609\n", "28\t52856\t78.3\t0\t52856\n", "29\t49881\t78.3\t0\t49881\n", "30\t50638\t78.3\t0\t50638\n", "31\t54245\t78.3\t0\t54245\n", "32\t51060\t78.3\t0\t51060\n", "33\t43734\t78.3\t0\t43734\n", "34\t41417\t78.3\t0\t41417\n", "35\t46770\t78.3\t0\t46770\n", "36\t56794\t78.3\t0\t56794\n", "37\t60645\t78.3\t0\t60645\n", "38\t46265\t78.3\t0\t46265\n", "39\t35696\t78.3\t0\t35696\n", "40\t32245\t78.3\t0\t32245\n", "41\t33070\t78.3\t0\t33070\n", "42\t35957\t78.3\t0\t35957\n", "43\t30530\t78.3\t0\t30530\n", "44\t24420\t78.3\t0\t24420\n", "45\t31064\t78.3\t0\t31064\n", "46\t37034\t78.3\t0\t37034\n", "47\t33729\t78.3\t0\t33729\n", "48\t35151\t78.3\t0\t35151\n", "49\t27727\t78.3\t0\t27727\n", "50\t25176\t78.3\t0\t25176\n", "51\t21864\t78.3\t0\t21864\n", "52\t21275\t78.3\t0\t21275\n", "53\t20852\t78.3\t0\t20852\n", "54\t24328\t78.3\t0\t24328\n", "55\t24057\t78.3\t0\t24057\n", "56\t20898\t78.3\t0\t20898\n", "57\t20237\t78.3\t0\t20237\n", "58\t25296\t78.3\t0\t25296\n", "59\t16722\t78.3\t0\t16722\n", "60\t12767\t78.3\t0\t12767\n", "61\t11976\t78.3\t0\t11976\n", "62\t9923\t78.3\t0\t9923\n", "63\t9859\t78.3\t0\t9859\n", "64\t10741\t78.3\t0\t10741\n", "65\t9592\t78.3\t0\t9592\n", "66\t7784\t78.3\t0\t7784\n", "67\t7629\t78.3\t0\t7629\n", "68\t7048\t78.3\t0\t7048\n", "69\t7231\t78.3\t0\t7231\n", "70\t7751\t78.3\t0\t7751\n", "71\t7453\t78.3\t0\t7453\n", "72\t5565\t78.3\t0\t5565\n", "73\t4643\t78.3\t0\t4643\n", "74\t4372\t78.3\t0\t4372\n", "75\t3915\t78.3\t0\t3915\n", "76\t3044\t78.3\t0\t3044\n", "77\t3140\t78.3\t0\t3140\n", "78\t3790\t78.3\t0\t3790\n", "79\t3287\t78.3\t0\t3287\n", "80\t3181\t78.3\t0\t3181\n", "81\t3256\t78.3\t0\t3256\n", "82\t3099\t78.3\t0\t3099\n", "83\t3329\t78.3\t0\t3329\n", "84\t3804\t78.3\t0\t3804\n", "85\t4721\t78.3\t0\t4721\n", "86\t4543\t78.3\t0\t4543\n", "87\t3442\t78.3\t0\t3442\n", "88\t3016\t78.3\t0\t3016\n", "89\t3283\t78.3\t0\t3283\n", "90\t3316\t78.3\t0\t3316\n", "91\t3326\t78.3\t0\t3326\n", "92\t3247\t78.3\t0\t3247\n", "93\t3436\t78.3\t0\t3436\n", "94\t3160\t78.3\t0\t3160\n", "95\t2818\t78.3\t0\t2818\n", "96\t2044\t78.3\t0\t2044\n", "97\t1407\t78.3\t0\t1407\n", "98\t828\t78.3\t0\t828\n", "99\t552\t78.3\t0\t552\n", "100\t485\t78.3\t0\t485\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 14915 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 52.4%\n", " C: 17.7%\n", " G: 0.0%\n", " T: 29.6%\n", " none/other: 0.4%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t7294\t80130.3\t0\t7294\n", "4\t1613\t20032.6\t0\t1613\n", "5\t755\t5008.1\t0\t755\n", "6\t635\t1252.0\t0\t635\n", "7\t78\t313.0\t0\t78\n", "8\t54\t78.3\t0\t54\n", "9\t42\t78.3\t0\t42\n", "10\t32\t78.3\t0\t32\n", "11\t33\t78.3\t0\t33\n", "12\t33\t78.3\t0\t33\n", "13\t48\t78.3\t0\t48\n", "14\t32\t78.3\t0\t32\n", "15\t43\t78.3\t0\t43\n", "16\t49\t78.3\t0\t49\n", "17\t43\t78.3\t0\t43\n", "18\t42\t78.3\t0\t42\n", "19\t48\t78.3\t0\t48\n", "20\t48\t78.3\t0\t48\n", "21\t45\t78.3\t0\t45\n", "22\t46\t78.3\t0\t46\n", "23\t41\t78.3\t0\t41\n", "24\t45\t78.3\t0\t45\n", "25\t63\t78.3\t0\t63\n", "26\t78\t78.3\t0\t78\n", "27\t86\t78.3\t0\t86\n", "28\t81\t78.3\t0\t81\n", "29\t128\t78.3\t0\t128\n", "30\t169\t78.3\t0\t169\n", "31\t195\t78.3\t0\t195\n", "32\t350\t78.3\t0\t350\n", "33\t303\t78.3\t0\t303\n", "34\t327\t78.3\t0\t327\n", "35\t430\t78.3\t0\t430\n", "36\t338\t78.3\t0\t338\n", "37\t131\t78.3\t0\t131\n", "38\t27\t78.3\t0\t27\n", "39\t10\t78.3\t0\t10\n", "40\t24\t78.3\t0\t24\n", "41\t6\t78.3\t0\t6\n", "42\t13\t78.3\t0\t13\n", "43\t18\t78.3\t0\t18\n", "44\t11\t78.3\t0\t11\n", "45\t20\t78.3\t0\t20\n", "46\t13\t78.3\t0\t13\n", "47\t14\t78.3\t0\t14\n", "48\t10\t78.3\t0\t10\n", "49\t14\t78.3\t0\t14\n", "50\t17\t78.3\t0\t17\n", "51\t14\t78.3\t0\t14\n", "52\t14\t78.3\t0\t14\n", "53\t15\t78.3\t0\t15\n", "54\t9\t78.3\t0\t9\n", "55\t17\t78.3\t0\t17\n", "56\t10\t78.3\t0\t10\n", "57\t17\t78.3\t0\t17\n", "58\t9\t78.3\t0\t9\n", "59\t9\t78.3\t0\t9\n", "60\t5\t78.3\t0\t5\n", "61\t14\t78.3\t0\t14\n", "62\t7\t78.3\t0\t7\n", "63\t8\t78.3\t0\t8\n", "64\t8\t78.3\t0\t8\n", "65\t5\t78.3\t0\t5\n", "66\t3\t78.3\t0\t3\n", "67\t4\t78.3\t0\t4\n", "68\t5\t78.3\t0\t5\n", "69\t2\t78.3\t0\t2\n", "70\t3\t78.3\t0\t3\n", "71\t8\t78.3\t0\t8\n", "72\t2\t78.3\t0\t2\n", "73\t1\t78.3\t0\t1\n", "74\t3\t78.3\t0\t3\n", "75\t4\t78.3\t0\t4\n", "76\t3\t78.3\t0\t3\n", "77\t2\t78.3\t0\t2\n", "78\t4\t78.3\t0\t4\n", "79\t2\t78.3\t0\t2\n", "80\t3\t78.3\t0\t3\n", "81\t3\t78.3\t0\t3\n", "82\t3\t78.3\t0\t3\n", "83\t2\t78.3\t0\t2\n", "84\t11\t78.3\t0\t11\n", "85\t3\t78.3\t0\t3\n", "86\t7\t78.3\t0\t7\n", "87\t7\t78.3\t0\t7\n", "88\t4\t78.3\t0\t4\n", "89\t9\t78.3\t0\t9\n", "90\t6\t78.3\t0\t6\n", "91\t4\t78.3\t0\t4\n", "92\t25\t78.3\t0\t25\n", "93\t48\t78.3\t0\t48\n", "94\t73\t78.3\t0\t73\n", "95\t105\t78.3\t0\t105\n", "96\t73\t78.3\t0\t73\n", "97\t83\t78.3\t0\t83\n", "98\t57\t78.3\t0\t57\n", "99\t85\t78.3\t0\t85\n", "100\t122\t78.3\t0\t122\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 88011 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.2%\n", " C: 19.2%\n", " G: 13.1%\n", " T: 22.4%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t65222\t80130.3\t0\t65222\n", "4\t14016\t20032.6\t0\t14016\n", "5\t3025\t5008.1\t0\t3025\n", "6\t187\t1252.0\t0\t187\n", "7\t69\t313.0\t0\t69\n", "8\t83\t313.0\t0\t83\n", "9\t75\t313.0\t0\t75\n", "10\t87\t313.0\t0\t87\n", "11\t72\t313.0\t0\t72\n", "12\t87\t313.0\t0\t87\n", "13\t69\t313.0\t0\t69\n", "14\t64\t313.0\t0\t64\n", "15\t67\t313.0\t0\t67\n", "16\t72\t313.0\t0\t72\n", "17\t69\t313.0\t0\t69\n", "18\t74\t313.0\t0\t74\n", "19\t56\t313.0\t0\t56\n", "20\t59\t313.0\t0\t59\n", "21\t64\t313.0\t0\t64\n", "22\t57\t313.0\t0\t57\n", "23\t50\t313.0\t0\t50\n", "24\t49\t313.0\t0\t49\n", "25\t56\t313.0\t0\t56\n", "26\t54\t313.0\t0\t54\n", "27\t69\t313.0\t0\t69\n", "28\t70\t313.0\t0\t70\n", "29\t49\t313.0\t0\t49\n", "30\t54\t313.0\t0\t54\n", "31\t65\t313.0\t0\t65\n", "32\t76\t313.0\t0\t76\n", "33\t63\t313.0\t0\t63\n", "34\t55\t313.0\t0\t55\n", "35\t50\t313.0\t0\t50\n", "36\t59\t313.0\t0\t59\n", "37\t54\t313.0\t0\t54\n", "38\t38\t313.0\t0\t38\n", "39\t70\t313.0\t0\t70\n", "40\t88\t313.0\t0\t88\n", "41\t49\t313.0\t0\t49\n", "42\t50\t313.0\t0\t50\n", "43\t43\t313.0\t0\t43\n", "44\t51\t313.0\t0\t51\n", "45\t62\t313.0\t0\t62\n", "46\t75\t313.0\t0\t75\n", "47\t65\t313.0\t0\t65\n", "48\t33\t313.0\t0\t33\n", "49\t39\t313.0\t0\t39\n", "50\t51\t313.0\t0\t51\n", "51\t39\t313.0\t0\t39\n", "52\t48\t313.0\t0\t48\n", "53\t59\t313.0\t0\t59\n", "54\t42\t313.0\t0\t42\n", "55\t27\t313.0\t0\t27\n", "56\t33\t313.0\t0\t33\n", "57\t41\t313.0\t0\t41\n", "58\t30\t313.0\t0\t30\n", "59\t28\t313.0\t0\t28\n", "60\t30\t313.0\t0\t30\n", "61\t37\t313.0\t0\t37\n", "62\t40\t313.0\t0\t40\n", "63\t33\t313.0\t0\t33\n", "64\t27\t313.0\t0\t27\n", "65\t32\t313.0\t0\t32\n", "66\t39\t313.0\t0\t39\n", "67\t50\t313.0\t0\t50\n", "68\t37\t313.0\t0\t37\n", "69\t46\t313.0\t0\t46\n", "70\t26\t313.0\t0\t26\n", "71\t41\t313.0\t0\t41\n", "72\t58\t313.0\t0\t58\n", "73\t47\t313.0\t0\t47\n", "74\t70\t313.0\t0\t70\n", "75\t48\t313.0\t0\t48\n", "76\t64\t313.0\t0\t64\n", "77\t75\t313.0\t0\t75\n", "78\t53\t313.0\t0\t53\n", "79\t79\t313.0\t0\t79\n", "80\t81\t313.0\t0\t81\n", "81\t82\t313.0\t0\t82\n", "82\t136\t313.0\t0\t136\n", "83\t121\t313.0\t0\t121\n", "84\t89\t313.0\t0\t89\n", "85\t93\t313.0\t0\t93\n", "86\t66\t313.0\t0\t66\n", "87\t82\t313.0\t0\t82\n", "88\t68\t313.0\t0\t68\n", "89\t44\t313.0\t0\t44\n", "90\t54\t313.0\t0\t54\n", "91\t44\t313.0\t0\t44\n", "92\t38\t313.0\t0\t38\n", "93\t43\t313.0\t0\t43\n", "94\t47\t313.0\t0\t47\n", "95\t36\t313.0\t0\t36\n", "96\t41\t313.0\t0\t41\n", "97\t75\t313.0\t0\t75\n", "98\t96\t313.0\t0\t96\n", "99\t112\t313.0\t0\t112\n", "100\t123\t313.0\t0\t123\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 533_S61_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/533.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 64.65 s (12 us/read; 4.99 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,373,610\n", "Reads with adapters: 2,266,656 (42.2%)\n", "Reads written (passing filters): 5,204,071 (96.8%)\n", "\n", "Total basepairs processed: 537,361,000 bp\n", "Quality-trimmed: 1,758,432 bp (0.3%)\n", "Total written (filtered): 457,919,337 bp (85.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2112771 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.4%\n", " G: 38.1%\n", " T: 34.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t132283\t83962.7\t0\t132283\n", "4\t65739\t20990.7\t0\t65739\n", "5\t44739\t5247.7\t0\t44739\n", "6\t35184\t1311.9\t0\t35184\n", "7\t28512\t328.0\t0\t28512\n", "8\t26785\t82.0\t0\t26785\n", "9\t27105\t82.0\t0\t27105\n", "10\t27357\t82.0\t0\t27357\n", "11\t28185\t82.0\t0\t28185\n", "12\t28534\t82.0\t0\t28534\n", "13\t36502\t82.0\t0\t36502\n", "14\t35920\t82.0\t0\t35920\n", "15\t31269\t82.0\t0\t31269\n", "16\t33266\t82.0\t0\t33266\n", "17\t33654\t82.0\t0\t33654\n", "18\t37731\t82.0\t0\t37731\n", "19\t33103\t82.0\t0\t33103\n", "20\t26087\t82.0\t0\t26087\n", "21\t24285\t82.0\t0\t24285\n", "22\t23178\t82.0\t0\t23178\n", "23\t25713\t82.0\t0\t25713\n", "24\t31051\t82.0\t0\t31051\n", "25\t33118\t82.0\t0\t33118\n", "26\t33307\t82.0\t0\t33307\n", "27\t30285\t82.0\t0\t30285\n", "28\t29931\t82.0\t0\t29931\n", "29\t28811\t82.0\t0\t28811\n", "30\t29304\t82.0\t0\t29304\n", "31\t32410\t82.0\t0\t32410\n", "32\t32585\t82.0\t0\t32585\n", "33\t31199\t82.0\t0\t31199\n", "34\t31980\t82.0\t0\t31980\n", "35\t35028\t82.0\t0\t35028\n", "36\t42435\t82.0\t0\t42435\n", "37\t46887\t82.0\t0\t46887\n", "38\t33520\t82.0\t0\t33520\n", "39\t26523\t82.0\t0\t26523\n", "40\t24251\t82.0\t0\t24251\n", "41\t25328\t82.0\t0\t25328\n", "42\t26423\t82.0\t0\t26423\n", "43\t23673\t82.0\t0\t23673\n", "44\t20168\t82.0\t0\t20168\n", "45\t23421\t82.0\t0\t23421\n", "46\t26256\t82.0\t0\t26256\n", "47\t24862\t82.0\t0\t24862\n", "48\t23525\t82.0\t0\t23525\n", "49\t20850\t82.0\t0\t20850\n", "50\t19545\t82.0\t0\t19545\n", "51\t19398\t82.0\t0\t19398\n", "52\t18515\t82.0\t0\t18515\n", "53\t18941\t82.0\t0\t18941\n", "54\t21223\t82.0\t0\t21223\n", "55\t21610\t82.0\t0\t21610\n", "56\t18760\t82.0\t0\t18760\n", "57\t16925\t82.0\t0\t16925\n", "58\t17301\t82.0\t0\t17301\n", "59\t15106\t82.0\t0\t15106\n", "60\t14114\t82.0\t0\t14114\n", "61\t13635\t82.0\t0\t13635\n", "62\t12439\t82.0\t0\t12439\n", "63\t11894\t82.0\t0\t11894\n", "64\t12517\t82.0\t0\t12517\n", "65\t12276\t82.0\t0\t12276\n", "66\t11862\t82.0\t0\t11862\n", "67\t12400\t82.0\t0\t12400\n", "68\t12643\t82.0\t0\t12643\n", "69\t13209\t82.0\t0\t13209\n", "70\t15395\t82.0\t0\t15395\n", "71\t15821\t82.0\t0\t15821\n", "72\t11385\t82.0\t0\t11385\n", "73\t9420\t82.0\t0\t9420\n", "74\t9181\t82.0\t0\t9181\n", "75\t8503\t82.0\t0\t8503\n", "76\t7660\t82.0\t0\t7660\n", "77\t7489\t82.0\t0\t7489\n", "78\t7749\t82.0\t0\t7749\n", "79\t7707\t82.0\t0\t7707\n", "80\t7889\t82.0\t0\t7889\n", "81\t7889\t82.0\t0\t7889\n", "82\t7705\t82.0\t0\t7705\n", "83\t8197\t82.0\t0\t8197\n", "84\t8892\t82.0\t0\t8892\n", "85\t9735\t82.0\t0\t9735\n", "86\t9837\t82.0\t0\t9837\n", "87\t8590\t82.0\t0\t8590\n", "88\t8569\t82.0\t0\t8569\n", "89\t8178\t82.0\t0\t8178\n", "90\t8089\t82.0\t0\t8089\n", "91\t7904\t82.0\t0\t7904\n", "92\t7893\t82.0\t0\t7893\n", "93\t7777\t82.0\t0\t7777\n", "94\t7478\t82.0\t0\t7478\n", "95\t6882\t82.0\t0\t6882\n", "96\t5300\t82.0\t0\t5300\n", "97\t3541\t82.0\t0\t3541\n", "98\t2214\t82.0\t0\t2214\n", "99\t1709\t82.0\t0\t1709\n", "100\t1618\t82.0\t0\t1618\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 39996 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 38.0%\n", " C: 35.6%\n", " G: 0.0%\n", " T: 26.1%\n", " none/other: 0.3%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t20532\t83962.7\t0\t20532\n", "4\t5746\t20990.7\t0\t5746\n", "5\t2266\t5247.7\t0\t2266\n", "6\t1189\t1311.9\t0\t1189\n", "7\t109\t328.0\t0\t109\n", "8\t85\t82.0\t0\t85\n", "9\t70\t82.0\t0\t70\n", "10\t85\t82.0\t0\t85\n", "11\t78\t82.0\t0\t78\n", "12\t61\t82.0\t0\t61\n", "13\t81\t82.0\t0\t81\n", "14\t79\t82.0\t0\t79\n", "15\t77\t82.0\t0\t77\n", "16\t73\t82.0\t0\t73\n", "17\t86\t82.0\t0\t86\n", "18\t117\t82.0\t0\t117\n", "19\t138\t82.0\t0\t138\n", "20\t265\t82.0\t0\t265\n", "21\t192\t82.0\t0\t192\n", "22\t134\t82.0\t0\t134\n", "23\t99\t82.0\t0\t99\n", "24\t88\t82.0\t0\t88\n", "25\t82\t82.0\t0\t82\n", "26\t119\t82.0\t0\t119\n", "27\t142\t82.0\t0\t142\n", "28\t143\t82.0\t0\t143\n", "29\t173\t82.0\t0\t173\n", "30\t291\t82.0\t0\t291\n", "31\t352\t82.0\t0\t352\n", "32\t611\t82.0\t0\t611\n", "33\t517\t82.0\t0\t517\n", "34\t554\t82.0\t0\t554\n", "35\t684\t82.0\t0\t684\n", "36\t697\t82.0\t0\t697\n", "37\t371\t82.0\t0\t371\n", "38\t57\t82.0\t0\t57\n", "39\t70\t82.0\t0\t70\n", "40\t39\t82.0\t0\t39\n", "41\t39\t82.0\t0\t39\n", "42\t44\t82.0\t0\t44\n", "43\t46\t82.0\t0\t46\n", "44\t33\t82.0\t0\t33\n", "45\t32\t82.0\t0\t32\n", "46\t44\t82.0\t0\t44\n", "47\t31\t82.0\t0\t31\n", "48\t24\t82.0\t0\t24\n", "49\t41\t82.0\t0\t41\n", "50\t31\t82.0\t0\t31\n", "51\t34\t82.0\t0\t34\n", "52\t21\t82.0\t0\t21\n", "53\t36\t82.0\t0\t36\n", "54\t26\t82.0\t0\t26\n", "55\t31\t82.0\t0\t31\n", "56\t13\t82.0\t0\t13\n", "57\t26\t82.0\t0\t26\n", "58\t23\t82.0\t0\t23\n", "59\t25\t82.0\t0\t25\n", "60\t15\t82.0\t0\t15\n", "61\t18\t82.0\t0\t18\n", "62\t23\t82.0\t0\t23\n", "63\t25\t82.0\t0\t25\n", "64\t29\t82.0\t0\t29\n", "65\t31\t82.0\t0\t31\n", "66\t19\t82.0\t0\t19\n", "67\t21\t82.0\t0\t21\n", "68\t16\t82.0\t0\t16\n", "69\t24\t82.0\t0\t24\n", "70\t17\t82.0\t0\t17\n", "71\t17\t82.0\t0\t17\n", "72\t16\t82.0\t0\t16\n", "73\t11\t82.0\t0\t11\n", "74\t10\t82.0\t0\t10\n", "75\t13\t82.0\t0\t13\n", "76\t11\t82.0\t0\t11\n", "77\t19\t82.0\t0\t19\n", "78\t25\t82.0\t0\t25\n", "79\t24\t82.0\t0\t24\n", "80\t19\t82.0\t0\t19\n", "81\t16\t82.0\t0\t16\n", "82\t12\t82.0\t0\t12\n", "83\t25\t82.0\t0\t25\n", "84\t25\t82.0\t0\t25\n", "85\t22\t82.0\t0\t22\n", "86\t26\t82.0\t0\t26\n", "87\t23\t82.0\t0\t23\n", "88\t31\t82.0\t0\t31\n", "89\t31\t82.0\t0\t31\n", "90\t37\t82.0\t0\t37\n", "91\t60\t82.0\t0\t60\n", "92\t87\t82.0\t0\t87\n", "93\t118\t82.0\t0\t118\n", "94\t191\t82.0\t0\t191\n", "95\t313\t82.0\t0\t313\n", "96\t286\t82.0\t0\t286\n", "97\t340\t82.0\t0\t340\n", "98\t259\t82.0\t0\t259\n", "99\t175\t82.0\t0\t175\n", "100\t364\t82.0\t0\t364\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 113889 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.6%\n", " C: 20.7%\n", " G: 18.3%\n", " T: 21.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t87219\t83962.7\t0\t87219\n", "4\t17052\t20990.7\t0\t17052\n", "5\t2627\t5247.7\t0\t2627\n", "6\t258\t1311.9\t0\t258\n", "7\t57\t328.0\t0\t57\n", "8\t80\t328.0\t0\t80\n", "9\t68\t328.0\t0\t68\n", "10\t72\t328.0\t0\t72\n", "11\t69\t328.0\t0\t69\n", "12\t77\t328.0\t0\t77\n", "13\t81\t328.0\t0\t81\n", "14\t83\t328.0\t0\t83\n", "15\t99\t328.0\t0\t99\n", "16\t86\t328.0\t0\t86\n", "17\t87\t328.0\t0\t87\n", "18\t74\t328.0\t0\t74\n", "19\t89\t328.0\t0\t89\n", "20\t74\t328.0\t0\t74\n", "21\t57\t328.0\t0\t57\n", "22\t58\t328.0\t0\t58\n", "23\t58\t328.0\t0\t58\n", "24\t48\t328.0\t0\t48\n", "25\t69\t328.0\t0\t69\n", "26\t51\t328.0\t0\t51\n", "27\t78\t328.0\t0\t78\n", "28\t74\t328.0\t0\t74\n", "29\t67\t328.0\t0\t67\n", "30\t69\t328.0\t0\t69\n", "31\t96\t328.0\t0\t96\n", "32\t99\t328.0\t0\t99\n", "33\t109\t328.0\t0\t109\n", "34\t80\t328.0\t0\t80\n", "35\t66\t328.0\t0\t66\n", "36\t77\t328.0\t0\t77\n", "37\t104\t328.0\t0\t104\n", "38\t92\t328.0\t0\t92\n", "39\t76\t328.0\t0\t76\n", "40\t107\t328.0\t0\t107\n", "41\t66\t328.0\t0\t66\n", "42\t50\t328.0\t0\t50\n", "43\t74\t328.0\t0\t74\n", "44\t61\t328.0\t0\t61\n", "45\t74\t328.0\t0\t74\n", "46\t80\t328.0\t0\t80\n", "47\t72\t328.0\t0\t72\n", "48\t80\t328.0\t0\t80\n", "49\t67\t328.0\t0\t67\n", "50\t59\t328.0\t0\t59\n", "51\t58\t328.0\t0\t58\n", "52\t65\t328.0\t0\t65\n", "53\t64\t328.0\t0\t64\n", "54\t55\t328.0\t0\t55\n", "55\t62\t328.0\t0\t62\n", "56\t69\t328.0\t0\t69\n", "57\t49\t328.0\t0\t49\n", "58\t80\t328.0\t0\t80\n", "59\t70\t328.0\t0\t70\n", "60\t79\t328.0\t0\t79\n", "61\t78\t328.0\t0\t78\n", "62\t88\t328.0\t0\t88\n", "63\t73\t328.0\t0\t73\n", "64\t60\t328.0\t0\t60\n", "65\t49\t328.0\t0\t49\n", "66\t54\t328.0\t0\t54\n", "67\t57\t328.0\t0\t57\n", "68\t52\t328.0\t0\t52\n", "69\t49\t328.0\t0\t49\n", "70\t56\t328.0\t0\t56\n", "71\t37\t328.0\t0\t37\n", "72\t52\t328.0\t0\t52\n", "73\t56\t328.0\t0\t56\n", "74\t54\t328.0\t0\t54\n", "75\t62\t328.0\t0\t62\n", "76\t67\t328.0\t0\t67\n", "77\t95\t328.0\t0\t95\n", "78\t69\t328.0\t0\t69\n", "79\t75\t328.0\t0\t75\n", "80\t62\t328.0\t0\t62\n", "81\t68\t328.0\t0\t68\n", "82\t79\t328.0\t0\t79\n", "83\t82\t328.0\t0\t82\n", "84\t111\t328.0\t0\t111\n", "85\t80\t328.0\t0\t80\n", "86\t72\t328.0\t0\t72\n", "87\t96\t328.0\t0\t96\n", "88\t111\t328.0\t0\t111\n", "89\t94\t328.0\t0\t94\n", "90\t74\t328.0\t0\t74\n", "91\t66\t328.0\t0\t66\n", "92\t47\t328.0\t0\t47\n", "93\t44\t328.0\t0\t44\n", "94\t50\t328.0\t0\t50\n", "95\t36\t328.0\t0\t36\n", "96\t48\t328.0\t0\t48\n", "97\t77\t328.0\t0\t77\n", "98\t72\t328.0\t0\t72\n", "99\t95\t328.0\t0\t95\n", "100\t121\t328.0\t0\t121\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 541_S41_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/541.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 94.56 s (13 us/read; 4.56 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,189,810\n", "Reads with adapters: 4,262,665 (59.3%)\n", "Reads written (passing filters): 7,018,861 (97.6%)\n", "\n", "Total basepairs processed: 718,981,000 bp\n", "Quality-trimmed: 2,020,605 bp (0.3%)\n", "Total written (filtered): 560,781,282 bp (78.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4097970 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.3%\n", " G: 38.4%\n", " T: 33.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t153366\t112340.8\t0\t153366\n", "4\t84898\t28085.2\t0\t84898\n", "5\t63516\t7021.3\t0\t63516\n", "6\t51097\t1755.3\t0\t51097\n", "7\t45016\t438.8\t0\t45016\n", "8\t45027\t109.7\t0\t45027\n", "9\t43922\t109.7\t0\t43922\n", "10\t41682\t109.7\t0\t41682\n", "11\t42350\t109.7\t0\t42350\n", "12\t42366\t109.7\t0\t42366\n", "13\t47007\t109.7\t0\t47007\n", "14\t47965\t109.7\t0\t47965\n", "15\t47115\t109.7\t0\t47115\n", "16\t49633\t109.7\t0\t49633\n", "17\t53949\t109.7\t0\t53949\n", "18\t62343\t109.7\t0\t62343\n", "19\t57184\t109.7\t0\t57184\n", "20\t48316\t109.7\t0\t48316\n", "21\t46328\t109.7\t0\t46328\n", "22\t43538\t109.7\t0\t43538\n", "23\t48568\t109.7\t0\t48568\n", "24\t57730\t109.7\t0\t57730\n", "25\t58419\t109.7\t0\t58419\n", "26\t66668\t109.7\t0\t66668\n", "27\t75419\t109.7\t0\t75419\n", "28\t70854\t109.7\t0\t70854\n", "29\t67525\t109.7\t0\t67525\n", "30\t71839\t109.7\t0\t71839\n", "31\t77250\t109.7\t0\t77250\n", "32\t73024\t109.7\t0\t73024\n", "33\t65794\t109.7\t0\t65794\n", "34\t64533\t109.7\t0\t64533\n", "35\t75473\t109.7\t0\t75473\n", "36\t94299\t109.7\t0\t94299\n", "37\t104668\t109.7\t0\t104668\n", "38\t81764\t109.7\t0\t81764\n", "39\t63491\t109.7\t0\t63491\n", "40\t59841\t109.7\t0\t59841\n", "41\t59101\t109.7\t0\t59101\n", "42\t64918\t109.7\t0\t64918\n", "43\t57263\t109.7\t0\t57263\n", "44\t47946\t109.7\t0\t47946\n", "45\t62005\t109.7\t0\t62005\n", "46\t75978\t109.7\t0\t75978\n", "47\t74997\t109.7\t0\t74997\n", "48\t74013\t109.7\t0\t74013\n", "49\t55189\t109.7\t0\t55189\n", "50\t51326\t109.7\t0\t51326\n", "51\t49431\t109.7\t0\t49431\n", "52\t49669\t109.7\t0\t49669\n", "53\t52524\t109.7\t0\t52524\n", "54\t64469\t109.7\t0\t64469\n", "55\t55921\t109.7\t0\t55921\n", "56\t45826\t109.7\t0\t45826\n", "57\t42708\t109.7\t0\t42708\n", "58\t46274\t109.7\t0\t46274\n", "59\t40107\t109.7\t0\t40107\n", "60\t35794\t109.7\t0\t35794\n", "61\t34058\t109.7\t0\t34058\n", "62\t27695\t109.7\t0\t27695\n", "63\t26867\t109.7\t0\t26867\n", "64\t29494\t109.7\t0\t29494\n", "65\t29833\t109.7\t0\t29833\n", "66\t27497\t109.7\t0\t27497\n", "67\t26258\t109.7\t0\t26258\n", "68\t24825\t109.7\t0\t24825\n", "69\t24710\t109.7\t0\t24710\n", "70\t26109\t109.7\t0\t26109\n", "71\t24585\t109.7\t0\t24585\n", "72\t20111\t109.7\t0\t20111\n", "73\t18537\t109.7\t0\t18537\n", "74\t18948\t109.7\t0\t18948\n", "75\t15703\t109.7\t0\t15703\n", "76\t13297\t109.7\t0\t13297\n", "77\t12011\t109.7\t0\t12011\n", "78\t12781\t109.7\t0\t12781\n", "79\t12532\t109.7\t0\t12532\n", "80\t12676\t109.7\t0\t12676\n", "81\t11416\t109.7\t0\t11416\n", "82\t10764\t109.7\t0\t10764\n", "83\t11457\t109.7\t0\t11457\n", "84\t12814\t109.7\t0\t12814\n", "85\t13974\t109.7\t0\t13974\n", "86\t12843\t109.7\t0\t12843\n", "87\t8608\t109.7\t0\t8608\n", "88\t7643\t109.7\t0\t7643\n", "89\t8180\t109.7\t0\t8180\n", "90\t8705\t109.7\t0\t8705\n", "91\t8305\t109.7\t0\t8305\n", "92\t8052\t109.7\t0\t8052\n", "93\t7839\t109.7\t0\t7839\n", "94\t7492\t109.7\t0\t7492\n", "95\t6556\t109.7\t0\t6556\n", "96\t5088\t109.7\t0\t5088\n", "97\t3482\t109.7\t0\t3482\n", "98\t2439\t109.7\t0\t2439\n", "99\t2802\t109.7\t0\t2802\n", "100\t1748\t109.7\t0\t1748\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28670 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 58.0%\n", " C: 19.7%\n", " G: 0.0%\n", " T: 22.2%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t12417\t112340.8\t0\t12417\n", "4\t2862\t28085.2\t0\t2862\n", "5\t1140\t7021.3\t0\t1140\n", "6\t801\t1755.3\t0\t801\n", "7\t291\t438.8\t0\t291\n", "8\t209\t109.7\t0\t209\n", "9\t197\t109.7\t0\t197\n", "10\t181\t109.7\t0\t181\n", "11\t185\t109.7\t0\t185\n", "12\t157\t109.7\t0\t157\n", "13\t147\t109.7\t0\t147\n", "14\t153\t109.7\t0\t153\n", "15\t132\t109.7\t0\t132\n", "16\t136\t109.7\t0\t136\n", "17\t151\t109.7\t0\t151\n", "18\t175\t109.7\t0\t175\n", "19\t234\t109.7\t0\t234\n", "20\t336\t109.7\t0\t336\n", "21\t281\t109.7\t0\t281\n", "22\t213\t109.7\t0\t213\n", "23\t170\t109.7\t0\t170\n", "24\t128\t109.7\t0\t128\n", "25\t134\t109.7\t0\t134\n", "26\t235\t109.7\t0\t235\n", "27\t238\t109.7\t0\t238\n", "28\t243\t109.7\t0\t243\n", "29\t276\t109.7\t0\t276\n", "30\t457\t109.7\t0\t457\n", "31\t503\t109.7\t0\t503\n", "32\t795\t109.7\t0\t795\n", "33\t741\t109.7\t0\t741\n", "34\t762\t109.7\t0\t762\n", "35\t1050\t109.7\t0\t1050\n", "36\t919\t109.7\t0\t919\n", "37\t392\t109.7\t0\t392\n", "38\t53\t109.7\t0\t53\n", "39\t29\t109.7\t0\t29\n", "40\t34\t109.7\t0\t34\n", "41\t29\t109.7\t0\t29\n", "42\t29\t109.7\t0\t29\n", "43\t25\t109.7\t0\t25\n", "44\t29\t109.7\t0\t29\n", "45\t23\t109.7\t0\t23\n", "46\t32\t109.7\t0\t32\n", "47\t37\t109.7\t0\t37\n", "48\t27\t109.7\t0\t27\n", "49\t26\t109.7\t0\t26\n", "50\t25\t109.7\t0\t25\n", "51\t24\t109.7\t0\t24\n", "52\t23\t109.7\t0\t23\n", "53\t28\t109.7\t0\t28\n", "54\t13\t109.7\t0\t13\n", "55\t16\t109.7\t0\t16\n", "56\t12\t109.7\t0\t12\n", "57\t19\t109.7\t0\t19\n", "58\t17\t109.7\t0\t17\n", "59\t13\t109.7\t0\t13\n", "60\t19\t109.7\t0\t19\n", "61\t8\t109.7\t0\t8\n", "62\t18\t109.7\t0\t18\n", "63\t8\t109.7\t0\t8\n", "64\t8\t109.7\t0\t8\n", "65\t13\t109.7\t0\t13\n", "66\t19\t109.7\t0\t19\n", "67\t8\t109.7\t0\t8\n", "68\t8\t109.7\t0\t8\n", "69\t8\t109.7\t0\t8\n", "70\t6\t109.7\t0\t6\n", "71\t12\t109.7\t0\t12\n", "72\t4\t109.7\t0\t4\n", "73\t4\t109.7\t0\t4\n", "74\t5\t109.7\t0\t5\n", "75\t6\t109.7\t0\t6\n", "76\t4\t109.7\t0\t4\n", "77\t9\t109.7\t0\t9\n", "78\t6\t109.7\t0\t6\n", "79\t4\t109.7\t0\t4\n", "80\t1\t109.7\t0\t1\n", "81\t4\t109.7\t0\t4\n", "82\t3\t109.7\t0\t3\n", "83\t6\t109.7\t0\t6\n", "84\t3\t109.7\t0\t3\n", "85\t6\t109.7\t0\t6\n", "86\t4\t109.7\t0\t4\n", "87\t9\t109.7\t0\t9\n", "88\t3\t109.7\t0\t3\n", "89\t8\t109.7\t0\t8\n", "90\t15\t109.7\t0\t15\n", "91\t7\t109.7\t0\t7\n", "92\t18\t109.7\t0\t18\n", "93\t24\t109.7\t0\t24\n", "94\t50\t109.7\t0\t50\n", "95\t79\t109.7\t0\t79\n", "96\t41\t109.7\t0\t41\n", "97\t56\t109.7\t0\t56\n", "98\t60\t109.7\t0\t60\n", "99\t35\t109.7\t0\t35\n", "100\t57\t109.7\t0\t57\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 136025 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.6%\n", " C: 20.6%\n", " G: 13.0%\n", " T: 25.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t96268\t112340.8\t0\t96268\n", "4\t22777\t28085.2\t0\t22777\n", "5\t3752\t7021.3\t0\t3752\n", "6\t355\t1755.3\t0\t355\n", "7\t221\t438.8\t0\t221\n", "8\t237\t438.8\t0\t237\n", "9\t211\t438.8\t0\t211\n", "10\t160\t438.8\t0\t160\n", "11\t219\t438.8\t0\t219\n", "12\t246\t438.8\t0\t246\n", "13\t188\t438.8\t0\t188\n", "14\t203\t438.8\t0\t203\n", "15\t185\t438.8\t0\t185\n", "16\t207\t438.8\t0\t207\n", "17\t203\t438.8\t0\t203\n", "18\t215\t438.8\t0\t215\n", "19\t196\t438.8\t0\t196\n", "20\t200\t438.8\t0\t200\n", "21\t200\t438.8\t0\t200\n", "22\t131\t438.8\t0\t131\n", "23\t179\t438.8\t0\t179\n", "24\t122\t438.8\t0\t122\n", "25\t160\t438.8\t0\t160\n", "26\t173\t438.8\t0\t173\n", "27\t151\t438.8\t0\t151\n", "28\t171\t438.8\t0\t171\n", "29\t164\t438.8\t0\t164\n", "30\t180\t438.8\t0\t180\n", "31\t159\t438.8\t0\t159\n", "32\t189\t438.8\t0\t189\n", "33\t152\t438.8\t0\t152\n", "34\t167\t438.8\t0\t167\n", "35\t181\t438.8\t0\t181\n", "36\t231\t438.8\t0\t231\n", "37\t119\t438.8\t0\t119\n", "38\t156\t438.8\t0\t156\n", "39\t224\t438.8\t0\t224\n", "40\t181\t438.8\t0\t181\n", "41\t178\t438.8\t0\t178\n", "42\t172\t438.8\t0\t172\n", "43\t202\t438.8\t0\t202\n", "44\t114\t438.8\t0\t114\n", "45\t162\t438.8\t0\t162\n", "46\t194\t438.8\t0\t194\n", "47\t136\t438.8\t0\t136\n", "48\t151\t438.8\t0\t151\n", "49\t128\t438.8\t0\t128\n", "50\t120\t438.8\t0\t120\n", "51\t131\t438.8\t0\t131\n", "52\t132\t438.8\t0\t132\n", "53\t143\t438.8\t0\t143\n", "54\t117\t438.8\t0\t117\n", "55\t129\t438.8\t0\t129\n", "56\t115\t438.8\t0\t115\n", "57\t116\t438.8\t0\t116\n", "58\t100\t438.8\t0\t100\n", "59\t85\t438.8\t0\t85\n", "60\t112\t438.8\t0\t112\n", "61\t104\t438.8\t0\t104\n", "62\t101\t438.8\t0\t101\n", "63\t78\t438.8\t0\t78\n", "64\t97\t438.8\t0\t97\n", "65\t100\t438.8\t0\t100\n", "66\t107\t438.8\t0\t107\n", "67\t92\t438.8\t0\t92\n", "68\t97\t438.8\t0\t97\n", "69\t60\t438.8\t0\t60\n", "70\t83\t438.8\t0\t83\n", "71\t73\t438.8\t0\t73\n", "72\t97\t438.8\t0\t97\n", "73\t99\t438.8\t0\t99\n", "74\t106\t438.8\t0\t106\n", "75\t56\t438.8\t0\t56\n", "76\t113\t438.8\t0\t113\n", "77\t141\t438.8\t0\t141\n", "78\t105\t438.8\t0\t105\n", "79\t103\t438.8\t0\t103\n", "80\t112\t438.8\t0\t112\n", "81\t116\t438.8\t0\t116\n", "82\t154\t438.8\t0\t154\n", "83\t136\t438.8\t0\t136\n", "84\t118\t438.8\t0\t118\n", "85\t95\t438.8\t0\t95\n", "86\t79\t438.8\t0\t79\n", "87\t118\t438.8\t0\t118\n", "88\t136\t438.8\t0\t136\n", "89\t101\t438.8\t0\t101\n", "90\t67\t438.8\t0\t67\n", "91\t64\t438.8\t0\t64\n", "92\t57\t438.8\t0\t57\n", "93\t35\t438.8\t0\t35\n", "94\t63\t438.8\t0\t63\n", "95\t53\t438.8\t0\t53\n", "96\t44\t438.8\t0\t44\n", "97\t107\t438.8\t0\t107\n", "98\t92\t438.8\t0\t92\n", "99\t137\t438.8\t0\t137\n", "100\t159\t438.8\t0\t159\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 542_S3_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/542.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 79.32 s (13 us/read; 4.76 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,287,099\n", "Reads with adapters: 3,570,868 (56.8%)\n", "Reads written (passing filters): 6,181,692 (98.3%)\n", "\n", "Total basepairs processed: 628,709,900 bp\n", "Quality-trimmed: 1,637,783 bp (0.3%)\n", "Total written (filtered): 500,750,253 bp (79.6%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3431498 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 23.3%\n", " G: 37.8%\n", " T: 38.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t139515\t98235.9\t0\t139515\n", "4\t75832\t24559.0\t0\t75832\n", "5\t60030\t6139.7\t0\t60030\n", "6\t44095\t1534.9\t0\t44095\n", "7\t35655\t383.7\t0\t35655\n", "8\t37542\t95.9\t0\t37542\n", "9\t35459\t95.9\t0\t35459\n", "10\t32302\t95.9\t0\t32302\n", "11\t31452\t95.9\t0\t31452\n", "12\t31163\t95.9\t0\t31163\n", "13\t32583\t95.9\t0\t32583\n", "14\t34302\t95.9\t0\t34302\n", "15\t35004\t95.9\t0\t35004\n", "16\t37163\t95.9\t0\t37163\n", "17\t40719\t95.9\t0\t40719\n", "18\t48572\t95.9\t0\t48572\n", "19\t46842\t95.9\t0\t46842\n", "20\t40216\t95.9\t0\t40216\n", "21\t40212\t95.9\t0\t40212\n", "22\t35940\t95.9\t0\t35940\n", "23\t41638\t95.9\t0\t41638\n", "24\t50902\t95.9\t0\t50902\n", "25\t51140\t95.9\t0\t51140\n", "26\t57633\t95.9\t0\t57633\n", "27\t69981\t95.9\t0\t69981\n", "28\t67197\t95.9\t0\t67197\n", "29\t64125\t95.9\t0\t64125\n", "30\t67878\t95.9\t0\t67878\n", "31\t71160\t95.9\t0\t71160\n", "32\t68995\t95.9\t0\t68995\n", "33\t58901\t95.9\t0\t58901\n", "34\t57126\t95.9\t0\t57126\n", "35\t66779\t95.9\t0\t66779\n", "36\t91408\t95.9\t0\t91408\n", "37\t107073\t95.9\t0\t107073\n", "38\t80971\t95.9\t0\t80971\n", "39\t54104\t95.9\t0\t54104\n", "40\t50268\t95.9\t0\t50268\n", "41\t48114\t95.9\t0\t48114\n", "42\t53856\t95.9\t0\t53856\n", "43\t46188\t95.9\t0\t46188\n", "44\t40608\t95.9\t0\t40608\n", "45\t53888\t95.9\t0\t53888\n", "46\t66253\t95.9\t0\t66253\n", "47\t62294\t95.9\t0\t62294\n", "48\t66282\t95.9\t0\t66282\n", "49\t50174\t95.9\t0\t50174\n", "50\t45462\t95.9\t0\t45462\n", "51\t41556\t95.9\t0\t41556\n", "52\t38579\t95.9\t0\t38579\n", "53\t39361\t95.9\t0\t39361\n", "54\t43650\t95.9\t0\t43650\n", "55\t50206\t95.9\t0\t50206\n", "56\t43092\t95.9\t0\t43092\n", "57\t41199\t95.9\t0\t41199\n", "58\t44461\t95.9\t0\t44461\n", "59\t29609\t95.9\t0\t29609\n", "60\t25061\t95.9\t0\t25061\n", "61\t25137\t95.9\t0\t25137\n", "62\t21696\t95.9\t0\t21696\n", "63\t22479\t95.9\t0\t22479\n", "64\t24988\t95.9\t0\t24988\n", "65\t22178\t95.9\t0\t22178\n", "66\t18551\t95.9\t0\t18551\n", "67\t18037\t95.9\t0\t18037\n", "68\t16650\t95.9\t0\t16650\n", "69\t17346\t95.9\t0\t17346\n", "70\t19112\t95.9\t0\t19112\n", "71\t18708\t95.9\t0\t18708\n", "72\t14819\t95.9\t0\t14819\n", "73\t12370\t95.9\t0\t12370\n", "74\t11585\t95.9\t0\t11585\n", "75\t9895\t95.9\t0\t9895\n", "76\t7797\t95.9\t0\t7797\n", "77\t7905\t95.9\t0\t7905\n", "78\t9202\t95.9\t0\t9202\n", "79\t7973\t95.9\t0\t7973\n", "80\t7541\t95.9\t0\t7541\n", "81\t7075\t95.9\t0\t7075\n", "82\t6649\t95.9\t0\t6649\n", "83\t6565\t95.9\t0\t6565\n", "84\t7624\t95.9\t0\t7624\n", "85\t8776\t95.9\t0\t8776\n", "86\t7989\t95.9\t0\t7989\n", "87\t5438\t95.9\t0\t5438\n", "88\t4586\t95.9\t0\t4586\n", "89\t4850\t95.9\t0\t4850\n", "90\t5047\t95.9\t0\t5047\n", "91\t4736\t95.9\t0\t4736\n", "92\t4296\t95.9\t0\t4296\n", "93\t4612\t95.9\t0\t4612\n", "94\t4530\t95.9\t0\t4530\n", "95\t4023\t95.9\t0\t4023\n", "96\t2877\t95.9\t0\t2877\n", "97\t2009\t95.9\t0\t2009\n", "98\t1303\t95.9\t0\t1303\n", "99\t1763\t95.9\t0\t1763\n", "100\t1011\t95.9\t0\t1011\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 20276 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 67.4%\n", " C: 11.7%\n", " G: 0.0%\n", " T: 20.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t7009\t98235.9\t0\t7009\n", "4\t1571\t24559.0\t0\t1571\n", "5\t663\t6139.7\t0\t663\n", "6\t521\t1534.9\t0\t521\n", "7\t151\t383.7\t0\t151\n", "8\t118\t95.9\t0\t118\n", "9\t117\t95.9\t0\t117\n", "10\t94\t95.9\t0\t94\n", "11\t89\t95.9\t0\t89\n", "12\t71\t95.9\t0\t71\n", "13\t88\t95.9\t0\t88\n", "14\t88\t95.9\t0\t88\n", "15\t96\t95.9\t0\t96\n", "16\t76\t95.9\t0\t76\n", "17\t109\t95.9\t0\t109\n", "18\t169\t95.9\t0\t169\n", "19\t232\t95.9\t0\t232\n", "20\t306\t95.9\t0\t306\n", "21\t206\t95.9\t0\t206\n", "22\t149\t95.9\t0\t149\n", "23\t88\t95.9\t0\t88\n", "24\t114\t95.9\t0\t114\n", "25\t108\t95.9\t0\t108\n", "26\t168\t95.9\t0\t168\n", "27\t198\t95.9\t0\t198\n", "28\t227\t95.9\t0\t227\n", "29\t254\t95.9\t0\t254\n", "30\t502\t95.9\t0\t502\n", "31\t575\t95.9\t0\t575\n", "32\t937\t95.9\t0\t937\n", "33\t826\t95.9\t0\t826\n", "34\t1022\t95.9\t0\t1022\n", "35\t1224\t95.9\t0\t1224\n", "36\t1109\t95.9\t0\t1109\n", "37\t398\t95.9\t0\t398\n", "38\t23\t95.9\t0\t23\n", "39\t27\t95.9\t0\t27\n", "40\t15\t95.9\t0\t15\n", "41\t9\t95.9\t0\t9\n", "42\t9\t95.9\t0\t9\n", "43\t16\t95.9\t0\t16\n", "44\t15\t95.9\t0\t15\n", "45\t16\t95.9\t0\t16\n", "46\t10\t95.9\t0\t10\n", "47\t8\t95.9\t0\t8\n", "48\t11\t95.9\t0\t11\n", "49\t17\t95.9\t0\t17\n", "50\t7\t95.9\t0\t7\n", "51\t5\t95.9\t0\t5\n", "52\t13\t95.9\t0\t13\n", "53\t13\t95.9\t0\t13\n", "54\t9\t95.9\t0\t9\n", "55\t11\t95.9\t0\t11\n", "56\t7\t95.9\t0\t7\n", "57\t3\t95.9\t0\t3\n", "58\t9\t95.9\t0\t9\n", "59\t4\t95.9\t0\t4\n", "60\t2\t95.9\t0\t2\n", "61\t7\t95.9\t0\t7\n", "62\t6\t95.9\t0\t6\n", "63\t7\t95.9\t0\t7\n", "64\t7\t95.9\t0\t7\n", "65\t4\t95.9\t0\t4\n", "66\t5\t95.9\t0\t5\n", "67\t7\t95.9\t0\t7\n", "68\t4\t95.9\t0\t4\n", "69\t2\t95.9\t0\t2\n", "70\t8\t95.9\t0\t8\n", "71\t1\t95.9\t0\t1\n", "72\t6\t95.9\t0\t6\n", "73\t4\t95.9\t0\t4\n", "74\t1\t95.9\t0\t1\n", "75\t2\t95.9\t0\t2\n", "77\t3\t95.9\t0\t3\n", "79\t4\t95.9\t0\t4\n", "80\t1\t95.9\t0\t1\n", "81\t1\t95.9\t0\t1\n", "82\t1\t95.9\t0\t1\n", "86\t3\t95.9\t0\t3\n", "87\t1\t95.9\t0\t1\n", "88\t2\t95.9\t0\t2\n", "89\t4\t95.9\t0\t4\n", "90\t1\t95.9\t0\t1\n", "91\t2\t95.9\t0\t2\n", "92\t7\t95.9\t0\t7\n", "93\t20\t95.9\t0\t20\n", "94\t38\t95.9\t0\t38\n", "95\t35\t95.9\t0\t35\n", "96\t25\t95.9\t0\t25\n", "97\t36\t95.9\t0\t36\n", "98\t23\t95.9\t0\t23\n", "99\t31\t95.9\t0\t31\n", "100\t35\t95.9\t0\t35\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 119094 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.5%\n", " C: 22.8%\n", " G: 8.9%\n", " T: 28.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t89154\t98235.9\t0\t89154\n", "4\t19598\t24559.0\t0\t19598\n", "5\t2261\t6139.7\t0\t2261\n", "6\t190\t1534.9\t0\t190\n", "7\t102\t383.7\t0\t102\n", "8\t114\t383.7\t0\t114\n", "9\t118\t383.7\t0\t118\n", "10\t148\t383.7\t0\t148\n", "11\t124\t383.7\t0\t124\n", "12\t118\t383.7\t0\t118\n", "13\t130\t383.7\t0\t130\n", "14\t129\t383.7\t0\t129\n", "15\t115\t383.7\t0\t115\n", "16\t134\t383.7\t0\t134\n", "17\t136\t383.7\t0\t136\n", "18\t110\t383.7\t0\t110\n", "19\t106\t383.7\t0\t106\n", "20\t97\t383.7\t0\t97\n", "21\t123\t383.7\t0\t123\n", "22\t118\t383.7\t0\t118\n", "23\t96\t383.7\t0\t96\n", "24\t109\t383.7\t0\t109\n", "25\t102\t383.7\t0\t102\n", "26\t114\t383.7\t0\t114\n", "27\t108\t383.7\t0\t108\n", "28\t109\t383.7\t0\t109\n", "29\t101\t383.7\t0\t101\n", "30\t120\t383.7\t0\t120\n", "31\t101\t383.7\t0\t101\n", "32\t102\t383.7\t0\t102\n", "33\t100\t383.7\t0\t100\n", "34\t95\t383.7\t0\t95\n", "35\t87\t383.7\t0\t87\n", "36\t78\t383.7\t0\t78\n", "37\t94\t383.7\t0\t94\n", "38\t103\t383.7\t0\t103\n", "39\t122\t383.7\t0\t122\n", "40\t83\t383.7\t0\t83\n", "41\t96\t383.7\t0\t96\n", "42\t70\t383.7\t0\t70\n", "43\t125\t383.7\t0\t125\n", "44\t40\t383.7\t0\t40\n", "45\t93\t383.7\t0\t93\n", "46\t117\t383.7\t0\t117\n", "47\t84\t383.7\t0\t84\n", "48\t82\t383.7\t0\t82\n", "49\t76\t383.7\t0\t76\n", "50\t57\t383.7\t0\t57\n", "51\t89\t383.7\t0\t89\n", "52\t78\t383.7\t0\t78\n", "53\t78\t383.7\t0\t78\n", "54\t57\t383.7\t0\t57\n", "55\t71\t383.7\t0\t71\n", "56\t65\t383.7\t0\t65\n", "57\t68\t383.7\t0\t68\n", "58\t64\t383.7\t0\t64\n", "59\t45\t383.7\t0\t45\n", "60\t71\t383.7\t0\t71\n", "61\t74\t383.7\t0\t74\n", "62\t66\t383.7\t0\t66\n", "63\t68\t383.7\t0\t68\n", "64\t84\t383.7\t0\t84\n", "65\t56\t383.7\t0\t56\n", "66\t46\t383.7\t0\t46\n", "67\t63\t383.7\t0\t63\n", "68\t43\t383.7\t0\t43\n", "69\t32\t383.7\t0\t32\n", "70\t41\t383.7\t0\t41\n", "71\t41\t383.7\t0\t41\n", "72\t64\t383.7\t0\t64\n", "73\t80\t383.7\t0\t80\n", "74\t98\t383.7\t0\t98\n", "75\t53\t383.7\t0\t53\n", "76\t73\t383.7\t0\t73\n", "77\t84\t383.7\t0\t84\n", "78\t64\t383.7\t0\t64\n", "79\t60\t383.7\t0\t60\n", "80\t85\t383.7\t0\t85\n", "81\t68\t383.7\t0\t68\n", "82\t93\t383.7\t0\t93\n", "83\t77\t383.7\t0\t77\n", "84\t83\t383.7\t0\t83\n", "85\t61\t383.7\t0\t61\n", "86\t47\t383.7\t0\t47\n", "87\t63\t383.7\t0\t63\n", "88\t68\t383.7\t0\t68\n", "89\t59\t383.7\t0\t59\n", "90\t33\t383.7\t0\t33\n", "91\t37\t383.7\t0\t37\n", "92\t39\t383.7\t0\t39\n", "93\t44\t383.7\t0\t44\n", "94\t42\t383.7\t0\t42\n", "95\t35\t383.7\t0\t35\n", "96\t32\t383.7\t0\t32\n", "97\t85\t383.7\t0\t85\n", "98\t116\t383.7\t0\t116\n", "99\t139\t383.7\t0\t139\n", "100\t123\t383.7\t0\t123\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 543_S29_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/543.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 51.97 s (13 us/read; 4.65 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 4,026,626\n", "Reads with adapters: 2,569,958 (63.8%)\n", "Reads written (passing filters): 3,923,848 (97.4%)\n", "\n", "Total basepairs processed: 402,662,600 bp\n", "Quality-trimmed: 1,173,201 bp (0.3%)\n", "Total written (filtered): 305,874,075 bp (76.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2503835 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 28.7%\n", " G: 35.8%\n", " T: 35.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t82046\t62916.0\t0\t82046\n", "4\t50126\t15729.0\t0\t50126\n", "5\t38457\t3932.3\t0\t38457\n", "6\t30894\t983.1\t0\t30894\n", "7\t27750\t245.8\t0\t27750\n", "8\t27282\t61.4\t0\t27282\n", "9\t26971\t61.4\t0\t26971\n", "10\t25695\t61.4\t0\t25695\n", "11\t26155\t61.4\t0\t26155\n", "12\t26384\t61.4\t0\t26384\n", "13\t26488\t61.4\t0\t26488\n", "14\t27729\t61.4\t0\t27729\n", "15\t28029\t61.4\t0\t28029\n", "16\t29773\t61.4\t0\t29773\n", "17\t33441\t61.4\t0\t33441\n", "18\t39362\t61.4\t0\t39362\n", "19\t36832\t61.4\t0\t36832\n", "20\t31217\t61.4\t0\t31217\n", "21\t30792\t61.4\t0\t30792\n", "22\t27867\t61.4\t0\t27867\n", "23\t30675\t61.4\t0\t30675\n", "24\t36438\t61.4\t0\t36438\n", "25\t37174\t61.4\t0\t37174\n", "26\t41872\t61.4\t0\t41872\n", "27\t46910\t61.4\t0\t46910\n", "28\t43323\t61.4\t0\t43323\n", "29\t41702\t61.4\t0\t41702\n", "30\t44246\t61.4\t0\t44246\n", "31\t48084\t61.4\t0\t48084\n", "32\t44986\t61.4\t0\t44986\n", "33\t40977\t61.4\t0\t40977\n", "34\t39070\t61.4\t0\t39070\n", "35\t44357\t61.4\t0\t44357\n", "36\t51687\t61.4\t0\t51687\n", "37\t52450\t61.4\t0\t52450\n", "38\t43971\t61.4\t0\t43971\n", "39\t37362\t61.4\t0\t37362\n", "40\t35304\t61.4\t0\t35304\n", "41\t37408\t61.4\t0\t37408\n", "42\t42018\t61.4\t0\t42018\n", "43\t37068\t61.4\t0\t37068\n", "44\t30548\t61.4\t0\t30548\n", "45\t38849\t61.4\t0\t38849\n", "46\t47337\t61.4\t0\t47337\n", "47\t46436\t61.4\t0\t46436\n", "48\t48644\t61.4\t0\t48644\n", "49\t36782\t61.4\t0\t36782\n", "50\t33845\t61.4\t0\t33845\n", "51\t31487\t61.4\t0\t31487\n", "52\t29937\t61.4\t0\t29937\n", "53\t29397\t61.4\t0\t29397\n", "54\t36334\t61.4\t0\t36334\n", "55\t40171\t61.4\t0\t40171\n", "56\t30786\t61.4\t0\t30786\n", "57\t29349\t61.4\t0\t29349\n", "58\t34340\t61.4\t0\t34340\n", "59\t27681\t61.4\t0\t27681\n", "60\t22385\t61.4\t0\t22385\n", "61\t21870\t61.4\t0\t21870\n", "62\t18098\t61.4\t0\t18098\n", "63\t17046\t61.4\t0\t17046\n", "64\t18829\t61.4\t0\t18829\n", "65\t18698\t61.4\t0\t18698\n", "66\t16587\t61.4\t0\t16587\n", "67\t15668\t61.4\t0\t15668\n", "68\t14711\t61.4\t0\t14711\n", "69\t15058\t61.4\t0\t15058\n", "70\t15408\t61.4\t0\t15408\n", "71\t14448\t61.4\t0\t14448\n", "72\t11897\t61.4\t0\t11897\n", "73\t10639\t61.4\t0\t10639\n", "74\t10628\t61.4\t0\t10628\n", "75\t8921\t61.4\t0\t8921\n", "76\t7325\t61.4\t0\t7325\n", "77\t6613\t61.4\t0\t6613\n", "78\t7266\t61.4\t0\t7266\n", "79\t7043\t61.4\t0\t7043\n", "80\t7050\t61.4\t0\t7050\n", "81\t6593\t61.4\t0\t6593\n", "82\t6001\t61.4\t0\t6001\n", "83\t6422\t61.4\t0\t6422\n", "84\t7291\t61.4\t0\t7291\n", "85\t7978\t61.4\t0\t7978\n", "86\t7946\t61.4\t0\t7946\n", "87\t5588\t61.4\t0\t5588\n", "88\t5134\t61.4\t0\t5134\n", "89\t5337\t61.4\t0\t5337\n", "90\t5607\t61.4\t0\t5607\n", "91\t5651\t61.4\t0\t5651\n", "92\t5286\t61.4\t0\t5286\n", "93\t5308\t61.4\t0\t5308\n", "94\t4771\t61.4\t0\t4771\n", "95\t3839\t61.4\t0\t3839\n", "96\t2594\t61.4\t0\t2594\n", "97\t1731\t61.4\t0\t1731\n", "98\t920\t61.4\t0\t920\n", "99\t819\t61.4\t0\t819\n", "100\t536\t61.4\t0\t536\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 11367 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 58.1%\n", " C: 14.9%\n", " G: 0.0%\n", " T: 26.5%\n", " none/other: 0.5%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t4794\t62916.0\t0\t4794\n", "4\t1043\t15729.0\t0\t1043\n", "5\t343\t3932.3\t0\t343\n", "6\t229\t983.1\t0\t229\n", "7\t44\t245.8\t0\t44\n", "8\t44\t61.4\t0\t44\n", "9\t40\t61.4\t0\t40\n", "10\t32\t61.4\t0\t32\n", "11\t54\t61.4\t0\t54\n", "12\t29\t61.4\t0\t29\n", "13\t34\t61.4\t0\t34\n", "14\t26\t61.4\t0\t26\n", "15\t49\t61.4\t0\t49\n", "16\t37\t61.4\t0\t37\n", "17\t31\t61.4\t0\t31\n", "18\t45\t61.4\t0\t45\n", "19\t68\t61.4\t0\t68\n", "20\t73\t61.4\t0\t73\n", "21\t76\t61.4\t0\t76\n", "22\t47\t61.4\t0\t47\n", "23\t49\t61.4\t0\t49\n", "24\t44\t61.4\t0\t44\n", "25\t39\t61.4\t0\t39\n", "26\t75\t61.4\t0\t75\n", "27\t77\t61.4\t0\t77\n", "28\t91\t61.4\t0\t91\n", "29\t119\t61.4\t0\t119\n", "30\t216\t61.4\t0\t216\n", "31\t224\t61.4\t0\t224\n", "32\t402\t61.4\t0\t402\n", "33\t409\t61.4\t0\t409\n", "34\t409\t61.4\t0\t409\n", "35\t574\t61.4\t0\t574\n", "36\t628\t61.4\t0\t628\n", "37\t237\t61.4\t0\t237\n", "38\t24\t61.4\t0\t24\n", "39\t15\t61.4\t0\t15\n", "40\t15\t61.4\t0\t15\n", "41\t15\t61.4\t0\t15\n", "42\t13\t61.4\t0\t13\n", "43\t13\t61.4\t0\t13\n", "44\t7\t61.4\t0\t7\n", "45\t17\t61.4\t0\t17\n", "46\t15\t61.4\t0\t15\n", "47\t8\t61.4\t0\t8\n", "48\t4\t61.4\t0\t4\n", "49\t13\t61.4\t0\t13\n", "50\t10\t61.4\t0\t10\n", "51\t12\t61.4\t0\t12\n", "52\t12\t61.4\t0\t12\n", "53\t6\t61.4\t0\t6\n", "54\t7\t61.4\t0\t7\n", "55\t8\t61.4\t0\t8\n", "56\t10\t61.4\t0\t10\n", "57\t8\t61.4\t0\t8\n", "58\t9\t61.4\t0\t9\n", "59\t10\t61.4\t0\t10\n", "60\t10\t61.4\t0\t10\n", "61\t8\t61.4\t0\t8\n", "62\t9\t61.4\t0\t9\n", "63\t4\t61.4\t0\t4\n", "64\t6\t61.4\t0\t6\n", "65\t5\t61.4\t0\t5\n", "66\t5\t61.4\t0\t5\n", "67\t6\t61.4\t0\t6\n", "68\t3\t61.4\t0\t3\n", "69\t4\t61.4\t0\t4\n", "70\t3\t61.4\t0\t3\n", "71\t3\t61.4\t0\t3\n", "72\t4\t61.4\t0\t4\n", "73\t3\t61.4\t0\t3\n", "74\t1\t61.4\t0\t1\n", "75\t1\t61.4\t0\t1\n", "76\t1\t61.4\t0\t1\n", "77\t1\t61.4\t0\t1\n", "78\t1\t61.4\t0\t1\n", "79\t7\t61.4\t0\t7\n", "80\t1\t61.4\t0\t1\n", "81\t4\t61.4\t0\t4\n", "82\t1\t61.4\t0\t1\n", "83\t1\t61.4\t0\t1\n", "85\t1\t61.4\t0\t1\n", "87\t2\t61.4\t0\t2\n", "90\t5\t61.4\t0\t5\n", "91\t11\t61.4\t0\t11\n", "92\t5\t61.4\t0\t5\n", "93\t16\t61.4\t0\t16\n", "94\t22\t61.4\t0\t22\n", "95\t52\t61.4\t0\t52\n", "96\t45\t61.4\t0\t45\n", "97\t26\t61.4\t0\t26\n", "98\t29\t61.4\t0\t29\n", "99\t28\t61.4\t0\t28\n", "100\t51\t61.4\t0\t51\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 54756 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.6%\n", " C: 19.0%\n", " G: 13.5%\n", " T: 23.8%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t39449\t62916.0\t0\t39449\n", "4\t9049\t15729.0\t0\t9049\n", "5\t1890\t3932.3\t0\t1890\n", "6\t115\t983.1\t0\t115\n", "7\t46\t245.8\t0\t46\n", "8\t52\t245.8\t0\t52\n", "9\t52\t245.8\t0\t52\n", "10\t64\t245.8\t0\t64\n", "11\t47\t245.8\t0\t47\n", "12\t71\t245.8\t0\t71\n", "13\t69\t245.8\t0\t69\n", "14\t60\t245.8\t0\t60\n", "15\t69\t245.8\t0\t69\n", "16\t49\t245.8\t0\t49\n", "17\t63\t245.8\t0\t63\n", "18\t58\t245.8\t0\t58\n", "19\t71\t245.8\t0\t71\n", "20\t62\t245.8\t0\t62\n", "21\t53\t245.8\t0\t53\n", "22\t41\t245.8\t0\t41\n", "23\t57\t245.8\t0\t57\n", "24\t45\t245.8\t0\t45\n", "25\t45\t245.8\t0\t45\n", "26\t50\t245.8\t0\t50\n", "27\t58\t245.8\t0\t58\n", "28\t51\t245.8\t0\t51\n", "29\t49\t245.8\t0\t49\n", "30\t47\t245.8\t0\t47\n", "31\t58\t245.8\t0\t58\n", "32\t58\t245.8\t0\t58\n", "33\t66\t245.8\t0\t66\n", "34\t44\t245.8\t0\t44\n", "35\t60\t245.8\t0\t60\n", "36\t39\t245.8\t0\t39\n", "37\t45\t245.8\t0\t45\n", "38\t50\t245.8\t0\t50\n", "39\t69\t245.8\t0\t69\n", "40\t70\t245.8\t0\t70\n", "41\t59\t245.8\t0\t59\n", "42\t40\t245.8\t0\t40\n", "43\t52\t245.8\t0\t52\n", "44\t26\t245.8\t0\t26\n", "45\t56\t245.8\t0\t56\n", "46\t67\t245.8\t0\t67\n", "47\t46\t245.8\t0\t46\n", "48\t23\t245.8\t0\t23\n", "49\t38\t245.8\t0\t38\n", "50\t30\t245.8\t0\t30\n", "51\t46\t245.8\t0\t46\n", "52\t43\t245.8\t0\t43\n", "53\t43\t245.8\t0\t43\n", "54\t38\t245.8\t0\t38\n", "55\t24\t245.8\t0\t24\n", "56\t37\t245.8\t0\t37\n", "57\t35\t245.8\t0\t35\n", "58\t25\t245.8\t0\t25\n", "59\t29\t245.8\t0\t29\n", "60\t30\t245.8\t0\t30\n", "61\t31\t245.8\t0\t31\n", "62\t35\t245.8\t0\t35\n", "63\t36\t245.8\t0\t36\n", "64\t42\t245.8\t0\t42\n", "65\t33\t245.8\t0\t33\n", "66\t24\t245.8\t0\t24\n", "67\t41\t245.8\t0\t41\n", "68\t26\t245.8\t0\t26\n", "69\t34\t245.8\t0\t34\n", "70\t14\t245.8\t0\t14\n", "71\t22\t245.8\t0\t22\n", "72\t32\t245.8\t0\t32\n", "73\t41\t245.8\t0\t41\n", "74\t46\t245.8\t0\t46\n", "75\t40\t245.8\t0\t40\n", "76\t55\t245.8\t0\t55\n", "77\t62\t245.8\t0\t62\n", "78\t35\t245.8\t0\t35\n", "79\t64\t245.8\t0\t64\n", "80\t42\t245.8\t0\t42\n", "81\t63\t245.8\t0\t63\n", "82\t76\t245.8\t0\t76\n", "83\t59\t245.8\t0\t59\n", "84\t45\t245.8\t0\t45\n", "85\t31\t245.8\t0\t31\n", "86\t30\t245.8\t0\t30\n", "87\t48\t245.8\t0\t48\n", "88\t43\t245.8\t0\t43\n", "89\t25\t245.8\t0\t25\n", "90\t36\t245.8\t0\t36\n", "91\t31\t245.8\t0\t31\n", "92\t27\t245.8\t0\t27\n", "93\t30\t245.8\t0\t30\n", "94\t24\t245.8\t0\t24\n", "95\t24\t245.8\t0\t24\n", "96\t35\t245.8\t0\t35\n", "97\t40\t245.8\t0\t40\n", "98\t38\t245.8\t0\t38\n", "99\t46\t245.8\t0\t46\n", "100\t72\t245.8\t0\t72\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 551_S24_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/551.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 98.45 s (13 us/read; 4.65 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 7,632,419\n", "Reads with adapters: 4,284,179 (56.1%)\n", "Reads written (passing filters): 7,462,460 (97.8%)\n", "\n", "Total basepairs processed: 763,241,900 bp\n", "Quality-trimmed: 1,756,741 bp (0.2%)\n", "Total written (filtered): 619,055,284 bp (81.1%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4132261 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.6%\n", " G: 35.8%\n", " T: 36.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t189239\t119256.5\t0\t189239\n", "4\t117897\t29814.1\t0\t117897\n", "5\t89765\t7453.5\t0\t89765\n", "6\t69939\t1863.4\t0\t69939\n", "7\t60293\t465.8\t0\t60293\n", "8\t57454\t116.5\t0\t57454\n", "9\t56407\t116.5\t0\t56407\n", "10\t53038\t116.5\t0\t53038\n", "11\t53092\t116.5\t0\t53092\n", "12\t53974\t116.5\t0\t53974\n", "13\t55611\t116.5\t0\t55611\n", "14\t56968\t116.5\t0\t56968\n", "15\t55977\t116.5\t0\t55977\n", "16\t58715\t116.5\t0\t58715\n", "17\t66232\t116.5\t0\t66232\n", "18\t76922\t116.5\t0\t76922\n", "19\t70725\t116.5\t0\t70725\n", "20\t58331\t116.5\t0\t58331\n", "21\t56525\t116.5\t0\t56525\n", "22\t50419\t116.5\t0\t50419\n", "23\t56233\t116.5\t0\t56233\n", "24\t66515\t116.5\t0\t66515\n", "25\t67542\t116.5\t0\t67542\n", "26\t76936\t116.5\t0\t76936\n", "27\t87734\t116.5\t0\t87734\n", "28\t79874\t116.5\t0\t79874\n", "29\t73126\t116.5\t0\t73126\n", "30\t77396\t116.5\t0\t77396\n", "31\t85241\t116.5\t0\t85241\n", "32\t74629\t116.5\t0\t74629\n", "33\t67685\t116.5\t0\t67685\n", "34\t63986\t116.5\t0\t63986\n", "35\t73336\t116.5\t0\t73336\n", "36\t87740\t116.5\t0\t87740\n", "37\t88709\t116.5\t0\t88709\n", "38\t73366\t116.5\t0\t73366\n", "39\t57633\t116.5\t0\t57633\n", "40\t53360\t116.5\t0\t53360\n", "41\t55764\t116.5\t0\t55764\n", "42\t60585\t116.5\t0\t60585\n", "43\t52976\t116.5\t0\t52976\n", "44\t42823\t116.5\t0\t42823\n", "45\t53587\t116.5\t0\t53587\n", "46\t64770\t116.5\t0\t64770\n", "47\t59107\t116.5\t0\t59107\n", "48\t61195\t116.5\t0\t61195\n", "49\t47865\t116.5\t0\t47865\n", "50\t43577\t116.5\t0\t43577\n", "51\t41522\t116.5\t0\t41522\n", "52\t37790\t116.5\t0\t37790\n", "53\t40206\t116.5\t0\t40206\n", "54\t45478\t116.5\t0\t45478\n", "55\t48120\t116.5\t0\t48120\n", "56\t36710\t116.5\t0\t36710\n", "57\t38768\t116.5\t0\t38768\n", "58\t47511\t116.5\t0\t47511\n", "59\t34543\t116.5\t0\t34543\n", "60\t26162\t116.5\t0\t26162\n", "61\t25485\t116.5\t0\t25485\n", "62\t21655\t116.5\t0\t21655\n", "63\t21455\t116.5\t0\t21455\n", "64\t23543\t116.5\t0\t23543\n", "65\t21904\t116.5\t0\t21904\n", "66\t18583\t116.5\t0\t18583\n", "67\t18093\t116.5\t0\t18093\n", "68\t17606\t116.5\t0\t17606\n", "69\t17628\t116.5\t0\t17628\n", "70\t18800\t116.5\t0\t18800\n", "71\t17886\t116.5\t0\t17886\n", "72\t14059\t116.5\t0\t14059\n", "73\t12654\t116.5\t0\t12654\n", "74\t12108\t116.5\t0\t12108\n", "75\t10316\t116.5\t0\t10316\n", "76\t8518\t116.5\t0\t8518\n", "77\t8248\t116.5\t0\t8248\n", "78\t9822\t116.5\t0\t9822\n", "79\t9033\t116.5\t0\t9033\n", "80\t9066\t116.5\t0\t9066\n", "81\t8709\t116.5\t0\t8709\n", "82\t8325\t116.5\t0\t8325\n", "83\t9126\t116.5\t0\t9126\n", "84\t10743\t116.5\t0\t10743\n", "85\t13210\t116.5\t0\t13210\n", "86\t12769\t116.5\t0\t12769\n", "87\t9519\t116.5\t0\t9519\n", "88\t8646\t116.5\t0\t8646\n", "89\t9083\t116.5\t0\t9083\n", "90\t9615\t116.5\t0\t9615\n", "91\t9432\t116.5\t0\t9432\n", "92\t9127\t116.5\t0\t9127\n", "93\t9039\t116.5\t0\t9039\n", "94\t8747\t116.5\t0\t8747\n", "95\t7540\t116.5\t0\t7540\n", "96\t5754\t116.5\t0\t5754\n", "97\t3694\t116.5\t0\t3694\n", "98\t2208\t116.5\t0\t2208\n", "99\t1555\t116.5\t0\t1555\n", "100\t1335\t116.5\t0\t1335\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 28015 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 57.4%\n", " C: 17.2%\n", " G: 0.0%\n", " T: 25.2%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t11496\t119256.5\t0\t11496\n", "4\t2692\t29814.1\t0\t2692\n", "5\t771\t7453.5\t0\t771\n", "6\t317\t1863.4\t0\t317\n", "7\t173\t465.8\t0\t173\n", "8\t112\t116.5\t0\t112\n", "9\t89\t116.5\t0\t89\n", "10\t97\t116.5\t0\t97\n", "11\t102\t116.5\t0\t102\n", "12\t100\t116.5\t0\t100\n", "13\t92\t116.5\t0\t92\n", "14\t83\t116.5\t0\t83\n", "15\t103\t116.5\t0\t103\n", "16\t99\t116.5\t0\t99\n", "17\t86\t116.5\t0\t86\n", "18\t108\t116.5\t0\t108\n", "19\t127\t116.5\t0\t127\n", "20\t155\t116.5\t0\t155\n", "21\t147\t116.5\t0\t147\n", "22\t130\t116.5\t0\t130\n", "23\t106\t116.5\t0\t106\n", "24\t114\t116.5\t0\t114\n", "25\t111\t116.5\t0\t111\n", "26\t180\t116.5\t0\t180\n", "27\t213\t116.5\t0\t213\n", "28\t265\t116.5\t0\t265\n", "29\t322\t116.5\t0\t322\n", "30\t573\t116.5\t0\t573\n", "31\t680\t116.5\t0\t680\n", "32\t1063\t116.5\t0\t1063\n", "33\t1022\t116.5\t0\t1022\n", "34\t1080\t116.5\t0\t1080\n", "35\t1509\t116.5\t0\t1509\n", "36\t1319\t116.5\t0\t1319\n", "37\t506\t116.5\t0\t506\n", "38\t44\t116.5\t0\t44\n", "39\t34\t116.5\t0\t34\n", "40\t34\t116.5\t0\t34\n", "41\t36\t116.5\t0\t36\n", "42\t30\t116.5\t0\t30\n", "43\t24\t116.5\t0\t24\n", "44\t25\t116.5\t0\t25\n", "45\t30\t116.5\t0\t30\n", "46\t36\t116.5\t0\t36\n", "47\t20\t116.5\t0\t20\n", "48\t22\t116.5\t0\t22\n", "49\t43\t116.5\t0\t43\n", "50\t33\t116.5\t0\t33\n", "51\t24\t116.5\t0\t24\n", "52\t19\t116.5\t0\t19\n", "53\t13\t116.5\t0\t13\n", "54\t21\t116.5\t0\t21\n", "55\t21\t116.5\t0\t21\n", "56\t21\t116.5\t0\t21\n", "57\t22\t116.5\t0\t22\n", "58\t23\t116.5\t0\t23\n", "59\t21\t116.5\t0\t21\n", "60\t16\t116.5\t0\t16\n", "61\t13\t116.5\t0\t13\n", "62\t20\t116.5\t0\t20\n", "63\t10\t116.5\t0\t10\n", "64\t11\t116.5\t0\t11\n", "65\t17\t116.5\t0\t17\n", "66\t13\t116.5\t0\t13\n", "67\t13\t116.5\t0\t13\n", "68\t6\t116.5\t0\t6\n", "69\t14\t116.5\t0\t14\n", "70\t8\t116.5\t0\t8\n", "71\t6\t116.5\t0\t6\n", "72\t9\t116.5\t0\t9\n", "73\t12\t116.5\t0\t12\n", "74\t4\t116.5\t0\t4\n", "75\t11\t116.5\t0\t11\n", "76\t7\t116.5\t0\t7\n", "77\t12\t116.5\t0\t12\n", "78\t9\t116.5\t0\t9\n", "79\t4\t116.5\t0\t4\n", "80\t8\t116.5\t0\t8\n", "81\t3\t116.5\t0\t3\n", "82\t10\t116.5\t0\t10\n", "83\t9\t116.5\t0\t9\n", "84\t10\t116.5\t0\t10\n", "85\t21\t116.5\t0\t21\n", "86\t10\t116.5\t0\t10\n", "87\t8\t116.5\t0\t8\n", "88\t5\t116.5\t0\t5\n", "89\t10\t116.5\t0\t10\n", "90\t9\t116.5\t0\t9\n", "91\t17\t116.5\t0\t17\n", "92\t24\t116.5\t0\t24\n", "93\t71\t116.5\t0\t71\n", "94\t126\t116.5\t0\t126\n", "95\t157\t116.5\t0\t157\n", "96\t93\t116.5\t0\t93\n", "97\t130\t116.5\t0\t130\n", "98\t85\t116.5\t0\t85\n", "99\t96\t116.5\t0\t96\n", "100\t160\t116.5\t0\t160\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 123903 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.2%\n", " C: 18.7%\n", " G: 15.1%\n", " T: 20.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t91256\t119256.5\t0\t91256\n", "4\t18923\t29814.1\t0\t18923\n", "5\t3917\t7453.5\t0\t3917\n", "6\t355\t1863.4\t0\t355\n", "7\t158\t465.8\t0\t158\n", "8\t137\t465.8\t0\t137\n", "9\t158\t465.8\t0\t158\n", "10\t148\t465.8\t0\t148\n", "11\t148\t465.8\t0\t148\n", "12\t159\t465.8\t0\t159\n", "13\t130\t465.8\t0\t130\n", "14\t134\t465.8\t0\t134\n", "15\t141\t465.8\t0\t141\n", "16\t135\t465.8\t0\t135\n", "17\t130\t465.8\t0\t130\n", "18\t129\t465.8\t0\t129\n", "19\t128\t465.8\t0\t128\n", "20\t142\t465.8\t0\t142\n", "21\t128\t465.8\t0\t128\n", "22\t116\t465.8\t0\t116\n", "23\t115\t465.8\t0\t115\n", "24\t120\t465.8\t0\t120\n", "25\t114\t465.8\t0\t114\n", "26\t97\t465.8\t0\t97\n", "27\t110\t465.8\t0\t110\n", "28\t140\t465.8\t0\t140\n", "29\t110\t465.8\t0\t110\n", "30\t115\t465.8\t0\t115\n", "31\t124\t465.8\t0\t124\n", "32\t118\t465.8\t0\t118\n", "33\t106\t465.8\t0\t106\n", "34\t111\t465.8\t0\t111\n", "35\t121\t465.8\t0\t121\n", "36\t101\t465.8\t0\t101\n", "37\t127\t465.8\t0\t127\n", "38\t99\t465.8\t0\t99\n", "39\t134\t465.8\t0\t134\n", "40\t148\t465.8\t0\t148\n", "41\t106\t465.8\t0\t106\n", "42\t81\t465.8\t0\t81\n", "43\t116\t465.8\t0\t116\n", "44\t50\t465.8\t0\t50\n", "45\t115\t465.8\t0\t115\n", "46\t108\t465.8\t0\t108\n", "47\t85\t465.8\t0\t85\n", "48\t92\t465.8\t0\t92\n", "49\t88\t465.8\t0\t88\n", "50\t83\t465.8\t0\t83\n", "51\t77\t465.8\t0\t77\n", "52\t69\t465.8\t0\t69\n", "53\t80\t465.8\t0\t80\n", "54\t65\t465.8\t0\t65\n", "55\t66\t465.8\t0\t66\n", "56\t63\t465.8\t0\t63\n", "57\t57\t465.8\t0\t57\n", "58\t60\t465.8\t0\t60\n", "59\t66\t465.8\t0\t66\n", "60\t71\t465.8\t0\t71\n", "61\t80\t465.8\t0\t80\n", "62\t51\t465.8\t0\t51\n", "63\t65\t465.8\t0\t65\n", "64\t58\t465.8\t0\t58\n", "65\t75\t465.8\t0\t75\n", "66\t72\t465.8\t0\t72\n", "67\t66\t465.8\t0\t66\n", "68\t69\t465.8\t0\t69\n", "69\t50\t465.8\t0\t50\n", "70\t48\t465.8\t0\t48\n", "71\t59\t465.8\t0\t59\n", "72\t94\t465.8\t0\t94\n", "73\t73\t465.8\t0\t73\n", "74\t98\t465.8\t0\t98\n", "75\t69\t465.8\t0\t69\n", "76\t91\t465.8\t0\t91\n", "77\t125\t465.8\t0\t125\n", "78\t88\t465.8\t0\t88\n", "79\t100\t465.8\t0\t100\n", "80\t121\t465.8\t0\t121\n", "81\t129\t465.8\t0\t129\n", "82\t169\t465.8\t0\t169\n", "83\t152\t465.8\t0\t152\n", "84\t111\t465.8\t0\t111\n", "85\t98\t465.8\t0\t98\n", "86\t75\t465.8\t0\t75\n", "87\t115\t465.8\t0\t115\n", "88\t79\t465.8\t0\t79\n", "89\t82\t465.8\t0\t82\n", "90\t78\t465.8\t0\t78\n", "91\t53\t465.8\t0\t53\n", "92\t49\t465.8\t0\t49\n", "93\t58\t465.8\t0\t58\n", "94\t71\t465.8\t0\t71\n", "95\t60\t465.8\t0\t60\n", "96\t73\t465.8\t0\t73\n", "97\t108\t465.8\t0\t108\n", "98\t108\t465.8\t0\t108\n", "99\t148\t465.8\t0\t148\n", "100\t155\t465.8\t0\t155\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 552b_S54_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/552b.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 55.38 s (13 us/read; 4.73 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 4,369,784\n", "Reads with adapters: 2,384,032 (54.6%)\n", "Reads written (passing filters): 4,239,829 (97.0%)\n", "\n", "Total basepairs processed: 436,978,400 bp\n", "Quality-trimmed: 1,233,591 bp (0.3%)\n", "Total written (filtered): 351,489,959 bp (80.4%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2285600 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.8%\n", " G: 35.8%\n", " T: 36.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t101033\t68277.9\t0\t101033\n", "4\t57271\t17069.5\t0\t57271\n", "5\t42904\t4267.4\t0\t42904\n", "6\t33985\t1066.8\t0\t33985\n", "7\t28368\t266.7\t0\t28368\n", "8\t26325\t66.7\t0\t26325\n", "9\t25724\t66.7\t0\t25724\n", "10\t25129\t66.7\t0\t25129\n", "11\t25129\t66.7\t0\t25129\n", "12\t26226\t66.7\t0\t26226\n", "13\t31054\t66.7\t0\t31054\n", "14\t31617\t66.7\t0\t31617\n", "15\t28678\t66.7\t0\t28678\n", "16\t29985\t66.7\t0\t29985\n", "17\t33124\t66.7\t0\t33124\n", "18\t38276\t66.7\t0\t38276\n", "19\t34154\t66.7\t0\t34154\n", "20\t29113\t66.7\t0\t29113\n", "21\t28243\t66.7\t0\t28243\n", "22\t25371\t66.7\t0\t25371\n", "23\t28363\t66.7\t0\t28363\n", "24\t34231\t66.7\t0\t34231\n", "25\t35390\t66.7\t0\t35390\n", "26\t40632\t66.7\t0\t40632\n", "27\t45507\t66.7\t0\t45507\n", "28\t42154\t66.7\t0\t42154\n", "29\t38981\t66.7\t0\t38981\n", "30\t40493\t66.7\t0\t40493\n", "31\t42834\t66.7\t0\t42834\n", "32\t39971\t66.7\t0\t39971\n", "33\t36514\t66.7\t0\t36514\n", "34\t36595\t66.7\t0\t36595\n", "35\t41647\t66.7\t0\t41647\n", "36\t52159\t66.7\t0\t52159\n", "37\t61227\t66.7\t0\t61227\n", "38\t43742\t66.7\t0\t43742\n", "39\t32504\t66.7\t0\t32504\n", "40\t30683\t66.7\t0\t30683\n", "41\t31401\t66.7\t0\t31401\n", "42\t33275\t66.7\t0\t33275\n", "43\t29308\t66.7\t0\t29308\n", "44\t24453\t66.7\t0\t24453\n", "45\t29235\t66.7\t0\t29235\n", "46\t35567\t66.7\t0\t35567\n", "47\t34093\t66.7\t0\t34093\n", "48\t34222\t66.7\t0\t34222\n", "49\t28002\t66.7\t0\t28002\n", "50\t25533\t66.7\t0\t25533\n", "51\t23615\t66.7\t0\t23615\n", "52\t22880\t66.7\t0\t22880\n", "53\t24288\t66.7\t0\t24288\n", "54\t24379\t66.7\t0\t24379\n", "55\t27328\t66.7\t0\t27328\n", "56\t26178\t66.7\t0\t26178\n", "57\t21870\t66.7\t0\t21870\n", "58\t26161\t66.7\t0\t26161\n", "59\t21069\t66.7\t0\t21069\n", "60\t17934\t66.7\t0\t17934\n", "61\t16137\t66.7\t0\t16137\n", "62\t13544\t66.7\t0\t13544\n", "63\t14346\t66.7\t0\t14346\n", "64\t16389\t66.7\t0\t16389\n", "65\t13476\t66.7\t0\t13476\n", "66\t12391\t66.7\t0\t12391\n", "67\t13364\t66.7\t0\t13364\n", "68\t12034\t66.7\t0\t12034\n", "69\t11745\t66.7\t0\t11745\n", "70\t13355\t66.7\t0\t13355\n", "71\t11787\t66.7\t0\t11787\n", "72\t8889\t66.7\t0\t8889\n", "73\t6238\t66.7\t0\t6238\n", "74\t5359\t66.7\t0\t5359\n", "75\t5099\t66.7\t0\t5099\n", "76\t4641\t66.7\t0\t4641\n", "77\t5497\t66.7\t0\t5497\n", "78\t6739\t66.7\t0\t6739\n", "79\t5954\t66.7\t0\t5954\n", "80\t5423\t66.7\t0\t5423\n", "81\t5692\t66.7\t0\t5692\n", "82\t5390\t66.7\t0\t5390\n", "83\t5347\t66.7\t0\t5347\n", "84\t6889\t66.7\t0\t6889\n", "85\t8454\t66.7\t0\t8454\n", "86\t9056\t66.7\t0\t9056\n", "87\t7216\t66.7\t0\t7216\n", "88\t6141\t66.7\t0\t6141\n", "89\t6194\t66.7\t0\t6194\n", "90\t6829\t66.7\t0\t6829\n", "91\t7106\t66.7\t0\t7106\n", "92\t7045\t66.7\t0\t7045\n", "93\t7587\t66.7\t0\t7587\n", "94\t7521\t66.7\t0\t7521\n", "95\t6805\t66.7\t0\t6805\n", "96\t5041\t66.7\t0\t5041\n", "97\t3418\t66.7\t0\t3418\n", "98\t2061\t66.7\t0\t2061\n", "99\t1737\t66.7\t0\t1737\n", "100\t1537\t66.7\t0\t1537\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 22206 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 58.1%\n", " C: 20.3%\n", " G: 0.0%\n", " T: 21.5%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t8189\t68277.9\t0\t8189\n", "4\t1937\t17069.5\t0\t1937\n", "5\t1025\t4267.4\t0\t1025\n", "6\t757\t1066.8\t0\t757\n", "7\t185\t266.7\t0\t185\n", "8\t152\t66.7\t0\t152\n", "9\t127\t66.7\t0\t127\n", "10\t143\t66.7\t0\t143\n", "11\t131\t66.7\t0\t131\n", "12\t117\t66.7\t0\t117\n", "13\t97\t66.7\t0\t97\n", "14\t110\t66.7\t0\t110\n", "15\t107\t66.7\t0\t107\n", "16\t113\t66.7\t0\t113\n", "17\t114\t66.7\t0\t114\n", "18\t145\t66.7\t0\t145\n", "19\t189\t66.7\t0\t189\n", "20\t169\t66.7\t0\t169\n", "21\t124\t66.7\t0\t124\n", "22\t106\t66.7\t0\t106\n", "23\t103\t66.7\t0\t103\n", "24\t183\t66.7\t0\t183\n", "25\t201\t66.7\t0\t201\n", "26\t247\t66.7\t0\t247\n", "27\t311\t66.7\t0\t311\n", "28\t325\t66.7\t0\t325\n", "29\t396\t66.7\t0\t396\n", "30\t567\t66.7\t0\t567\n", "31\t682\t66.7\t0\t682\n", "32\t897\t66.7\t0\t897\n", "33\t774\t66.7\t0\t774\n", "34\t880\t66.7\t0\t880\n", "35\t934\t66.7\t0\t934\n", "36\t540\t66.7\t0\t540\n", "37\t132\t66.7\t0\t132\n", "38\t20\t66.7\t0\t20\n", "39\t10\t66.7\t0\t10\n", "40\t16\t66.7\t0\t16\n", "41\t17\t66.7\t0\t17\n", "42\t14\t66.7\t0\t14\n", "43\t24\t66.7\t0\t24\n", "44\t17\t66.7\t0\t17\n", "45\t16\t66.7\t0\t16\n", "46\t17\t66.7\t0\t17\n", "47\t9\t66.7\t0\t9\n", "48\t24\t66.7\t0\t24\n", "49\t9\t66.7\t0\t9\n", "50\t10\t66.7\t0\t10\n", "51\t12\t66.7\t0\t12\n", "52\t19\t66.7\t0\t19\n", "53\t4\t66.7\t0\t4\n", "54\t17\t66.7\t0\t17\n", "55\t11\t66.7\t0\t11\n", "56\t3\t66.7\t0\t3\n", "57\t9\t66.7\t0\t9\n", "58\t6\t66.7\t0\t6\n", "59\t5\t66.7\t0\t5\n", "60\t4\t66.7\t0\t4\n", "61\t3\t66.7\t0\t3\n", "62\t2\t66.7\t0\t2\n", "63\t3\t66.7\t0\t3\n", "64\t11\t66.7\t0\t11\n", "65\t5\t66.7\t0\t5\n", "66\t8\t66.7\t0\t8\n", "67\t4\t66.7\t0\t4\n", "68\t9\t66.7\t0\t9\n", "69\t3\t66.7\t0\t3\n", "70\t6\t66.7\t0\t6\n", "71\t5\t66.7\t0\t5\n", "72\t6\t66.7\t0\t6\n", "73\t3\t66.7\t0\t3\n", "74\t1\t66.7\t0\t1\n", "75\t4\t66.7\t0\t4\n", "76\t2\t66.7\t0\t2\n", "77\t2\t66.7\t0\t2\n", "78\t2\t66.7\t0\t2\n", "79\t4\t66.7\t0\t4\n", "80\t3\t66.7\t0\t3\n", "81\t5\t66.7\t0\t5\n", "82\t7\t66.7\t0\t7\n", "83\t5\t66.7\t0\t5\n", "84\t3\t66.7\t0\t3\n", "85\t5\t66.7\t0\t5\n", "86\t2\t66.7\t0\t2\n", "87\t6\t66.7\t0\t6\n", "88\t7\t66.7\t0\t7\n", "89\t7\t66.7\t0\t7\n", "90\t5\t66.7\t0\t5\n", "91\t8\t66.7\t0\t8\n", "92\t26\t66.7\t0\t26\n", "93\t44\t66.7\t0\t44\n", "94\t69\t66.7\t0\t69\n", "95\t77\t66.7\t0\t77\n", "96\t72\t66.7\t0\t72\n", "97\t91\t66.7\t0\t91\n", "98\t61\t66.7\t0\t61\n", "99\t53\t66.7\t0\t53\n", "100\t65\t66.7\t0\t65\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 76226 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.2%\n", " C: 24.9%\n", " G: 12.5%\n", " T: 22.3%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t56691\t68277.9\t0\t56691\n", "4\t11057\t17069.5\t0\t11057\n", "5\t2051\t4267.4\t0\t2051\n", "6\t163\t1066.8\t0\t163\n", "7\t88\t266.7\t0\t88\n", "8\t94\t266.7\t0\t94\n", "9\t109\t266.7\t0\t109\n", "10\t106\t266.7\t0\t106\n", "11\t108\t266.7\t0\t108\n", "12\t107\t266.7\t0\t107\n", "13\t105\t266.7\t0\t105\n", "14\t117\t266.7\t0\t117\n", "15\t131\t266.7\t0\t131\n", "16\t121\t266.7\t0\t121\n", "17\t135\t266.7\t0\t135\n", "18\t130\t266.7\t0\t130\n", "19\t115\t266.7\t0\t115\n", "20\t125\t266.7\t0\t125\n", "21\t102\t266.7\t0\t102\n", "22\t93\t266.7\t0\t93\n", "23\t78\t266.7\t0\t78\n", "24\t88\t266.7\t0\t88\n", "25\t68\t266.7\t0\t68\n", "26\t100\t266.7\t0\t100\n", "27\t100\t266.7\t0\t100\n", "28\t84\t266.7\t0\t84\n", "29\t86\t266.7\t0\t86\n", "30\t104\t266.7\t0\t104\n", "31\t75\t266.7\t0\t75\n", "32\t89\t266.7\t0\t89\n", "33\t82\t266.7\t0\t82\n", "34\t91\t266.7\t0\t91\n", "35\t88\t266.7\t0\t88\n", "36\t59\t266.7\t0\t59\n", "37\t66\t266.7\t0\t66\n", "38\t64\t266.7\t0\t64\n", "39\t76\t266.7\t0\t76\n", "40\t82\t266.7\t0\t82\n", "41\t55\t266.7\t0\t55\n", "42\t74\t266.7\t0\t74\n", "43\t69\t266.7\t0\t69\n", "44\t29\t266.7\t0\t29\n", "45\t61\t266.7\t0\t61\n", "46\t96\t266.7\t0\t96\n", "47\t66\t266.7\t0\t66\n", "48\t45\t266.7\t0\t45\n", "49\t67\t266.7\t0\t67\n", "50\t34\t266.7\t0\t34\n", "51\t50\t266.7\t0\t50\n", "52\t68\t266.7\t0\t68\n", "53\t55\t266.7\t0\t55\n", "54\t23\t266.7\t0\t23\n", "55\t50\t266.7\t0\t50\n", "56\t40\t266.7\t0\t40\n", "57\t56\t266.7\t0\t56\n", "58\t41\t266.7\t0\t41\n", "59\t24\t266.7\t0\t24\n", "60\t43\t266.7\t0\t43\n", "61\t35\t266.7\t0\t35\n", "62\t34\t266.7\t0\t34\n", "63\t49\t266.7\t0\t49\n", "64\t44\t266.7\t0\t44\n", "65\t33\t266.7\t0\t33\n", "66\t36\t266.7\t0\t36\n", "67\t45\t266.7\t0\t45\n", "68\t46\t266.7\t0\t46\n", "69\t44\t266.7\t0\t44\n", "70\t28\t266.7\t0\t28\n", "71\t25\t266.7\t0\t25\n", "72\t54\t266.7\t0\t54\n", "73\t33\t266.7\t0\t33\n", "74\t58\t266.7\t0\t58\n", "75\t45\t266.7\t0\t45\n", "76\t58\t266.7\t0\t58\n", "77\t45\t266.7\t0\t45\n", "78\t49\t266.7\t0\t49\n", "79\t68\t266.7\t0\t68\n", "80\t51\t266.7\t0\t51\n", "81\t66\t266.7\t0\t66\n", "82\t58\t266.7\t0\t58\n", "83\t66\t266.7\t0\t66\n", "84\t62\t266.7\t0\t62\n", "85\t45\t266.7\t0\t45\n", "86\t55\t266.7\t0\t55\n", "87\t58\t266.7\t0\t58\n", "88\t57\t266.7\t0\t57\n", "89\t47\t266.7\t0\t47\n", "90\t37\t266.7\t0\t37\n", "91\t35\t266.7\t0\t35\n", "92\t54\t266.7\t0\t54\n", "93\t30\t266.7\t0\t30\n", "94\t35\t266.7\t0\t35\n", "95\t30\t266.7\t0\t30\n", "96\t41\t266.7\t0\t41\n", "97\t62\t266.7\t0\t62\n", "98\t74\t266.7\t0\t74\n", "99\t68\t266.7\t0\t68\n", "100\t92\t266.7\t0\t92\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 553_S23_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/553.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 59.08 s (12 us/read; 5.01 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 4,933,901\n", "Reads with adapters: 2,344,193 (47.5%)\n", "Reads written (passing filters): 4,827,655 (97.8%)\n", "\n", "Total basepairs processed: 493,390,100 bp\n", "Quality-trimmed: 1,147,314 bp (0.2%)\n", "Total written (filtered): 413,224,412 bp (83.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2210397 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.1%\n", " G: 39.0%\n", " T: 29.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t117225\t77092.2\t0\t117225\n", "4\t62767\t19273.1\t0\t62767\n", "5\t42850\t4818.3\t0\t42850\n", "6\t34124\t1204.6\t0\t34124\n", "7\t29780\t301.1\t0\t29780\n", "8\t28754\t75.3\t0\t28754\n", "9\t28139\t75.3\t0\t28139\n", "10\t27157\t75.3\t0\t27157\n", "11\t27816\t75.3\t0\t27816\n", "12\t28645\t75.3\t0\t28645\n", "13\t30789\t75.3\t0\t30789\n", "14\t31366\t75.3\t0\t31366\n", "15\t30661\t75.3\t0\t30661\n", "16\t31245\t75.3\t0\t31245\n", "17\t33991\t75.3\t0\t33991\n", "18\t39036\t75.3\t0\t39036\n", "19\t35381\t75.3\t0\t35381\n", "20\t29543\t75.3\t0\t29543\n", "21\t27494\t75.3\t0\t27494\n", "22\t25527\t75.3\t0\t25527\n", "23\t28136\t75.3\t0\t28136\n", "24\t32152\t75.3\t0\t32152\n", "25\t32732\t75.3\t0\t32732\n", "26\t36956\t75.3\t0\t36956\n", "27\t40261\t75.3\t0\t40261\n", "28\t36378\t75.3\t0\t36378\n", "29\t34581\t75.3\t0\t34581\n", "30\t34635\t75.3\t0\t34635\n", "31\t37462\t75.3\t0\t37462\n", "32\t38559\t75.3\t0\t38559\n", "33\t34981\t75.3\t0\t34981\n", "34\t34113\t75.3\t0\t34113\n", "35\t37538\t75.3\t0\t37538\n", "36\t43425\t75.3\t0\t43425\n", "37\t44446\t75.3\t0\t44446\n", "38\t36722\t75.3\t0\t36722\n", "39\t31773\t75.3\t0\t31773\n", "40\t30064\t75.3\t0\t30064\n", "41\t32548\t75.3\t0\t32548\n", "42\t36029\t75.3\t0\t36029\n", "43\t31279\t75.3\t0\t31279\n", "44\t24908\t75.3\t0\t24908\n", "45\t30742\t75.3\t0\t30742\n", "46\t35474\t75.3\t0\t35474\n", "47\t32243\t75.3\t0\t32243\n", "48\t32385\t75.3\t0\t32385\n", "49\t26994\t75.3\t0\t26994\n", "50\t25890\t75.3\t0\t25890\n", "51\t21956\t75.3\t0\t21956\n", "52\t20667\t75.3\t0\t20667\n", "53\t21347\t75.3\t0\t21347\n", "54\t25136\t75.3\t0\t25136\n", "55\t27214\t75.3\t0\t27214\n", "56\t24477\t75.3\t0\t24477\n", "57\t23333\t75.3\t0\t23333\n", "58\t23005\t75.3\t0\t23005\n", "59\t18026\t75.3\t0\t18026\n", "60\t15793\t75.3\t0\t15793\n", "61\t14936\t75.3\t0\t14936\n", "62\t12262\t75.3\t0\t12262\n", "63\t11896\t75.3\t0\t11896\n", "64\t13504\t75.3\t0\t13504\n", "65\t13364\t75.3\t0\t13364\n", "66\t11327\t75.3\t0\t11327\n", "67\t11478\t75.3\t0\t11478\n", "68\t11324\t75.3\t0\t11324\n", "69\t11425\t75.3\t0\t11425\n", "70\t12213\t75.3\t0\t12213\n", "71\t12028\t75.3\t0\t12028\n", "72\t9418\t75.3\t0\t9418\n", "73\t7946\t75.3\t0\t7946\n", "74\t8145\t75.3\t0\t8145\n", "75\t7117\t75.3\t0\t7117\n", "76\t5860\t75.3\t0\t5860\n", "77\t5768\t75.3\t0\t5768\n", "78\t6719\t75.3\t0\t6719\n", "79\t6309\t75.3\t0\t6309\n", "80\t6121\t75.3\t0\t6121\n", "81\t5940\t75.3\t0\t5940\n", "82\t5854\t75.3\t0\t5854\n", "83\t5955\t75.3\t0\t5955\n", "84\t6674\t75.3\t0\t6674\n", "85\t7337\t75.3\t0\t7337\n", "86\t7244\t75.3\t0\t7244\n", "87\t5679\t75.3\t0\t5679\n", "88\t5507\t75.3\t0\t5507\n", "89\t5559\t75.3\t0\t5559\n", "90\t5625\t75.3\t0\t5625\n", "91\t5572\t75.3\t0\t5572\n", "92\t5375\t75.3\t0\t5375\n", "93\t5181\t75.3\t0\t5181\n", "94\t4688\t75.3\t0\t4688\n", "95\t3950\t75.3\t0\t3950\n", "96\t2840\t75.3\t0\t2840\n", "97\t1877\t75.3\t0\t1877\n", "98\t1276\t75.3\t0\t1276\n", "99\t1384\t75.3\t0\t1384\n", "100\t1070\t75.3\t0\t1070\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 25781 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.2%\n", " C: 28.1%\n", " G: 0.0%\n", " T: 28.6%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t14945\t77092.2\t0\t14945\n", "4\t3346\t19273.1\t0\t3346\n", "5\t1120\t4818.3\t0\t1120\n", "6\t619\t1204.6\t0\t619\n", "7\t102\t301.1\t0\t102\n", "8\t73\t75.3\t0\t73\n", "9\t86\t75.3\t0\t86\n", "10\t66\t75.3\t0\t66\n", "11\t72\t75.3\t0\t72\n", "12\t61\t75.3\t0\t61\n", "13\t71\t75.3\t0\t71\n", "14\t70\t75.3\t0\t70\n", "15\t82\t75.3\t0\t82\n", "16\t64\t75.3\t0\t64\n", "17\t70\t75.3\t0\t70\n", "18\t92\t75.3\t0\t92\n", "19\t104\t75.3\t0\t104\n", "20\t122\t75.3\t0\t122\n", "21\t96\t75.3\t0\t96\n", "22\t74\t75.3\t0\t74\n", "23\t76\t75.3\t0\t76\n", "24\t58\t75.3\t0\t58\n", "25\t71\t75.3\t0\t71\n", "26\t73\t75.3\t0\t73\n", "27\t108\t75.3\t0\t108\n", "28\t82\t75.3\t0\t82\n", "29\t128\t75.3\t0\t128\n", "30\t162\t75.3\t0\t162\n", "31\t207\t75.3\t0\t207\n", "32\t284\t75.3\t0\t284\n", "33\t279\t75.3\t0\t279\n", "34\t267\t75.3\t0\t267\n", "35\t320\t75.3\t0\t320\n", "36\t322\t75.3\t0\t322\n", "37\t150\t75.3\t0\t150\n", "38\t54\t75.3\t0\t54\n", "39\t32\t75.3\t0\t32\n", "40\t37\t75.3\t0\t37\n", "41\t48\t75.3\t0\t48\n", "42\t32\t75.3\t0\t32\n", "43\t47\t75.3\t0\t47\n", "44\t44\t75.3\t0\t44\n", "45\t34\t75.3\t0\t34\n", "46\t38\t75.3\t0\t38\n", "47\t46\t75.3\t0\t46\n", "48\t41\t75.3\t0\t41\n", "49\t49\t75.3\t0\t49\n", "50\t41\t75.3\t0\t41\n", "51\t32\t75.3\t0\t32\n", "52\t36\t75.3\t0\t36\n", "53\t33\t75.3\t0\t33\n", "54\t29\t75.3\t0\t29\n", "55\t23\t75.3\t0\t23\n", "56\t24\t75.3\t0\t24\n", "57\t26\t75.3\t0\t26\n", "58\t26\t75.3\t0\t26\n", "59\t12\t75.3\t0\t12\n", "60\t29\t75.3\t0\t29\n", "61\t21\t75.3\t0\t21\n", "62\t27\t75.3\t0\t27\n", "63\t30\t75.3\t0\t30\n", "64\t21\t75.3\t0\t21\n", "65\t22\t75.3\t0\t22\n", "66\t19\t75.3\t0\t19\n", "67\t15\t75.3\t0\t15\n", "68\t12\t75.3\t0\t12\n", "69\t20\t75.3\t0\t20\n", "70\t20\t75.3\t0\t20\n", "71\t12\t75.3\t0\t12\n", "72\t9\t75.3\t0\t9\n", "73\t11\t75.3\t0\t11\n", "74\t12\t75.3\t0\t12\n", "75\t8\t75.3\t0\t8\n", "76\t7\t75.3\t0\t7\n", "77\t15\t75.3\t0\t15\n", "78\t11\t75.3\t0\t11\n", "79\t9\t75.3\t0\t9\n", "80\t11\t75.3\t0\t11\n", "81\t6\t75.3\t0\t6\n", "82\t16\t75.3\t0\t16\n", "83\t12\t75.3\t0\t12\n", "84\t9\t75.3\t0\t9\n", "85\t11\t75.3\t0\t11\n", "86\t4\t75.3\t0\t4\n", "87\t14\t75.3\t0\t14\n", "88\t11\t75.3\t0\t11\n", "89\t18\t75.3\t0\t18\n", "90\t14\t75.3\t0\t14\n", "91\t26\t75.3\t0\t26\n", "92\t25\t75.3\t0\t25\n", "93\t45\t75.3\t0\t45\n", "94\t59\t75.3\t0\t59\n", "95\t79\t75.3\t0\t79\n", "96\t77\t75.3\t0\t77\n", "97\t103\t75.3\t0\t103\n", "98\t71\t75.3\t0\t71\n", "99\t41\t75.3\t0\t41\n", "100\t93\t75.3\t0\t93\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 108015 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.0%\n", " C: 22.0%\n", " G: 18.0%\n", " T: 21.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t81288\t77092.2\t0\t81288\n", "4\t16168\t19273.1\t0\t16168\n", "5\t2882\t4818.3\t0\t2882\n", "6\t284\t1204.6\t0\t284\n", "7\t102\t301.1\t0\t102\n", "8\t87\t301.1\t0\t87\n", "9\t106\t301.1\t0\t106\n", "10\t103\t301.1\t0\t103\n", "11\t95\t301.1\t0\t95\n", "12\t124\t301.1\t0\t124\n", "13\t86\t301.1\t0\t86\n", "14\t104\t301.1\t0\t104\n", "15\t78\t301.1\t0\t78\n", "16\t80\t301.1\t0\t80\n", "17\t100\t301.1\t0\t100\n", "18\t75\t301.1\t0\t75\n", "19\t91\t301.1\t0\t91\n", "20\t70\t301.1\t0\t70\n", "21\t82\t301.1\t0\t82\n", "22\t77\t301.1\t0\t77\n", "23\t62\t301.1\t0\t62\n", "24\t65\t301.1\t0\t65\n", "25\t81\t301.1\t0\t81\n", "26\t69\t301.1\t0\t69\n", "27\t73\t301.1\t0\t73\n", "28\t99\t301.1\t0\t99\n", "29\t78\t301.1\t0\t78\n", "30\t87\t301.1\t0\t87\n", "31\t85\t301.1\t0\t85\n", "32\t78\t301.1\t0\t78\n", "33\t74\t301.1\t0\t74\n", "34\t90\t301.1\t0\t90\n", "35\t74\t301.1\t0\t74\n", "36\t84\t301.1\t0\t84\n", "37\t78\t301.1\t0\t78\n", "38\t74\t301.1\t0\t74\n", "39\t85\t301.1\t0\t85\n", "40\t106\t301.1\t0\t106\n", "41\t80\t301.1\t0\t80\n", "42\t71\t301.1\t0\t71\n", "43\t91\t301.1\t0\t91\n", "44\t73\t301.1\t0\t73\n", "45\t83\t301.1\t0\t83\n", "46\t110\t301.1\t0\t110\n", "47\t111\t301.1\t0\t111\n", "48\t57\t301.1\t0\t57\n", "49\t53\t301.1\t0\t53\n", "50\t66\t301.1\t0\t66\n", "51\t61\t301.1\t0\t61\n", "52\t68\t301.1\t0\t68\n", "53\t82\t301.1\t0\t82\n", "54\t68\t301.1\t0\t68\n", "55\t66\t301.1\t0\t66\n", "56\t57\t301.1\t0\t57\n", "57\t83\t301.1\t0\t83\n", "58\t52\t301.1\t0\t52\n", "59\t77\t301.1\t0\t77\n", "60\t68\t301.1\t0\t68\n", "61\t85\t301.1\t0\t85\n", "62\t64\t301.1\t0\t64\n", "63\t78\t301.1\t0\t78\n", "64\t70\t301.1\t0\t70\n", "65\t56\t301.1\t0\t56\n", "66\t79\t301.1\t0\t79\n", "67\t63\t301.1\t0\t63\n", "68\t73\t301.1\t0\t73\n", "69\t62\t301.1\t0\t62\n", "70\t63\t301.1\t0\t63\n", "71\t66\t301.1\t0\t66\n", "72\t66\t301.1\t0\t66\n", "73\t66\t301.1\t0\t66\n", "74\t87\t301.1\t0\t87\n", "75\t74\t301.1\t0\t74\n", "76\t84\t301.1\t0\t84\n", "77\t102\t301.1\t0\t102\n", "78\t90\t301.1\t0\t90\n", "79\t98\t301.1\t0\t98\n", "80\t88\t301.1\t0\t88\n", "81\t97\t301.1\t0\t97\n", "82\t105\t301.1\t0\t105\n", "83\t87\t301.1\t0\t87\n", "84\t95\t301.1\t0\t95\n", "85\t80\t301.1\t0\t80\n", "86\t71\t301.1\t0\t71\n", "87\t98\t301.1\t0\t98\n", "88\t112\t301.1\t0\t112\n", "89\t83\t301.1\t0\t83\n", "90\t75\t301.1\t0\t75\n", "91\t56\t301.1\t0\t56\n", "92\t44\t301.1\t0\t44\n", "93\t43\t301.1\t0\t43\n", "94\t65\t301.1\t0\t65\n", "95\t40\t301.1\t0\t40\n", "96\t42\t301.1\t0\t42\n", "97\t57\t301.1\t0\t57\n", "98\t73\t301.1\t0\t73\n", "99\t97\t301.1\t0\t97\n", "100\t80\t301.1\t0\t80\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 554_S13_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/554.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 105.77 s (13 us/read; 4.62 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,147,322\n", "Reads with adapters: 4,534,048 (55.7%)\n", "Reads written (passing filters): 7,993,552 (98.1%)\n", "\n", "Total basepairs processed: 814,732,200 bp\n", "Quality-trimmed: 2,013,867 bp (0.2%)\n", "Total written (filtered): 659,086,247 bp (80.9%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 4340349 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 31.3%\n", " G: 41.3%\n", " T: 27.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t184570\t127301.9\t0\t184570\n", "4\t101465\t31825.5\t0\t101465\n", "5\t76211\t7956.4\t0\t76211\n", "6\t64604\t1989.1\t0\t64604\n", "7\t57716\t497.3\t0\t57716\n", "8\t57201\t124.3\t0\t57201\n", "9\t56446\t124.3\t0\t56446\n", "10\t55302\t124.3\t0\t55302\n", "11\t55741\t124.3\t0\t55741\n", "12\t56713\t124.3\t0\t56713\n", "13\t62352\t124.3\t0\t62352\n", "14\t63676\t124.3\t0\t63676\n", "15\t60802\t124.3\t0\t60802\n", "16\t63202\t124.3\t0\t63202\n", "17\t67468\t124.3\t0\t67468\n", "18\t78387\t124.3\t0\t78387\n", "19\t72570\t124.3\t0\t72570\n", "20\t60629\t124.3\t0\t60629\n", "21\t58588\t124.3\t0\t58588\n", "22\t53075\t124.3\t0\t53075\n", "23\t57482\t124.3\t0\t57482\n", "24\t65439\t124.3\t0\t65439\n", "25\t67105\t124.3\t0\t67105\n", "26\t76192\t124.3\t0\t76192\n", "27\t84127\t124.3\t0\t84127\n", "28\t75885\t124.3\t0\t75885\n", "29\t70797\t124.3\t0\t70797\n", "30\t72624\t124.3\t0\t72624\n", "31\t79916\t124.3\t0\t79916\n", "32\t76073\t124.3\t0\t76073\n", "33\t72435\t124.3\t0\t72435\n", "34\t67473\t124.3\t0\t67473\n", "35\t77550\t124.3\t0\t77550\n", "36\t90050\t124.3\t0\t90050\n", "37\t87809\t124.3\t0\t87809\n", "38\t73082\t124.3\t0\t73082\n", "39\t61798\t124.3\t0\t61798\n", "40\t60214\t124.3\t0\t60214\n", "41\t67760\t124.3\t0\t67760\n", "42\t78239\t124.3\t0\t78239\n", "43\t66787\t124.3\t0\t66787\n", "44\t51357\t124.3\t0\t51357\n", "45\t63495\t124.3\t0\t63495\n", "46\t74373\t124.3\t0\t74373\n", "47\t67996\t124.3\t0\t67996\n", "48\t65366\t124.3\t0\t65366\n", "49\t53618\t124.3\t0\t53618\n", "50\t50566\t124.3\t0\t50566\n", "51\t45580\t124.3\t0\t45580\n", "52\t48070\t124.3\t0\t48070\n", "53\t50250\t124.3\t0\t50250\n", "54\t50786\t124.3\t0\t50786\n", "55\t50129\t124.3\t0\t50129\n", "56\t46590\t124.3\t0\t46590\n", "57\t45028\t124.3\t0\t45028\n", "58\t51380\t124.3\t0\t51380\n", "59\t40784\t124.3\t0\t40784\n", "60\t32429\t124.3\t0\t32429\n", "61\t30503\t124.3\t0\t30503\n", "62\t25566\t124.3\t0\t25566\n", "63\t23636\t124.3\t0\t23636\n", "64\t26767\t124.3\t0\t26767\n", "65\t26199\t124.3\t0\t26199\n", "66\t22193\t124.3\t0\t22193\n", "67\t22126\t124.3\t0\t22126\n", "68\t21862\t124.3\t0\t21862\n", "69\t22489\t124.3\t0\t22489\n", "70\t23236\t124.3\t0\t23236\n", "71\t21987\t124.3\t0\t21987\n", "72\t17049\t124.3\t0\t17049\n", "73\t14731\t124.3\t0\t14731\n", "74\t14593\t124.3\t0\t14593\n", "75\t12721\t124.3\t0\t12721\n", "76\t10144\t124.3\t0\t10144\n", "77\t9929\t124.3\t0\t9929\n", "78\t11313\t124.3\t0\t11313\n", "79\t10535\t124.3\t0\t10535\n", "80\t10179\t124.3\t0\t10179\n", "81\t9394\t124.3\t0\t9394\n", "82\t8937\t124.3\t0\t8937\n", "83\t9142\t124.3\t0\t9142\n", "84\t10224\t124.3\t0\t10224\n", "85\t11190\t124.3\t0\t11190\n", "86\t10659\t124.3\t0\t10659\n", "87\t8030\t124.3\t0\t8030\n", "88\t7448\t124.3\t0\t7448\n", "89\t7358\t124.3\t0\t7358\n", "90\t7697\t124.3\t0\t7697\n", "91\t7863\t124.3\t0\t7863\n", "92\t7773\t124.3\t0\t7773\n", "93\t8228\t124.3\t0\t8228\n", "94\t7461\t124.3\t0\t7461\n", "95\t6122\t124.3\t0\t6122\n", "96\t4401\t124.3\t0\t4401\n", "97\t2812\t124.3\t0\t2812\n", "98\t1684\t124.3\t0\t1684\n", "99\t1725\t124.3\t0\t1725\n", "100\t1091\t124.3\t0\t1091\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 42628 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 43.1%\n", " C: 32.4%\n", " G: 0.0%\n", " T: 24.4%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t23095\t127301.9\t0\t23095\n", "4\t5348\t31825.5\t0\t5348\n", "5\t1978\t7956.4\t0\t1978\n", "6\t1463\t1989.1\t0\t1463\n", "7\t234\t497.3\t0\t234\n", "8\t151\t124.3\t0\t151\n", "9\t140\t124.3\t0\t140\n", "10\t137\t124.3\t0\t137\n", "11\t152\t124.3\t0\t152\n", "12\t135\t124.3\t0\t135\n", "13\t125\t124.3\t0\t125\n", "14\t125\t124.3\t0\t125\n", "15\t143\t124.3\t0\t143\n", "16\t130\t124.3\t0\t130\n", "17\t132\t124.3\t0\t132\n", "18\t146\t124.3\t0\t146\n", "19\t174\t124.3\t0\t174\n", "20\t199\t124.3\t0\t199\n", "21\t150\t124.3\t0\t150\n", "22\t147\t124.3\t0\t147\n", "23\t145\t124.3\t0\t145\n", "24\t146\t124.3\t0\t146\n", "25\t150\t124.3\t0\t150\n", "26\t186\t124.3\t0\t186\n", "27\t183\t124.3\t0\t183\n", "28\t196\t124.3\t0\t196\n", "29\t240\t124.3\t0\t240\n", "30\t361\t124.3\t0\t361\n", "31\t434\t124.3\t0\t434\n", "32\t673\t124.3\t0\t673\n", "33\t560\t124.3\t0\t560\n", "34\t590\t124.3\t0\t590\n", "35\t701\t124.3\t0\t701\n", "36\t653\t124.3\t0\t653\n", "37\t247\t124.3\t0\t247\n", "38\t95\t124.3\t0\t95\n", "39\t85\t124.3\t0\t85\n", "40\t83\t124.3\t0\t83\n", "41\t68\t124.3\t0\t68\n", "42\t62\t124.3\t0\t62\n", "43\t71\t124.3\t0\t71\n", "44\t58\t124.3\t0\t58\n", "45\t50\t124.3\t0\t50\n", "46\t64\t124.3\t0\t64\n", "47\t69\t124.3\t0\t69\n", "48\t58\t124.3\t0\t58\n", "49\t61\t124.3\t0\t61\n", "50\t65\t124.3\t0\t65\n", "51\t68\t124.3\t0\t68\n", "52\t61\t124.3\t0\t61\n", "53\t46\t124.3\t0\t46\n", "54\t53\t124.3\t0\t53\n", "55\t49\t124.3\t0\t49\n", "56\t41\t124.3\t0\t41\n", "57\t53\t124.3\t0\t53\n", "58\t36\t124.3\t0\t36\n", "59\t38\t124.3\t0\t38\n", "60\t49\t124.3\t0\t49\n", "61\t38\t124.3\t0\t38\n", "62\t38\t124.3\t0\t38\n", "63\t29\t124.3\t0\t29\n", "64\t31\t124.3\t0\t31\n", "65\t28\t124.3\t0\t28\n", "66\t35\t124.3\t0\t35\n", "67\t37\t124.3\t0\t37\n", "68\t34\t124.3\t0\t34\n", "69\t29\t124.3\t0\t29\n", "70\t19\t124.3\t0\t19\n", "71\t11\t124.3\t0\t11\n", "72\t22\t124.3\t0\t22\n", "73\t11\t124.3\t0\t11\n", "74\t16\t124.3\t0\t16\n", "75\t16\t124.3\t0\t16\n", "76\t13\t124.3\t0\t13\n", "77\t6\t124.3\t0\t6\n", "78\t16\t124.3\t0\t16\n", "79\t19\t124.3\t0\t19\n", "80\t9\t124.3\t0\t9\n", "81\t16\t124.3\t0\t16\n", "82\t13\t124.3\t0\t13\n", "83\t19\t124.3\t0\t19\n", "84\t18\t124.3\t0\t18\n", "85\t18\t124.3\t0\t18\n", "86\t18\t124.3\t0\t18\n", "87\t12\t124.3\t0\t12\n", "88\t12\t124.3\t0\t12\n", "89\t18\t124.3\t0\t18\n", "90\t24\t124.3\t0\t24\n", "91\t15\t124.3\t0\t15\n", "92\t44\t124.3\t0\t44\n", "93\t64\t124.3\t0\t64\n", "94\t85\t124.3\t0\t85\n", "95\t107\t124.3\t0\t107\n", "96\t122\t124.3\t0\t122\n", "97\t123\t124.3\t0\t123\n", "98\t95\t124.3\t0\t95\n", "99\t67\t124.3\t0\t67\n", "100\t129\t124.3\t0\t129\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 151071 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.9%\n", " C: 20.5%\n", " G: 18.0%\n", " T: 20.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t112208\t127301.9\t0\t112208\n", "4\t22703\t31825.5\t0\t22703\n", "5\t4184\t7956.4\t0\t4184\n", "6\t399\t1989.1\t0\t399\n", "7\t119\t497.3\t0\t119\n", "8\t150\t497.3\t0\t150\n", "9\t162\t497.3\t0\t162\n", "10\t125\t497.3\t0\t125\n", "11\t182\t497.3\t0\t182\n", "12\t158\t497.3\t0\t158\n", "13\t173\t497.3\t0\t173\n", "14\t176\t497.3\t0\t176\n", "15\t183\t497.3\t0\t183\n", "16\t162\t497.3\t0\t162\n", "17\t209\t497.3\t0\t209\n", "18\t167\t497.3\t0\t167\n", "19\t161\t497.3\t0\t161\n", "20\t153\t497.3\t0\t153\n", "21\t163\t497.3\t0\t163\n", "22\t159\t497.3\t0\t159\n", "23\t138\t497.3\t0\t138\n", "24\t139\t497.3\t0\t139\n", "25\t140\t497.3\t0\t140\n", "26\t119\t497.3\t0\t119\n", "27\t153\t497.3\t0\t153\n", "28\t152\t497.3\t0\t152\n", "29\t150\t497.3\t0\t150\n", "30\t155\t497.3\t0\t155\n", "31\t130\t497.3\t0\t130\n", "32\t144\t497.3\t0\t144\n", "33\t154\t497.3\t0\t154\n", "34\t162\t497.3\t0\t162\n", "35\t135\t497.3\t0\t135\n", "36\t126\t497.3\t0\t126\n", "37\t133\t497.3\t0\t133\n", "38\t150\t497.3\t0\t150\n", "39\t168\t497.3\t0\t168\n", "40\t164\t497.3\t0\t164\n", "41\t130\t497.3\t0\t130\n", "42\t103\t497.3\t0\t103\n", "43\t142\t497.3\t0\t142\n", "44\t94\t497.3\t0\t94\n", "45\t125\t497.3\t0\t125\n", "46\t129\t497.3\t0\t129\n", "47\t138\t497.3\t0\t138\n", "48\t120\t497.3\t0\t120\n", "49\t109\t497.3\t0\t109\n", "50\t106\t497.3\t0\t106\n", "51\t101\t497.3\t0\t101\n", "52\t123\t497.3\t0\t123\n", "53\t117\t497.3\t0\t117\n", "54\t79\t497.3\t0\t79\n", "55\t104\t497.3\t0\t104\n", "56\t92\t497.3\t0\t92\n", "57\t75\t497.3\t0\t75\n", "58\t105\t497.3\t0\t105\n", "59\t71\t497.3\t0\t71\n", "60\t96\t497.3\t0\t96\n", "61\t101\t497.3\t0\t101\n", "62\t106\t497.3\t0\t106\n", "63\t73\t497.3\t0\t73\n", "64\t91\t497.3\t0\t91\n", "65\t93\t497.3\t0\t93\n", "66\t90\t497.3\t0\t90\n", "67\t85\t497.3\t0\t85\n", "68\t86\t497.3\t0\t86\n", "69\t73\t497.3\t0\t73\n", "70\t66\t497.3\t0\t66\n", "71\t86\t497.3\t0\t86\n", "72\t91\t497.3\t0\t91\n", "73\t92\t497.3\t0\t92\n", "74\t109\t497.3\t0\t109\n", "75\t96\t497.3\t0\t96\n", "76\t147\t497.3\t0\t147\n", "77\t151\t497.3\t0\t151\n", "78\t117\t497.3\t0\t117\n", "79\t118\t497.3\t0\t118\n", "80\t121\t497.3\t0\t121\n", "81\t117\t497.3\t0\t117\n", "82\t138\t497.3\t0\t138\n", "83\t148\t497.3\t0\t148\n", "84\t96\t497.3\t0\t96\n", "85\t102\t497.3\t0\t102\n", "86\t104\t497.3\t0\t104\n", "87\t131\t497.3\t0\t131\n", "88\t178\t497.3\t0\t178\n", "89\t127\t497.3\t0\t127\n", "90\t93\t497.3\t0\t93\n", "91\t96\t497.3\t0\t96\n", "92\t70\t497.3\t0\t70\n", "93\t62\t497.3\t0\t62\n", "94\t94\t497.3\t0\t94\n", "95\t59\t497.3\t0\t59\n", "96\t70\t497.3\t0\t70\n", "97\t91\t497.3\t0\t91\n", "98\t127\t497.3\t0\t127\n", "99\t160\t497.3\t0\t160\n", "100\t149\t497.3\t0\t149\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 561_S69_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/561.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 85.42 s (13 us/read; 4.50 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 6,408,963\n", "Reads with adapters: 2,733,028 (42.6%)\n", "Reads written (passing filters): 6,343,297 (99.0%)\n", "\n", "Total basepairs processed: 640,896,300 bp\n", "Quality-trimmed: 992,037 bp (0.2%)\n", "Total written (filtered): 563,361,097 bp (87.9%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2521852 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 27.3%\n", " G: 35.7%\n", " T: 37.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t189024\t100140.0\t0\t189024\n", "4\t105975\t25035.0\t0\t105975\n", "5\t73314\t6258.8\t0\t73314\n", "6\t53634\t1564.7\t0\t53634\n", "7\t47622\t391.2\t0\t47622\n", "8\t43776\t97.8\t0\t43776\n", "9\t43184\t97.8\t0\t43184\n", "10\t40009\t97.8\t0\t40009\n", "11\t40019\t97.8\t0\t40019\n", "12\t38138\t97.8\t0\t38138\n", "13\t38575\t97.8\t0\t38575\n", "14\t39180\t97.8\t0\t39180\n", "15\t39508\t97.8\t0\t39508\n", "16\t40688\t97.8\t0\t40688\n", "17\t46565\t97.8\t0\t46565\n", "18\t53094\t97.8\t0\t53094\n", "19\t53276\t97.8\t0\t53276\n", "20\t44028\t97.8\t0\t44028\n", "21\t38953\t97.8\t0\t38953\n", "22\t34238\t97.8\t0\t34238\n", "23\t38618\t97.8\t0\t38618\n", "24\t46536\t97.8\t0\t46536\n", "25\t49259\t97.8\t0\t49259\n", "26\t50154\t97.8\t0\t50154\n", "27\t46862\t97.8\t0\t46862\n", "28\t45040\t97.8\t0\t45040\n", "29\t43852\t97.8\t0\t43852\n", "30\t47966\t97.8\t0\t47966\n", "31\t49724\t97.8\t0\t49724\n", "32\t44076\t97.8\t0\t44076\n", "33\t39934\t97.8\t0\t39934\n", "34\t37560\t97.8\t0\t37560\n", "35\t41599\t97.8\t0\t41599\n", "36\t49048\t97.8\t0\t49048\n", "37\t51933\t97.8\t0\t51933\n", "38\t41415\t97.8\t0\t41415\n", "39\t31697\t97.8\t0\t31697\n", "40\t28562\t97.8\t0\t28562\n", "41\t28283\t97.8\t0\t28283\n", "42\t29274\t97.8\t0\t29274\n", "43\t25249\t97.8\t0\t25249\n", "44\t21468\t97.8\t0\t21468\n", "45\t26660\t97.8\t0\t26660\n", "46\t32045\t97.8\t0\t32045\n", "47\t32256\t97.8\t0\t32256\n", "48\t32220\t97.8\t0\t32220\n", "49\t25390\t97.8\t0\t25390\n", "50\t20562\t97.8\t0\t20562\n", "51\t21186\t97.8\t0\t21186\n", "52\t20157\t97.8\t0\t20157\n", "53\t18247\t97.8\t0\t18247\n", "54\t19550\t97.8\t0\t19550\n", "55\t21840\t97.8\t0\t21840\n", "56\t19537\t97.8\t0\t19537\n", "57\t16068\t97.8\t0\t16068\n", "58\t16854\t97.8\t0\t16854\n", "59\t13299\t97.8\t0\t13299\n", "60\t11634\t97.8\t0\t11634\n", "61\t11039\t97.8\t0\t11039\n", "62\t8868\t97.8\t0\t8868\n", "63\t9193\t97.8\t0\t9193\n", "64\t9877\t97.8\t0\t9877\n", "65\t8720\t97.8\t0\t8720\n", "66\t8293\t97.8\t0\t8293\n", "67\t7627\t97.8\t0\t7627\n", "68\t6796\t97.8\t0\t6796\n", "69\t6431\t97.8\t0\t6431\n", "70\t6247\t97.8\t0\t6247\n", "71\t5886\t97.8\t0\t5886\n", "72\t5078\t97.8\t0\t5078\n", "73\t4812\t97.8\t0\t4812\n", "74\t4653\t97.8\t0\t4653\n", "75\t3619\t97.8\t0\t3619\n", "76\t3335\t97.8\t0\t3335\n", "77\t2964\t97.8\t0\t2964\n", "78\t3045\t97.8\t0\t3045\n", "79\t2995\t97.8\t0\t2995\n", "80\t3282\t97.8\t0\t3282\n", "81\t2934\t97.8\t0\t2934\n", "82\t2870\t97.8\t0\t2870\n", "83\t2959\t97.8\t0\t2959\n", "84\t3565\t97.8\t0\t3565\n", "85\t3919\t97.8\t0\t3919\n", "86\t3488\t97.8\t0\t3488\n", "87\t2507\t97.8\t0\t2507\n", "88\t2561\t97.8\t0\t2561\n", "89\t2460\t97.8\t0\t2460\n", "90\t2455\t97.8\t0\t2455\n", "91\t2584\t97.8\t0\t2584\n", "92\t2886\t97.8\t0\t2886\n", "93\t3638\t97.8\t0\t3638\n", "94\t3964\t97.8\t0\t3964\n", "95\t4060\t97.8\t0\t4060\n", "96\t3487\t97.8\t0\t3487\n", "97\t3012\t97.8\t0\t3012\n", "98\t2249\t97.8\t0\t2249\n", "99\t3191\t97.8\t0\t3191\n", "100\t1889\t97.8\t0\t1889\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 99469 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 86.9%\n", " C: 4.7%\n", " G: 0.0%\n", " T: 8.4%\n", " none/other: 0.1%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t7644\t100140.0\t0\t7644\n", "4\t1735\t25035.0\t0\t1735\n", "5\t594\t6258.8\t0\t594\n", "6\t447\t1564.7\t0\t447\n", "7\t1074\t391.2\t0\t1074\n", "8\t4402\t97.8\t0\t4402\n", "9\t241\t97.8\t0\t241\n", "10\t91\t97.8\t0\t91\n", "11\t87\t97.8\t0\t87\n", "12\t77\t97.8\t0\t77\n", "13\t90\t97.8\t0\t90\n", "14\t86\t97.8\t0\t86\n", "15\t88\t97.8\t0\t88\n", "16\t129\t97.8\t0\t129\n", "17\t186\t97.8\t0\t186\n", "18\t289\t97.8\t0\t289\n", "19\t500\t97.8\t0\t500\n", "20\t1189\t97.8\t0\t1189\n", "21\t724\t97.8\t0\t724\n", "22\t436\t97.8\t0\t436\n", "23\t264\t97.8\t0\t264\n", "24\t221\t97.8\t0\t221\n", "25\t229\t97.8\t0\t229\n", "26\t409\t97.8\t0\t409\n", "27\t554\t97.8\t0\t554\n", "28\t811\t97.8\t0\t811\n", "29\t1356\t97.8\t0\t1356\n", "30\t3010\t97.8\t0\t3010\n", "31\t3931\t97.8\t0\t3931\n", "32\t7642\t97.8\t0\t7642\n", "33\t8415\t97.8\t0\t8415\n", "34\t10488\t97.8\t0\t10488\n", "35\t15582\t97.8\t0\t15582\n", "36\t15571\t97.8\t0\t15571\n", "37\t9307\t97.8\t0\t9307\n", "38\t403\t97.8\t0\t403\n", "39\t207\t97.8\t0\t207\n", "40\t12\t97.8\t0\t12\n", "41\t9\t97.8\t0\t9\n", "42\t5\t97.8\t0\t5\n", "43\t18\t97.8\t0\t18\n", "44\t8\t97.8\t0\t8\n", "45\t8\t97.8\t0\t8\n", "46\t3\t97.8\t0\t3\n", "47\t7\t97.8\t0\t7\n", "48\t8\t97.8\t0\t8\n", "49\t11\t97.8\t0\t11\n", "50\t8\t97.8\t0\t8\n", "51\t8\t97.8\t0\t8\n", "52\t2\t97.8\t0\t2\n", "53\t2\t97.8\t0\t2\n", "54\t7\t97.8\t0\t7\n", "55\t3\t97.8\t0\t3\n", "56\t1\t97.8\t0\t1\n", "57\t5\t97.8\t0\t5\n", "58\t2\t97.8\t0\t2\n", "59\t3\t97.8\t0\t3\n", "60\t1\t97.8\t0\t1\n", "61\t4\t97.8\t0\t4\n", "62\t3\t97.8\t0\t3\n", "64\t4\t97.8\t0\t4\n", "65\t1\t97.8\t0\t1\n", "67\t1\t97.8\t0\t1\n", "69\t2\t97.8\t0\t2\n", "70\t8\t97.8\t0\t8\n", "72\t1\t97.8\t0\t1\n", "73\t2\t97.8\t0\t2\n", "74\t9\t97.8\t0\t9\n", "75\t3\t97.8\t0\t3\n", "76\t6\t97.8\t0\t6\n", "78\t7\t97.8\t0\t7\n", "80\t4\t97.8\t0\t4\n", "81\t12\t97.8\t0\t12\n", "85\t1\t97.8\t0\t1\n", "86\t1\t97.8\t0\t1\n", "87\t2\t97.8\t0\t2\n", "88\t17\t97.8\t0\t17\n", "89\t1\t97.8\t0\t1\n", "92\t15\t97.8\t0\t15\n", "93\t64\t97.8\t0\t64\n", "94\t71\t97.8\t0\t71\n", "95\t109\t97.8\t0\t109\n", "96\t84\t97.8\t0\t84\n", "97\t33\t97.8\t0\t33\n", "98\t131\t97.8\t0\t131\n", "99\t47\t97.8\t0\t47\n", "100\t186\t97.8\t0\t186\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 111707 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 45.6%\n", " C: 19.0%\n", " G: 13.6%\n", " T: 21.7%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t80203\t100140.0\t0\t80203\n", "4\t17569\t25035.0\t0\t17569\n", "5\t3536\t6258.8\t0\t3536\n", "6\t197\t1564.7\t0\t197\n", "7\t73\t391.2\t0\t73\n", "8\t75\t391.2\t0\t75\n", "9\t34\t391.2\t0\t34\n", "10\t40\t391.2\t0\t40\n", "11\t69\t391.2\t0\t69\n", "12\t49\t391.2\t0\t49\n", "13\t53\t391.2\t0\t53\n", "14\t33\t391.2\t0\t33\n", "15\t58\t391.2\t0\t58\n", "16\t72\t391.2\t0\t72\n", "17\t64\t391.2\t0\t64\n", "18\t48\t391.2\t0\t48\n", "19\t118\t391.2\t0\t118\n", "20\t87\t391.2\t0\t87\n", "21\t92\t391.2\t0\t92\n", "22\t30\t391.2\t0\t30\n", "23\t71\t391.2\t0\t71\n", "24\t77\t391.2\t0\t77\n", "25\t92\t391.2\t0\t92\n", "26\t81\t391.2\t0\t81\n", "27\t75\t391.2\t0\t75\n", "28\t98\t391.2\t0\t98\n", "29\t87\t391.2\t0\t87\n", "30\t88\t391.2\t0\t88\n", "31\t73\t391.2\t0\t73\n", "32\t96\t391.2\t0\t96\n", "33\t119\t391.2\t0\t119\n", "34\t86\t391.2\t0\t86\n", "35\t91\t391.2\t0\t91\n", "36\t87\t391.2\t0\t87\n", "37\t63\t391.2\t0\t63\n", "38\t152\t391.2\t0\t152\n", "39\t92\t391.2\t0\t92\n", "40\t96\t391.2\t0\t96\n", "41\t96\t391.2\t0\t96\n", "42\t90\t391.2\t0\t90\n", "43\t100\t391.2\t0\t100\n", "44\t47\t391.2\t0\t47\n", "45\t60\t391.2\t0\t60\n", "46\t87\t391.2\t0\t87\n", "47\t96\t391.2\t0\t96\n", "48\t50\t391.2\t0\t50\n", "49\t91\t391.2\t0\t91\n", "50\t83\t391.2\t0\t83\n", "51\t99\t391.2\t0\t99\n", "52\t117\t391.2\t0\t117\n", "53\t99\t391.2\t0\t99\n", "54\t81\t391.2\t0\t81\n", "55\t85\t391.2\t0\t85\n", "56\t80\t391.2\t0\t80\n", "57\t90\t391.2\t0\t90\n", "58\t202\t391.2\t0\t202\n", "59\t105\t391.2\t0\t105\n", "60\t135\t391.2\t0\t135\n", "61\t172\t391.2\t0\t172\n", "62\t134\t391.2\t0\t134\n", "63\t114\t391.2\t0\t114\n", "64\t235\t391.2\t0\t235\n", "65\t181\t391.2\t0\t181\n", "66\t148\t391.2\t0\t148\n", "67\t97\t391.2\t0\t97\n", "68\t89\t391.2\t0\t89\n", "69\t45\t391.2\t0\t45\n", "70\t57\t391.2\t0\t57\n", "71\t86\t391.2\t0\t86\n", "72\t155\t391.2\t0\t155\n", "73\t174\t391.2\t0\t174\n", "74\t172\t391.2\t0\t172\n", "75\t144\t391.2\t0\t144\n", "76\t1290\t391.2\t0\t1290\n", "77\t180\t391.2\t0\t180\n", "78\t104\t391.2\t0\t104\n", "79\t143\t391.2\t0\t143\n", "80\t56\t391.2\t0\t56\n", "81\t135\t391.2\t0\t135\n", "82\t268\t391.2\t0\t268\n", "83\t132\t391.2\t0\t132\n", "84\t83\t391.2\t0\t83\n", "85\t93\t391.2\t0\t93\n", "86\t60\t391.2\t0\t60\n", "87\t133\t391.2\t0\t133\n", "88\t95\t391.2\t0\t95\n", "89\t87\t391.2\t0\t87\n", "90\t50\t391.2\t0\t50\n", "91\t25\t391.2\t0\t25\n", "92\t28\t391.2\t0\t28\n", "93\t50\t391.2\t0\t50\n", "94\t39\t391.2\t0\t39\n", "95\t55\t391.2\t0\t55\n", "96\t97\t391.2\t0\t97\n", "97\t88\t391.2\t0\t88\n", "98\t67\t391.2\t0\t67\n", "99\t74\t391.2\t0\t74\n", "100\t255\t391.2\t0\t255\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 562_S77_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/562.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 228.06 s (14 us/read; 4.23 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 16,068,123\n", "Reads with adapters: 10,958,886 (68.2%)\n", "Reads written (passing filters): 14,984,547 (93.3%)\n", "\n", "Total basepairs processed: 1,606,812,300 bp\n", "Quality-trimmed: 4,107,656 bp (0.3%)\n", "Total written (filtered): 1,152,759,422 bp (71.7%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 9394561 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 24.8%\n", " G: 47.5%\n", " T: 27.7%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t267693\t251064.4\t0\t267693\n", "4\t150421\t62766.1\t0\t150421\n", "5\t117264\t15691.5\t0\t117264\n", "6\t96161\t3922.9\t0\t96161\n", "7\t89016\t980.7\t0\t89016\n", "8\t84693\t245.2\t0\t84693\n", "9\t87662\t245.2\t0\t87662\n", "10\t91851\t245.2\t0\t91851\n", "11\t93792\t245.2\t0\t93792\n", "12\t104608\t245.2\t0\t104608\n", "13\t175469\t245.2\t0\t175469\n", "14\t163922\t245.2\t0\t163922\n", "15\t123589\t245.2\t0\t123589\n", "16\t129048\t245.2\t0\t129048\n", "17\t137324\t245.2\t0\t137324\n", "18\t154965\t245.2\t0\t154965\n", "19\t115019\t245.2\t0\t115019\n", "20\t90730\t245.2\t0\t90730\n", "21\t85527\t245.2\t0\t85527\n", "22\t79510\t245.2\t0\t79510\n", "23\t88619\t245.2\t0\t88619\n", "24\t106382\t245.2\t0\t106382\n", "25\t111494\t245.2\t0\t111494\n", "26\t131312\t245.2\t0\t131312\n", "27\t153134\t245.2\t0\t153134\n", "28\t152563\t245.2\t0\t152563\n", "29\t159014\t245.2\t0\t159014\n", "30\t174703\t245.2\t0\t174703\n", "31\t178879\t245.2\t0\t178879\n", "32\t162615\t245.2\t0\t162615\n", "33\t136045\t245.2\t0\t136045\n", "34\t136058\t245.2\t0\t136058\n", "35\t160222\t245.2\t0\t160222\n", "36\t201265\t245.2\t0\t201265\n", "37\t239327\t245.2\t0\t239327\n", "38\t176789\t245.2\t0\t176789\n", "39\t126499\t245.2\t0\t126499\n", "40\t113264\t245.2\t0\t113264\n", "41\t108426\t245.2\t0\t108426\n", "42\t114230\t245.2\t0\t114230\n", "43\t97146\t245.2\t0\t97146\n", "44\t79629\t245.2\t0\t79629\n", "45\t103438\t245.2\t0\t103438\n", "46\t127257\t245.2\t0\t127257\n", "47\t127323\t245.2\t0\t127323\n", "48\t127018\t245.2\t0\t127018\n", "49\t103951\t245.2\t0\t103951\n", "50\t90123\t245.2\t0\t90123\n", "51\t78681\t245.2\t0\t78681\n", "52\t79841\t245.2\t0\t79841\n", "53\t87347\t245.2\t0\t87347\n", "54\t103467\t245.2\t0\t103467\n", "55\t122451\t245.2\t0\t122451\n", "56\t112895\t245.2\t0\t112895\n", "57\t98862\t245.2\t0\t98862\n", "58\t126240\t245.2\t0\t126240\n", "59\t76979\t245.2\t0\t76979\n", "60\t58969\t245.2\t0\t58969\n", "61\t59899\t245.2\t0\t59899\n", "62\t50204\t245.2\t0\t50204\n", "63\t53040\t245.2\t0\t53040\n", "64\t58342\t245.2\t0\t58342\n", "65\t57859\t245.2\t0\t57859\n", "66\t57638\t245.2\t0\t57638\n", "67\t61662\t245.2\t0\t61662\n", "68\t63941\t245.2\t0\t63941\n", "69\t72892\t245.2\t0\t72892\n", "70\t91896\t245.2\t0\t91896\n", "71\t97795\t245.2\t0\t97795\n", "72\t68236\t245.2\t0\t68236\n", "73\t58158\t245.2\t0\t58158\n", "74\t60726\t245.2\t0\t60726\n", "75\t49696\t245.2\t0\t49696\n", "76\t43602\t245.2\t0\t43602\n", "77\t39206\t245.2\t0\t39206\n", "78\t41491\t245.2\t0\t41491\n", "79\t41102\t245.2\t0\t41102\n", "80\t46657\t245.2\t0\t46657\n", "81\t44915\t245.2\t0\t44915\n", "82\t40059\t245.2\t0\t40059\n", "83\t48695\t245.2\t0\t48695\n", "84\t60920\t245.2\t0\t60920\n", "85\t73550\t245.2\t0\t73550\n", "86\t67547\t245.2\t0\t67547\n", "87\t44939\t245.2\t0\t44939\n", "88\t42942\t245.2\t0\t42942\n", "89\t51714\t245.2\t0\t51714\n", "90\t61625\t245.2\t0\t61625\n", "91\t67164\t245.2\t0\t67164\n", "92\t69902\t245.2\t0\t69902\n", "93\t73537\t245.2\t0\t73537\n", "94\t76215\t245.2\t0\t76215\n", "95\t70407\t245.2\t0\t70407\n", "96\t54379\t245.2\t0\t54379\n", "97\t39448\t245.2\t0\t39448\n", "98\t24800\t245.2\t0\t24800\n", "99\t18908\t245.2\t0\t18908\n", "100\t18132\t245.2\t0\t18132\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 1390381 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 91.0%\n", " C: 4.0%\n", " G: 0.0%\n", " T: 5.0%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t26120\t251064.4\t0\t26120\n", "4\t11034\t62766.1\t0\t11034\n", "5\t9440\t15691.5\t0\t9440\n", "6\t7070\t3922.9\t0\t7070\n", "7\t4473\t980.7\t0\t4473\n", "8\t3731\t245.2\t0\t3731\n", "9\t4379\t245.2\t0\t4379\n", "10\t4272\t245.2\t0\t4272\n", "11\t5734\t245.2\t0\t5734\n", "12\t4519\t245.2\t0\t4519\n", "13\t4160\t245.2\t0\t4160\n", "14\t3973\t245.2\t0\t3973\n", "15\t3604\t245.2\t0\t3604\n", "16\t3639\t245.2\t0\t3639\n", "17\t4037\t245.2\t0\t4037\n", "18\t5378\t245.2\t0\t5378\n", "19\t5778\t245.2\t0\t5778\n", "20\t8681\t245.2\t0\t8681\n", "21\t7603\t245.2\t0\t7603\n", "22\t7305\t245.2\t0\t7305\n", "23\t6485\t245.2\t0\t6485\n", "24\t7569\t245.2\t0\t7569\n", "25\t10265\t245.2\t0\t10265\n", "26\t19830\t245.2\t0\t19830\n", "27\t21512\t245.2\t0\t21512\n", "28\t23912\t245.2\t0\t23912\n", "29\t29765\t245.2\t0\t29765\n", "30\t60354\t245.2\t0\t60354\n", "31\t75766\t245.2\t0\t75766\n", "32\t137733\t245.2\t0\t137733\n", "33\t147717\t245.2\t0\t147717\n", "34\t163176\t245.2\t0\t163176\n", "35\t220823\t245.2\t0\t220823\n", "36\t229836\t245.2\t0\t229836\n", "37\t93718\t245.2\t0\t93718\n", "38\t2483\t245.2\t0\t2483\n", "39\t463\t245.2\t0\t463\n", "40\t48\t245.2\t0\t48\n", "41\t36\t245.2\t0\t36\n", "42\t30\t245.2\t0\t30\n", "43\t21\t245.2\t0\t21\n", "44\t25\t245.2\t0\t25\n", "45\t36\t245.2\t0\t36\n", "46\t43\t245.2\t0\t43\n", "47\t31\t245.2\t0\t31\n", "48\t17\t245.2\t0\t17\n", "49\t38\t245.2\t0\t38\n", "50\t33\t245.2\t0\t33\n", "51\t44\t245.2\t0\t44\n", "52\t52\t245.2\t0\t52\n", "53\t44\t245.2\t0\t44\n", "54\t39\t245.2\t0\t39\n", "55\t19\t245.2\t0\t19\n", "56\t34\t245.2\t0\t34\n", "57\t31\t245.2\t0\t31\n", "58\t13\t245.2\t0\t13\n", "59\t22\t245.2\t0\t22\n", "60\t24\t245.2\t0\t24\n", "61\t19\t245.2\t0\t19\n", "62\t15\t245.2\t0\t15\n", "63\t12\t245.2\t0\t12\n", "64\t9\t245.2\t0\t9\n", "65\t8\t245.2\t0\t8\n", "66\t17\t245.2\t0\t17\n", "67\t10\t245.2\t0\t10\n", "68\t7\t245.2\t0\t7\n", "69\t8\t245.2\t0\t8\n", "70\t4\t245.2\t0\t4\n", "71\t2\t245.2\t0\t2\n", "72\t6\t245.2\t0\t6\n", "73\t7\t245.2\t0\t7\n", "74\t7\t245.2\t0\t7\n", "75\t5\t245.2\t0\t5\n", "76\t10\t245.2\t0\t10\n", "77\t4\t245.2\t0\t4\n", "78\t9\t245.2\t0\t9\n", "79\t5\t245.2\t0\t5\n", "80\t4\t245.2\t0\t4\n", "81\t9\t245.2\t0\t9\n", "82\t10\t245.2\t0\t10\n", "83\t15\t245.2\t0\t15\n", "84\t16\t245.2\t0\t16\n", "85\t5\t245.2\t0\t5\n", "86\t21\t245.2\t0\t21\n", "87\t10\t245.2\t0\t10\n", "88\t29\t245.2\t0\t29\n", "89\t20\t245.2\t0\t20\n", "90\t22\t245.2\t0\t22\n", "91\t28\t245.2\t0\t28\n", "92\t58\t245.2\t0\t58\n", "93\t125\t245.2\t0\t125\n", "94\t203\t245.2\t0\t203\n", "95\t630\t245.2\t0\t630\n", "96\t471\t245.2\t0\t471\n", "97\t520\t245.2\t0\t520\n", "98\t478\t245.2\t0\t478\n", "99\t291\t245.2\t0\t291\n", "100\t235\t245.2\t0\t235\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 173944 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 47.3%\n", " C: 18.8%\n", " G: 11.5%\n", " T: 22.4%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t112810\t251064.4\t0\t112810\n", "4\t24898\t62766.1\t0\t24898\n", "5\t4245\t15691.5\t0\t4245\n", "6\t596\t3922.9\t0\t596\n", "7\t459\t980.7\t0\t459\n", "8\t577\t980.7\t0\t577\n", "9\t614\t980.7\t0\t614\n", "10\t542\t980.7\t0\t542\n", "11\t556\t980.7\t0\t556\n", "12\t727\t980.7\t0\t727\n", "13\t882\t980.7\t0\t882\n", "14\t802\t980.7\t0\t802\n", "15\t936\t980.7\t0\t936\n", "16\t820\t980.7\t0\t820\n", "17\t1013\t980.7\t0\t1013\n", "18\t1074\t980.7\t0\t1074\n", "19\t739\t980.7\t0\t739\n", "20\t895\t980.7\t0\t895\n", "21\t753\t980.7\t0\t753\n", "22\t651\t980.7\t0\t651\n", "23\t493\t980.7\t0\t493\n", "24\t519\t980.7\t0\t519\n", "25\t372\t980.7\t0\t372\n", "26\t319\t980.7\t0\t319\n", "27\t361\t980.7\t0\t361\n", "28\t367\t980.7\t0\t367\n", "29\t293\t980.7\t0\t293\n", "30\t407\t980.7\t0\t407\n", "31\t288\t980.7\t0\t288\n", "32\t384\t980.7\t0\t384\n", "33\t276\t980.7\t0\t276\n", "34\t445\t980.7\t0\t445\n", "35\t243\t980.7\t0\t243\n", "36\t271\t980.7\t0\t271\n", "37\t200\t980.7\t0\t200\n", "38\t274\t980.7\t0\t274\n", "39\t346\t980.7\t0\t346\n", "40\t339\t980.7\t0\t339\n", "41\t263\t980.7\t0\t263\n", "42\t222\t980.7\t0\t222\n", "43\t396\t980.7\t0\t396\n", "44\t124\t980.7\t0\t124\n", "45\t251\t980.7\t0\t251\n", "46\t211\t980.7\t0\t211\n", "47\t263\t980.7\t0\t263\n", "48\t314\t980.7\t0\t314\n", "49\t287\t980.7\t0\t287\n", "50\t329\t980.7\t0\t329\n", "51\t308\t980.7\t0\t308\n", "52\t393\t980.7\t0\t393\n", "53\t476\t980.7\t0\t476\n", "54\t569\t980.7\t0\t569\n", "55\t714\t980.7\t0\t714\n", "56\t667\t980.7\t0\t667\n", "57\t522\t980.7\t0\t522\n", "58\t514\t980.7\t0\t514\n", "59\t378\t980.7\t0\t378\n", "60\t435\t980.7\t0\t435\n", "61\t321\t980.7\t0\t321\n", "62\t300\t980.7\t0\t300\n", "63\t243\t980.7\t0\t243\n", "64\t168\t980.7\t0\t168\n", "65\t197\t980.7\t0\t197\n", "66\t234\t980.7\t0\t234\n", "67\t191\t980.7\t0\t191\n", "68\t209\t980.7\t0\t209\n", "69\t96\t980.7\t0\t96\n", "70\t72\t980.7\t0\t72\n", "71\t138\t980.7\t0\t138\n", "72\t145\t980.7\t0\t145\n", "73\t135\t980.7\t0\t135\n", "74\t190\t980.7\t0\t190\n", "75\t93\t980.7\t0\t93\n", "76\t94\t980.7\t0\t94\n", "77\t122\t980.7\t0\t122\n", "78\t85\t980.7\t0\t85\n", "79\t74\t980.7\t0\t74\n", "80\t77\t980.7\t0\t77\n", "81\t98\t980.7\t0\t98\n", "82\t117\t980.7\t0\t117\n", "83\t121\t980.7\t0\t121\n", "84\t101\t980.7\t0\t101\n", "85\t119\t980.7\t0\t119\n", "86\t63\t980.7\t0\t63\n", "87\t88\t980.7\t0\t88\n", "88\t109\t980.7\t0\t109\n", "89\t97\t980.7\t0\t97\n", "90\t72\t980.7\t0\t72\n", "91\t73\t980.7\t0\t73\n", "92\t64\t980.7\t0\t64\n", "93\t50\t980.7\t0\t50\n", "94\t96\t980.7\t0\t96\n", "95\t84\t980.7\t0\t84\n", "96\t97\t980.7\t0\t97\n", "97\t217\t980.7\t0\t217\n", "98\t178\t980.7\t0\t178\n", "99\t282\t980.7\t0\t282\n", "100\t212\t980.7\t0\t212\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 563_S59_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/563.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 108.91 s (13 us/read; 4.59 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 8,332,688\n", "Reads with adapters: 4,065,811 (48.8%)\n", "Reads written (passing filters): 8,250,108 (99.0%)\n", "\n", "Total basepairs processed: 833,268,800 bp\n", "Quality-trimmed: 1,684,343 bp (0.2%)\n", "Total written (filtered): 704,074,978 bp (84.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3863219 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 26.2%\n", " G: 32.8%\n", " T: 41.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t234457\t130198.2\t0\t234457\n", "4\t119921\t32549.6\t0\t119921\n", "5\t80226\t8137.4\t0\t80226\n", "6\t58028\t2034.3\t0\t58028\n", "7\t51857\t508.6\t0\t51857\n", "8\t50496\t127.1\t0\t50496\n", "9\t48950\t127.1\t0\t48950\n", "10\t45876\t127.1\t0\t45876\n", "11\t47342\t127.1\t0\t47342\n", "12\t44118\t127.1\t0\t44118\n", "13\t44823\t127.1\t0\t44823\n", "14\t46071\t127.1\t0\t46071\n", "15\t50493\t127.1\t0\t50493\n", "16\t52481\t127.1\t0\t52481\n", "17\t58553\t127.1\t0\t58553\n", "18\t68329\t127.1\t0\t68329\n", "19\t62123\t127.1\t0\t62123\n", "20\t51903\t127.1\t0\t51903\n", "21\t50057\t127.1\t0\t50057\n", "22\t46342\t127.1\t0\t46342\n", "23\t53513\t127.1\t0\t53513\n", "24\t65253\t127.1\t0\t65253\n", "25\t63934\t127.1\t0\t63934\n", "26\t72136\t127.1\t0\t72136\n", "27\t86008\t127.1\t0\t86008\n", "28\t77252\t127.1\t0\t77252\n", "29\t70747\t127.1\t0\t70747\n", "30\t72812\t127.1\t0\t72812\n", "31\t75902\t127.1\t0\t75902\n", "32\t74999\t127.1\t0\t74999\n", "33\t65652\t127.1\t0\t65652\n", "34\t63428\t127.1\t0\t63428\n", "35\t74167\t127.1\t0\t74167\n", "36\t91765\t127.1\t0\t91765\n", "37\t98551\t127.1\t0\t98551\n", "38\t79855\t127.1\t0\t79855\n", "39\t60494\t127.1\t0\t60494\n", "40\t53870\t127.1\t0\t53870\n", "41\t53266\t127.1\t0\t53266\n", "42\t57265\t127.1\t0\t57265\n", "43\t49305\t127.1\t0\t49305\n", "44\t40925\t127.1\t0\t40925\n", "45\t53121\t127.1\t0\t53121\n", "46\t68663\t127.1\t0\t68663\n", "47\t69977\t127.1\t0\t69977\n", "48\t58019\t127.1\t0\t58019\n", "49\t43078\t127.1\t0\t43078\n", "50\t41010\t127.1\t0\t41010\n", "51\t42335\t127.1\t0\t42335\n", "52\t39511\t127.1\t0\t39511\n", "53\t33444\t127.1\t0\t33444\n", "54\t37278\t127.1\t0\t37278\n", "55\t44898\t127.1\t0\t44898\n", "56\t43644\t127.1\t0\t43644\n", "57\t36076\t127.1\t0\t36076\n", "58\t32284\t127.1\t0\t32284\n", "59\t27370\t127.1\t0\t27370\n", "60\t24496\t127.1\t0\t24496\n", "61\t24093\t127.1\t0\t24093\n", "62\t19985\t127.1\t0\t19985\n", "63\t19840\t127.1\t0\t19840\n", "64\t21666\t127.1\t0\t21666\n", "65\t20357\t127.1\t0\t20357\n", "66\t18157\t127.1\t0\t18157\n", "67\t17008\t127.1\t0\t17008\n", "68\t15042\t127.1\t0\t15042\n", "69\t14679\t127.1\t0\t14679\n", "70\t15011\t127.1\t0\t15011\n", "71\t14356\t127.1\t0\t14356\n", "72\t12123\t127.1\t0\t12123\n", "73\t11067\t127.1\t0\t11067\n", "74\t11685\t127.1\t0\t11685\n", "75\t9260\t127.1\t0\t9260\n", "76\t7710\t127.1\t0\t7710\n", "77\t6799\t127.1\t0\t6799\n", "78\t7217\t127.1\t0\t7217\n", "79\t6771\t127.1\t0\t6771\n", "80\t7451\t127.1\t0\t7451\n", "81\t6248\t127.1\t0\t6248\n", "82\t5841\t127.1\t0\t5841\n", "83\t6183\t127.1\t0\t6183\n", "84\t6719\t127.1\t0\t6719\n", "85\t7447\t127.1\t0\t7447\n", "86\t7052\t127.1\t0\t7052\n", "87\t4470\t127.1\t0\t4470\n", "88\t3865\t127.1\t0\t3865\n", "89\t4204\t127.1\t0\t4204\n", "90\t4119\t127.1\t0\t4119\n", "91\t3591\t127.1\t0\t3591\n", "92\t2925\t127.1\t0\t2925\n", "93\t2715\t127.1\t0\t2715\n", "94\t2378\t127.1\t0\t2378\n", "95\t1966\t127.1\t0\t1966\n", "96\t1457\t127.1\t0\t1457\n", "97\t1015\t127.1\t0\t1015\n", "98\t750\t127.1\t0\t750\n", "99\t741\t127.1\t0\t741\n", "100\t507\t127.1\t0\t507\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 27013 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 64.1%\n", " C: 10.9%\n", " G: 0.0%\n", " T: 25.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t10790\t130198.2\t0\t10790\n", "4\t2030\t32549.6\t0\t2030\n", "5\t496\t8137.4\t0\t496\n", "6\t195\t2034.3\t0\t195\n", "7\t103\t508.6\t0\t103\n", "8\t60\t127.1\t0\t60\n", "9\t66\t127.1\t0\t66\n", "10\t60\t127.1\t0\t60\n", "11\t53\t127.1\t0\t53\n", "12\t63\t127.1\t0\t63\n", "13\t57\t127.1\t0\t57\n", "14\t64\t127.1\t0\t64\n", "15\t64\t127.1\t0\t64\n", "16\t60\t127.1\t0\t60\n", "17\t74\t127.1\t0\t74\n", "18\t82\t127.1\t0\t82\n", "19\t123\t127.1\t0\t123\n", "20\t240\t127.1\t0\t240\n", "21\t140\t127.1\t0\t140\n", "22\t82\t127.1\t0\t82\n", "23\t81\t127.1\t0\t81\n", "24\t66\t127.1\t0\t66\n", "25\t59\t127.1\t0\t59\n", "26\t101\t127.1\t0\t101\n", "27\t116\t127.1\t0\t116\n", "28\t139\t127.1\t0\t139\n", "29\t233\t127.1\t0\t233\n", "30\t432\t127.1\t0\t432\n", "31\t650\t127.1\t0\t650\n", "32\t1093\t127.1\t0\t1093\n", "33\t1306\t127.1\t0\t1306\n", "34\t1573\t127.1\t0\t1573\n", "35\t2220\t127.1\t0\t2220\n", "36\t2108\t127.1\t0\t2108\n", "37\t1216\t127.1\t0\t1216\n", "38\t87\t127.1\t0\t87\n", "39\t71\t127.1\t0\t71\n", "40\t17\t127.1\t0\t17\n", "41\t14\t127.1\t0\t14\n", "42\t15\t127.1\t0\t15\n", "43\t21\t127.1\t0\t21\n", "44\t11\t127.1\t0\t11\n", "45\t11\t127.1\t0\t11\n", "46\t13\t127.1\t0\t13\n", "47\t5\t127.1\t0\t5\n", "48\t12\t127.1\t0\t12\n", "49\t9\t127.1\t0\t9\n", "50\t5\t127.1\t0\t5\n", "51\t11\t127.1\t0\t11\n", "52\t7\t127.1\t0\t7\n", "53\t7\t127.1\t0\t7\n", "54\t9\t127.1\t0\t9\n", "55\t5\t127.1\t0\t5\n", "56\t9\t127.1\t0\t9\n", "57\t10\t127.1\t0\t10\n", "58\t5\t127.1\t0\t5\n", "59\t4\t127.1\t0\t4\n", "60\t7\t127.1\t0\t7\n", "61\t8\t127.1\t0\t8\n", "62\t5\t127.1\t0\t5\n", "63\t2\t127.1\t0\t2\n", "64\t6\t127.1\t0\t6\n", "65\t13\t127.1\t0\t13\n", "66\t7\t127.1\t0\t7\n", "67\t6\t127.1\t0\t6\n", "68\t3\t127.1\t0\t3\n", "69\t3\t127.1\t0\t3\n", "70\t4\t127.1\t0\t4\n", "71\t2\t127.1\t0\t2\n", "72\t8\t127.1\t0\t8\n", "73\t1\t127.1\t0\t1\n", "74\t1\t127.1\t0\t1\n", "75\t2\t127.1\t0\t2\n", "76\t2\t127.1\t0\t2\n", "77\t2\t127.1\t0\t2\n", "78\t3\t127.1\t0\t3\n", "79\t2\t127.1\t0\t2\n", "80\t1\t127.1\t0\t1\n", "81\t3\t127.1\t0\t3\n", "83\t4\t127.1\t0\t4\n", "84\t5\t127.1\t0\t5\n", "85\t4\t127.1\t0\t4\n", "86\t2\t127.1\t0\t2\n", "87\t2\t127.1\t0\t2\n", "88\t3\t127.1\t0\t3\n", "89\t2\t127.1\t0\t2\n", "90\t4\t127.1\t0\t4\n", "91\t2\t127.1\t0\t2\n", "92\t8\t127.1\t0\t8\n", "93\t16\t127.1\t0\t16\n", "94\t52\t127.1\t0\t52\n", "95\t46\t127.1\t0\t46\n", "96\t18\t127.1\t0\t18\n", "97\t21\t127.1\t0\t21\n", "98\t29\t127.1\t0\t29\n", "99\t23\t127.1\t0\t23\n", "100\t28\t127.1\t0\t28\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 175579 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 38.1%\n", " C: 16.4%\n", " G: 8.3%\n", " T: 37.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t126807\t130198.2\t0\t126807\n", "4\t38278\t32549.6\t0\t38278\n", "5\t3588\t8137.4\t0\t3588\n", "6\t158\t2034.3\t0\t158\n", "7\t36\t508.6\t0\t36\n", "8\t47\t508.6\t0\t47\n", "9\t28\t508.6\t0\t28\n", "10\t40\t508.6\t0\t40\n", "11\t31\t508.6\t0\t31\n", "12\t44\t508.6\t0\t44\n", "13\t40\t508.6\t0\t40\n", "14\t36\t508.6\t0\t36\n", "15\t44\t508.6\t0\t44\n", "16\t46\t508.6\t0\t46\n", "17\t35\t508.6\t0\t35\n", "18\t35\t508.6\t0\t35\n", "19\t25\t508.6\t0\t25\n", "20\t28\t508.6\t0\t28\n", "21\t28\t508.6\t0\t28\n", "22\t36\t508.6\t0\t36\n", "23\t33\t508.6\t0\t33\n", "24\t32\t508.6\t0\t32\n", "25\t45\t508.6\t0\t45\n", "26\t38\t508.6\t0\t38\n", "27\t51\t508.6\t0\t51\n", "28\t36\t508.6\t0\t36\n", "29\t31\t508.6\t0\t31\n", "30\t61\t508.6\t0\t61\n", "31\t40\t508.6\t0\t40\n", "32\t42\t508.6\t0\t42\n", "33\t48\t508.6\t0\t48\n", "34\t35\t508.6\t0\t35\n", "35\t40\t508.6\t0\t40\n", "36\t23\t508.6\t0\t23\n", "37\t36\t508.6\t0\t36\n", "38\t55\t508.6\t0\t55\n", "39\t53\t508.6\t0\t53\n", "40\t45\t508.6\t0\t45\n", "41\t62\t508.6\t0\t62\n", "42\t49\t508.6\t0\t49\n", "43\t64\t508.6\t0\t64\n", "44\t74\t508.6\t0\t74\n", "45\t59\t508.6\t0\t59\n", "46\t62\t508.6\t0\t62\n", "47\t78\t508.6\t0\t78\n", "48\t58\t508.6\t0\t58\n", "49\t51\t508.6\t0\t51\n", "50\t67\t508.6\t0\t67\n", "51\t62\t508.6\t0\t62\n", "52\t72\t508.6\t0\t72\n", "53\t77\t508.6\t0\t77\n", "54\t62\t508.6\t0\t62\n", "55\t54\t508.6\t0\t54\n", "56\t46\t508.6\t0\t46\n", "57\t53\t508.6\t0\t53\n", "58\t74\t508.6\t0\t74\n", "59\t54\t508.6\t0\t54\n", "60\t67\t508.6\t0\t67\n", "61\t97\t508.6\t0\t97\n", "62\t75\t508.6\t0\t75\n", "63\t96\t508.6\t0\t96\n", "64\t67\t508.6\t0\t67\n", "65\t49\t508.6\t0\t49\n", "66\t63\t508.6\t0\t63\n", "67\t42\t508.6\t0\t42\n", "68\t41\t508.6\t0\t41\n", "69\t58\t508.6\t0\t58\n", "70\t58\t508.6\t0\t58\n", "71\t78\t508.6\t0\t78\n", "72\t105\t508.6\t0\t105\n", "73\t142\t508.6\t0\t142\n", "74\t131\t508.6\t0\t131\n", "75\t75\t508.6\t0\t75\n", "76\t127\t508.6\t0\t127\n", "77\t153\t508.6\t0\t153\n", "78\t116\t508.6\t0\t116\n", "79\t132\t508.6\t0\t132\n", "80\t141\t508.6\t0\t141\n", "81\t147\t508.6\t0\t147\n", "82\t186\t508.6\t0\t186\n", "83\t151\t508.6\t0\t151\n", "84\t94\t508.6\t0\t94\n", "85\t125\t508.6\t0\t125\n", "86\t92\t508.6\t0\t92\n", "87\t127\t508.6\t0\t127\n", "88\t110\t508.6\t0\t110\n", "89\t88\t508.6\t0\t88\n", "90\t71\t508.6\t0\t71\n", "91\t59\t508.6\t0\t59\n", "92\t41\t508.6\t0\t41\n", "93\t48\t508.6\t0\t48\n", "94\t68\t508.6\t0\t68\n", "95\t55\t508.6\t0\t55\n", "96\t76\t508.6\t0\t76\n", "97\t156\t508.6\t0\t156\n", "98\t184\t508.6\t0\t184\n", "99\t196\t508.6\t0\t196\n", "100\t260\t508.6\t0\t260\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 564_S32_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/564.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 55.66 s (12 us/read; 4.91 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 4,557,229\n", "Reads with adapters: 2,227,163 (48.9%)\n", "Reads written (passing filters): 4,478,206 (98.3%)\n", "\n", "Total basepairs processed: 455,722,900 bp\n", "Quality-trimmed: 949,380 bp (0.2%)\n", "Total written (filtered): 383,640,458 bp (84.2%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2112534 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.4%\n", " G: 38.5%\n", " T: 31.0%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t110301\t71206.7\t0\t110301\n", "4\t60479\t17801.7\t0\t60479\n", "5\t43425\t4450.4\t0\t43425\n", "6\t35303\t1112.6\t0\t35303\n", "7\t30647\t278.2\t0\t30647\n", "8\t30343\t69.5\t0\t30343\n", "9\t29563\t69.5\t0\t29563\n", "10\t28884\t69.5\t0\t28884\n", "11\t29432\t69.5\t0\t29432\n", "12\t30116\t69.5\t0\t30116\n", "13\t34280\t69.5\t0\t34280\n", "14\t33973\t69.5\t0\t33973\n", "15\t31004\t69.5\t0\t31004\n", "16\t32078\t69.5\t0\t32078\n", "17\t34766\t69.5\t0\t34766\n", "18\t40467\t69.5\t0\t40467\n", "19\t36806\t69.5\t0\t36806\n", "20\t30410\t69.5\t0\t30410\n", "21\t29372\t69.5\t0\t29372\n", "22\t26419\t69.5\t0\t26419\n", "23\t28780\t69.5\t0\t28780\n", "24\t33895\t69.5\t0\t33895\n", "25\t34063\t69.5\t0\t34063\n", "26\t38110\t69.5\t0\t38110\n", "27\t41854\t69.5\t0\t41854\n", "28\t38126\t69.5\t0\t38126\n", "29\t35653\t69.5\t0\t35653\n", "30\t35925\t69.5\t0\t35925\n", "31\t39342\t69.5\t0\t39342\n", "32\t38220\t69.5\t0\t38220\n", "33\t34559\t69.5\t0\t34559\n", "34\t33230\t69.5\t0\t33230\n", "35\t37761\t69.5\t0\t37761\n", "36\t44018\t69.5\t0\t44018\n", "37\t46010\t69.5\t0\t46010\n", "38\t36068\t69.5\t0\t36068\n", "39\t30015\t69.5\t0\t30015\n", "40\t27617\t69.5\t0\t27617\n", "41\t30329\t69.5\t0\t30329\n", "42\t33367\t69.5\t0\t33367\n", "43\t28841\t69.5\t0\t28841\n", "44\t22591\t69.5\t0\t22591\n", "45\t27696\t69.5\t0\t27696\n", "46\t33137\t69.5\t0\t33137\n", "47\t29956\t69.5\t0\t29956\n", "48\t29554\t69.5\t0\t29554\n", "49\t25250\t69.5\t0\t25250\n", "50\t23769\t69.5\t0\t23769\n", "51\t19853\t69.5\t0\t19853\n", "52\t19244\t69.5\t0\t19244\n", "53\t18552\t69.5\t0\t18552\n", "54\t20040\t69.5\t0\t20040\n", "55\t21883\t69.5\t0\t21883\n", "56\t19869\t69.5\t0\t19869\n", "57\t18261\t69.5\t0\t18261\n", "58\t21585\t69.5\t0\t21585\n", "59\t17594\t69.5\t0\t17594\n", "60\t14594\t69.5\t0\t14594\n", "61\t12697\t69.5\t0\t12697\n", "62\t10456\t69.5\t0\t10456\n", "63\t9887\t69.5\t0\t9887\n", "64\t10654\t69.5\t0\t10654\n", "65\t10407\t69.5\t0\t10407\n", "66\t9134\t69.5\t0\t9134\n", "67\t8938\t69.5\t0\t8938\n", "68\t8637\t69.5\t0\t8637\n", "69\t8771\t69.5\t0\t8771\n", "70\t9370\t69.5\t0\t9370\n", "71\t8736\t69.5\t0\t8736\n", "72\t6804\t69.5\t0\t6804\n", "73\t5937\t69.5\t0\t5937\n", "74\t5890\t69.5\t0\t5890\n", "75\t5268\t69.5\t0\t5268\n", "76\t4436\t69.5\t0\t4436\n", "77\t4181\t69.5\t0\t4181\n", "78\t4642\t69.5\t0\t4642\n", "79\t4442\t69.5\t0\t4442\n", "80\t4597\t69.5\t0\t4597\n", "81\t4323\t69.5\t0\t4323\n", "82\t4215\t69.5\t0\t4215\n", "83\t4299\t69.5\t0\t4299\n", "84\t4934\t69.5\t0\t4934\n", "85\t5466\t69.5\t0\t5466\n", "86\t5524\t69.5\t0\t5524\n", "87\t4247\t69.5\t0\t4247\n", "88\t4039\t69.5\t0\t4039\n", "89\t4132\t69.5\t0\t4132\n", "90\t4093\t69.5\t0\t4093\n", "91\t4103\t69.5\t0\t4103\n", "92\t4019\t69.5\t0\t4019\n", "93\t4189\t69.5\t0\t4189\n", "94\t3985\t69.5\t0\t3985\n", "95\t3516\t69.5\t0\t3516\n", "96\t2453\t69.5\t0\t2453\n", "97\t1583\t69.5\t0\t1583\n", "98\t921\t69.5\t0\t921\n", "99\t741\t69.5\t0\t741\n", "100\t589\t69.5\t0\t589\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 21780 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 44.4%\n", " C: 28.8%\n", " G: 0.0%\n", " T: 26.6%\n", " none/other: 0.2%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t11827\t71206.7\t0\t11827\n", "4\t2963\t17801.7\t0\t2963\n", "5\t1252\t4450.4\t0\t1252\n", "6\t537\t1112.6\t0\t537\n", "7\t107\t278.2\t0\t107\n", "8\t76\t69.5\t0\t76\n", "9\t61\t69.5\t0\t61\n", "10\t71\t69.5\t0\t71\n", "11\t72\t69.5\t0\t72\n", "12\t68\t69.5\t0\t68\n", "13\t69\t69.5\t0\t69\n", "14\t65\t69.5\t0\t65\n", "15\t66\t69.5\t0\t66\n", "16\t67\t69.5\t0\t67\n", "17\t57\t69.5\t0\t57\n", "18\t67\t69.5\t0\t67\n", "19\t90\t69.5\t0\t90\n", "20\t104\t69.5\t0\t104\n", "21\t81\t69.5\t0\t81\n", "22\t54\t69.5\t0\t54\n", "23\t39\t69.5\t0\t39\n", "24\t43\t69.5\t0\t43\n", "25\t68\t69.5\t0\t68\n", "26\t78\t69.5\t0\t78\n", "27\t79\t69.5\t0\t79\n", "28\t95\t69.5\t0\t95\n", "29\t120\t69.5\t0\t120\n", "30\t182\t69.5\t0\t182\n", "31\t195\t69.5\t0\t195\n", "32\t304\t69.5\t0\t304\n", "33\t263\t69.5\t0\t263\n", "34\t281\t69.5\t0\t281\n", "35\t343\t69.5\t0\t343\n", "36\t358\t69.5\t0\t358\n", "37\t154\t69.5\t0\t154\n", "38\t49\t69.5\t0\t49\n", "39\t32\t69.5\t0\t32\n", "40\t30\t69.5\t0\t30\n", "41\t18\t69.5\t0\t18\n", "42\t16\t69.5\t0\t16\n", "43\t20\t69.5\t0\t20\n", "44\t24\t69.5\t0\t24\n", "45\t37\t69.5\t0\t37\n", "46\t37\t69.5\t0\t37\n", "47\t29\t69.5\t0\t29\n", "48\t23\t69.5\t0\t23\n", "49\t25\t69.5\t0\t25\n", "50\t22\t69.5\t0\t22\n", "51\t29\t69.5\t0\t29\n", "52\t18\t69.5\t0\t18\n", "53\t19\t69.5\t0\t19\n", "54\t16\t69.5\t0\t16\n", "55\t27\t69.5\t0\t27\n", "56\t16\t69.5\t0\t16\n", "57\t10\t69.5\t0\t10\n", "58\t18\t69.5\t0\t18\n", "59\t14\t69.5\t0\t14\n", "60\t19\t69.5\t0\t19\n", "61\t16\t69.5\t0\t16\n", "62\t16\t69.5\t0\t16\n", "63\t17\t69.5\t0\t17\n", "64\t13\t69.5\t0\t13\n", "65\t9\t69.5\t0\t9\n", "66\t12\t69.5\t0\t12\n", "67\t13\t69.5\t0\t13\n", "68\t24\t69.5\t0\t24\n", "69\t8\t69.5\t0\t8\n", "70\t16\t69.5\t0\t16\n", "71\t7\t69.5\t0\t7\n", "72\t5\t69.5\t0\t5\n", "73\t8\t69.5\t0\t8\n", "74\t8\t69.5\t0\t8\n", "75\t10\t69.5\t0\t10\n", "76\t7\t69.5\t0\t7\n", "78\t5\t69.5\t0\t5\n", "79\t9\t69.5\t0\t9\n", "80\t7\t69.5\t0\t7\n", "81\t13\t69.5\t0\t13\n", "82\t14\t69.5\t0\t14\n", "83\t8\t69.5\t0\t8\n", "84\t14\t69.5\t0\t14\n", "85\t6\t69.5\t0\t6\n", "86\t12\t69.5\t0\t12\n", "87\t7\t69.5\t0\t7\n", "88\t9\t69.5\t0\t9\n", "89\t13\t69.5\t0\t13\n", "90\t8\t69.5\t0\t8\n", "91\t20\t69.5\t0\t20\n", "92\t15\t69.5\t0\t15\n", "93\t47\t69.5\t0\t47\n", "94\t59\t69.5\t0\t59\n", "95\t77\t69.5\t0\t77\n", "96\t82\t69.5\t0\t82\n", "97\t65\t69.5\t0\t65\n", "98\t63\t69.5\t0\t63\n", "99\t40\t69.5\t0\t40\n", "100\t94\t69.5\t0\t94\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 92849 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 39.8%\n", " C: 22.9%\n", " G: 16.4%\n", " T: 20.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t70849\t71206.7\t0\t70849\n", "4\t13167\t17801.7\t0\t13167\n", "5\t2489\t4450.4\t0\t2489\n", "6\t220\t1112.6\t0\t220\n", "7\t79\t278.2\t0\t79\n", "8\t69\t278.2\t0\t69\n", "9\t67\t278.2\t0\t67\n", "10\t89\t278.2\t0\t89\n", "11\t82\t278.2\t0\t82\n", "12\t78\t278.2\t0\t78\n", "13\t84\t278.2\t0\t84\n", "14\t74\t278.2\t0\t74\n", "15\t103\t278.2\t0\t103\n", "16\t98\t278.2\t0\t98\n", "17\t74\t278.2\t0\t74\n", "18\t100\t278.2\t0\t100\n", "19\t69\t278.2\t0\t69\n", "20\t85\t278.2\t0\t85\n", "21\t60\t278.2\t0\t60\n", "22\t66\t278.2\t0\t66\n", "23\t75\t278.2\t0\t75\n", "24\t52\t278.2\t0\t52\n", "25\t77\t278.2\t0\t77\n", "26\t66\t278.2\t0\t66\n", "27\t72\t278.2\t0\t72\n", "28\t80\t278.2\t0\t80\n", "29\t58\t278.2\t0\t58\n", "30\t58\t278.2\t0\t58\n", "31\t60\t278.2\t0\t60\n", "32\t77\t278.2\t0\t77\n", "33\t71\t278.2\t0\t71\n", "34\t50\t278.2\t0\t50\n", "35\t63\t278.2\t0\t63\n", "36\t61\t278.2\t0\t61\n", "37\t73\t278.2\t0\t73\n", "38\t71\t278.2\t0\t71\n", "39\t55\t278.2\t0\t55\n", "40\t66\t278.2\t0\t66\n", "41\t57\t278.2\t0\t57\n", "42\t53\t278.2\t0\t53\n", "43\t59\t278.2\t0\t59\n", "44\t58\t278.2\t0\t58\n", "45\t73\t278.2\t0\t73\n", "46\t51\t278.2\t0\t51\n", "47\t55\t278.2\t0\t55\n", "48\t46\t278.2\t0\t46\n", "49\t59\t278.2\t0\t59\n", "50\t57\t278.2\t0\t57\n", "51\t64\t278.2\t0\t64\n", "52\t46\t278.2\t0\t46\n", "53\t45\t278.2\t0\t45\n", "54\t72\t278.2\t0\t72\n", "55\t49\t278.2\t0\t49\n", "56\t47\t278.2\t0\t47\n", "57\t71\t278.2\t0\t71\n", "58\t52\t278.2\t0\t52\n", "59\t49\t278.2\t0\t49\n", "60\t61\t278.2\t0\t61\n", "61\t72\t278.2\t0\t72\n", "62\t52\t278.2\t0\t52\n", "63\t52\t278.2\t0\t52\n", "64\t56\t278.2\t0\t56\n", "65\t43\t278.2\t0\t43\n", "66\t60\t278.2\t0\t60\n", "67\t47\t278.2\t0\t47\n", "68\t53\t278.2\t0\t53\n", "69\t37\t278.2\t0\t37\n", "70\t46\t278.2\t0\t46\n", "71\t62\t278.2\t0\t62\n", "72\t67\t278.2\t0\t67\n", "73\t46\t278.2\t0\t46\n", "74\t62\t278.2\t0\t62\n", "75\t51\t278.2\t0\t51\n", "76\t65\t278.2\t0\t65\n", "77\t94\t278.2\t0\t94\n", "78\t61\t278.2\t0\t61\n", "79\t53\t278.2\t0\t53\n", "80\t82\t278.2\t0\t82\n", "81\t91\t278.2\t0\t91\n", "82\t105\t278.2\t0\t105\n", "83\t83\t278.2\t0\t83\n", "84\t78\t278.2\t0\t78\n", "85\t69\t278.2\t0\t69\n", "86\t64\t278.2\t0\t64\n", "87\t86\t278.2\t0\t86\n", "88\t86\t278.2\t0\t86\n", "89\t81\t278.2\t0\t81\n", "90\t53\t278.2\t0\t53\n", "91\t54\t278.2\t0\t54\n", "92\t39\t278.2\t0\t39\n", "93\t47\t278.2\t0\t47\n", "94\t41\t278.2\t0\t41\n", "95\t37\t278.2\t0\t37\n", "96\t39\t278.2\t0\t39\n", "97\t51\t278.2\t0\t51\n", "98\t74\t278.2\t0\t74\n", "99\t89\t278.2\t0\t89\n", "100\t110\t278.2\t0\t110\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 565_S67_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/565.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 70.59 s (13 us/read; 4.79 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 5,638,974\n", "Reads with adapters: 2,617,958 (46.4%)\n", "Reads written (passing filters): 5,459,207 (96.8%)\n", "\n", "Total basepairs processed: 563,897,400 bp\n", "Quality-trimmed: 1,740,066 bp (0.3%)\n", "Total written (filtered): 465,432,034 bp (82.5%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 2465700 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 23.4%\n", " G: 53.1%\n", " T: 23.5%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t125927\t88109.0\t0\t125927\n", "4\t54794\t22027.2\t0\t54794\n", "5\t40676\t5506.8\t0\t40676\n", "6\t34305\t1376.7\t0\t34305\n", "7\t30994\t344.2\t0\t30994\n", "8\t30412\t86.0\t0\t30412\n", "9\t31993\t86.0\t0\t31993\n", "10\t32146\t86.0\t0\t32146\n", "11\t29505\t86.0\t0\t29505\n", "12\t30467\t86.0\t0\t30467\n", "13\t40659\t86.0\t0\t40659\n", "14\t39276\t86.0\t0\t39276\n", "15\t32406\t86.0\t0\t32406\n", "16\t36646\t86.0\t0\t36646\n", "17\t36600\t86.0\t0\t36600\n", "18\t41866\t86.0\t0\t41866\n", "19\t34140\t86.0\t0\t34140\n", "20\t28620\t86.0\t0\t28620\n", "21\t27737\t86.0\t0\t27737\n", "22\t26431\t86.0\t0\t26431\n", "23\t27159\t86.0\t0\t27159\n", "24\t29727\t86.0\t0\t29727\n", "25\t29952\t86.0\t0\t29952\n", "26\t34694\t86.0\t0\t34694\n", "27\t38547\t86.0\t0\t38547\n", "28\t36302\t86.0\t0\t36302\n", "29\t35463\t86.0\t0\t35463\n", "30\t34616\t86.0\t0\t34616\n", "31\t38924\t86.0\t0\t38924\n", "32\t39438\t86.0\t0\t39438\n", "33\t39732\t86.0\t0\t39732\n", "34\t38867\t86.0\t0\t38867\n", "35\t41490\t86.0\t0\t41490\n", "36\t47184\t86.0\t0\t47184\n", "37\t55158\t86.0\t0\t55158\n", "38\t38911\t86.0\t0\t38911\n", "39\t32173\t86.0\t0\t32173\n", "40\t29720\t86.0\t0\t29720\n", "41\t31257\t86.0\t0\t31257\n", "42\t32895\t86.0\t0\t32895\n", "43\t29175\t86.0\t0\t29175\n", "44\t23007\t86.0\t0\t23007\n", "45\t28559\t86.0\t0\t28559\n", "46\t28394\t86.0\t0\t28394\n", "47\t26201\t86.0\t0\t26201\n", "48\t24792\t86.0\t0\t24792\n", "49\t23502\t86.0\t0\t23502\n", "50\t23609\t86.0\t0\t23609\n", "51\t22471\t86.0\t0\t22471\n", "52\t22916\t86.0\t0\t22916\n", "53\t21133\t86.0\t0\t21133\n", "54\t22293\t86.0\t0\t22293\n", "55\t24608\t86.0\t0\t24608\n", "56\t26969\t86.0\t0\t26969\n", "57\t25333\t86.0\t0\t25333\n", "58\t25138\t86.0\t0\t25138\n", "59\t21183\t86.0\t0\t21183\n", "60\t19439\t86.0\t0\t19439\n", "61\t18119\t86.0\t0\t18119\n", "62\t16918\t86.0\t0\t16918\n", "63\t14528\t86.0\t0\t14528\n", "64\t15982\t86.0\t0\t15982\n", "65\t16295\t86.0\t0\t16295\n", "66\t15693\t86.0\t0\t15693\n", "67\t18959\t86.0\t0\t18959\n", "68\t20382\t86.0\t0\t20382\n", "69\t24437\t86.0\t0\t24437\n", "70\t32417\t86.0\t0\t32417\n", "71\t35504\t86.0\t0\t35504\n", "72\t21818\t86.0\t0\t21818\n", "73\t15839\t86.0\t0\t15839\n", "74\t15074\t86.0\t0\t15074\n", "75\t13477\t86.0\t0\t13477\n", "76\t11822\t86.0\t0\t11822\n", "77\t10949\t86.0\t0\t10949\n", "78\t12163\t86.0\t0\t12163\n", "79\t11692\t86.0\t0\t11692\n", "80\t11244\t86.0\t0\t11244\n", "81\t10187\t86.0\t0\t10187\n", "82\t9123\t86.0\t0\t9123\n", "83\t9308\t86.0\t0\t9308\n", "84\t10131\t86.0\t0\t10131\n", "85\t11073\t86.0\t0\t11073\n", "86\t10338\t86.0\t0\t10338\n", "87\t7575\t86.0\t0\t7575\n", "88\t7196\t86.0\t0\t7196\n", "89\t6786\t86.0\t0\t6786\n", "90\t7298\t86.0\t0\t7298\n", "91\t7513\t86.0\t0\t7513\n", "92\t8024\t86.0\t0\t8024\n", "93\t8216\t86.0\t0\t8216\n", "94\t8037\t86.0\t0\t8037\n", "95\t6927\t86.0\t0\t6927\n", "96\t5445\t86.0\t0\t5445\n", "97\t4399\t86.0\t0\t4399\n", "98\t4553\t86.0\t0\t4553\n", "99\t7346\t86.0\t0\t7346\n", "100\t6382\t86.0\t0\t6382\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 52930 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 31.6%\n", " C: 50.8%\n", " G: 0.0%\n", " T: 17.6%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t27790\t88109.0\t0\t27790\n", "4\t8002\t22027.2\t0\t8002\n", "5\t3997\t5506.8\t0\t3997\n", "6\t2488\t1376.7\t0\t2488\n", "7\t155\t344.2\t0\t155\n", "8\t147\t86.0\t0\t147\n", "9\t140\t86.0\t0\t140\n", "10\t128\t86.0\t0\t128\n", "11\t146\t86.0\t0\t146\n", "12\t107\t86.0\t0\t107\n", "13\t140\t86.0\t0\t140\n", "14\t114\t86.0\t0\t114\n", "15\t116\t86.0\t0\t116\n", "16\t120\t86.0\t0\t120\n", "17\t130\t86.0\t0\t130\n", "18\t187\t86.0\t0\t187\n", "19\t289\t86.0\t0\t289\n", "20\t685\t86.0\t0\t685\n", "21\t362\t86.0\t0\t362\n", "22\t246\t86.0\t0\t246\n", "23\t158\t86.0\t0\t158\n", "24\t156\t86.0\t0\t156\n", "25\t120\t86.0\t0\t120\n", "26\t162\t86.0\t0\t162\n", "27\t178\t86.0\t0\t178\n", "28\t166\t86.0\t0\t166\n", "29\t223\t86.0\t0\t223\n", "30\t401\t86.0\t0\t401\n", "31\t436\t86.0\t0\t436\n", "32\t717\t86.0\t0\t717\n", "33\t564\t86.0\t0\t564\n", "34\t660\t86.0\t0\t660\n", "35\t698\t86.0\t0\t698\n", "36\t672\t86.0\t0\t672\n", "37\t340\t86.0\t0\t340\n", "38\t36\t86.0\t0\t36\n", "39\t42\t86.0\t0\t42\n", "40\t37\t86.0\t0\t37\n", "41\t14\t86.0\t0\t14\n", "42\t23\t86.0\t0\t23\n", "43\t23\t86.0\t0\t23\n", "44\t34\t86.0\t0\t34\n", "45\t26\t86.0\t0\t26\n", "46\t24\t86.0\t0\t24\n", "47\t20\t86.0\t0\t20\n", "48\t19\t86.0\t0\t19\n", "49\t15\t86.0\t0\t15\n", "50\t14\t86.0\t0\t14\n", "51\t16\t86.0\t0\t16\n", "52\t15\t86.0\t0\t15\n", "53\t24\t86.0\t0\t24\n", "54\t29\t86.0\t0\t29\n", "55\t8\t86.0\t0\t8\n", "56\t18\t86.0\t0\t18\n", "57\t23\t86.0\t0\t23\n", "58\t19\t86.0\t0\t19\n", "59\t23\t86.0\t0\t23\n", "60\t20\t86.0\t0\t20\n", "61\t12\t86.0\t0\t12\n", "62\t13\t86.0\t0\t13\n", "63\t17\t86.0\t0\t17\n", "64\t17\t86.0\t0\t17\n", "65\t21\t86.0\t0\t21\n", "66\t21\t86.0\t0\t21\n", "67\t15\t86.0\t0\t15\n", "68\t10\t86.0\t0\t10\n", "69\t3\t86.0\t0\t3\n", "70\t7\t86.0\t0\t7\n", "71\t11\t86.0\t0\t11\n", "72\t13\t86.0\t0\t13\n", "73\t22\t86.0\t0\t22\n", "74\t7\t86.0\t0\t7\n", "75\t26\t86.0\t0\t26\n", "76\t16\t86.0\t0\t16\n", "77\t20\t86.0\t0\t20\n", "78\t25\t86.0\t0\t25\n", "79\t9\t86.0\t0\t9\n", "80\t13\t86.0\t0\t13\n", "81\t22\t86.0\t0\t22\n", "82\t13\t86.0\t0\t13\n", "83\t5\t86.0\t0\t5\n", "84\t8\t86.0\t0\t8\n", "85\t13\t86.0\t0\t13\n", "86\t10\t86.0\t0\t10\n", "87\t5\t86.0\t0\t5\n", "88\t4\t86.0\t0\t4\n", "89\t16\t86.0\t0\t16\n", "90\t15\t86.0\t0\t15\n", "91\t28\t86.0\t0\t28\n", "92\t32\t86.0\t0\t32\n", "93\t52\t86.0\t0\t52\n", "94\t75\t86.0\t0\t75\n", "95\t117\t86.0\t0\t117\n", "96\t146\t86.0\t0\t146\n", "97\t100\t86.0\t0\t100\n", "98\t126\t86.0\t0\t126\n", "99\t83\t86.0\t0\t83\n", "100\t100\t86.0\t0\t100\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 99328 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 40.3%\n", " C: 25.2%\n", " G: 16.2%\n", " T: 18.2%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t74685\t88109.0\t0\t74685\n", "4\t13596\t22027.2\t0\t13596\n", "5\t1684\t5506.8\t0\t1684\n", "6\t203\t1376.7\t0\t203\n", "7\t57\t344.2\t0\t57\n", "8\t83\t344.2\t0\t83\n", "9\t66\t344.2\t0\t66\n", "10\t98\t344.2\t0\t98\n", "11\t123\t344.2\t0\t123\n", "12\t142\t344.2\t0\t142\n", "13\t161\t344.2\t0\t161\n", "14\t146\t344.2\t0\t146\n", "15\t121\t344.2\t0\t121\n", "16\t102\t344.2\t0\t102\n", "17\t148\t344.2\t0\t148\n", "18\t148\t344.2\t0\t148\n", "19\t145\t344.2\t0\t145\n", "20\t155\t344.2\t0\t155\n", "21\t166\t344.2\t0\t166\n", "22\t100\t344.2\t0\t100\n", "23\t65\t344.2\t0\t65\n", "24\t65\t344.2\t0\t65\n", "25\t39\t344.2\t0\t39\n", "26\t100\t344.2\t0\t100\n", "27\t87\t344.2\t0\t87\n", "28\t94\t344.2\t0\t94\n", "29\t103\t344.2\t0\t103\n", "30\t133\t344.2\t0\t133\n", "31\t141\t344.2\t0\t141\n", "32\t149\t344.2\t0\t149\n", "33\t82\t344.2\t0\t82\n", "34\t159\t344.2\t0\t159\n", "35\t116\t344.2\t0\t116\n", "36\t122\t344.2\t0\t122\n", "37\t98\t344.2\t0\t98\n", "38\t116\t344.2\t0\t116\n", "39\t108\t344.2\t0\t108\n", "40\t125\t344.2\t0\t125\n", "41\t91\t344.2\t0\t91\n", "42\t78\t344.2\t0\t78\n", "43\t88\t344.2\t0\t88\n", "44\t33\t344.2\t0\t33\n", "45\t73\t344.2\t0\t73\n", "46\t90\t344.2\t0\t90\n", "47\t83\t344.2\t0\t83\n", "48\t47\t344.2\t0\t47\n", "49\t73\t344.2\t0\t73\n", "50\t61\t344.2\t0\t61\n", "51\t50\t344.2\t0\t50\n", "52\t95\t344.2\t0\t95\n", "53\t82\t344.2\t0\t82\n", "54\t60\t344.2\t0\t60\n", "55\t61\t344.2\t0\t61\n", "56\t136\t344.2\t0\t136\n", "57\t165\t344.2\t0\t165\n", "58\t327\t344.2\t0\t327\n", "59\t165\t344.2\t0\t165\n", "60\t307\t344.2\t0\t307\n", "61\t267\t344.2\t0\t267\n", "62\t261\t344.2\t0\t261\n", "63\t147\t344.2\t0\t147\n", "64\t214\t344.2\t0\t214\n", "65\t170\t344.2\t0\t170\n", "66\t180\t344.2\t0\t180\n", "67\t99\t344.2\t0\t99\n", "68\t89\t344.2\t0\t89\n", "69\t50\t344.2\t0\t50\n", "70\t21\t344.2\t0\t21\n", "71\t49\t344.2\t0\t49\n", "72\t52\t344.2\t0\t52\n", "73\t79\t344.2\t0\t79\n", "74\t61\t344.2\t0\t61\n", "75\t57\t344.2\t0\t57\n", "76\t43\t344.2\t0\t43\n", "77\t33\t344.2\t0\t33\n", "78\t25\t344.2\t0\t25\n", "79\t53\t344.2\t0\t53\n", "80\t24\t344.2\t0\t24\n", "81\t64\t344.2\t0\t64\n", "82\t50\t344.2\t0\t50\n", "83\t64\t344.2\t0\t64\n", "84\t49\t344.2\t0\t49\n", "85\t51\t344.2\t0\t51\n", "86\t62\t344.2\t0\t62\n", "87\t66\t344.2\t0\t66\n", "88\t147\t344.2\t0\t147\n", "89\t69\t344.2\t0\t69\n", "90\t85\t344.2\t0\t85\n", "91\t45\t344.2\t0\t45\n", "92\t14\t344.2\t0\t14\n", "93\t35\t344.2\t0\t35\n", "94\t38\t344.2\t0\t38\n", "95\t34\t344.2\t0\t34\n", "96\t25\t344.2\t0\t25\n", "97\t52\t344.2\t0\t52\n", "98\t31\t344.2\t0\t31\n", "99\t86\t344.2\t0\t86\n", "100\t91\t344.2\t0\t91\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: 571_S76_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/571.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 21.22 s (15 us/read; 3.96 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 1,401,824\n", "Reads with adapters: 1,193,426 (85.1%)\n", "Reads written (passing filters): 730,357 (52.1%)\n", "\n", "Total basepairs processed: 140,182,400 bp\n", "Quality-trimmed: 5,962,356 bp (4.3%)\n", "Total written (filtered): 48,749,775 bp (34.8%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 950296 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 32.1%\n", " G: 46.3%\n", " T: 21.5%\n", " none/other: 0.1%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t9624\t21903.5\t0\t9624\n", "4\t3960\t5475.9\t0\t3960\n", "5\t2554\t1369.0\t0\t2554\n", "6\t1301\t342.2\t0\t1301\n", "7\t1621\t85.6\t0\t1621\n", "8\t1361\t21.4\t0\t1361\n", "9\t1815\t21.4\t0\t1815\n", "10\t1068\t21.4\t0\t1068\n", "11\t1308\t21.4\t0\t1308\n", "12\t1906\t21.4\t0\t1906\n", "13\t1309\t21.4\t0\t1309\n", "14\t1986\t21.4\t0\t1986\n", "15\t1870\t21.4\t0\t1870\n", "16\t1709\t21.4\t0\t1709\n", "17\t1319\t21.4\t0\t1319\n", "18\t2233\t21.4\t0\t2233\n", "19\t2554\t21.4\t0\t2554\n", "20\t2284\t21.4\t0\t2284\n", "21\t2416\t21.4\t0\t2416\n", "22\t1461\t21.4\t0\t1461\n", "23\t2035\t21.4\t0\t2035\n", "24\t1519\t21.4\t0\t1519\n", "25\t1686\t21.4\t0\t1686\n", "26\t2044\t21.4\t0\t2044\n", "27\t2155\t21.4\t0\t2155\n", "28\t1761\t21.4\t0\t1761\n", "29\t1523\t21.4\t0\t1523\n", "30\t1844\t21.4\t0\t1844\n", "31\t2136\t21.4\t0\t2136\n", "32\t2030\t21.4\t0\t2030\n", "33\t1972\t21.4\t0\t1972\n", "34\t1596\t21.4\t0\t1596\n", "35\t1866\t21.4\t0\t1866\n", "36\t2519\t21.4\t0\t2519\n", "37\t2728\t21.4\t0\t2728\n", "38\t2322\t21.4\t0\t2322\n", "39\t2598\t21.4\t0\t2598\n", "40\t1953\t21.4\t0\t1953\n", "41\t1607\t21.4\t0\t1607\n", "42\t1954\t21.4\t0\t1954\n", "43\t2271\t21.4\t0\t2271\n", "44\t2305\t21.4\t0\t2305\n", "45\t2326\t21.4\t0\t2326\n", "46\t3041\t21.4\t0\t3041\n", "47\t3011\t21.4\t0\t3011\n", "48\t3071\t21.4\t0\t3071\n", "49\t3017\t21.4\t0\t3017\n", "50\t3414\t21.4\t0\t3414\n", "51\t3964\t21.4\t0\t3964\n", "52\t4611\t21.4\t0\t4611\n", "53\t4752\t21.4\t0\t4752\n", "54\t5175\t21.4\t0\t5175\n", "55\t4990\t21.4\t0\t4990\n", "56\t5271\t21.4\t0\t5271\n", "57\t6153\t21.4\t0\t6153\n", "58\t6515\t21.4\t0\t6515\n", "59\t6143\t21.4\t0\t6143\n", "60\t6539\t21.4\t0\t6539\n", "61\t6814\t21.4\t0\t6814\n", "62\t7673\t21.4\t0\t7673\n", "63\t8028\t21.4\t0\t8028\n", "64\t8855\t21.4\t0\t8855\n", "65\t9425\t21.4\t0\t9425\n", "66\t9443\t21.4\t0\t9443\n", "67\t11835\t21.4\t0\t11835\n", "68\t19418\t21.4\t0\t19418\n", "69\t27322\t21.4\t0\t27322\n", "70\t19913\t21.4\t0\t19913\n", "71\t12647\t21.4\t0\t12647\n", "72\t9482\t21.4\t0\t9482\n", "73\t8690\t21.4\t0\t8690\n", "74\t10561\t21.4\t0\t10561\n", "75\t14490\t21.4\t0\t14490\n", "76\t18196\t21.4\t0\t18196\n", "77\t16403\t21.4\t0\t16403\n", "78\t16957\t21.4\t0\t16957\n", "79\t12009\t21.4\t0\t12009\n", "80\t9515\t21.4\t0\t9515\n", "81\t9366\t21.4\t0\t9366\n", "82\t8468\t21.4\t0\t8468\n", "83\t8534\t21.4\t0\t8534\n", "84\t8784\t21.4\t0\t8784\n", "85\t8497\t21.4\t0\t8497\n", "86\t7724\t21.4\t0\t7724\n", "87\t6811\t21.4\t0\t6811\n", "88\t6611\t21.4\t0\t6611\n", "89\t7103\t21.4\t0\t7103\n", "90\t7761\t21.4\t0\t7761\n", "91\t10224\t21.4\t0\t10224\n", "92\t15054\t21.4\t0\t15054\n", "93\t20839\t21.4\t0\t20839\n", "94\t25531\t21.4\t0\t25531\n", "95\t32212\t21.4\t0\t32212\n", "96\t37551\t21.4\t0\t37551\n", "97\t41389\t21.4\t0\t41389\n", "98\t60752\t21.4\t0\t60752\n", "99\t104575\t21.4\t0\t104575\n", "100\t102758\t21.4\t0\t102758\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 116712 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 89.8%\n", " C: 4.5%\n", " G: 0.0%\n", " T: 5.8%\n", " none/other: 0.0%\n", "WARNING:\n", " The adapter is preceded by \"A\" extremely often.\n", " The provided adapter sequence could be incomplete at its 3' end.\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t2830\t21903.5\t0\t2830\n", "4\t512\t5475.9\t0\t512\n", "5\t634\t1369.0\t0\t634\n", "6\t211\t342.2\t0\t211\n", "7\t753\t85.6\t0\t753\n", "8\t635\t21.4\t0\t635\n", "9\t612\t21.4\t0\t612\n", "10\t531\t21.4\t0\t531\n", "11\t537\t21.4\t0\t537\n", "12\t502\t21.4\t0\t502\n", "13\t617\t21.4\t0\t617\n", "14\t666\t21.4\t0\t666\n", "15\t608\t21.4\t0\t608\n", "16\t817\t21.4\t0\t817\n", "17\t1230\t21.4\t0\t1230\n", "18\t2844\t21.4\t0\t2844\n", "19\t5952\t21.4\t0\t5952\n", "20\t12993\t21.4\t0\t12993\n", "21\t8387\t21.4\t0\t8387\n", "22\t5249\t21.4\t0\t5249\n", "23\t2876\t21.4\t0\t2876\n", "24\t2037\t21.4\t0\t2037\n", "25\t1560\t21.4\t0\t1560\n", "26\t1656\t21.4\t0\t1656\n", "27\t1286\t21.4\t0\t1286\n", "28\t1670\t21.4\t0\t1670\n", "29\t1930\t21.4\t0\t1930\n", "30\t3695\t21.4\t0\t3695\n", "31\t4439\t21.4\t0\t4439\n", "32\t6366\t21.4\t0\t6366\n", "33\t6948\t21.4\t0\t6948\n", "34\t7552\t21.4\t0\t7552\n", "35\t10357\t21.4\t0\t10357\n", "36\t10508\t21.4\t0\t10508\n", "37\t5812\t21.4\t0\t5812\n", "38\t459\t21.4\t0\t459\n", "39\t197\t21.4\t0\t197\n", "40\t10\t21.4\t0\t10\n", "41\t3\t21.4\t0\t3\n", "44\t2\t21.4\t0\t2\n", "46\t3\t21.4\t0\t3\n", "47\t3\t21.4\t0\t3\n", "48\t2\t21.4\t0\t2\n", "49\t1\t21.4\t0\t1\n", "50\t1\t21.4\t0\t1\n", "51\t1\t21.4\t0\t1\n", "52\t3\t21.4\t0\t3\n", "55\t1\t21.4\t0\t1\n", "56\t90\t21.4\t0\t90\n", "58\t1\t21.4\t0\t1\n", "63\t1\t21.4\t0\t1\n", "84\t1\t21.4\t0\t1\n", "87\t5\t21.4\t0\t5\n", "88\t105\t21.4\t0\t105\n", "92\t1\t21.4\t0\t1\n", "93\t1\t21.4\t0\t1\n", "94\t1\t21.4\t0\t1\n", "95\t1\t21.4\t0\t1\n", "99\t7\t21.4\t0\t7\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 126418 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 18.8%\n", " C: 24.9%\n", " G: 36.2%\n", " T: 20.1%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t7495\t21903.5\t0\t7495\n", "4\t1653\t5475.9\t0\t1653\n", "5\t827\t1369.0\t0\t827\n", "6\t783\t342.2\t0\t783\n", "7\t645\t85.6\t0\t645\n", "8\t1156\t85.6\t0\t1156\n", "9\t547\t85.6\t0\t547\n", "10\t691\t85.6\t0\t691\n", "11\t896\t85.6\t0\t896\n", "12\t920\t85.6\t0\t920\n", "13\t715\t85.6\t0\t715\n", "14\t1319\t85.6\t0\t1319\n", "15\t694\t85.6\t0\t694\n", "16\t469\t85.6\t0\t469\n", "17\t778\t85.6\t0\t778\n", "18\t585\t85.6\t0\t585\n", "19\t384\t85.6\t0\t384\n", "20\t832\t85.6\t0\t832\n", "21\t500\t85.6\t0\t500\n", "22\t201\t85.6\t0\t201\n", "23\t985\t85.6\t0\t985\n", "24\t501\t85.6\t0\t501\n", "25\t655\t85.6\t0\t655\n", "26\t1019\t85.6\t0\t1019\n", "27\t1132\t85.6\t0\t1132\n", "28\t1674\t85.6\t0\t1674\n", "29\t1196\t85.6\t0\t1196\n", "30\t2339\t85.6\t0\t2339\n", "31\t1730\t85.6\t0\t1730\n", "32\t1789\t85.6\t0\t1789\n", "33\t1919\t85.6\t0\t1919\n", "34\t2344\t85.6\t0\t2344\n", "35\t1955\t85.6\t0\t1955\n", "36\t2410\t85.6\t0\t2410\n", "37\t1412\t85.6\t0\t1412\n", "38\t1742\t85.6\t0\t1742\n", "39\t1702\t85.6\t0\t1702\n", "40\t1943\t85.6\t0\t1943\n", "41\t1413\t85.6\t0\t1413\n", "42\t1715\t85.6\t0\t1715\n", "43\t2524\t85.6\t0\t2524\n", "44\t504\t85.6\t0\t504\n", "45\t1000\t85.6\t0\t1000\n", "46\t853\t85.6\t0\t853\n", "47\t979\t85.6\t0\t979\n", "48\t557\t85.6\t0\t557\n", "49\t1497\t85.6\t0\t1497\n", "50\t1388\t85.6\t0\t1388\n", "51\t964\t85.6\t0\t964\n", "52\t670\t85.6\t0\t670\n", "53\t907\t85.6\t0\t907\n", "54\t461\t85.6\t0\t461\n", "55\t1128\t85.6\t0\t1128\n", "56\t1560\t85.6\t0\t1560\n", "57\t2863\t85.6\t0\t2863\n", "58\t5225\t85.6\t0\t5225\n", "59\t2598\t85.6\t0\t2598\n", "60\t5030\t85.6\t0\t5030\n", "61\t6233\t85.6\t0\t6233\n", "62\t4557\t85.6\t0\t4557\n", "63\t2819\t85.6\t0\t2819\n", "64\t7001\t85.6\t0\t7001\n", "65\t3036\t85.6\t0\t3036\n", "66\t3184\t85.6\t0\t3184\n", "67\t2218\t85.6\t0\t2218\n", "68\t1473\t85.6\t0\t1473\n", "69\t497\t85.6\t0\t497\n", "70\t676\t85.6\t0\t676\n", "71\t840\t85.6\t0\t840\n", "72\t912\t85.6\t0\t912\n", "73\t853\t85.6\t0\t853\n", "74\t494\t85.6\t0\t494\n", "75\t172\t85.6\t0\t172\n", "76\t167\t85.6\t0\t167\n", "77\t25\t85.6\t0\t25\n", "78\t9\t85.6\t0\t9\n", "79\t18\t85.6\t0\t18\n", "80\t10\t85.6\t0\t10\n", "81\t17\t85.6\t0\t17\n", "82\t29\t85.6\t0\t29\n", "83\t102\t85.6\t0\t102\n", "84\t46\t85.6\t0\t46\n", "85\t117\t85.6\t0\t117\n", "86\t396\t85.6\t0\t396\n", "87\t598\t85.6\t0\t598\n", "88\t1993\t85.6\t0\t1993\n", "89\t1715\t85.6\t0\t1715\n", "90\t651\t85.6\t0\t651\n", "91\t482\t85.6\t0\t482\n", "92\t223\t85.6\t0\t223\n", "93\t134\t85.6\t0\t134\n", "94\t241\t85.6\t0\t241\n", "95\t77\t85.6\t0\t77\n", "96\t19\t85.6\t0\t19\n", "97\t3\t85.6\t0\t3\n", "98\t3\t85.6\t0\t3\n", "99\t2\t85.6\t0\t2\n", "100\t3\t85.6\t0\t3\n", "\n", "\n", "WARNING:\n", " One or more of your adapter sequences may be incomplete.\n", " Please see the detailed output above.\n", "This is cutadapt 2.10 with Python 3.7.7\n", "Command line parameters: Undetermined_S0_L002_R1_001.fastq -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 -o ../../qc-processing/cutadapt/Undetermined.trim.fastq\n", "Processing reads on 1 core in single-end mode ...\n", "Finished in 164.27 s (12 us/read; 4.98 M reads/minute).\n", "\n", "=== Summary ===\n", "\n", "Total reads processed: 13,639,330\n", "Reads with adapters: 3,942,151 (28.9%)\n", "Reads written (passing filters): 13,289,142 (97.4%)\n", "\n", "Total basepairs processed: 1,363,933,000 bp\n", "Quality-trimmed: 3,160,356 bp (0.2%)\n", "Total written (filtered): 1,213,719,138 bp (89.0%)\n", "\n", "=== Adapter 1 ===\n", "\n", "Sequence: AAAAAAAA; Type: regular 3'; Length: 8; Trimmed: 3513669 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 0.0%\n", " C: 30.3%\n", " G: 31.9%\n", " T: 37.8%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t273867\t213114.5\t0\t273867\n", "4\t120566\t53278.6\t0\t120566\n", "5\t68642\t13319.7\t0\t68642\n", "6\t41328\t3329.9\t0\t41328\n", "7\t33409\t832.5\t0\t33409\n", "8\t30860\t208.1\t0\t30860\n", "9\t31050\t208.1\t0\t31050\n", "10\t29625\t208.1\t0\t29625\n", "11\t30250\t208.1\t0\t30250\n", "12\t30993\t208.1\t0\t30993\n", "13\t34782\t208.1\t0\t34782\n", "14\t35678\t208.1\t0\t35678\n", "15\t34818\t208.1\t0\t34818\n", "16\t35976\t208.1\t0\t35976\n", "17\t38292\t208.1\t0\t38292\n", "18\t43548\t208.1\t0\t43548\n", "19\t40400\t208.1\t0\t40400\n", "20\t35919\t208.1\t0\t35919\n", "21\t35483\t208.1\t0\t35483\n", "22\t33110\t208.1\t0\t33110\n", "23\t34927\t208.1\t0\t34927\n", "24\t39114\t208.1\t0\t39114\n", "25\t40479\t208.1\t0\t40479\n", "26\t45725\t208.1\t0\t45725\n", "27\t52015\t208.1\t0\t52015\n", "28\t49568\t208.1\t0\t49568\n", "29\t49794\t208.1\t0\t49794\n", "30\t50755\t208.1\t0\t50755\n", "31\t52831\t208.1\t0\t52831\n", "32\t50819\t208.1\t0\t50819\n", "33\t47722\t208.1\t0\t47722\n", "34\t47727\t208.1\t0\t47727\n", "35\t51722\t208.1\t0\t51722\n", "36\t57903\t208.1\t0\t57903\n", "37\t61226\t208.1\t0\t61226\n", "38\t52132\t208.1\t0\t52132\n", "39\t43183\t208.1\t0\t43183\n", "40\t41728\t208.1\t0\t41728\n", "41\t43140\t208.1\t0\t43140\n", "42\t46331\t208.1\t0\t46331\n", "43\t42119\t208.1\t0\t42119\n", "44\t37366\t208.1\t0\t37366\n", "45\t43572\t208.1\t0\t43572\n", "46\t49331\t208.1\t0\t49331\n", "47\t48419\t208.1\t0\t48419\n", "48\t48816\t208.1\t0\t48816\n", "49\t42943\t208.1\t0\t42943\n", "50\t39934\t208.1\t0\t39934\n", "51\t38830\t208.1\t0\t38830\n", "52\t37689\t208.1\t0\t37689\n", "53\t37811\t208.1\t0\t37811\n", "54\t40263\t208.1\t0\t40263\n", "55\t41593\t208.1\t0\t41593\n", "56\t39330\t208.1\t0\t39330\n", "57\t37638\t208.1\t0\t37638\n", "58\t38962\t208.1\t0\t38962\n", "59\t32154\t208.1\t0\t32154\n", "60\t29660\t208.1\t0\t29660\n", "61\t27303\t208.1\t0\t27303\n", "62\t25776\t208.1\t0\t25776\n", "63\t26726\t208.1\t0\t26726\n", "64\t26004\t208.1\t0\t26004\n", "65\t25064\t208.1\t0\t25064\n", "66\t25686\t208.1\t0\t25686\n", "67\t25140\t208.1\t0\t25140\n", "68\t24298\t208.1\t0\t24298\n", "69\t24994\t208.1\t0\t24994\n", "70\t25153\t208.1\t0\t25153\n", "71\t22469\t208.1\t0\t22469\n", "72\t20534\t208.1\t0\t20534\n", "73\t19061\t208.1\t0\t19061\n", "74\t18575\t208.1\t0\t18575\n", "75\t17163\t208.1\t0\t17163\n", "76\t17086\t208.1\t0\t17086\n", "77\t17256\t208.1\t0\t17256\n", "78\t16842\t208.1\t0\t16842\n", "79\t16751\t208.1\t0\t16751\n", "80\t16876\t208.1\t0\t16876\n", "81\t16687\t208.1\t0\t16687\n", "82\t16731\t208.1\t0\t16731\n", "83\t17349\t208.1\t0\t17349\n", "84\t18401\t208.1\t0\t18401\n", "85\t18926\t208.1\t0\t18926\n", "86\t18876\t208.1\t0\t18876\n", "87\t18432\t208.1\t0\t18432\n", "88\t20011\t208.1\t0\t20011\n", "89\t18934\t208.1\t0\t18934\n", "90\t17541\t208.1\t0\t17541\n", "91\t17462\t208.1\t0\t17462\n", "92\t17345\t208.1\t0\t17345\n", "93\t17193\t208.1\t0\t17193\n", "94\t16355\t208.1\t0\t16355\n", "95\t14826\t208.1\t0\t14826\n", "96\t12593\t208.1\t0\t12593\n", "97\t11396\t208.1\t0\t11396\n", "98\t10845\t208.1\t0\t10845\n", "99\t14063\t208.1\t0\t14063\n", "100\t17079\t208.1\t0\t17079\n", "\n", "\n", "=== Adapter 2 ===\n", "\n", "Sequence: GGGGGGGG; Type: regular 3'; Length: 8; Trimmed: 160071 times\n", "\n", "No. of allowed errors:\n", "0-8 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 62.9%\n", " C: 16.2%\n", " G: 0.0%\n", " T: 20.9%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t50559\t213114.5\t0\t50559\n", "4\t11580\t53278.6\t0\t11580\n", "5\t2771\t13319.7\t0\t2771\n", "6\t1377\t3329.9\t0\t1377\n", "7\t908\t832.5\t0\t908\n", "8\t750\t208.1\t0\t750\n", "9\t645\t208.1\t0\t645\n", "10\t525\t208.1\t0\t525\n", "11\t644\t208.1\t0\t644\n", "12\t601\t208.1\t0\t601\n", "13\t631\t208.1\t0\t631\n", "14\t584\t208.1\t0\t584\n", "15\t713\t208.1\t0\t713\n", "16\t758\t208.1\t0\t758\n", "17\t704\t208.1\t0\t704\n", "18\t762\t208.1\t0\t762\n", "19\t1020\t208.1\t0\t1020\n", "20\t1126\t208.1\t0\t1126\n", "21\t1408\t208.1\t0\t1408\n", "22\t1263\t208.1\t0\t1263\n", "23\t1124\t208.1\t0\t1124\n", "24\t977\t208.1\t0\t977\n", "25\t952\t208.1\t0\t952\n", "26\t1143\t208.1\t0\t1143\n", "27\t1502\t208.1\t0\t1502\n", "28\t1491\t208.1\t0\t1491\n", "29\t1778\t208.1\t0\t1778\n", "30\t2494\t208.1\t0\t2494\n", "31\t3576\t208.1\t0\t3576\n", "32\t4830\t208.1\t0\t4830\n", "33\t6735\t208.1\t0\t6735\n", "34\t8080\t208.1\t0\t8080\n", "35\t10158\t208.1\t0\t10158\n", "36\t10688\t208.1\t0\t10688\n", "37\t9561\t208.1\t0\t9561\n", "38\t5248\t208.1\t0\t5248\n", "39\t1586\t208.1\t0\t1586\n", "40\t727\t208.1\t0\t727\n", "41\t538\t208.1\t0\t538\n", "42\t482\t208.1\t0\t482\n", "43\t467\t208.1\t0\t467\n", "44\t429\t208.1\t0\t429\n", "45\t383\t208.1\t0\t383\n", "46\t369\t208.1\t0\t369\n", "47\t377\t208.1\t0\t377\n", "48\t309\t208.1\t0\t309\n", "49\t292\t208.1\t0\t292\n", "50\t247\t208.1\t0\t247\n", "51\t257\t208.1\t0\t257\n", "52\t276\t208.1\t0\t276\n", "53\t258\t208.1\t0\t258\n", "54\t176\t208.1\t0\t176\n", "55\t212\t208.1\t0\t212\n", "56\t171\t208.1\t0\t171\n", "57\t167\t208.1\t0\t167\n", "58\t175\t208.1\t0\t175\n", "59\t159\t208.1\t0\t159\n", "60\t132\t208.1\t0\t132\n", "61\t138\t208.1\t0\t138\n", "62\t113\t208.1\t0\t113\n", "63\t107\t208.1\t0\t107\n", "64\t176\t208.1\t0\t176\n", "65\t140\t208.1\t0\t140\n", "66\t122\t208.1\t0\t122\n", "67\t110\t208.1\t0\t110\n", "68\t121\t208.1\t0\t121\n", "69\t127\t208.1\t0\t127\n", "70\t181\t208.1\t0\t181\n", "71\t140\t208.1\t0\t140\n", "72\t83\t208.1\t0\t83\n", "73\t15\t208.1\t0\t15\n", "74\t12\t208.1\t0\t12\n", "75\t6\t208.1\t0\t6\n", "76\t9\t208.1\t0\t9\n", "77\t3\t208.1\t0\t3\n", "78\t9\t208.1\t0\t9\n", "79\t7\t208.1\t0\t7\n", "80\t8\t208.1\t0\t8\n", "81\t3\t208.1\t0\t3\n", "82\t3\t208.1\t0\t3\n", "83\t4\t208.1\t0\t4\n", "84\t5\t208.1\t0\t5\n", "85\t7\t208.1\t0\t7\n", "86\t6\t208.1\t0\t6\n", "87\t4\t208.1\t0\t4\n", "88\t6\t208.1\t0\t6\n", "89\t6\t208.1\t0\t6\n", "90\t15\t208.1\t0\t15\n", "91\t18\t208.1\t0\t18\n", "92\t25\t208.1\t0\t25\n", "93\t40\t208.1\t0\t40\n", "94\t61\t208.1\t0\t61\n", "95\t65\t208.1\t0\t65\n", "96\t58\t208.1\t0\t58\n", "97\t58\t208.1\t0\t58\n", "98\t72\t208.1\t0\t72\n", "99\t63\t208.1\t0\t63\n", "100\t70\t208.1\t0\t70\n", "\n", "\n", "=== Adapter 3 ===\n", "\n", "Sequence: AGATCGG; Type: regular 3'; Length: 7; Trimmed: 268411 times\n", "\n", "No. of allowed errors:\n", "0-7 bp: 0\n", "\n", "Bases preceding removed adapters:\n", " A: 34.2%\n", " C: 27.2%\n", " G: 21.0%\n", " T: 17.6%\n", " none/other: 0.0%\n", "\n", "Overview of removed sequences\n", "length\tcount\texpect\tmax.err\terror counts\n", "3\t203655\t213114.5\t0\t203655\n", "4\t41522\t53278.6\t0\t41522\n", "5\t2592\t13319.7\t0\t2592\n", "6\t605\t3329.9\t0\t605\n", "7\t528\t832.5\t0\t528\n", "8\t594\t832.5\t0\t594\n", "9\t352\t832.5\t0\t352\n", "10\t493\t832.5\t0\t493\n", "11\t474\t832.5\t0\t474\n", "12\t440\t832.5\t0\t440\n", "13\t504\t832.5\t0\t504\n", "14\t521\t832.5\t0\t521\n", "15\t495\t832.5\t0\t495\n", "16\t493\t832.5\t0\t493\n", "17\t437\t832.5\t0\t437\n", "18\t406\t832.5\t0\t406\n", "19\t357\t832.5\t0\t357\n", "20\t423\t832.5\t0\t423\n", "21\t353\t832.5\t0\t353\n", "22\t357\t832.5\t0\t357\n", "23\t346\t832.5\t0\t346\n", "24\t303\t832.5\t0\t303\n", "25\t328\t832.5\t0\t328\n", "26\t315\t832.5\t0\t315\n", "27\t324\t832.5\t0\t324\n", "28\t328\t832.5\t0\t328\n", "29\t307\t832.5\t0\t307\n", "30\t307\t832.5\t0\t307\n", "31\t266\t832.5\t0\t266\n", "32\t268\t832.5\t0\t268\n", "33\t277\t832.5\t0\t277\n", "34\t311\t832.5\t0\t311\n", "35\t303\t832.5\t0\t303\n", "36\t266\t832.5\t0\t266\n", "37\t229\t832.5\t0\t229\n", "38\t237\t832.5\t0\t237\n", "39\t255\t832.5\t0\t255\n", "40\t335\t832.5\t0\t335\n", "41\t129\t832.5\t0\t129\n", "42\t220\t832.5\t0\t220\n", "43\t177\t832.5\t0\t177\n", "44\t202\t832.5\t0\t202\n", "45\t159\t832.5\t0\t159\n", "46\t176\t832.5\t0\t176\n", "47\t191\t832.5\t0\t191\n", "48\t159\t832.5\t0\t159\n", "49\t165\t832.5\t0\t165\n", "50\t172\t832.5\t0\t172\n", "51\t144\t832.5\t0\t144\n", "52\t177\t832.5\t0\t177\n", "53\t154\t832.5\t0\t154\n", "54\t153\t832.5\t0\t153\n", "55\t154\t832.5\t0\t154\n", "56\t171\t832.5\t0\t171\n", "57\t230\t832.5\t0\t230\n", "58\t195\t832.5\t0\t195\n", "59\t327\t832.5\t0\t327\n", "60\t302\t832.5\t0\t302\n", "61\t260\t832.5\t0\t260\n", "62\t220\t832.5\t0\t220\n", "63\t345\t832.5\t0\t345\n", "64\t178\t832.5\t0\t178\n", "65\t189\t832.5\t0\t189\n", "66\t126\t832.5\t0\t126\n", "67\t122\t832.5\t0\t122\n", "68\t92\t832.5\t0\t92\n", "69\t75\t832.5\t0\t75\n", "70\t160\t832.5\t0\t160\n", "71\t85\t832.5\t0\t85\n", "72\t88\t832.5\t0\t88\n", "73\t87\t832.5\t0\t87\n", "74\t65\t832.5\t0\t65\n", "75\t60\t832.5\t0\t60\n", "76\t59\t832.5\t0\t59\n", "77\t60\t832.5\t0\t60\n", "78\t52\t832.5\t0\t52\n", "79\t59\t832.5\t0\t59\n", "80\t65\t832.5\t0\t65\n", "81\t73\t832.5\t0\t73\n", "82\t70\t832.5\t0\t70\n", "83\t80\t832.5\t0\t80\n", "84\t57\t832.5\t0\t57\n", "85\t71\t832.5\t0\t71\n", "86\t65\t832.5\t0\t65\n", "87\t74\t832.5\t0\t74\n", "88\t132\t832.5\t0\t132\n", "89\t116\t832.5\t0\t116\n", "90\t57\t832.5\t0\t57\n", "91\t48\t832.5\t0\t48\n", "92\t44\t832.5\t0\t44\n", "93\t28\t832.5\t0\t28\n", "94\t40\t832.5\t0\t40\n", "95\t15\t832.5\t0\t15\n", "96\t42\t832.5\t0\t42\n", "97\t44\t832.5\t0\t44\n", "98\t57\t832.5\t0\t57\n", "99\t62\t832.5\t0\t62\n", "100\t126\t832.5\t0\t126\n" ] } ], "source": [ "%%bash\n", "\n", "# create output file names (with location in relative path)\n", "for file in *_L002_R1_001.fastq\n", "do\n", "sample=\"$(basename -a $file | cut -d \"_\" -f 1)\"\n", "trimmed_file=\"$sample.trim.fastq\"\n", "\n", "# run cutadapt on each file\n", "/Users/laura/.local/bin/cutadapt $file -a A{8} -a G{8} -a AGATCGG -q 15 -m 20 \\\n", "-o ../../qc-processing/cutadapt/$trimmed_file\n", "done" ] }, { "cell_type": "code", "execution_count": 66, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 147\r\n" ] } ], "source": [ "# Check that the total # files\n", "! ls {workingdir}qc-processing/cutadapt/ | wc -l" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Assess reads after trimming " ] }, { "cell_type": "code", "execution_count": 67, "metadata": {}, "outputs": [], "source": [ "! mkdir {workingdir}qc-processing/fastqc/trimmed/" ] }, { "cell_type": "code", "execution_count": 68, "metadata": {}, "outputs": [], "source": [ "!{fastqc}fastqc \\\n", "{workingdir}qc-processing/cutadapt/*.fastq \\\n", "--outdir {workingdir}qc-processing/fastqc/trimmed/ \\\n", "--quiet" ] }, { "cell_type": "code", "execution_count": 69, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;30m[INFO ]\u001b[0m multiqc : This is MultiQC v1.9.dev0\n", "\u001b[1;30m[INFO ]\u001b[0m multiqc : Template : default\n", "\u001b[1;30m[INFO ]\u001b[0m multiqc : Searching : /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/fastqc/trimmed\n", "\u001b[1;30m[INFO ]\u001b[0m fastqc : Found 147 reports\n", "\u001b[1;30m[INFO ]\u001b[0m multiqc : Compressing plot data\n", "\u001b[1;30m[INFO ]\u001b[0m multiqc : Report : ../../qc-processing/fastqc/trimmed/multiqc_report_trimmed.html\n", "\u001b[1;30m[INFO ]\u001b[0m multiqc : Data : ../../qc-processing/fastqc/trimmed/multiqc_report_trimmed_data\n", 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              \n", "

              Download the raw data used to create the plots in this report below:

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              \n", " \n", "

              Note that additional data was saved in /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/fastqc/trimmed/multiqc_report_trimmed_data when this report was generated.

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              Choose Plots
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              If you use plots from MultiQC in a publication or presentation, please cite:

              \n", "
              \n", " MultiQC: Summarize analysis results for multiple tools and samples in a single report
              \n", " Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
              \n", " Bioinformatics (2016)
              \n", " doi: 10.1093/bioinformatics/btw354
              \n", " PMID: 27312411\n", "
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              Save Settings

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              You can save the toolbox settings for this report to the browser.

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              \n", "

              About MultiQC

              \n", "

              This report was generated using MultiQC, version 1.9.dev0

              \n", "

              You can see a YouTube video describing how to use MultiQC reports here:\n", " https://youtu.be/qPbIlO_KWN0

              \n", "

              For more information about MultiQC, including other videos and\n", " extensive documentation, please visit http://multiqc.info

              \n", "

              You can report bugs, suggest improvements and find the source code for MultiQC on GitHub:\n", " https://github.com/ewels/MultiQC

              \n", "

              MultiQC is published in Bioinformatics:

              \n", "
              \n", " MultiQC: Summarize analysis results for multiple tools and samples in a single report
              \n", " Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
              \n", " Bioinformatics (2016)
              \n", " doi: 10.1093/bioinformatics/btw354
              \n", " PMID: 27312411\n", "
              \n", "
              \n", "\n", "
              \n", " \n", "
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              \n", "\n", " \n", "\n", "

              \n", " \n", " \n", " \n", " \n", "

              \n", "\n", "\n", "\n", "

              \n", " A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.\n", "

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               Loading report..
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              \n", "

              Report generated on 2020-05-19, 20:40 based on data in:\n", " /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/fastqc/trimmed\n", " \n", "

              \n", "\n", "\n", "\n", "
              \n", "\n", "
              \n", " \n", " \n", " \n", " Welcome! Not sure where to start?  \n", " Watch a tutorial video\n", "   (6:06)\n", "
              \n", "\n", "\n", "\n", " \n", "\n", "\n", "
              \n", "

              General Statistics

              \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " Showing 147/147 rows and 4/5 columns.\n", " \n", "
              \n", "
              \n", " \n", "
              Sample Name% Dups% GCLength% FailedM Seqs
              137.trim
              45.2%
              38%
              83 bp
              9%
              6.2
              139.trim
              34.1%
              38%
              81 bp
              9%
              2.2
              140.trim
              45.9%
              36%
              82 bp
              9%
              5.7
              141.trim
              34.3%
              37%
              83 bp
              9%
              2.0
              156.trim
              55.4%
              35%
              84 bp
              18%
              5.1
              159.trim
              56.3%
              35%
              79 bp
              9%
              9.0
              161.trim
              44.3%
              37%
              82 bp
              9%
              6.8
              162.trim
              46.1%
              35%
              79 bp
              0%
              6.0
              168.trim
              44.4%
              36%
              83 bp
              0%
              3.0
              169.trim
              52.5%
              37%
              82 bp
              18%
              10.6
              171.trim
              50.4%
              36%
              81 bp
              9%
              8.0
              172.trim
              40.7%
              37%
              82 bp
              9%
              4.8
              181.trim
              52.4%
              34%
              80 bp
              9%
              2.7
              183.trim
              44.0%
              37%
              83 bp
              9%
              9.3
              184.trim
              38.8%
              38%
              82 bp
              9%
              3.3
              185.trim
              43.1%
              37%
              83 bp
              9%
              2.1
              291.trim
              40.9%
              38%
              81 bp
              9%
              7.0
              292.trim
              33.9%
              41%
              71 bp
              0%
              4.7
              293.trim
              36.0%
              41%
              74 bp
              0%
              4.9
              294.trim
              43.0%
              38%
              74 bp
              9%
              7.1
              295.trim
              37.9%
              39%
              80 bp
              0%
              9.3
              296.trim
              38.1%
              37%
              70 bp
              9%
              11.6
              298.trim
              33.2%
              38%
              73 bp
              9%
              6.3
              299.trim
              35.0%
              40%
              66 bp
              0%
              9.1
              301.trim
              36.8%
              38%
              70 bp
              0%
              7.1
              302.trim
              31.8%
              38%
              71 bp
              0%
              9.8
              303.trim
              35.3%
              38%
              78 bp
              9%
              7.6
              304.trim
              34.0%
              39%
              65 bp
              9%
              8.3
              305.trim
              38.0%
              38%
              77 bp
              9%
              6.0
              306.trim
              43.7%
              37%
              82 bp
              9%
              7.6
              307.trim
              43.2%
              37%
              85 bp
              9%
              7.3
              308.trim
              47.0%
              38%
              80 bp
              9%
              8.0
              309.trim
              36.6%
              38%
              78 bp
              9%
              8.4
              311.trim
              35.8%
              38%
              79 bp
              0%
              6.9
              312.trim
              37.9%
              38%
              79 bp
              0%
              6.9
              313.trim
              40.2%
              39%
              79 bp
              9%
              6.8
              314.trim
              53.5%
              39%
              88 bp
              18%
              5.3
              315.trim
              36.3%
              39%
              68 bp
              0%
              8.5
              316.trim
              37.0%
              39%
              76 bp
              0%
              9.5
              317.trim
              32.1%
              39%
              79 bp
              0%
              5.6
              318.trim
              37.6%
              38%
              78 bp
              9%
              6.2
              319.trim
              56.9%
              37%
              83 bp
              18%
              7.8
              321.trim
              31.7%
              38%
              79 bp
              9%
              6.0
              322.trim
              39.1%
              38%
              78 bp
              9%
              7.3
              323.trim
              34.0%
              39%
              69 bp
              0%
              9.5
              324.trim
              41.7%
              38%
              73 bp
              0%
              8.3
              325.trim
              31.9%
              38%
              78 bp
              9%
              7.6
              326.trim
              40.4%
              37%
              79 bp
              9%
              8.9
              327.trim
              36.7%
              38%
              81 bp
              9%
              5.8
              328.trim
              31.3%
              40%
              65 bp
              0%
              12.0
              329.trim
              42.9%
              38%
              86 bp
              9%
              8.3
              331.trim
              57.7%
              41%
              79 bp
              18%
              6.5
              332.trim
              47.0%
              37%
              78 bp
              9%
              5.4
              333.trim
              36.0%
              38%
              81 bp
              9%
              5.2
              334.trim
              54.6%
              38%
              86 bp
              18%
              5.7
              335.trim
              35.7%
              38%
              78 bp
              9%
              5.1
              336.trim
              53.4%
              37%
              83 bp
              18%
              7.6
              337.trim
              44.2%
              37%
              76 bp
              9%
              10.5
              338.trim
              39.9%
              38%
              81 bp
              9%
              6.3
              339.trim
              43.2%
              38%
              75 bp
              9%
              7.2
              34.trim
              75.8%
              39%
              83 bp
              18%
              6.7
              341.trim
              35.8%
              39%
              75 bp
              9%
              5.5
              342.trim
              40.8%
              38%
              76 bp
              9%
              8.5
              343.trim
              29.3%
              39%
              67 bp
              9%
              7.4
              344.trim
              49.3%
              41%
              62 bp
              9%
              10.0
              345.trim
              28.2%
              38%
              67 bp
              0%
              5.5
              346.trim
              32.5%
              39%
              75 bp
              0%
              5.7
              347.trim
              41.0%
              37%
              87 bp
              0%
              6.5
              348.trim
              41.8%
              38%
              80 bp
              9%
              7.1
              349.trim
              33.0%
              40%
              68 bp
              0%
              5.5
              35.trim
              80.2%
              46%
              67 bp
              27%
              2.2
              37.trim
              84.9%
              40%
              81 bp
              27%
              7.4
              39.trim
              45.8%
              38%
              80 bp
              9%
              5.8
              401.trim
              65.4%
              40%
              90 bp
              18%
              4.1
              402.trim
              45.9%
              39%
              77 bp
              9%
              5.7
              403.trim
              37.8%
              38%
              81 bp
              9%
              6.6
              404.trim
              53.9%
              37%
              84 bp
              18%
              6.9
              41.trim
              72.6%
              39%
              88 bp
              18%
              8.2
              411.trim
              48.8%
              38%
              82 bp
              9%
              6.5
              412.trim
              83.8%
              38%
              84 bp
              36%
              6.7
              413.trim
              48.5%
              37%
              81 bp
              9%
              6.3
              414.trim
              41.1%
              41%
              54 bp
              9%
              4.9
              421.trim
              40.1%
              39%
              83 bp
              9%
              7.4
              43.trim
              44.1%
              39%
              77 bp
              9%
              7.1
              431b.trim
              54.3%
              40%
              84 bp
              18%
              6.2
              432.trim
              93.3%
              44%
              91 bp
              27%
              5.9
              434.trim
              56.1%
              35%
              82 bp
              9%
              7.0
              44.trim
              68.3%
              50%
              57 bp
              36%
              1.0
              441.trim
              92.9%
              39%
              73 bp
              36%
              8.1
              442b.trim
              60.0%
              38%
              76 bp
              9%
              5.0
              443.trim
              53.5%
              36%
              80 bp
              9%
              6.0
              444.trim
              54.7%
              33%
              82 bp
              9%
              7.9
              445.trim
              39.5%
              38%
              83 bp
              9%
              6.5
              45.trim
              69.2%
              39%
              76 bp
              18%
              7.0
              451.trim
              47.0%
              37%
              78 bp
              0%
              8.8
              452b.trim
              51.1%
              39%
              83 bp
              18%
              5.4
              453.trim
              39.5%
              38%
              78 bp
              9%
              5.2
              46.trim
              75.8%
              38%
              83 bp
              18%
              7.4
              461b.trim
              45.9%
              36%
              84 bp
              9%
              4.5
              462b.trim
              58.7%
              35%
              72 bp
              9%
              9.6
              47.trim
              49.5%
              38%
              86 bp
              9%
              5.4
              471b.trim
              46.1%
              37%
              83 bp
              9%
              6.2
              472b.trim
              46.3%
              37%
              77 bp
              9%
              6.1
              473.trim
              45.9%
              37%
              85 bp
              9%
              6.5
              474.trim
              49.4%
              36%
              85 bp
              0%
              8.4
              475.trim
              47.6%
              36%
              84 bp
              0%
              7.3
              476.trim
              48.6%
              33%
              82 bp
              0%
              4.7
              477.trim
              43.8%
              39%
              86 bp
              9%
              6.5
              481.trim
              50.3%
              37%
              74 bp
              18%
              7.2
              482.trim
              51.8%
              33%
              81 bp
              9%
              5.4
              483.trim
              55.0%
              39%
              65 bp
              18%
              5.7
              484.trim
              46.2%
              40%
              81 bp
              9%
              5.1
              485.trim
              42.2%
              38%
              85 bp
              9%
              7.0
              487.trim
              50.4%
              38%
              79 bp
              18%
              7.2
              488.trim
              51.1%
              33%
              82 bp
              9%
              6.9
              489.trim
              41.5%
              40%
              83 bp
              9%
              7.3
              490.trim
              40.2%
              38%
              80 bp
              9%
              5.8
              491.trim
              54.2%
              34%
              82 bp
              9%
              6.4
              492.trim
              53.6%
              35%
              76 bp
              9%
              7.8
              506.trim
              60.9%
              33%
              74 bp
              9%
              5.7
              513.trim
              40.4%
              38%
              73 bp
              9%
              6.3
              521.trim
              74.0%
              37%
              76 bp
              18%
              11.5
              522.trim
              56.0%
              36%
              79 bp
              18%
              5.8
              523.trim
              58.7%
              38%
              80 bp
              18%
              6.9
              524.trim
              48.7%
              35%
              83 bp
              0%
              6.1
              525.trim
              35.9%
              39%
              81 bp
              9%
              5.3
              526.trim
              40.9%
              38%
              85 bp
              9%
              5.2
              527.trim
              50.5%
              37%
              75 bp
              18%
              7.8
              528.trim
              44.3%
              36%
              77 bp
              0%
              8.6
              529.trim
              58.0%
              33%
              83 bp
              9%
              6.9
              531.trim
              39.6%
              39%
              79 bp
              9%
              4.9
              532.trim
              47.5%
              36%
              85 bp
              0%
              5.1
              533.trim
              50.1%
              39%
              88 bp
              18%
              5.2
              541.trim
              55.5%
              37%
              80 bp
              18%
              7.0
              542.trim
              65.1%
              36%
              81 bp
              18%
              6.2
              543.trim
              39.1%
              35%
              78 bp
              0%
              3.9
              551.trim
              47.1%
              35%
              83 bp
              0%
              7.5
              552b.trim
              49.5%
              37%
              83 bp
              9%
              4.2
              553.trim
              36.7%
              38%
              85 bp
              9%
              4.8
              554.trim
              40.8%
              39%
              82 bp
              9%
              8.0
              561.trim
              86.3%
              35%
              89 bp
              27%
              6.3
              562.trim
              77.2%
              40%
              77 bp
              18%
              15.0
              563.trim
              64.7%
              35%
              85 bp
              27%
              8.3
              564.trim
              39.6%
              38%
              85 bp
              9%
              4.5
              565.trim
              76.5%
              42%
              85 bp
              18%
              5.5
              571.trim
              82.3%
              46%
              66 bp
              18%
              0.7
              Undetermined.trim
              71.5%
              41%
              91 bp
              18%
              13.3
              \n", " \n", "
              \n", "
              \n", "
              \n", "
              \n", " \n", "

              General Statistics: Columns

              \n", "
              \n", "
              \n", "

              Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

              \n", "

              \n", " \n", " \n", "

              \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
              SortVisibleGroupColumnDescriptionIDScale
              ||\n", " \n", " FastQC% Dups% Duplicate Readspercent_duplicatesNone
              ||\n", " \n", " FastQC% GCAverage % GC Contentpercent_gcNone
              ||\n", " \n", " FastQCLengthAverage Sequence Length (bp)avg_sequence_lengthNone
              ||\n", " \n", " FastQC% FailedPercentage of modules failed in FastQC report (includes those not plotted here)percent_failsNone
              ||\n", " \n", " FastQCM SeqsTotal Sequences (millions)total_sequencesread_count
              \n", "
              \n", "
              \n", "
              \n", "
              \n", "\n", "\n", " \n", "\n", "\n", " \n", "
              \n", "

              FastQC

              \n", "

              FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

              \n", " \n", " \n", " \n", " \n", "
              \n", " \n", "

              \n", " Sequence Counts\n", " \n", " \n", " \n", "

              \n", " \n", "

              Sequence counts for each sample. Duplicate read counts are an estimate only.

              \n", " \n", " \n", "
              \n", "

              This plot show the total number of reads, broken down into unique and duplicate\n", "if possible (only more recent versions of FastQC give duplicate info).

              \n", "

              You can read more about duplicate calculation in the\n", "FastQC documentation.\n", "A small part has been copied here for convenience:

              \n", "

              Only sequences which first appear in the first 100,000 sequences\n", "in each file are analysed. This should be enough to get a good impression\n", "for the duplication levels in the whole file. Each sequence is tracked to\n", "the end of the file to give a representative count of the overall duplication level.

              \n", "

              The duplication detection requires an exact sequence match over the whole length of\n", "the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

              \n", "
              \n", " \n", "

              Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

              \n", " \n", " \n", "
              \n", " \n", "
              \n", "
              \n", " \n", " \n", " \n", " \n", "
              \n", " \n", "

              \n", " Sequence Quality Histograms\n", " \n", " \n", " \n", "

              \n", " \n", "

              The mean quality value across each base position in the read.

              \n", " \n", " \n", "
              \n", "

              To enable multiple samples to be plotted on the same graph, only the mean quality\n", "scores are plotted (unlike the box plots seen in FastQC reports).

              \n", "

              Taken from the FastQC help:

              \n", "

              The y-axis on the graph shows the quality scores. The higher the score, the better\n", "the base call. The background of the graph divides the y axis into very good quality\n", "calls (green), calls of reasonable quality (orange), and calls of poor quality (red).\n", "The quality of calls on most platforms will degrade as the run progresses, so it is\n", "common to see base calls falling into the orange area towards the end of a read.

              \n", "
              \n", " \n", "

              Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

              \n", " \n", "
              \n", "
              \n", " \n", " \n", " \n", " \n", "
              \n", " \n", "

              \n", " Per Sequence Quality Scores\n", " \n", " \n", " \n", "

              \n", " \n", "

              The number of reads with average quality scores. Shows if a subset of reads has poor quality.

              \n", " \n", " \n", "
              \n", "

              From the FastQC help:

              \n", "

              The per sequence quality score report allows you to see if a subset of your\n", "sequences have universally low quality values. It is often the case that a\n", "subset of sequences will have universally poor quality, however these should\n", "represent only a small percentage of the total sequences.

              \n", "
              \n", " \n", "

              Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

              \n", " \n", "
              \n", "
              \n", " \n", " \n", " \n", " \n", "
              \n", " \n", "

              \n", " Per Base Sequence Content\n", " \n", " \n", " \n", "

              \n", " \n", "

              The proportion of each base position for which each of the four normal DNA bases has been called.

              \n", " \n", " \n", "
              \n", "

              To enable multiple samples to be shown in a single plot, the base composition data\n", "is shown as a heatmap. The colours represent the balance between the four bases:\n", "an even distribution should give an even muddy brown colour. Hover over the plot\n", "to see the percentage of the four bases under the cursor.

              \n", "

              To see the data as a line plot, as in the original FastQC graph, click on a sample track.

              \n", "

              From the FastQC help:

              \n", "

              Per Base Sequence Content plots out the proportion of each base position in a\n", "file for which each of the four normal DNA bases has been called.

              \n", "

              In a random library you would expect that there would be little to no difference\n", "between the different bases of a sequence run, so the lines in this plot should\n", "run parallel with each other. The relative amount of each base should reflect\n", "the overall amount of these bases in your genome, but in any case they should\n", "not be hugely imbalanced from each other.

              \n", "

              It's worth noting that some types of library will always produce biased sequence\n", "composition, normally at the start of the read. Libraries produced by priming\n", "using random hexamers (including nearly all RNA-Seq libraries) and those which\n", "were fragmented using transposases inherit an intrinsic bias in the positions\n", "at which reads start. This bias does not concern an absolute sequence, but instead\n", "provides enrichement of a number of different K-mers at the 5' end of the reads.\n", "Whilst this is a true technical bias, it isn't something which can be corrected\n", "by trimming and in most cases doesn't seem to adversely affect the downstream\n", "analysis.

              \n", "
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              \n", " \n", " Click a sample row to see a line plot for that dataset.\n", "
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              Rollover for sample name
              \n", " \n", "
              \n", " Position: -\n", "
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              \n", " Per Sequence GC Content\n", " \n", " \n", " \n", "

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              The average GC content of reads. Normal random library typically have a\n", " roughly normal distribution of GC content.

              \n", " \n", " \n", "
              \n", "

              From the FastQC help:

              \n", "

              This module measures the GC content across the whole length of each sequence\n", "in a file and compares it to a modelled normal distribution of GC content.

              \n", "

              In a normal random library you would expect to see a roughly normal distribution\n", "of GC content where the central peak corresponds to the overall GC content of\n", "the underlying genome. Since we don't know the the GC content of the genome the\n", "modal GC content is calculated from the observed data and used to build a\n", "reference distribution.

              \n", "

              An unusually shaped distribution could indicate a contaminated library or\n", "some other kinds of biased subset. A normal distribution which is shifted\n", "indicates some systematic bias which is independent of base position. If there\n", "is a systematic bias which creates a shifted normal distribution then this won't\n", "be flagged as an error by the module since it doesn't know what your genome's\n", "GC content should be.

              \n", "
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              Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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              \n", " Per Base N Content\n", " \n", " \n", " \n", "

              \n", " \n", "

              The percentage of base calls at each position for which an N was called.

              \n", " \n", " \n", "
              \n", "

              From the FastQC help:

              \n", "

              If a sequencer is unable to make a base call with sufficient confidence then it will\n", "normally substitute an N rather than a conventional base call. This graph shows the\n", "percentage of base calls at each position for which an N was called.

              \n", "

              It's not unusual to see a very low proportion of Ns appearing in a sequence, especially\n", "nearer the end of a sequence. However, if this proportion rises above a few percent\n", "it suggests that the analysis pipeline was unable to interpret the data well enough to\n", "make valid base calls.

              \n", "
              \n", " \n", "

              Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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              \n", " Sequence Length Distribution\n", " \n", "

              \n", " \n", "

              The distribution of fragment sizes (read lengths) found.\n", " See the FastQC help

              \n", " \n", " \n", "

              Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

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              \n", " Sequence Duplication Levels\n", " \n", " \n", " \n", "

              \n", " \n", "

              The relative level of duplication found for every sequence.

              \n", " \n", " \n", "
              \n", "

              From the FastQC Help:

              \n", "

              In a diverse library most sequences will occur only once in the final set.\n", "A low level of duplication may indicate a very high level of coverage of the\n", "target sequence, but a high level of duplication is more likely to indicate\n", "some kind of enrichment bias (eg PCR over amplification). This graph shows\n", "the degree of duplication for every sequence in a library: the relative\n", "number of sequences with different degrees of duplication.

              \n", "

              Only sequences which first appear in the first 100,000 sequences\n", "in each file are analysed. This should be enough to get a good impression\n", "for the duplication levels in the whole file. Each sequence is tracked to\n", "the end of the file to give a representative count of the overall duplication level.

              \n", "

              The duplication detection requires an exact sequence match over the whole length of\n", "the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

              \n", "

              In a properly diverse library most sequences should fall into the far left of the\n", "plot in both the red and blue lines. A general level of enrichment, indicating broad\n", "oversequencing in the library will tend to flatten the lines, lowering the low end\n", "and generally raising other categories. More specific enrichments of subsets, or\n", "the presence of low complexity contaminants will tend to produce spikes towards the\n", "right of the plot.

              \n", "
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              Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

              \n", " \n", "
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              \n", " \n", "

              \n", " Overrepresented sequences\n", " \n", " \n", " \n", "

              \n", " \n", "

              The total amount of overrepresented sequences found in each library.

              \n", " \n", " \n", "
              \n", "

              FastQC calculates and lists overrepresented sequences in FastQ files. It would not be\n", "possible to show this for all samples in a MultiQC report, so instead this plot shows\n", "the number of sequences categorized as over represented.

              \n", "

              Sometimes, a single sequence may account for a large number of reads in a dataset.\n", "To show this, the bars are split into two: the first shows the overrepresented reads\n", "that come from the single most common sequence. The second shows the total count\n", "from all remaining overrepresented sequences.

              \n", "

              From the FastQC Help:

              \n", "

              A normal high-throughput library will contain a diverse set of sequences, with no\n", "individual sequence making up a tiny fraction of the whole. Finding that a single\n", "sequence is very overrepresented in the set either means that it is highly biologically\n", "significant, or indicates that the library is contaminated, or not as diverse as you expected.

              \n", "

              FastQC lists all of the sequences which make up more than 0.1% of the total.\n", "To conserve memory only sequences which appear in the first 100,000 sequences are tracked\n", "to the end of the file. It is therefore possible that a sequence which is overrepresented\n", "but doesn't appear at the start of the file for some reason could be missed by this module.

              \n", "
              \n", " \n", "

              Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

              \n", " \n", "
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              \n", " Adapter Content\n", " \n", " \n", " \n", "

              \n", " \n", "

              The cumulative percentage count of the proportion of your\n", " library which has seen each of the adapter sequences at each position.

              \n", " \n", " \n", "
              \n", "

              Note that only samples with ≥ 0.1% adapter contamination are shown.

              \n", "

              There may be several lines per sample, as one is shown for each adapter\n", "detected in the file.

              \n", "

              From the FastQC Help:

              \n", "

              The plot shows a cumulative percentage count of the proportion\n", "of your library which has seen each of the adapter sequences at each position.\n", "Once a sequence has been seen in a read it is counted as being present\n", "right through to the end of the read so the percentages you see will only\n", "increase as the read length goes on.

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              \n", " Status Checks\n", " \n", " \n", " \n", "

              \n", " \n", "

              Status for each FastQC section showing whether results seem entirely normal (green),\n", "slightly abnormal (orange) or very unusual (red).

              \n", " \n", " \n", "
              \n", "

              FastQC assigns a status for each section of the report.\n", "These give a quick evaluation of whether the results of the analysis seem\n", "entirely normal (green), slightly abnormal (orange) or very unusual (red).

              \n", "

              It is important to stress that although the analysis results appear to give a pass/fail result,\n", "these evaluations must be taken in the context of what you expect from your library.\n", "A 'normal' sample as far as FastQC is concerned is random and diverse.\n", "Some experiments may be expected to produce libraries which are biased in particular ways.\n", "You should treat the summary evaluations therefore as pointers to where you should concentrate\n", "your attention and understand why your library may not look random and diverse.

              \n", "

              Specific guidance on how to interpret the output of each module can be found in the relevant\n", "report section, or in the FastQC help.

              \n", "

              In this heatmap, we summarise all of these into a single heatmap for a quick overview.\n", "Note that not all FastQC sections have plots in MultiQC reports, but all status checks\n", "are shown in this heatmap.

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              \n", " \n", " \n", " \n", " \n", " MultiQC v1.9.dev0\n", " \n", " - Written by Phil Ewels,\n", " available on GitHub.\n", "

              \n", "

              \n", " This report uses HighCharts,\n", " jQuery,\n", " jQuery UI,\n", " Bootstrap,\n", " FileSaver.js and\n", " clipboard.js.\n", "

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              Plot Table Data

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              \n", " Please select two table columns.\n", "
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              Regex Help

              \n", "
              \n", "
              \n", "

              Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.

              \n", "
              \n", "
              \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
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              \n",
       "samp_1\n",
       "samp_1_edited\n",
       "samp_2\n",
       "samp_2_edited\n",
       "samp_3\n",
       "samp_3_edited\n",
       "prepended_samp_1\n",
       "tmp_samp_1_edited\n",
       "tmpp_samp_1_edited\n",
       "tmppp_samp_1_edited\n",
       "#samp_1_edited.tmp\n",
       "samp_11\n",
       "samp_11111\n",
       "
              \n", "

              See regex101.com for a more heavy duty testing suite.

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              \n", "\n", "\n", "\n" ], "text/plain": [ "" ] }, "execution_count": 70, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import IPython\n", "IPython.display.HTML(filename='/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/fastqc/trimmed/multiqc_report_trimmed.html')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Count total no. reads before and after trimming " ] }, { "cell_type": "code", "execution_count": 96, "metadata": {}, "outputs": [], "source": [ "# Before trimming \n", "! wc -l {workingdir}raw-data/Batch1_69plex_lane1_done/*.fastq \\\n", "{workingdir}raw-data/Batch2_77plex_lane2_done/*.fastq > {workingdir}raw-data/read-count-untrimmed.txt" ] }, { "cell_type": "code", "execution_count": 97, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 25618784 /Volumes/Bumblebee/O.lurida_QuantSeq-2020/raw-data/Batch1_69plex_lane1_done/137_S63_L001_R1_001.fastq\r\n", " 9396844 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/Volumes/Bumblebee/O.lurida_QuantSeq-2020/raw-data/Batch2_77plex_lane2_done/565_S67_L002_R1_001.fastq\r\n", " 5607296 /Volumes/Bumblebee/O.lurida_QuantSeq-2020/raw-data/Batch2_77plex_lane2_done/571_S76_L002_R1_001.fastq\r\n", " 54557320 /Volumes/Bumblebee/O.lurida_QuantSeq-2020/raw-data/Batch2_77plex_lane2_done/Undetermined_S0_L002_R1_001.fastq\r\n", " 4102334876 total\r\n" ] } ], "source": [ "! cat {workingdir}raw-data/read-count-untrimmed.txt" ] }, { "cell_type": "code", "execution_count": 98, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 24995332 /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/cutadapt/137.trim.fastq\r\n", " 8948620 /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/cutadapt/139.trim.fastq\r\n", " 22791972 /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/cutadapt/140.trim.fastq\r\n", " 7898348 /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/cutadapt/141.trim.fastq\r\n", " 20483872 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/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/cutadapt/565.trim.fastq\r\n", " 2921428 /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/cutadapt/571.trim.fastq\r\n", " 53156568 /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/cutadapt/Undetermined.trim.fastq\r\n", " 3915145660 total\r\n" ] } ], "source": [ "# After trimming\n", "! wc -l {workingdir}qc-processing/cutadapt/*.fastq > {workingdir}qc-processing/cutadapt/read-count-trimmed.txt\n", "! cat {workingdir}qc-processing/cutadapt/read-count-trimmed.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 95.44% reads remain after trimming and filtering \n", "\n", "- 3,915,145,660 reads after trimming\n", "- 4,102,334,876 reads before " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# 4. Align reads" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Download O. lurida genome \n", "(If needed)" ] }, { "cell_type": "code", "execution_count": 88, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " % Total % Received % Xferd Average Speed Time Time Time Current\n", " Dload Upload Total Spent Left Speed\n", "100 1090M 100 1090M 0 0 1960k 0 0:09:29 0:09:29 --:--:-- 2198k21k 0 0:08:46 0:00:17 0:08:29 2021k 0 0 2183k 0 0:08:31 0:01:11 0:07:20 2193k 0 2183k 0 0:08:31 0:01:14 0:07:17 2202k9 0:07:11 2212k1939k 0 0:09:35 0:01:45 0:07:50 1024k 0 1765k 0 0:10:32 0:02:00 0:08:32 497k 0 0 1752k 0 0:10:36 0:03:40 0:06:56 2190k 0 1748k 0 0:10:38 0:03:50 0:06:48 1105k 1855k 0 0:10:01 0:05:01 0:05:00 2215k 0 0 1861k 0 0:09:59 0:05:07 0:04:52 2191k 0 1881k 0 0:09:53 0:05:25 0:04:28 2222k931k 0 0:09:38 0:07:31 0:02:07 2169k 1929k 0 0:09:38 0:08:03 0:01:35 2179k 0 1933k 0 0:09:37 0:08:11 0:01:26 2200k 0 0:09:35 0:08:42 0:00:53 2212k\n" ] } ], "source": [ "! curl http://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081.fa > {workingdir}/references/Olurida_v081.fa" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "MD5 (/Volumes/Bumblebee/QuantSeq-04-21-2020/references/Olurida_v081.fa) = 3ac56372bd62038f264d27eef0883bd3\r\n" ] } ], "source": [ "# MD5 should = 3ac56372bd62038f264d27eef0883bd3\n", "! md5 {workingdir}references/Olurida_v081.fa" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Align reads using Bowtie2\n", "\n", "See the [Bowtie2 manual](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml) for details\n", "\n", "Updated Bowtie2 using homebrew\n", "\n", "`brew upgrade bowtie2` \n", "\n", "Version before update: version 2.3.4.3 \n", "Version after update: version 2.4.1" ] }, { "cell_type": "code", "execution_count": 74, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/usr/local/bin/../Cellar/bowtie2/2.4.1/bin/bowtie2-align-s version 2.4.1\r\n", "64-bit\r\n", "Built on \r\n", "Wed Mar 4 02:33:44 UTC 2020\r\n", "Compiler: InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin\r\n", "Options: -O3 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\r\n", "Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}\r\n" ] } ], "source": [ "# make sure bowtie2 is in path and working\n", "! bowtie2 --version" ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [], "source": [ "! mkdir {workingdir}qc-processing/bowtie/" ] }, { "cell_type": "code", "execution_count": 75, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie\n" ] } ], "source": [ "cd {workingdir}qc-processing/bowtie/" ] }, { "cell_type": "code", "execution_count": 262, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Settings:\n", " Output files: \"Olurida_v081.fa.*.bt2\"\n", " Line rate: 6 (line is 64 bytes)\n", " Lines per side: 1 (side is 64 bytes)\n", " Offset rate: 4 (one in 16)\n", " FTable chars: 10\n", " Strings: unpacked\n", " Max bucket size: default\n", " Max bucket size, sqrt multiplier: default\n", " Max bucket size, len divisor: 4\n", " Difference-cover sample period: 1024\n", " Endianness: little\n", " Actual local endianness: little\n", " Sanity checking: disabled\n", " Assertions: disabled\n", " Random seed: 0\n", " Sizeofs: void*:8, int:4, long:8, size_t:8\n", "Input files DNA, FASTA:\n", " ../../references/Olurida_v081.fa\n", "Reading reference sizes\n", " Time reading reference sizes: 00:00:11\n", "Calculating joined length\n", "Writing header\n", "Reserving space for joined string\n", "Joining reference sequences\n", " Time to join reference sequences: 00:00:07\n", "bmax according to bmaxDivN setting: 269313774\n", "Using parameters --bmax 201985331 --dcv 1024\n", " Doing ahead-of-time memory usage test\n", " Passed! Constructing with these parameters: --bmax 201985331 --dcv 1024\n", "Constructing suffix-array element generator\n", "Building DifferenceCoverSample\n", " Building sPrime\n", " Building sPrimeOrder\n", " V-Sorting samples\n", " V-Sorting samples time: 00:00:24\n", " Allocating rank array\n", " Ranking v-sort output\n", " Ranking v-sort output time: 00:00:07\n", " Invoking Larsson-Sadakane on ranks\n", " Invoking Larsson-Sadakane on ranks time: 00:00:10\n", " Sanity-checking and returning\n", "Building samples\n", "Reserving space for 12 sample suffixes\n", "Generating random suffixes\n", "QSorting 12 sample offsets, eliminating duplicates\n", "QSorting sample offsets, eliminating duplicates time: 00:00:00\n", "Multikey QSorting 12 samples\n", " (Using difference cover)\n", " Multikey QSorting samples time: 00:00:00\n", "Calculating bucket sizes\n", "Splitting and merging\n", " Splitting and merging time: 00:00:00\n", "Avg bucket size: 1.07726e+09 (target: 201985330)\n", "Converting suffix-array elements to index image\n", "Allocating ftab, absorbFtab\n", "Entering Ebwt loop\n", "Getting block 1 of 1\n", " No samples; assembling all-inclusive block\n", " Sorting block of length 1077255099 for bucket 1\n", " (Using difference cover)\n", " Sorting block time: 00:12:51\n", "Returning block of 1077255100 for bucket 1\n", "Exited Ebwt loop\n", "fchr[A]: 0\n", "fchr[C]: 341519526\n", "fchr[G]: 538577822\n", "fchr[T]: 735626959\n", "fchr[$]: 1077255099\n", "Exiting Ebwt::buildToDisk()\n", "Returning from initFromVector\n", "Wrote 371984998 bytes to primary EBWT file: Olurida_v081.fa.1.bt2\n", "Wrote 269313780 bytes to secondary EBWT file: Olurida_v081.fa.2.bt2\n", "Re-opening _in1 and _in2 as input streams\n", "Returning from Ebwt constructor\n", "Headers:\n", " len: 1077255099\n", " bwtLen: 1077255100\n", " sz: 269313775\n", " bwtSz: 269313775\n", " lineRate: 6\n", " offRate: 4\n", " offMask: 0xfffffff0\n", " ftabChars: 10\n", " eftabLen: 20\n", " eftabSz: 80\n", " ftabLen: 1048577\n", " ftabSz: 4194308\n", " offsLen: 67328444\n", " offsSz: 269313776\n", " lineSz: 64\n", " sideSz: 64\n", " sideBwtSz: 48\n", " sideBwtLen: 192\n", " numSides: 5610704\n", " numLines: 5610704\n", " ebwtTotLen: 359085056\n", " ebwtTotSz: 359085056\n", " color: 0\n", " reverse: 0\n", "Total time for call to driver() for forward index: 00:17:15\n", "Reading reference sizes\n", " Time reading reference sizes: 00:00:09\n", "Calculating joined length\n", "Writing header\n", "Reserving space for joined string\n", "Joining reference sequences\n", " Time to join reference sequences: 00:00:07\n", " Time to reverse reference sequence: 00:00:01\n", "bmax according to bmaxDivN setting: 269313774\n", "Using parameters --bmax 201985331 --dcv 1024\n", " Doing ahead-of-time memory usage test\n", " Passed! Constructing with these parameters: --bmax 201985331 --dcv 1024\n", "Constructing suffix-array element generator\n", "Building DifferenceCoverSample\n", " Building sPrime\n", " Building sPrimeOrder\n", " V-Sorting samples\n", " V-Sorting samples time: 00:00:24\n", " Allocating rank array\n", " Ranking v-sort output\n", " Ranking v-sort output time: 00:00:08\n", " Invoking Larsson-Sadakane on ranks\n", " Invoking Larsson-Sadakane on ranks time: 00:00:11\n", " Sanity-checking and returning\n", "Building samples\n", "Reserving space for 12 sample suffixes\n", "Generating random suffixes\n", "QSorting 12 sample offsets, eliminating duplicates\n", "QSorting sample offsets, eliminating duplicates time: 00:00:00\n", "Multikey QSorting 12 samples\n", " (Using difference cover)\n", " Multikey QSorting samples time: 00:00:00\n", "Calculating bucket sizes\n", "Splitting and merging\n", " Splitting and merging time: 00:00:00\n", "Avg bucket size: 1.07726e+09 (target: 201985330)\n", "Converting suffix-array elements to index image\n", "Allocating ftab, absorbFtab\n", "Entering Ebwt loop\n", "Getting block 1 of 1\n", " No samples; assembling all-inclusive block\n", " Sorting block of length 1077255099 for bucket 1\n", " (Using difference cover)\n", " Sorting block time: 00:14:01\n", "Returning block of 1077255100 for bucket 1\n", "Exited Ebwt loop\n", "fchr[A]: 0\n", "fchr[C]: 341519526\n", "fchr[G]: 538577822\n", "fchr[T]: 735626959\n", "fchr[$]: 1077255099\n", "Exiting Ebwt::buildToDisk()\n", "Returning from initFromVector\n", "Wrote 371984998 bytes to primary EBWT file: Olurida_v081.fa.rev.1.bt2\n", "Wrote 269313780 bytes to secondary EBWT file: Olurida_v081.fa.rev.2.bt2\n", "Re-opening _in1 and _in2 as input streams\n", "Returning from Ebwt constructor\n", "Headers:\n", " len: 1077255099\n", " bwtLen: 1077255100\n", " sz: 269313775\n", " bwtSz: 269313775\n", " lineRate: 6\n", " offRate: 4\n", " offMask: 0xfffffff0\n", " ftabChars: 10\n", " eftabLen: 20\n", " eftabSz: 80\n", " ftabLen: 1048577\n", " ftabSz: 4194308\n", " offsLen: 67328444\n", " offsSz: 269313776\n", " lineSz: 64\n", " sideSz: 64\n", " sideBwtSz: 48\n", " sideBwtLen: 192\n", " numSides: 5610704\n", " numLines: 5610704\n", " ebwtTotLen: 359085056\n", " ebwtTotSz: 359085056\n", " color: 0\n", " reverse: 1\n", "Total time for backward call to driver() for mirror index: 00:18:21\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Building a SMALL index\n" ] } ], "source": [ "### creating bowtie2 index for Oly genome v081:\n", "! bowtie2-build \\\n", "{workingdir}references/Olurida_v081.fa \\\n", "Olurida_v081.fa" ] }, { "cell_type": "code", "execution_count": 78, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[31mOlurida_v081.fa.1.bt2\u001b[m\u001b[m* \u001b[31mOlurida_v081.fa.rev.1.bt2\u001b[m\u001b[m*\r\n", "\u001b[31mOlurida_v081.fa.2.bt2\u001b[m\u001b[m* \u001b[31mOlurida_v081.fa.rev.2.bt2\u001b[m\u001b[m*\r\n", "\u001b[31mOlurida_v081.fa.3.bt2\u001b[m\u001b[m* \u001b[30m\u001b[43mmapped\u001b[m\u001b[m/\r\n", "\u001b[31mOlurida_v081.fa.4.bt2\u001b[m\u001b[m*\r\n" ] } ], "source": [ "ls {workingdir}qc-processing/bowtie/" ] }, { "cell_type": "code", "execution_count": 77, "metadata": {}, "outputs": [], "source": [ "! mkdir {workingdir}qc-processing/bowtie/mapped/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Candidate options from the Bowtie2 manual \n", "\n", "### Local alignment \n", "\n", "When the `–-local` option is specified, Bowtie 2 performs local read alignment. In this mode, Bowtie 2 might “trim” or “clip” some read characters from one or both ends of the alignment if doing so maximizes the alignment score.\n", "\n", "The following is a “local” alignment because some of the characters at the ends of the read do not participate. In this case, 4 characters are omitted (or “soft trimmed” or “soft clipped”) from the beginning and 3 characters are omitted from the end. This sort of alignment can be produced by Bowtie 2 only in local mode.\n", "\n", " Read: ACGGTTGCGTTAATCCGCCACG \n", " Reference: TAACTTGCGTTAAATCCGCCTGG \n", "\n", " Alignment: \n", " Read: ACGGTTGCGTTAA-TCCGCCACG\n", " ||||||||| ||||||\n", " Reference: TAACTTGCGTTAAATCCGCCTGG\n", "\n", "### Distinct alignments map a read to different places \n", "\n", "Two alignments for the same individual read are “distinct” if they map the same read to different places. Default mode: search for multiple alignments, report the best one. **In -k mode, Bowtie 2 searches for up to N distinct, valid alignments for each read**, where N equals the integer specified with the -k parameter. That is, if -k 2 is specified, Bowtie 2 will search for at most 2 distinct alignments. It reports all alignments found, in descending order by alignment score. \n", "\n", "Bowtie 2 does not “find” alignments in any specific order, so for reads that have more than N distinct, valid alignments, Bowtie 2 does not guarantee that the N alignments reported are the best possible in terms of alignment score. Still, this mode can be effective and fast in situations where the user cares more about whether a read aligns (or aligns a certain number of times) than where exactly it originated.\n", "\n", "### Using multiple cores \n", "\n", "If your computer has multiple processors/cores, use `-p/--threads N`\n", "\n", "The `-p/--threads` option causes Bowtie 2 to launch a specified number of parallel search threads. Each thread runs on a different processor/core and all threads find alignments in parallel, increasing alignment throughput by approximately a multiple of the number of threads (though in practice, speedup is somewhat worse than linear).\n", "\n", "_note: my computer is a quad-core, so I can use up to 8 threads_ \n", "\n", "`-x`: The basename of the index for the reference genome. \n", "`-U`: Comma-separated list of files containing unpaired reads to be aligned, e.g. lane1.fq,lane2.fq,lane3.fq,lane4.fq. \n", "`-S`: File to write SAM alignments to. By default, alignments are written to the “standard out” or “stdout” filehandle (i.e. the console). \n", "`-q`: Reads are FASTQ files. FASTQ files usually have extension .fq or .fastq. FASTQ is the default format. \n", "`--trim5`: Trim N bases from 5’ (left) end of each read before alignment (default: 0). \n", "`--trim3`: Trim N bases from 3’ (right) end of each read before alignment (default: 0). \n", " \n", "### Presets: setting many settings at once\n", "\n", "Bowtie 2 comes with some useful combinations of parameters packaged into shorter “preset” parameters. For example, running Bowtie 2 with the --very-sensitive option is the same as running with options: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50. The preset options that come with Bowtie 2 are designed to cover a wide area of the speed/sensitivity/accuracy trade-off space, with the presets ending in fast generally being faster but less sensitive and less accurate, and the presets ending in sensitive generally being slower but more sensitive and more accurate. See the documentation for the preset options for details.\n", "\n", "#### Preset options in `--local` mode \n", "`--very-fast-local` - Same as: -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 \n", "`--fast-local` - Same as: -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 \n", "`--sensitive-local` - Same as: -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default in --local mode) \n", "`--very-sensitive-local` Same as: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 \n", "\n", "##### Preset options \n", "`-D` - Up to N consecutive seed extension attempts can “fail” before Bowtie 2 moves on, using the alignments found so far. A seed extension “fails” if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. \n", "\n", "`-R` - The maximum number of times Bowtie 2 will “re-seed” reads with repetitive seeds. When “re-seeding,” Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. \n", "\n", "`-N` - No. mismatches allowed in seed alignment. \n", "\n", "`-L` - Sets the length of the seed substrings to align during multiseed alignment. Smaller values make alignment slower but more sensitive. \n", "\n", "`-i S,1,0.75` - Sets a function governing the interval between seed substrings to use during multiseed alignment. For instance, if the read has 30 characters, and seed length is 10, and the seed interval is 6, the seeds extracted will be:\n", "\n", " Read: TAGCTACGCTCTACGCTATCATGCATAAAC\n", " Seed 1 fw: TAGCTACGCT\n", " Seed 1 rc: AGCGTAGCTA\n", " Seed 2 fw: CGCTCTACGC\n", " Seed 2 rc: GCGTAGAGCG\n", " Seed 3 fw: ACGCTATCAT\n", " Seed 3 rc: ATGATAGCGT\n", " Seed 4 fw: TCATGCATAA\n", " Seed 4 rc: TTATGCATGA\n", "\n", "Since it’s best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number.\n", "\n", "### SAM output \n", "\n", "The following settings were recommended by the TagSeq pipeline \n", "\n", " --no-unal = suppress SAM records for unaligned reads \n", " --no-sq = suppress @SQ header lines \n", " --no-hd = suppress SAM header lines (starting with @) \n", " \n", "When I analigned my preliminary QuantSeq data I used the `--no-unal` option, so I'll do that again here. That will also make the downtream processing step easier (don't have to filter out unaligned reads) " ] }, { "cell_type": "code", "execution_count": 91, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie\r\n" ] } ], "source": [ "# confirm that current directory is bowtie/ \n", "! pwd" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Run Bowtie on trimmed reads, pre-set option= `--sensitive-local`" ] }, { "cell_type": "code", "execution_count": 92, "metadata": {}, "outputs": [], "source": [ "%%bash \n", "\n", "for file in ../cutadapt/*.trim.fastq\n", "do\n", "sample=\"$(basename -a $file | cut -d \".\" -f 1)\"\n", "map_file=\"$sample.bowtie.sam\"\n", "\n", "# run Bowtie2 on each file\n", "bowtie2 \\\n", "--local \\\n", "-x Olurida_v081.fa \\\n", "--sensitive-local \\\n", "--threads 8 \\\n", "--no-unal \\\n", "-k 5 \\\n", "-U $file \\\n", "-S mapped/$map_file; \\\n", "done >> mapped/bowtieout.txt 2>&1" ] }, { "cell_type": "code", "execution_count": 94, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6248833 reads; of these:\r\n", " 6248833 (100.00%) were unpaired; of these:\r\n", " 1773790 (28.39%) aligned 0 times\r\n", " 2757197 (44.12%) aligned exactly 1 time\r\n", " 1717846 (27.49%) aligned >1 times\r\n", "71.61% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "2237155 reads; of these:\r\n", " 2237155 (100.00%) were unpaired; of these:\r\n", " 608066 (27.18%) aligned 0 times\r\n", " 1019006 (45.55%) aligned exactly 1 time\r\n", " 610083 (27.27%) aligned >1 times\r\n", "72.82% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5697993 reads; of these:\r\n", " 5697993 (100.00%) were unpaired; of these:\r\n", " 1862083 (32.68%) aligned 0 times\r\n", " 2520128 (44.23%) aligned exactly 1 time\r\n", " 1315782 (23.09%) aligned >1 times\r\n", "67.32% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "1974587 reads; of these:\r\n", " 1974587 (100.00%) were unpaired; of these:\r\n", " 555265 (28.12%) aligned 0 times\r\n", " 895775 (45.37%) aligned exactly 1 time\r\n", " 523547 (26.51%) aligned >1 times\r\n", "71.88% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5120968 reads; of these:\r\n", " 5120968 (100.00%) were unpaired; of these:\r\n", " 1690944 (33.02%) aligned 0 times\r\n", " 2287249 (44.66%) aligned exactly 1 time\r\n", " 1142775 (22.32%) aligned >1 times\r\n", "66.98% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "9025275 reads; of these:\r\n", " 9025275 (100.00%) were unpaired; of these:\r\n", " 2448337 (27.13%) aligned 0 times\r\n", " 4313084 (47.79%) aligned exactly 1 time\r\n", " 2263854 (25.08%) aligned >1 times\r\n", "72.87% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6763567 reads; of these:\r\n", " 6763567 (100.00%) were unpaired; of these:\r\n", " 2493448 (36.87%) aligned 0 times\r\n", " 2776687 (41.05%) aligned exactly 1 time\r\n", " 1493432 (22.08%) aligned >1 times\r\n", "63.13% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6049165 reads; of these:\r\n", " 6049165 (100.00%) were unpaired; of these:\r\n", " 2217655 (36.66%) aligned 0 times\r\n", " 2564592 (42.40%) aligned exactly 1 time\r\n", " 1266918 (20.94%) aligned >1 times\r\n", "63.34% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "2986013 reads; of these:\r\n", " 2986013 (100.00%) were unpaired; of these:\r\n", " 882761 (29.56%) aligned 0 times\r\n", " 1384455 (46.36%) aligned exactly 1 time\r\n", " 718797 (24.07%) aligned >1 times\r\n", "70.44% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "10573113 reads; of these:\r\n", " 10573113 (100.00%) were unpaired; of these:\r\n", " 2598856 (24.58%) aligned 0 times\r\n", " 4901437 (46.36%) aligned exactly 1 time\r\n", " 3072820 (29.06%) aligned >1 times\r\n", "75.42% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8008438 reads; of these:\r\n", " 8008438 (100.00%) were unpaired; of these:\r\n", " 2275501 (28.41%) aligned 0 times\r\n", " 3729846 (46.57%) aligned exactly 1 time\r\n", " 2003091 (25.01%) aligned >1 times\r\n", "71.59% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "4809404 reads; of these:\r\n", " 4809404 (100.00%) were unpaired; of these:\r\n", " 1244279 (25.87%) aligned 0 times\r\n", " 2250698 (46.80%) aligned exactly 1 time\r\n", " 1314427 (27.33%) aligned >1 times\r\n", "74.13% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "2688049 reads; of these:\r\n", " 2688049 (100.00%) were unpaired; of these:\r\n", " 617833 (22.98%) aligned 0 times\r\n", " 1370874 (51.00%) aligned exactly 1 time\r\n", " 699342 (26.02%) aligned >1 times\r\n", "77.02% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "9300823 reads; of these:\r\n", " 9300823 (100.00%) were unpaired; of these:\r\n", " 2944832 (31.66%) aligned 0 times\r\n", " 4070861 (43.77%) aligned exactly 1 time\r\n", " 2285130 (24.57%) aligned >1 times\r\n", "68.34% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "3260956 reads; of these:\r\n", " 3260956 (100.00%) were unpaired; of these:\r\n", " 839154 (25.73%) aligned 0 times\r\n", " 1489906 (45.69%) aligned exactly 1 time\r\n", " 931896 (28.58%) aligned >1 times\r\n", "74.27% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "2097649 reads; of these:\r\n", " 2097649 (100.00%) were unpaired; of these:\r\n", " 734548 (35.02%) aligned 0 times\r\n", " 878255 (41.87%) aligned exactly 1 time\r\n", " 484846 (23.11%) aligned >1 times\r\n", "64.98% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6950103 reads; of these:\r\n", " 6950103 (100.00%) were unpaired; of these:\r\n", " 1653367 (23.79%) aligned 0 times\r\n", " 2983749 (42.93%) aligned exactly 1 time\r\n", " 2312987 (33.28%) aligned >1 times\r\n", "76.21% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "4745334 reads; of these:\r\n", " 4745334 (100.00%) were unpaired; of these:\r\n", " 918604 (19.36%) aligned 0 times\r\n", " 2302612 (48.52%) aligned exactly 1 time\r\n", " 1524118 (32.12%) aligned >1 times\r\n", "80.64% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "4921084 reads; of these:\r\n", " 4921084 (100.00%) were unpaired; of these:\r\n", " 837679 (17.02%) aligned 0 times\r\n", " 2193572 (44.57%) aligned exactly 1 time\r\n", " 1889833 (38.40%) aligned >1 times\r\n", "82.98% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7135974 reads; of these:\r\n", " 7135974 (100.00%) were unpaired; of these:\r\n", " 1453785 (20.37%) aligned 0 times\r\n", " 3458236 (48.46%) aligned exactly 1 time\r\n", " 2223953 (31.17%) aligned >1 times\r\n", "79.63% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "9324833 reads; of these:\r\n", " 9324833 (100.00%) were unpaired; of these:\r\n", " 1609637 (17.26%) aligned 0 times\r\n", " 4444051 (47.66%) aligned exactly 1 time\r\n", " 3271145 (35.08%) aligned >1 times\r\n", "82.74% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "11560606 reads; of these:\r\n", " 11560606 (100.00%) were unpaired; of these:\r\n", " 2575746 (22.28%) aligned 0 times\r\n", " 5594277 (48.39%) aligned exactly 1 time\r\n", " 3390583 (29.33%) aligned >1 times\r\n", "77.72% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6324004 reads; of these:\r\n", " 6324004 (100.00%) were unpaired; of these:\r\n", " 1326130 (20.97%) aligned 0 times\r\n", " 2999729 (47.43%) aligned exactly 1 time\r\n", " 1998145 (31.60%) aligned >1 times\r\n", "79.03% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "9113464 reads; of these:\r\n", " 9113464 (100.00%) were unpaired; of these:\r\n", " 1981579 (21.74%) aligned 0 times\r\n", " 4220263 (46.31%) aligned exactly 1 time\r\n", " 2911622 (31.95%) aligned >1 times\r\n", "78.26% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7081848 reads; of these:\r\n", " 7081848 (100.00%) were unpaired; of these:\r\n", " 1586730 (22.41%) aligned 0 times\r\n", " 3320577 (46.89%) aligned exactly 1 time\r\n", " 2174541 (30.71%) aligned >1 times\r\n", "77.59% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "9834992 reads; of these:\r\n", " 9834992 (100.00%) were unpaired; of these:\r\n", " 2045376 (20.80%) aligned 0 times\r\n", " 4767165 (48.47%) aligned exactly 1 time\r\n", " 3022451 (30.73%) aligned >1 times\r\n", "79.20% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7583861 reads; of these:\r\n", " 7583861 (100.00%) were unpaired; of these:\r\n", " 1651124 (21.77%) aligned 0 times\r\n", " 3712415 (48.95%) aligned exactly 1 time\r\n", " 2220322 (29.28%) aligned >1 times\r\n", "78.23% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8289824 reads; of these:\r\n", " 8289824 (100.00%) were unpaired; of these:\r\n", " 1859534 (22.43%) aligned 0 times\r\n", " 4019472 (48.49%) aligned exactly 1 time\r\n", " 2410818 (29.08%) aligned >1 times\r\n", "77.57% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5956268 reads; of these:\r\n", " 5956268 (100.00%) were unpaired; of these:\r\n", " 1512760 (25.40%) aligned 0 times\r\n", " 2368364 (39.76%) aligned exactly 1 time\r\n", " 2075144 (34.84%) aligned >1 times\r\n", "74.60% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7630183 reads; of these:\r\n", " 7630183 (100.00%) were unpaired; of these:\r\n", " 1941772 (25.45%) aligned 0 times\r\n", " 3400866 (44.57%) aligned exactly 1 time\r\n", " 2287545 (29.98%) aligned >1 times\r\n", "74.55% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7296222 reads; of these:\r\n", " 7296222 (100.00%) were unpaired; of these:\r\n", " 1993171 (27.32%) aligned 0 times\r\n", " 3186814 (43.68%) aligned exactly 1 time\r\n", " 2116237 (29.00%) aligned >1 times\r\n", "72.68% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8014531 reads; of these:\r\n", " 8014531 (100.00%) were unpaired; of these:\r\n", " 1729954 (21.59%) aligned 0 times\r\n", " 3639631 (45.41%) aligned exactly 1 time\r\n", " 2644946 (33.00%) aligned >1 times\r\n", "78.41% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8376279 reads; of these:\r\n", " 8376279 (100.00%) were unpaired; of these:\r\n", " 1716284 (20.49%) aligned 0 times\r\n", " 3848189 (45.94%) aligned exactly 1 time\r\n", " 2811806 (33.57%) aligned >1 times\r\n", "79.51% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6870080 reads; of these:\r\n", " 6870080 (100.00%) were unpaired; of these:\r\n", " 1444863 (21.03%) aligned 0 times\r\n", " 3118398 (45.39%) aligned exactly 1 time\r\n", " 2306819 (33.58%) aligned >1 times\r\n", "78.97% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6899004 reads; of these:\r\n", " 6899004 (100.00%) were unpaired; of these:\r\n", " 1601906 (23.22%) aligned 0 times\r\n", " 3040442 (44.07%) aligned exactly 1 time\r\n", " 2256656 (32.71%) aligned >1 times\r\n", "76.78% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6811884 reads; of these:\r\n", " 6811884 (100.00%) were unpaired; of these:\r\n", " 1435558 (21.07%) aligned 0 times\r\n", " 3113731 (45.71%) aligned exactly 1 time\r\n", " 2262595 (33.22%) aligned >1 times\r\n", "78.93% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5277805 reads; of these:\r\n", " 5277805 (100.00%) were unpaired; of these:\r\n", " 1606846 (30.45%) aligned 0 times\r\n", " 1809474 (34.28%) aligned exactly 1 time\r\n", " 1861485 (35.27%) aligned >1 times\r\n", "69.55% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8512680 reads; of these:\r\n", " 8512680 (100.00%) were unpaired; of these:\r\n", " 1851698 (21.75%) aligned 0 times\r\n", " 3974539 (46.69%) aligned exactly 1 time\r\n", " 2686443 (31.56%) aligned >1 times\r\n", "78.25% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "9498546 reads; of these:\r\n", " 9498546 (100.00%) were unpaired; of these:\r\n", " 1808077 (19.04%) aligned 0 times\r\n", " 4408422 (46.41%) aligned exactly 1 time\r\n", " 3282047 (34.55%) aligned >1 times\r\n", "80.96% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5632419 reads; of these:\r\n", " 5632419 (100.00%) were unpaired; of these:\r\n", " 1113071 (19.76%) aligned 0 times\r\n", " 2577058 (45.75%) aligned exactly 1 time\r\n", " 1942290 (34.48%) aligned >1 times\r\n", "80.24% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6174885 reads; of these:\r\n", " 6174885 (100.00%) were unpaired; of these:\r\n", " 1265772 (20.50%) aligned 0 times\r\n", " 2920049 (47.29%) aligned exactly 1 time\r\n", " 1989064 (32.21%) aligned >1 times\r\n", "79.50% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7780353 reads; of these:\r\n", " 7780353 (100.00%) were unpaired; of these:\r\n", " 2202550 (28.31%) aligned 0 times\r\n", " 3316193 (42.62%) aligned exactly 1 time\r\n", " 2261610 (29.07%) aligned >1 times\r\n", "71.69% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6027317 reads; of these:\r\n", " 6027317 (100.00%) were unpaired; of these:\r\n", " 1319319 (21.89%) aligned 0 times\r\n", " 2688543 (44.61%) aligned exactly 1 time\r\n", " 2019455 (33.51%) aligned >1 times\r\n", "78.11% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7301694 reads; of these:\r\n", " 7301694 (100.00%) were unpaired; of these:\r\n", " 1555174 (21.30%) aligned 0 times\r\n", " 3410758 (46.71%) aligned exactly 1 time\r\n", " 2335762 (31.99%) aligned >1 times\r\n", "78.70% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "9545280 reads; of these:\r\n", " 9545280 (100.00%) were unpaired; of these:\r\n", " 1963161 (20.57%) aligned 0 times\r\n", " 4631618 (48.52%) aligned exactly 1 time\r\n", " 2950501 (30.91%) aligned >1 times\r\n", "79.43% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8321889 reads; of these:\r\n", " 8321889 (100.00%) were unpaired; of these:\r\n", " 1729867 (20.79%) aligned 0 times\r\n", " 3990338 (47.95%) aligned exactly 1 time\r\n", " 2601684 (31.26%) aligned >1 times\r\n", "79.21% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7590400 reads; of these:\r\n", " 7590400 (100.00%) were unpaired; of these:\r\n", " 1557562 (20.52%) aligned 0 times\r\n", " 3547400 (46.74%) aligned exactly 1 time\r\n", " 2485438 (32.74%) aligned >1 times\r\n", "79.48% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8911376 reads; of these:\r\n", " 8911376 (100.00%) were unpaired; of these:\r\n", " 1892455 (21.24%) aligned 0 times\r\n", " 4381413 (49.17%) aligned exactly 1 time\r\n", " 2637508 (29.60%) aligned >1 times\r\n", "78.76% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5777410 reads; of these:\r\n", " 5777410 (100.00%) were unpaired; of these:\r\n", " 1110949 (19.23%) aligned 0 times\r\n", " 2713720 (46.97%) aligned exactly 1 time\r\n", " 1952741 (33.80%) aligned >1 times\r\n", "80.77% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "11991890 reads; of these:\r\n", " 11991890 (100.00%) were unpaired; of these:\r\n", " 2457580 (20.49%) aligned 0 times\r\n", " 5760562 (48.04%) aligned exactly 1 time\r\n", " 3773748 (31.47%) aligned >1 times\r\n", "79.51% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8346864 reads; of these:\r\n", " 8346864 (100.00%) were unpaired; of these:\r\n", " 1959447 (23.48%) aligned 0 times\r\n", " 3681628 (44.11%) aligned exactly 1 time\r\n", " 2705789 (32.42%) aligned >1 times\r\n", "76.52% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r", "\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6491194 reads; of these:\r\n", " 6491194 (100.00%) were unpaired; of these:\r\n", " 1798278 (27.70%) aligned 0 times\r\n", " 2233577 (34.41%) aligned exactly 1 time\r\n", " 2459339 (37.89%) aligned >1 times\r\n", "72.30% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5401456 reads; of these:\r\n", " 5401456 (100.00%) were unpaired; of these:\r\n", " 1700466 (31.48%) aligned 0 times\r\n", " 2100335 (38.88%) aligned exactly 1 time\r\n", " 1600655 (29.63%) aligned >1 times\r\n", "68.52% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5178798 reads; of these:\r\n", " 5178798 (100.00%) were unpaired; of these:\r\n", " 1140957 (22.03%) aligned 0 times\r\n", " 2427396 (46.87%) aligned exactly 1 time\r\n", " 1610445 (31.10%) aligned >1 times\r\n", "77.97% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5704064 reads; of these:\r\n", " 5704064 (100.00%) were unpaired; of these:\r\n", " 1745890 (30.61%) aligned 0 times\r\n", " 1929208 (33.82%) aligned exactly 1 time\r\n", " 2028966 (35.57%) aligned >1 times\r\n", "69.39% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5117435 reads; of these:\r\n", " 5117435 (100.00%) were unpaired; of these:\r\n", " 1124527 (21.97%) aligned 0 times\r\n", " 2423215 (47.35%) aligned exactly 1 time\r\n", " 1569693 (30.67%) aligned >1 times\r\n", "78.03% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7615302 reads; of these:\r\n", " 7615302 (100.00%) were unpaired; of these:\r\n", " 2636045 (34.62%) aligned 0 times\r\n", " 2811129 (36.91%) aligned exactly 1 time\r\n", " 2168128 (28.47%) aligned >1 times\r\n", "65.38% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "10460927 reads; of these:\r\n", " 10460927 (100.00%) were unpaired; of these:\r\n", " 2497969 (23.88%) aligned 0 times\r\n", " 4963703 (47.45%) aligned exactly 1 time\r\n", " 2999255 (28.67%) aligned >1 times\r\n", "76.12% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6309501 reads; of these:\r\n", " 6309501 (100.00%) were unpaired; of these:\r\n", " 1534019 (24.31%) aligned 0 times\r\n", " 2597790 (41.17%) aligned exactly 1 time\r\n", " 2177692 (34.51%) aligned >1 times\r\n", "75.69% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7152967 reads; of these:\r\n", " 7152967 (100.00%) were unpaired; of these:\r\n", " 1697971 (23.74%) aligned 0 times\r\n", " 3120262 (43.62%) aligned exactly 1 time\r\n", " 2334734 (32.64%) aligned >1 times\r\n", "76.26% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6737872 reads; of these:\r\n", " 6737872 (100.00%) were unpaired; of these:\r\n", " 1607945 (23.86%) aligned 0 times\r\n", " 2356661 (34.98%) aligned exactly 1 time\r\n", " 2773266 (41.16%) aligned >1 times\r\n", "76.14% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5451087 reads; of these:\r\n", " 5451087 (100.00%) were unpaired; of these:\r\n", " 1355847 (24.87%) aligned 0 times\r\n", " 2339964 (42.93%) aligned exactly 1 time\r\n", " 1755276 (32.20%) aligned >1 times\r\n", "75.13% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8496317 reads; of these:\r\n", " 8496317 (100.00%) were unpaired; of these:\r\n", " 1684533 (19.83%) aligned 0 times\r\n", " 4071809 (47.92%) aligned exactly 1 time\r\n", " 2739975 (32.25%) aligned >1 times\r\n", "80.17% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7400336 reads; of these:\r\n", " 7400336 (100.00%) were unpaired; of these:\r\n", " 1666374 (22.52%) aligned 0 times\r\n", " 3164453 (42.76%) aligned exactly 1 time\r\n", " 2569509 (34.72%) aligned >1 times\r\n", "77.48% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "10029720 reads; of these:\r\n", " 10029720 (100.00%) were unpaired; of these:\r\n", " 3039957 (30.31%) aligned 0 times\r\n", " 3742896 (37.32%) aligned exactly 1 time\r\n", " 3246867 (32.37%) aligned >1 times\r\n", "69.69% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5460373 reads; of these:\r\n", " 5460373 (100.00%) were unpaired; of these:\r\n", " 1206099 (22.09%) aligned 0 times\r\n", " 2681482 (49.11%) aligned exactly 1 time\r\n", " 1572792 (28.80%) aligned >1 times\r\n", "77.91% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5675956 reads; of these:\r\n", " 5675956 (100.00%) were unpaired; of these:\r\n", " 1132211 (19.95%) aligned 0 times\r\n", " 2568705 (45.26%) aligned exactly 1 time\r\n", " 1975040 (34.80%) aligned >1 times\r\n", "80.05% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6508706 reads; of these:\r\n", " 6508706 (100.00%) were unpaired; of these:\r\n", " 1470107 (22.59%) aligned 0 times\r\n", " 3121145 (47.95%) aligned exactly 1 time\r\n", " 1917454 (29.46%) aligned >1 times\r\n", "77.41% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7102992 reads; of these:\r\n", " 7102992 (100.00%) were unpaired; of these:\r\n", " 1516419 (21.35%) aligned 0 times\r\n", " 3115047 (43.86%) aligned exactly 1 time\r\n", " 2471526 (34.80%) aligned >1 times\r\n", "78.65% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5518471 reads; of these:\r\n", " 5518471 (100.00%) were unpaired; of these:\r\n", " 1192177 (21.60%) aligned 0 times\r\n", " 2571063 (46.59%) aligned exactly 1 time\r\n", " 1755231 (31.81%) aligned >1 times\r\n", "78.40% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "2162122 reads; of these:\r\n", " 2162122 (100.00%) were unpaired; of these:\r\n", " 629175 (29.10%) aligned 0 times\r\n", " 439646 (20.33%) aligned exactly 1 time\r\n", " 1093301 (50.57%) aligned >1 times\r\n", "70.90% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7420499 reads; of these:\r\n", " 7420499 (100.00%) were unpaired; of these:\r\n", " 2964240 (39.95%) aligned 0 times\r\n", " 1874387 (25.26%) aligned exactly 1 time\r\n", " 2581872 (34.79%) aligned >1 times\r\n", "60.05% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5800354 reads; of these:\r\n", " 5800354 (100.00%) were unpaired; of these:\r\n", " 1796522 (30.97%) aligned 0 times\r\n", " 2438829 (42.05%) aligned exactly 1 time\r\n", " 1565003 (26.98%) aligned >1 times\r\n", "69.03% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "4090721 reads; of these:\r\n", " 4090721 (100.00%) were unpaired; of these:\r\n", " 1198060 (29.29%) aligned 0 times\r\n", " 1409314 (34.45%) aligned exactly 1 time\r\n", " 1483347 (36.26%) aligned >1 times\r\n", "70.71% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5669857 reads; of these:\r\n", " 5669857 (100.00%) were unpaired; of these:\r\n", " 1480933 (26.12%) aligned 0 times\r\n", " 2561923 (45.18%) aligned exactly 1 time\r\n", " 1627001 (28.70%) aligned >1 times\r\n", "73.88% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6633816 reads; of these:\r\n", " 6633816 (100.00%) were unpaired; of these:\r\n", " 1607194 (24.23%) aligned 0 times\r\n", " 3343989 (50.41%) aligned exactly 1 time\r\n", " 1682633 (25.36%) aligned >1 times\r\n", "75.77% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6901932 reads; of these:\r\n", " 6901932 (100.00%) were unpaired; of these:\r\n", " 2026122 (29.36%) aligned 0 times\r\n", " 3290792 (47.68%) aligned exactly 1 time\r\n", " 1585018 (22.96%) aligned >1 times\r\n", "70.64% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8171671 reads; of these:\r\n", " 8171671 (100.00%) were unpaired; of these:\r\n", " 2021528 (24.74%) aligned 0 times\r\n", " 3010880 (36.85%) aligned exactly 1 time\r\n", " 3139263 (38.42%) aligned >1 times\r\n", "75.26% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6514655 reads; of these:\r\n", " 6514655 (100.00%) were unpaired; of these:\r\n", " 1799423 (27.62%) aligned 0 times\r\n", " 3001892 (46.08%) aligned exactly 1 time\r\n", " 1713340 (26.30%) aligned >1 times\r\n", "72.38% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6700690 reads; of these:\r\n", " 6700690 (100.00%) were unpaired; of these:\r\n", " 4359429 (65.06%) aligned 0 times\r\n", " 933927 (13.94%) aligned exactly 1 time\r\n", " 1407334 (21.00%) aligned >1 times\r\n", "34.94% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6340392 reads; of these:\r\n", " 6340392 (100.00%) were unpaired; of these:\r\n", " 1605112 (25.32%) aligned 0 times\r\n", " 3282496 (51.77%) aligned exactly 1 time\r\n", " 1452784 (22.91%) aligned >1 times\r\n", "74.68% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "4860031 reads; of these:\r\n", " 4860031 (100.00%) were unpaired; of these:\r\n", " 1442201 (29.67%) aligned 0 times\r\n", " 2252150 (46.34%) aligned exactly 1 time\r\n", " 1165680 (23.99%) aligned >1 times\r\n", "70.33% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7424325 reads; of these:\r\n", " 7424325 (100.00%) were unpaired; of these:\r\n", " 1763697 (23.76%) aligned 0 times\r\n", " 3275449 (44.12%) aligned exactly 1 time\r\n", " 2385179 (32.13%) aligned >1 times\r\n", "76.24% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7115207 reads; of these:\r\n", " 7115207 (100.00%) were unpaired; of these:\r\n", " 1880445 (26.43%) aligned 0 times\r\n", " 3215757 (45.20%) aligned exactly 1 time\r\n", " 2019005 (28.38%) aligned >1 times\r\n", "73.57% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6226370 reads; of these:\r\n", " 6226370 (100.00%) were unpaired; of these:\r\n", " 1454634 (23.36%) aligned 0 times\r\n", " 2677604 (43.00%) aligned exactly 1 time\r\n", " 2094132 (33.63%) aligned >1 times\r\n", "76.64% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5883347 reads; of these:\r\n", " 5883347 (100.00%) were unpaired; of these:\r\n", " 1042589 (17.72%) aligned 0 times\r\n", " 1144460 (19.45%) aligned exactly 1 time\r\n", " 3696298 (62.83%) aligned >1 times\r\n", "82.28% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6970399 reads; of these:\r\n", " 6970399 (100.00%) were unpaired; of these:\r\n", " 2444457 (35.07%) aligned 0 times\r\n", " 3291999 (47.23%) aligned exactly 1 time\r\n", " 1233943 (17.70%) aligned >1 times\r\n", "64.93% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "990849 reads; of these:\r\n", " 990849 (100.00%) were unpaired; of these:\r\n", " 588349 (59.38%) aligned 0 times\r\n", " 97500 (9.84%) aligned exactly 1 time\r\n", " 305000 (30.78%) aligned >1 times\r\n", "40.62% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8072265 reads; of these:\r\n", " 8072265 (100.00%) were unpaired; of these:\r\n", " 1592545 (19.73%) aligned 0 times\r\n", " 2886221 (35.75%) aligned exactly 1 time\r\n", " 3593499 (44.52%) aligned >1 times\r\n", "80.27% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5025993 reads; of these:\r\n", " 5025993 (100.00%) were unpaired; of these:\r\n", " 1478254 (29.41%) aligned 0 times\r\n", " 2040774 (40.60%) aligned exactly 1 time\r\n", " 1506965 (29.98%) aligned >1 times\r\n", "70.59% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6046395 reads; of these:\r\n", " 6046395 (100.00%) were unpaired; of these:\r\n", " 1787976 (29.57%) aligned 0 times\r\n", " 3051910 (50.47%) aligned exactly 1 time\r\n", " 1206509 (19.95%) aligned >1 times\r\n", "70.43% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7946834 reads; of these:\r\n", " 7946834 (100.00%) were unpaired; of these:\r\n", " 2392768 (30.11%) aligned 0 times\r\n", " 4136071 (52.05%) aligned exactly 1 time\r\n", " 1417995 (17.84%) aligned >1 times\r\n", "69.89% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6518991 reads; of these:\r\n", " 6518991 (100.00%) were unpaired; of these:\r\n", " 1487253 (22.81%) aligned 0 times\r\n", " 3262451 (50.05%) aligned exactly 1 time\r\n", " 1769287 (27.14%) aligned >1 times\r\n", "77.19% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6994794 reads; of these:\r\n", " 6994794 (100.00%) were unpaired; of these:\r\n", " 2461507 (35.19%) aligned 0 times\r\n", " 2498909 (35.73%) aligned exactly 1 time\r\n", " 2034378 (29.08%) aligned >1 times\r\n", "64.81% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8825897 reads; of these:\r\n", " 8825897 (100.00%) were unpaired; of these:\r\n", " 2484604 (28.15%) aligned 0 times\r\n", " 4454279 (50.47%) aligned exactly 1 time\r\n", " 1887014 (21.38%) aligned >1 times\r\n", "71.85% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5437883 reads; of these:\r\n", " 5437883 (100.00%) were unpaired; of these:\r\n", " 1435743 (26.40%) aligned 0 times\r\n", " 2357819 (43.36%) aligned exactly 1 time\r\n", " 1644321 (30.24%) aligned >1 times\r\n", "73.60% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5209585 reads; of these:\r\n", " 5209585 (100.00%) were unpaired; of these:\r\n", " 1233885 (23.68%) aligned 0 times\r\n", " 2662283 (51.10%) aligned exactly 1 time\r\n", " 1313417 (25.21%) aligned >1 times\r\n", "76.32% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7381449 reads; of these:\r\n", " 7381449 (100.00%) were unpaired; of these:\r\n", " 2190889 (29.68%) aligned 0 times\r\n", " 2999956 (40.64%) aligned exactly 1 time\r\n", " 2190604 (29.68%) aligned >1 times\r\n", "70.32% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "4537377 reads; of these:\r\n", " 4537377 (100.00%) were unpaired; of these:\r\n", " 1208728 (26.64%) aligned 0 times\r\n", " 2219556 (48.92%) aligned exactly 1 time\r\n", " 1109093 (24.44%) aligned >1 times\r\n", "73.36% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "9643294 reads; of these:\r\n", " 9643294 (100.00%) were unpaired; of these:\r\n", " 3078779 (31.93%) aligned 0 times\r\n", " 4806311 (49.84%) aligned exactly 1 time\r\n", " 1758204 (18.23%) aligned >1 times\r\n", "68.07% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5363627 reads; of these:\r\n", " 5363627 (100.00%) were unpaired; of these:\r\n", " 1512705 (28.20%) aligned 0 times\r\n", " 2366175 (44.12%) aligned exactly 1 time\r\n", " 1484747 (27.68%) aligned >1 times\r\n", "71.80% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6249764 reads; of these:\r\n", " 6249764 (100.00%) were unpaired; of these:\r\n", " 1645445 (26.33%) aligned 0 times\r\n", " 2971247 (47.54%) aligned exactly 1 time\r\n", " 1633072 (26.13%) aligned >1 times\r\n", "73.67% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6074913 reads; of these:\r\n", " 6074913 (100.00%) were unpaired; of these:\r\n", " 1575430 (25.93%) aligned 0 times\r\n", " 3005437 (49.47%) aligned exactly 1 time\r\n", " 1494046 (24.59%) aligned >1 times\r\n", "74.07% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6549731 reads; of these:\r\n", " 6549731 (100.00%) were unpaired; of these:\r\n", " 1690030 (25.80%) aligned 0 times\r\n", " 3317548 (50.65%) aligned exactly 1 time\r\n", " 1542153 (23.55%) aligned >1 times\r\n", "74.20% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8402514 reads; of these:\r\n", " 8402514 (100.00%) were unpaired; of these:\r\n", " 2301969 (27.40%) aligned 0 times\r\n", " 4320274 (51.42%) aligned exactly 1 time\r\n", " 1780271 (21.19%) aligned >1 times\r\n", "72.60% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7267714 reads; of these:\r\n", " 7267714 (100.00%) were unpaired; of these:\r\n", " 1692861 (23.29%) aligned 0 times\r\n", " 3960955 (54.50%) aligned exactly 1 time\r\n", " 1613898 (22.21%) aligned >1 times\r\n", "76.71% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "4670118 reads; of these:\r\n", " 4670118 (100.00%) were unpaired; of these:\r\n", " 1129980 (24.20%) aligned 0 times\r\n", " 2613752 (55.97%) aligned exactly 1 time\r\n", " 926386 (19.84%) aligned >1 times\r\n", "75.80% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6454707 reads; of these:\r\n", " 6454707 (100.00%) were unpaired; of these:\r\n", " 1476326 (22.87%) aligned 0 times\r\n", " 2994628 (46.39%) aligned exactly 1 time\r\n", " 1983753 (30.73%) aligned >1 times\r\n", "77.13% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7191139 reads; of these:\r\n", " 7191139 (100.00%) were unpaired; of these:\r\n", " 2353213 (32.72%) aligned 0 times\r\n", " 3150903 (43.82%) aligned exactly 1 time\r\n", " 1687023 (23.46%) aligned >1 times\r\n", "67.28% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5356061 reads; of these:\r\n", " 5356061 (100.00%) were unpaired; of these:\r\n", " 1481908 (27.67%) aligned 0 times\r\n", " 2837487 (52.98%) aligned exactly 1 time\r\n", " 1036666 (19.36%) aligned >1 times\r\n", "72.33% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5681617 reads; of these:\r\n", " 5681617 (100.00%) were unpaired; of these:\r\n", " 1912268 (33.66%) aligned 0 times\r\n", " 2459659 (43.29%) aligned exactly 1 time\r\n", " 1309690 (23.05%) aligned >1 times\r\n", "66.34% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5100265 reads; of these:\r\n", " 5100265 (100.00%) were unpaired; of these:\r\n", " 1329192 (26.06%) aligned 0 times\r\n", " 2136646 (41.89%) aligned exactly 1 time\r\n", " 1634427 (32.05%) aligned >1 times\r\n", "73.94% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7025728 reads; of these:\r\n", " 7025728 (100.00%) were unpaired; of these:\r\n", " 1775822 (25.28%) aligned 0 times\r\n", " 3428212 (48.80%) aligned exactly 1 time\r\n", " 1821694 (25.93%) aligned >1 times\r\n", "74.72% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7171226 reads; of these:\r\n", " 7171226 (100.00%) were unpaired; of these:\r\n", " 1614078 (22.51%) aligned 0 times\r\n", " 3635312 (50.69%) aligned exactly 1 time\r\n", " 1921836 (26.80%) aligned >1 times\r\n", "77.49% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6865968 reads; of these:\r\n", " 6865968 (100.00%) were unpaired; of these:\r\n", " 1674836 (24.39%) aligned 0 times\r\n", " 3826106 (55.73%) aligned exactly 1 time\r\n", " 1365026 (19.88%) aligned >1 times\r\n", "75.61% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7259955 reads; of these:\r\n", " 7259955 (100.00%) were unpaired; of these:\r\n", " 1610992 (22.19%) aligned 0 times\r\n", " 3224357 (44.41%) aligned exactly 1 time\r\n", " 2424606 (33.40%) aligned >1 times\r\n", "77.81% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5790529 reads; of these:\r\n", " 5790529 (100.00%) were unpaired; of these:\r\n", " 1545547 (26.69%) aligned 0 times\r\n", " 2826028 (48.80%) aligned exactly 1 time\r\n", " 1418954 (24.50%) aligned >1 times\r\n", "73.31% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6417993 reads; of these:\r\n", " 6417993 (100.00%) were unpaired; of these:\r\n", " 2279136 (35.51%) aligned 0 times\r\n", " 3054950 (47.60%) aligned exactly 1 time\r\n", " 1083907 (16.89%) aligned >1 times\r\n", "64.49% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7797298 reads; of these:\r\n", " 7797298 (100.00%) were unpaired; of these:\r\n", " 2191711 (28.11%) aligned 0 times\r\n", " 4069344 (52.19%) aligned exactly 1 time\r\n", " 1536243 (19.70%) aligned >1 times\r\n", "71.89% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5742555 reads; of these:\r\n", " 5742555 (100.00%) were unpaired; of these:\r\n", " 2485094 (43.28%) aligned 0 times\r\n", " 2409229 (41.95%) aligned exactly 1 time\r\n", " 848232 (14.77%) aligned >1 times\r\n", "56.72% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6258815 reads; of these:\r\n", " 6258815 (100.00%) were unpaired; of these:\r\n", " 1746253 (27.90%) aligned 0 times\r\n", " 3021723 (48.28%) aligned exactly 1 time\r\n", " 1490839 (23.82%) aligned >1 times\r\n", "72.10% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "11458532 reads; of these:\r\n", " 11458532 (100.00%) were unpaired; of these:\r\n", " 4423204 (38.60%) aligned 0 times\r\n", " 4230689 (36.92%) aligned exactly 1 time\r\n", " 2804639 (24.48%) aligned >1 times\r\n", "61.40% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5760534 reads; of these:\r\n", " 5760534 (100.00%) were unpaired; of these:\r\n", " 2058700 (35.74%) aligned 0 times\r\n", " 2606012 (45.24%) aligned exactly 1 time\r\n", " 1095822 (19.02%) aligned >1 times\r\n", "64.26% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6915805 reads; of these:\r\n", " 6915805 (100.00%) were unpaired; of these:\r\n", " 1945131 (28.13%) aligned 0 times\r\n", " 3034504 (43.88%) aligned exactly 1 time\r\n", " 1936170 (28.00%) aligned >1 times\r\n", "71.87% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6095565 reads; of these:\r\n", " 6095565 (100.00%) were unpaired; of these:\r\n", " 1718975 (28.20%) aligned 0 times\r\n", " 3144415 (51.59%) aligned exactly 1 time\r\n", " 1232175 (20.21%) aligned >1 times\r\n", "71.80% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5336335 reads; of these:\r\n", " 5336335 (100.00%) were unpaired; of these:\r\n", " 1161455 (21.77%) aligned 0 times\r\n", " 2582059 (48.39%) aligned exactly 1 time\r\n", " 1592821 (29.85%) aligned >1 times\r\n", "78.23% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5230794 reads; of these:\r\n", " 5230794 (100.00%) were unpaired; of these:\r\n", " 1489000 (28.47%) aligned 0 times\r\n", " 2398871 (45.86%) aligned exactly 1 time\r\n", " 1342923 (25.67%) aligned >1 times\r\n", "71.53% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7826889 reads; of these:\r\n", " 7826889 (100.00%) were unpaired; of these:\r\n", " 1929471 (24.65%) aligned 0 times\r\n", " 4115521 (52.58%) aligned exactly 1 time\r\n", " 1781897 (22.77%) aligned >1 times\r\n", "75.35% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8623428 reads; of these:\r\n", " 8623428 (100.00%) were unpaired; of these:\r\n", " 2280745 (26.45%) aligned 0 times\r\n", " 4496855 (52.15%) aligned exactly 1 time\r\n", " 1845828 (21.40%) aligned >1 times\r\n", "73.55% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6863657 reads; of these:\r\n", " 6863657 (100.00%) were unpaired; of these:\r\n", " 2210404 (32.20%) aligned 0 times\r\n", " 3435370 (50.05%) aligned exactly 1 time\r\n", " 1217883 (17.74%) aligned >1 times\r\n", "67.80% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "4945903 reads; of these:\r\n", " 4945903 (100.00%) were unpaired; of these:\r\n", " 1268749 (25.65%) aligned 0 times\r\n", " 2219534 (44.88%) aligned exactly 1 time\r\n", " 1457620 (29.47%) aligned >1 times\r\n", "74.35% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5065262 reads; of these:\r\n", " 5065262 (100.00%) were unpaired; of these:\r\n", " 1473796 (29.10%) aligned 0 times\r\n", " 2513222 (49.62%) aligned exactly 1 time\r\n", " 1078244 (21.29%) aligned >1 times\r\n", "70.90% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5204071 reads; of these:\r\n", " 5204071 (100.00%) were unpaired; of these:\r\n", " 1303197 (25.04%) aligned 0 times\r\n", " 2294927 (44.10%) aligned exactly 1 time\r\n", " 1605947 (30.86%) aligned >1 times\r\n", "74.96% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7018861 reads; of these:\r\n", " 7018861 (100.00%) were unpaired; of these:\r\n", " 2238280 (31.89%) aligned 0 times\r\n", " 3277159 (46.69%) aligned exactly 1 time\r\n", " 1503422 (21.42%) aligned >1 times\r\n", "68.11% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6181692 reads; of these:\r\n", " 6181692 (100.00%) were unpaired; of these:\r\n", " 3005636 (48.62%) aligned 0 times\r\n", " 2171125 (35.12%) aligned exactly 1 time\r\n", " 1004931 (16.26%) aligned >1 times\r\n", "51.38% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "3923848 reads; of these:\r\n", " 3923848 (100.00%) were unpaired; of these:\r\n", " 1082741 (27.59%) aligned 0 times\r\n", " 2029336 (51.72%) aligned exactly 1 time\r\n", " 811771 (20.69%) aligned >1 times\r\n", "72.41% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7462460 reads; of these:\r\n", " 7462460 (100.00%) were unpaired; of these:\r\n", " 2043909 (27.39%) aligned 0 times\r\n", " 3825088 (51.26%) aligned exactly 1 time\r\n", " 1593463 (21.35%) aligned >1 times\r\n", "72.61% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "4239829 reads; of these:\r\n", " 4239829 (100.00%) were unpaired; of these:\r\n", " 1336030 (31.51%) aligned 0 times\r\n", " 1944441 (45.86%) aligned exactly 1 time\r\n", " 959358 (22.63%) aligned >1 times\r\n", "68.49% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "4827655 reads; of these:\r\n", " 4827655 (100.00%) were unpaired; of these:\r\n", " 1143674 (23.69%) aligned 0 times\r\n", " 2354270 (48.77%) aligned exactly 1 time\r\n", " 1329711 (27.54%) aligned >1 times\r\n", "76.31% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "7993552 reads; of these:\r\n", " 7993552 (100.00%) were unpaired; of these:\r\n", " 1836741 (22.98%) aligned 0 times\r\n", " 3741076 (46.80%) aligned exactly 1 time\r\n", " 2415735 (30.22%) aligned >1 times\r\n", "77.02% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "6343297 reads; of these:\r\n", " 6343297 (100.00%) were unpaired; of these:\r\n", " 2304902 (36.34%) aligned 0 times\r\n", " 2928187 (46.16%) aligned exactly 1 time\r\n", " 1110208 (17.50%) aligned >1 times\r\n", "63.66% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "14984547 reads; of these:\r\n", " 14984547 (100.00%) were unpaired; of these:\r\n", " 5003490 (33.39%) aligned 0 times\r\n", " 5242520 (34.99%) aligned exactly 1 time\r\n", " 4738537 (31.62%) aligned >1 times\r\n", "66.61% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "8250108 reads; of these:\r\n", " 8250108 (100.00%) were unpaired; of these:\r\n", " 3690477 (44.73%) aligned 0 times\r\n", " 3376082 (40.92%) aligned exactly 1 time\r\n", " 1183549 (14.35%) aligned >1 times\r\n", "55.27% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "4478206 reads; of these:\r\n", " 4478206 (100.00%) were unpaired; of these:\r\n", " 1224129 (27.34%) aligned 0 times\r\n", " 2076156 (46.36%) aligned exactly 1 time\r\n", " 1177921 (26.30%) aligned >1 times\r\n", "72.66% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "5459207 reads; of these:\r\n", " 5459207 (100.00%) were unpaired; of these:\r\n", " 1096629 (20.09%) aligned 0 times\r\n", " 1674939 (30.68%) aligned exactly 1 time\r\n", " 2687639 (49.23%) aligned >1 times\r\n", "79.91% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "730357 reads; of these:\r\n", " 730357 (100.00%) were unpaired; of these:\r\n", " 494937 (67.77%) aligned 0 times\r\n", " 63423 (8.68%) aligned exactly 1 time\r\n", " 171997 (23.55%) aligned >1 times\r\n", "32.23% overall alignment rate\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\r\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\r\n", "13289142 reads; of these:\r\n", " 13289142 (100.00%) were unpaired; of these:\r\n", " 10576512 (79.59%) aligned 0 times\r\n", " 1730846 (13.02%) aligned exactly 1 time\r\n", " 981784 (7.39%) aligned >1 times\r\n", "20.41% overall alignment rate\r\n" ] } ], "source": [ "! cat {workingdir}qc-processing/bowtie/mapped/bowtieout.txt" ] }, { "cell_type": "code", "execution_count": 99, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "71.61% overall alignment rate\r\n", "72.82% overall alignment rate\r\n", "67.32% overall alignment rate\r\n", "71.88% overall alignment rate\r\n", "66.98% overall alignment rate\r\n", "72.87% overall alignment rate\r\n", "63.13% overall alignment rate\r\n", "63.34% overall alignment rate\r\n", "70.44% overall alignment rate\r\n", "75.42% overall alignment rate\r\n", "71.59% overall alignment rate\r\n", "74.13% overall alignment rate\r\n", "77.02% overall alignment rate\r\n", "68.34% overall alignment rate\r\n", "74.27% overall alignment rate\r\n", "64.98% overall alignment rate\r\n", "76.21% overall alignment rate\r\n", "80.64% overall alignment rate\r\n", "82.98% overall alignment rate\r\n", "79.63% overall alignment rate\r\n", "82.74% overall alignment rate\r\n", "77.72% overall alignment rate\r\n", "79.03% overall alignment rate\r\n", "78.26% overall alignment rate\r\n", "77.59% overall alignment rate\r\n", "79.20% overall alignment rate\r\n", "78.23% overall alignment rate\r\n", "77.57% overall alignment rate\r\n", "74.60% overall alignment rate\r\n", "74.55% overall alignment rate\r\n", "72.68% overall alignment rate\r\n", "78.41% overall alignment rate\r\n", "79.51% overall alignment rate\r\n", "78.97% overall alignment rate\r\n", "76.78% overall alignment rate\r\n", "78.93% overall alignment rate\r\n", "69.55% overall alignment rate\r\n", "78.25% overall alignment rate\r\n", "80.96% overall alignment rate\r\n", "80.24% overall alignment rate\r\n", "79.50% overall alignment rate\r\n", "71.69% overall alignment rate\r\n", "78.11% overall alignment rate\r\n", "78.70% overall alignment rate\r\n", "79.43% overall alignment rate\r\n", "79.21% overall alignment rate\r\n", "79.48% overall alignment rate\r\n", "78.76% overall alignment rate\r\n", "80.77% overall alignment rate\r\n", "79.51% overall alignment rate\r\n", "76.52% overall alignment rate\r\n", "72.30% overall alignment rate\r\n", "68.52% overall alignment rate\r\n", "77.97% overall alignment rate\r\n", "69.39% overall alignment rate\r\n", "78.03% overall alignment rate\r\n", "65.38% overall alignment rate\r\n", "76.12% overall alignment rate\r\n", "75.69% overall alignment rate\r\n", "76.26% overall alignment rate\r\n", "76.14% overall alignment rate\r\n", "75.13% overall alignment rate\r\n", "80.17% overall alignment rate\r\n", "77.48% overall alignment rate\r\n", "69.69% overall alignment rate\r\n", "77.91% overall alignment rate\r\n", "80.05% overall alignment rate\r\n", "77.41% overall alignment rate\r\n", "78.65% overall alignment rate\r\n", "78.40% overall alignment rate\r\n", "70.90% overall alignment rate\r\n", "60.05% overall alignment rate\r\n", "69.03% overall alignment rate\r\n", "70.71% overall alignment rate\r\n", "73.88% overall alignment rate\r\n", "75.77% overall alignment rate\r\n", "70.64% overall alignment rate\r\n", "75.26% overall alignment rate\r\n", "72.38% overall alignment rate\r\n", "34.94% overall alignment rate\r\n", "74.68% overall alignment rate\r\n", "70.33% overall alignment rate\r\n", "76.24% overall alignment rate\r\n", "73.57% overall alignment rate\r\n", "76.64% overall alignment rate\r\n", "82.28% overall alignment rate\r\n", "64.93% overall alignment rate\r\n", "40.62% overall alignment rate\r\n", "80.27% overall alignment rate\r\n", "70.59% overall alignment rate\r\n", "70.43% overall alignment rate\r\n", "69.89% overall alignment rate\r\n", "77.19% overall alignment rate\r\n", "64.81% overall alignment rate\r\n", "71.85% overall alignment rate\r\n", "73.60% overall alignment rate\r\n", "76.32% overall alignment rate\r\n", "70.32% overall alignment rate\r\n", "73.36% overall alignment rate\r\n", "68.07% overall alignment rate\r\n", "71.80% overall alignment rate\r\n", "73.67% overall alignment rate\r\n", "74.07% overall alignment rate\r\n", "74.20% overall alignment rate\r\n", "72.60% overall alignment rate\r\n", "76.71% overall alignment rate\r\n", "75.80% overall alignment rate\r\n", "77.13% overall alignment rate\r\n", "67.28% overall alignment rate\r\n", "72.33% overall alignment rate\r\n", "66.34% overall alignment rate\r\n", "73.94% overall alignment rate\r\n", "74.72% overall alignment rate\r\n", "77.49% overall alignment rate\r\n", "75.61% overall alignment rate\r\n", "77.81% overall alignment rate\r\n", "73.31% overall alignment rate\r\n", "64.49% overall alignment rate\r\n", "71.89% overall alignment rate\r\n", "56.72% overall alignment rate\r\n", "72.10% overall alignment rate\r\n", "61.40% overall alignment rate\r\n", "64.26% overall alignment rate\r\n", "71.87% overall alignment rate\r\n", "71.80% overall alignment rate\r\n", "78.23% overall alignment rate\r\n", "71.53% overall alignment rate\r\n", "75.35% overall alignment rate\r\n", "73.55% overall alignment rate\r\n", "67.80% overall alignment rate\r\n", "74.35% overall alignment rate\r\n", "70.90% overall alignment rate\r\n", "74.96% overall alignment rate\r\n", "68.11% overall alignment rate\r\n", "51.38% overall alignment rate\r\n", "72.41% overall alignment rate\r\n", "72.61% overall alignment rate\r\n", "68.49% overall alignment rate\r\n", "76.31% overall alignment rate\r\n", "77.02% overall alignment rate\r\n", "63.66% overall alignment rate\r\n", "66.61% overall alignment rate\r\n", "55.27% overall alignment rate\r\n", "72.66% overall alignment rate\r\n", "79.91% overall alignment rate\r\n", "32.23% overall alignment rate\r\n", "20.41% overall alignment rate\r\n" ] } ], "source": [ "# alignment rates:\n", "! grep \"overall alignment rate\" {workingdir}qc-processing/bowtie/mapped/bowtieout.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### External hard drive may have run out of space at the very end of the Bowtie run. Re-align sample 571 (2nd to last sample that ran, had 32.23% overall alignment - last one is the \"undetermined\" reads) " ] }, { "cell_type": "code", "execution_count": 101, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 423.\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 423.\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\n", "Use of uninitialized value in exists at /usr/local/bin/bowtie2 line 81.\n", "Use of uninitialized value $bt2_args[8] in join or string at /usr/local/bin/bowtie2 line 459.\n", "Use of uninitialized value $bt2_args[9] in join or string at /usr/local/bin/bowtie2 line 459.\n", "730357 reads; of these:\n", " 730357 (100.00%) were unpaired; of these:\n", " 494937 (67.77%) aligned 0 times\n", " 63423 (8.68%) aligned exactly 1 time\n", " 171997 (23.55%) aligned >1 times\n", "32.23% overall alignment rate\n" ] } ], "source": [ "# run Bowtie2 on 571 again to see if file size changes \n", "! bowtie2 \\\n", "--local \\\n", "-x Olurida_v081.fa \\\n", "--sensitive-local \\\n", "--threads 8 \\\n", "--no-unal \\\n", "-k 5 \\\n", "-U {workingdir}qc-processing/cutadapt/571.trim.fastq \\\n", "-S {workingdir}qc-processing/bowtie/mapped/571.bowtie.sam" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Same alignment rate as the full run. Good to move forward with .sam --> .bam conversion " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Convert .sam files to .bam files & sort" ] }, { "cell_type": "code", "execution_count": 104, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Bumblebee/O.lurida_QuantSeq-2020\n" ] } ], "source": [ "cd {workingdir}" ] }, { "cell_type": "code", "execution_count": 105, "metadata": {}, "outputs": [], "source": [ "# Create new bowtie/ subdirectory for sorted .bam files \n", "mkdir {workingdir}qc-processing/bowtie/mapped-sorted/" ] }, { "cell_type": "code", "execution_count": 121, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "[bam_sort_core] merging from 3 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 1 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 2 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 2 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 3 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 2 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 2 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 1 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 5 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 3 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 2 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 1 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 4 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 1 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 4 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 2 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 3 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 3 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 6 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 6 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 3 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 5 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 3 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 5 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 4 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 4 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 3 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 4 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 3 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 4 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 5 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 4 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 4 files and 1 in-memory blocks...\n", "[bam_sort_core] merging 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"[bam_sort_core] merging from 4 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 2 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 7 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 2 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 2 files and 1 in-memory blocks...\n", "[bam_sort_core] merging from 4 files and 1 in-memory blocks...\n", "[W::sam_read1] Parse error at line 369269\n", "[main_samview] truncated file.\n" ] } ], "source": [ "%%bash\n", "\n", "for file in qc-processing/bowtie/mapped/*.bowtie.sam\n", "do\n", "sample=\"$(basename -a $file | cut -d \".\" -f 1)\"\n", "sorted_file=\"$sample.sorted.bam\"\n", "samtools view -b $file | samtools sort -o qc-processing/bowtie/mapped-sorted/$sorted_file\n", "done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Deduplicate reads (optional)\n", "\n", "After running the entire pipeline and analyzing the juvenile samples w/ and w/o deduplicating, I have decided to deduplicate reads, since I only saw slight differences in the #DEGs among groups w/o and w/o deduplicating, and when I spot-checked DEGs in IGV, the reads that had not been deduplicated clearly had some PCR duplication (tons of reads stacked up at exactly the same start & stop). Here I will use the `Picard` tool w/n the `gatk` tool library to deduplicate (since I have that program already, which I use to identify SNPs). " ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "# Create directory to house deduplicated .bam files \n", "! mkdir ../qc-processing/bowtie/deduplicated/" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "%%bash \n", "\n", "for file in ../qc-processing/bowtie/mapped-sorted/*.bam\n", "do\n", "sample=\"$(basename -a $file | cut -b 1,2,3)\"\n", "dedup_file=\"$sample.dedup.bam\"\n", "\n", "# deduplicate using picard, output will have duplicates removed \n", "/Applications/bioinformatics/gatk-4.1.9.0/gatk MarkDuplicates \\\n", "I=$file \\\n", "O=\"../qc-processing/bowtie/deduplicated/$dedup_file\" \\\n", "M=\"../qc-processing/bowtie/deduplicated/$sample.dup_metrics.txt\" \\\n", "REMOVE_DUPLICATES=true\n", "done >> \"../qc-processing/bowtie/deduplicated/dedup_stout.txt\" 2>&1" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "INFO\t2021-03-14 18:23:57\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/137.sorted.bam -O ../qc-processing/bowtie/deduplicated/137.dedup.bam -M ../qc-processing/bowtie/deduplicated/137.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:23:57.757 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:23:58 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/137.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/137.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/137.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:23:58 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:23:58 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:23:58\tMarkDuplicates\tStart of doWork freeMemory: 67869712; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:23:58\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:23:58\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:24:01\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig6669:2,710\r\n", "INFO\t2021-03-14 18:24:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:03\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: Contig27126:25,668\r\n", "INFO\t2021-03-14 18:24:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:05\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig36557:11,314\r\n", "INFO\t2021-03-14 18:24:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:06\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig46967:1,169\r\n", "INFO\t2021-03-14 18:24:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:08\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig63991:717\r\n", "INFO\t2021-03-14 18:24:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:10\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig74566:11,537\r\n", "INFO\t2021-03-14 18:24:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:12\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,566\r\n", "INFO\t2021-03-14 18:24:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:13\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig203572:1,231\r\n", "INFO\t2021-03-14 18:24:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:14\tMarkDuplicates\tRead 8215035 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:24:14\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1167565400; totalMemory: 1673527296; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:24:14\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:24:15\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:24:15\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:24:15\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:24:15\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1615308160; totalMemory: 2748317696; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:24:15\tMarkDuplicates\tMarking 3000708 records as duplicates.\r\n", "INFO\t2021-03-14 18:24:15\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:24:16\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:24:29\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:24:29\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:24:29\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:24:29\tMarkDuplicates\tBefore output close freeMemory: 263547368; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:24:29\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:24:29\tMarkDuplicates\tAfter output close freeMemory: 262955320; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:24:29 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.53 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/137.sorted.bam O=../qc-processing/bowtie/deduplicated/137.dedup.bam M=../qc-processing/bowtie/deduplicated/137.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:24:31\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/139.sorted.bam -O ../qc-processing/bowtie/deduplicated/139.dedup.bam -M ../qc-processing/bowtie/deduplicated/139.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:24:31.775 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:24:31 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/139.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/139.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/139.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:24:31 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:24:31 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:24:32\tMarkDuplicates\tStart of doWork freeMemory: 72062600; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:24:32\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:24:32\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:24:35\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig35213:1,244\r\n", "INFO\t2021-03-14 18:24:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:37\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,809\r\n", "INFO\t2021-03-14 18:24:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:38\tMarkDuplicates\tRead 2959909 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:24:39\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 716064328; totalMemory: 1017118720; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:24:39\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:24:39\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:24:39\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:24:39\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:24:40\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 958898400; totalMemory: 2091909120; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:24:40\tMarkDuplicates\tMarking 894339 records as duplicates.\r\n", "INFO\t2021-03-14 18:24:40\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:24:40\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:24:46\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:24:46\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:24:46\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:24:46\tMarkDuplicates\tBefore output close freeMemory: 268296456; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:24:46\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:24:46\tMarkDuplicates\tAfter output close freeMemory: 258759248; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:24:46 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.24 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/139.sorted.bam O=../qc-processing/bowtie/deduplicated/139.dedup.bam M=../qc-processing/bowtie/deduplicated/139.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:24:48\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/140.sorted.bam -O ../qc-processing/bowtie/deduplicated/140.dedup.bam -M ../qc-processing/bowtie/deduplicated/140.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:24:48.234 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:24:48 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/140.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/140.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/140.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:24:48 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:24:48 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:24:48\tMarkDuplicates\tStart of doWork freeMemory: 72064224; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:24:48\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:24:48\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:24:51\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig16788:4,765\r\n", "INFO\t2021-03-14 18:24:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:54\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: Contig33224:2,663\r\n", "INFO\t2021-03-14 18:24:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:56\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig44127:2,347\r\n", "INFO\t2021-03-14 18:24:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:58\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig63634:4,870\r\n", "INFO\t2021-03-14 18:24:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:24:59\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig86127:727\r\n", "INFO\t2021-03-14 18:24:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:25:01\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig138416:6,522\r\n", "INFO\t2021-03-14 18:25:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:25:02\tMarkDuplicates\tRead 6554977 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:25:02\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1085657072; totalMemory: 1545601024; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:25:02\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:25:03\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:25:03\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:25:04\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:25:04\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1487381824; totalMemory: 2620391424; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:25:04\tMarkDuplicates\tMarking 2530853 records as duplicates.\r\n", "INFO\t2021-03-14 18:25:04\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:25:05\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:25:21\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:25:21\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:25:21\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:25:21\tMarkDuplicates\tBefore output close freeMemory: 818914624; totalMemory: 2620391424; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:25:21\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:25:21\tMarkDuplicates\tAfter output close freeMemory: 258761072; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:25:21 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.55 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/140.sorted.bam O=../qc-processing/bowtie/deduplicated/140.dedup.bam M=../qc-processing/bowtie/deduplicated/140.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:25:24\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/141.sorted.bam -O ../qc-processing/bowtie/deduplicated/141.dedup.bam -M ../qc-processing/bowtie/deduplicated/141.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:25:24.232 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:25:24 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/141.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/141.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/141.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:25:24 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:25:24 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:25:24\tMarkDuplicates\tStart of doWork freeMemory: 67870664; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:25:24\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:25:24\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:25:28\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: Contig38783:3,115\r\n", "INFO\t2021-03-14 18:25:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:25:30\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: Contig94656:10,928\r\n", "INFO\t2021-03-14 18:25:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:25:31\tMarkDuplicates\tRead 2538247 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:25:31\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 682934792; totalMemory: 968884224; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:25:31\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:25:32\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:25:32\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:25:32\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:25:32\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 910664400; totalMemory: 2043674624; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:25:32\tMarkDuplicates\tMarking 782861 records as duplicates.\r\n", "INFO\t2021-03-14 18:25:32\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:25:33\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:25:38\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:25:38\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:25:38\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:25:38\tMarkDuplicates\tBefore output close freeMemory: 264520856; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:25:38\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:25:38\tMarkDuplicates\tAfter output close freeMemory: 262953896; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:25:38 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.24 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/141.sorted.bam O=../qc-processing/bowtie/deduplicated/141.dedup.bam M=../qc-processing/bowtie/deduplicated/141.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:25:40\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/156.sorted.bam -O ../qc-processing/bowtie/deduplicated/156.dedup.bam -M ../qc-processing/bowtie/deduplicated/156.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:25:40.346 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:25:40 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/156.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/156.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/156.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:25:40 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:25:40 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:25:40\tMarkDuplicates\tStart of doWork freeMemory: 72062888; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:25:40\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:25:40\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:25:44\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig20210:18,604\r\n", "INFO\t2021-03-14 18:25:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:25:46\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: Contig36057:6,843\r\n", "INFO\t2021-03-14 18:25:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:25:48\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig52757:1,474\r\n", "INFO\t2021-03-14 18:25:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:25:50\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig71173:8,003\r\n", "INFO\t2021-03-14 18:25:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:25:52\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig124918:1,863\r\n", "INFO\t2021-03-14 18:25:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:25:53\tMarkDuplicates\tRead 5611214 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:25:53\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1013168264; totalMemory: 1443889152; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:25:53\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:25:53\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:25:53\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:25:54\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:25:54\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1385669720; totalMemory: 2518679552; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:25:54\tMarkDuplicates\tMarking 2613891 records as duplicates.\r\n", "INFO\t2021-03-14 18:25:54\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:25:55\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:26:05\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:26:05\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:26:05\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:26:06\tMarkDuplicates\tBefore output close freeMemory: 266095472; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:26:06\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:26:06\tMarkDuplicates\tAfter output close freeMemory: 262954608; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:26:06 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.43 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/156.sorted.bam O=../qc-processing/bowtie/deduplicated/156.dedup.bam M=../qc-processing/bowtie/deduplicated/156.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:26:08\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/159.sorted.bam -O ../qc-processing/bowtie/deduplicated/159.dedup.bam -M ../qc-processing/bowtie/deduplicated/159.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:26:08.560 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:26:08 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/159.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/159.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/159.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:26:08 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:26:08 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:26:08\tMarkDuplicates\tStart of doWork freeMemory: 72062472; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:26:08\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:26:08\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:26:12\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3018:8,594\r\n", "INFO\t2021-03-14 18:26:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:26:14\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig19438:13,623\r\n", "INFO\t2021-03-14 18:26:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:26:16\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig30555:37,097\r\n", "INFO\t2021-03-14 18:26:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:26:18\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig36767:905\r\n", "INFO\t2021-03-14 18:26:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:26:19\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig43042:1,725\r\n", "INFO\t2021-03-14 18:26:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:26:21\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig54850:2,425\r\n", "INFO\t2021-03-14 18:26:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:26:23\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig66247:2,701\r\n", "INFO\t2021-03-14 18:26:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:26:24\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig80374:5,873\r\n", "INFO\t2021-03-14 18:26:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:26:26\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig103041:521\r\n", "INFO\t2021-03-14 18:26:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:26:27\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig150704:1,077\r\n", "INFO\t2021-03-14 18:26:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:26:29\tMarkDuplicates\tRead 10773184 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:26:29\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 791832480; totalMemory: 1449132032; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:26:29\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:26:29\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:26:29\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:26:31\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:26:31\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1390911680; totalMemory: 2523922432; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:26:31\tMarkDuplicates\tMarking 5421619 records as duplicates.\r\n", "INFO\t2021-03-14 18:26:31\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:26:32\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:26:50\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:26:50\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:26:50\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:26:50\tMarkDuplicates\tBefore output close freeMemory: 262353240; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:26:50\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:26:51\tMarkDuplicates\tAfter output close freeMemory: 255613808; totalMemory: 363855872; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:26:51 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.71 minutes.\r\n", "Runtime.totalMemory()=363855872\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/159.sorted.bam O=../qc-processing/bowtie/deduplicated/159.dedup.bam M=../qc-processing/bowtie/deduplicated/159.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:26:52\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/161.sorted.bam -O ../qc-processing/bowtie/deduplicated/161.dedup.bam -M ../qc-processing/bowtie/deduplicated/161.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:26:52.843 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:26:52 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/161.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/161.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/161.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:26:53 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:26:53 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:26:53\tMarkDuplicates\tStart of doWork freeMemory: 67873536; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:26:53\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:26:53\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:26:56\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig8182:1,101\r\n", "INFO\t2021-03-14 18:26:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:26:58\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: Contig26402:9,052\r\n", "INFO\t2021-03-14 18:26:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:00\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig36682:230\r\n", "INFO\t2021-03-14 18:27:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:02\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig51337:2,870\r\n", "INFO\t2021-03-14 18:27:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:04\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig68185:2,553\r\n", "INFO\t2021-03-14 18:27:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:06\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig90312:2,801\r\n", "INFO\t2021-03-14 18:27:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:07\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig137778:2,754\r\n", "INFO\t2021-03-14 18:27:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:09\tMarkDuplicates\tRead 7701698 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:27:09\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1100531504; totalMemory: 1591738368; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:27:09\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:27:09\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:27:09\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:27:10\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:27:11\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1533519224; totalMemory: 2666528768; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:27:11\tMarkDuplicates\tMarking 2615842 records as duplicates.\r\n", "INFO\t2021-03-14 18:27:11\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:27:11\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:27:25\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:27:25\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:27:25\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:27:26\tMarkDuplicates\tBefore output close freeMemory: 266714976; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:27:26\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:27:26\tMarkDuplicates\tAfter output close freeMemory: 262955104; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:27:26 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.56 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/161.sorted.bam O=../qc-processing/bowtie/deduplicated/161.dedup.bam M=../qc-processing/bowtie/deduplicated/161.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:27:28\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/162.sorted.bam -O ../qc-processing/bowtie/deduplicated/162.dedup.bam -M ../qc-processing/bowtie/deduplicated/162.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:27:28.070 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:27:28 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/162.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/162.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/162.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:27:28 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:27:28 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:27:28\tMarkDuplicates\tStart of doWork freeMemory: 72065416; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:27:28\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:27:28\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:27:32\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig16595:34,145\r\n", "INFO\t2021-03-14 18:27:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:34\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: Contig30879:27,671\r\n", "INFO\t2021-03-14 18:27:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:36\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: Contig42436:7,996\r\n", "INFO\t2021-03-14 18:27:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:38\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig60239:5,847\r\n", "INFO\t2021-03-14 18:27:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:39\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig85010:16,644\r\n", "INFO\t2021-03-14 18:27:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:41\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig136321:1,929\r\n", "INFO\t2021-03-14 18:27:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:27:42\tMarkDuplicates\tRead 6639584 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:27:42\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 879405040; totalMemory: 1339031552; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:27:42\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:27:43\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:27:43\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:27:43\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:27:44\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1280813424; totalMemory: 2413821952; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:27:44\tMarkDuplicates\tMarking 2507433 records as duplicates.\r\n", "INFO\t2021-03-14 18:27:44\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:27:44\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:27:55\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:27:55\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:27:55\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:27:55\tMarkDuplicates\tBefore output close freeMemory: 271407064; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:27:55\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:27:56\tMarkDuplicates\tAfter output close freeMemory: 258761816; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:27:56 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.47 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/162.sorted.bam O=../qc-processing/bowtie/deduplicated/162.dedup.bam M=../qc-processing/bowtie/deduplicated/162.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:27:57\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/168.sorted.bam -O ../qc-processing/bowtie/deduplicated/168.dedup.bam -M ../qc-processing/bowtie/deduplicated/168.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:27:57.963 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:27:58 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/168.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/168.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/168.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:27:58 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:27:58 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:27:58\tMarkDuplicates\tStart of doWork freeMemory: 72067144; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:27:58\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:27:58\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:28:01\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig32542:18,032\r\n", "INFO\t2021-03-14 18:28:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:03\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig57586:1,981\r\n", "INFO\t2021-03-14 18:28:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:04\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig105506:8,234\r\n", "INFO\t2021-03-14 18:28:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:05\tMarkDuplicates\tRead 3509744 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:28:05\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 797268464; totalMemory: 1132462080; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:28:05\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:28:06\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:28:06\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:28:06\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:28:06\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1074242192; totalMemory: 2207252480; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:28:06\tMarkDuplicates\tMarking 1442402 records as duplicates.\r\n", "INFO\t2021-03-14 18:28:06\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:28:07\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:28:15\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:28:15\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:28:15\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:28:15\tMarkDuplicates\tBefore output close freeMemory: 262949616; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:28:15\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:28:16\tMarkDuplicates\tAfter output close freeMemory: 262954480; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:28:16 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.30 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/168.sorted.bam O=../qc-processing/bowtie/deduplicated/168.dedup.bam M=../qc-processing/bowtie/deduplicated/168.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:28:18\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/169.sorted.bam -O ../qc-processing/bowtie/deduplicated/169.dedup.bam -M ../qc-processing/bowtie/deduplicated/169.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:28:18.302 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:28:18 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/169.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/169.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/169.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:28:18 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:28:18 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:28:18\tMarkDuplicates\tStart of doWork freeMemory: 72062464; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:28:18\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:28:18\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:28:22\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig1699:19,616\r\n", "INFO\t2021-03-14 18:28:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:24\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig15298:857\r\n", "INFO\t2021-03-14 18:28:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:26\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig23200:4,720\r\n", "INFO\t2021-03-14 18:28:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:28\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig31405:9,632\r\n", "INFO\t2021-03-14 18:28:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:29\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig36057:7,071\r\n", "INFO\t2021-03-14 18:28:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:31\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig42435:21,752\r\n", "INFO\t2021-03-14 18:28:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:32\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig47503:8,697\r\n", "INFO\t2021-03-14 18:28:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:34\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig56693:11,741\r\n", "INFO\t2021-03-14 18:28:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:36\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig64789:2,789\r\n", "INFO\t2021-03-14 18:28:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:37\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig70334:9,786\r\n", "INFO\t2021-03-14 18:28:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:39\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig84562:1,585\r\n", "INFO\t2021-03-14 18:28:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:41\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,751\r\n", "INFO\t2021-03-14 18:28:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:43\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: Contig130284:6,245\r\n", "INFO\t2021-03-14 18:28:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:44\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: Contig194722:1,063\r\n", "INFO\t2021-03-14 18:28:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:28:45\tMarkDuplicates\tRead 14466237 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:28:45\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 561202528; totalMemory: 1319108608; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:28:45\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:28:46\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:28:46\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:28:47\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:28:48\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1260887504; totalMemory: 2393899008; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:28:48\tMarkDuplicates\tMarking 6189939 records as duplicates.\r\n", "INFO\t2021-03-14 18:28:48\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:28:48\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:29:14\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:29:14\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:29:14\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:29:15\tMarkDuplicates\tBefore output close freeMemory: 268520624; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:29:15\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:29:15\tMarkDuplicates\tAfter output close freeMemory: 266099088; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:29:15 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.95 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/169.sorted.bam O=../qc-processing/bowtie/deduplicated/169.dedup.bam M=../qc-processing/bowtie/deduplicated/169.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:29:17\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/171.sorted.bam -O ../qc-processing/bowtie/deduplicated/171.dedup.bam -M ../qc-processing/bowtie/deduplicated/171.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:29:17.126 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:29:17 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/171.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/171.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/171.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:29:17 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:29:17 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:29:17\tMarkDuplicates\tStart of doWork freeMemory: 64728408; totalMemory: 91226112; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:29:17\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:29:17\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:29:21\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4035:804\r\n", "INFO\t2021-03-14 18:29:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:29:22\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig22257:13,195\r\n", "INFO\t2021-03-14 18:29:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:29:24\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig34479:1\r\n", "INFO\t2021-03-14 18:29:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:29:26\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig42072:19,471\r\n", "INFO\t2021-03-14 18:29:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:29:27\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig50647:500\r\n", "INFO\t2021-03-14 18:29:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:29:29\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig64427:9,249\r\n", "INFO\t2021-03-14 18:29:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:29:31\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig77522:6,732\r\n", "INFO\t2021-03-14 18:29:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:29:32\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig101302:2,438\r\n", "INFO\t2021-03-14 18:29:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:29:34\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig149841:1,610\r\n", "INFO\t2021-03-14 18:29:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:29:35\tMarkDuplicates\tRead 9737759 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:29:35\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 917614560; totalMemory: 1514143744; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:29:35\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:29:36\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:29:36\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:29:37\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:29:37\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1455925752; totalMemory: 2588934144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:29:37\tMarkDuplicates\tMarking 4340697 records as duplicates.\r\n", "INFO\t2021-03-14 18:29:37\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:29:38\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:29:52\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:29:52\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:29:52\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:29:53\tMarkDuplicates\tBefore output close freeMemory: 266096992; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:29:53\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:29:53\tMarkDuplicates\tAfter output close freeMemory: 262956000; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:29:53 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.60 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/171.sorted.bam O=../qc-processing/bowtie/deduplicated/171.dedup.bam M=../qc-processing/bowtie/deduplicated/171.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:29:54\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/172.sorted.bam -O ../qc-processing/bowtie/deduplicated/172.dedup.bam -M ../qc-processing/bowtie/deduplicated/172.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:29:54.961 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:29:55 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/172.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/172.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/172.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:29:55 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:29:55 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:29:55\tMarkDuplicates\tStart of doWork freeMemory: 72064144; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:29:55\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:29:55\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:29:58\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig17120:4,297\r\n", "INFO\t2021-03-14 18:29:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:29:59\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig35026:10,391\r\n", "INFO\t2021-03-14 18:29:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:01\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig46355:20,730\r\n", "INFO\t2021-03-14 18:30:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:03\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig67033:4,974\r\n", "INFO\t2021-03-14 18:30:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:04\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig95218:1,123\r\n", "INFO\t2021-03-14 18:30:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:06\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig170685:812\r\n", "INFO\t2021-03-14 18:30:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:06\tMarkDuplicates\tRead 6309512 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:30:07\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1042239176; totalMemory: 1482686464; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:30:07\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:30:07\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:30:07\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:30:08\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:30:08\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1424467408; totalMemory: 2557476864; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:30:08\tMarkDuplicates\tMarking 2397405 records as duplicates.\r\n", "INFO\t2021-03-14 18:30:08\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:30:08\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:30:18\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:30:18\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:30:18\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:30:18\tMarkDuplicates\tBefore output close freeMemory: 261879856; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:30:18\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:30:18\tMarkDuplicates\tAfter output close freeMemory: 262955488; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:30:18 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.40 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/172.sorted.bam O=../qc-processing/bowtie/deduplicated/172.dedup.bam M=../qc-processing/bowtie/deduplicated/172.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:30:20\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/181.sorted.bam -O ../qc-processing/bowtie/deduplicated/181.dedup.bam -M ../qc-processing/bowtie/deduplicated/181.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:30:20.744 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:30:20 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/181.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/181.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/181.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:30:20 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:30:20 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:30:20\tMarkDuplicates\tStart of doWork freeMemory: 75212624; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:30:20\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:30:20\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:30:24\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig31688:46,079\r\n", "INFO\t2021-03-14 18:30:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:25\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig57586:2,002\r\n", "INFO\t2021-03-14 18:30:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:27\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig129088:996\r\n", "INFO\t2021-03-14 18:30:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:28\tMarkDuplicates\tRead 3374761 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:30:28\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 786018224; totalMemory: 1118830592; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:30:28\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:30:28\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:30:28\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:30:29\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:30:29\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1060613440; totalMemory: 2193620992; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:30:29\tMarkDuplicates\tMarking 1570013 records as duplicates.\r\n", "INFO\t2021-03-14 18:30:29\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:30:29\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:30:35\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:30:35\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:30:35\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:30:35\tMarkDuplicates\tBefore output close freeMemory: 266097968; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:30:35\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:30:35\tMarkDuplicates\tAfter output close freeMemory: 266102832; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:30:35 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.24 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/181.sorted.bam O=../qc-processing/bowtie/deduplicated/181.dedup.bam M=../qc-processing/bowtie/deduplicated/181.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:30:37\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/183.sorted.bam -O ../qc-processing/bowtie/deduplicated/183.dedup.bam -M ../qc-processing/bowtie/deduplicated/183.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:30:37.089 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:30:37 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/183.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/183.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/183.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:30:37 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:30:37 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:30:37\tMarkDuplicates\tStart of doWork freeMemory: 72063664; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:30:37\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:30:37\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:30:40\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2973:6,068\r\n", "INFO\t2021-03-14 18:30:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:42\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig18527:16,246\r\n", "INFO\t2021-03-14 18:30:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:44\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig26702:12,979\r\n", "INFO\t2021-03-14 18:30:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:46\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig35026:45,565\r\n", "INFO\t2021-03-14 18:30:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:47\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig41141:1,660\r\n", "INFO\t2021-03-14 18:30:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:49\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig51347:15,900\r\n", "INFO\t2021-03-14 18:30:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:51\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig61480:2,233\r\n", "INFO\t2021-03-14 18:30:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:53\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,891\r\n", "INFO\t2021-03-14 18:30:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:54\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig89720:19,337\r\n", "INFO\t2021-03-14 18:30:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:56\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig110929:7,647\r\n", "INFO\t2021-03-14 18:30:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:58\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig166726:3,649\r\n", "INFO\t2021-03-14 18:30:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:30:59\tMarkDuplicates\tRead 11658116 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:30:59\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 838149000; totalMemory: 1479540736; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:30:59\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:31:00\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:31:00\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:31:01\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:31:01\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1421320080; totalMemory: 2554331136; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:31:01\tMarkDuplicates\tMarking 4120081 records as duplicates.\r\n", "INFO\t2021-03-14 18:31:01\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:31:01\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:31:22\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:31:22\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:31:22\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:31:22\tMarkDuplicates\tBefore output close freeMemory: 265153800; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:31:22\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:31:22\tMarkDuplicates\tAfter output close freeMemory: 258759160; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:31:22 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.76 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/183.sorted.bam O=../qc-processing/bowtie/deduplicated/183.dedup.bam M=../qc-processing/bowtie/deduplicated/183.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:31:24\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/184.sorted.bam -O ../qc-processing/bowtie/deduplicated/184.dedup.bam -M ../qc-processing/bowtie/deduplicated/184.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:31:24.662 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:31:24 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/184.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/184.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/184.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:31:25 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:31:25 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:31:25\tMarkDuplicates\tStart of doWork freeMemory: 72061096; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:31:25\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:31:25\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:31:28\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig25558:32,037\r\n", "INFO\t2021-03-14 18:31:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:31:30\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig44324:13,005\r\n", "INFO\t2021-03-14 18:31:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:31:31\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig69409:10,984\r\n", "INFO\t2021-03-14 18:31:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:31:33\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig137005:5,549\r\n", "INFO\t2021-03-14 18:31:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:31:34\tMarkDuplicates\tRead 4368139 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:31:34\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 847730504; totalMemory: 1205862400; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:31:34\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:31:34\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:31:34\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:31:35\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:31:35\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1147639976; totalMemory: 2280652800; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:31:35\tMarkDuplicates\tMarking 1535740 records as duplicates.\r\n", "INFO\t2021-03-14 18:31:35\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:31:36\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:31:43\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:31:43\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:31:43\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:31:43\tMarkDuplicates\tBefore output close freeMemory: 262351576; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:31:43\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:31:43\tMarkDuplicates\tAfter output close freeMemory: 255611392; totalMemory: 363855872; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:31:43 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.32 minutes.\r\n", "Runtime.totalMemory()=363855872\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/184.sorted.bam O=../qc-processing/bowtie/deduplicated/184.dedup.bam M=../qc-processing/bowtie/deduplicated/184.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:31:45\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/185.sorted.bam -O ../qc-processing/bowtie/deduplicated/185.dedup.bam -M ../qc-processing/bowtie/deduplicated/185.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:31:45.612 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:31:45 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/185.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/185.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/185.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:31:45 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:31:45 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:31:45\tMarkDuplicates\tStart of doWork freeMemory: 67870624; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:31:45\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:31:45\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:31:49\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig42436:8,000\r\n", "INFO\t2021-03-14 18:31:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:31:50\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig104701:4,807\r\n", "INFO\t2021-03-14 18:31:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:31:51\tMarkDuplicates\tRead 2341517 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:31:51\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 669158248; totalMemory: 951058432; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:31:51\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:31:51\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:31:51\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:31:52\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:31:52\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 892840672; totalMemory: 2025848832; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:31:52\tMarkDuplicates\tMarking 851956 records as duplicates.\r\n", "INFO\t2021-03-14 18:31:52\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:31:53\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:31:56\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:31:56\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:31:56\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:31:57\tMarkDuplicates\tBefore output close freeMemory: 262325008; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:31:57\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:31:57\tMarkDuplicates\tAfter output close freeMemory: 258761944; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:31:57 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.19 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/185.sorted.bam O=../qc-processing/bowtie/deduplicated/185.dedup.bam M=../qc-processing/bowtie/deduplicated/185.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:31:58\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/291.sorted.bam -O ../qc-processing/bowtie/deduplicated/291.dedup.bam -M ../qc-processing/bowtie/deduplicated/291.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:31:58.775 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:31:58 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/291.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/291.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/291.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:31:58 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:31:58 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:31:58\tMarkDuplicates\tStart of doWork freeMemory: 72062688; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:31:58\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:31:58\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:32:02\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4488:6,212\r\n", "INFO\t2021-03-14 18:32:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:03\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig20865:53,989\r\n", "INFO\t2021-03-14 18:32:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:05\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30614:21,755\r\n", "INFO\t2021-03-14 18:32:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:07\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35841:1,508\r\n", "INFO\t2021-03-14 18:32:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:09\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig46265:4,039\r\n", "INFO\t2021-03-14 18:32:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:10\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig56693:9,308\r\n", "INFO\t2021-03-14 18:32:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:12\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig68037:876\r\n", "INFO\t2021-03-14 18:32:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:14\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig73139:2,271\r\n", "INFO\t2021-03-14 18:32:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:15\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig96826:9,748\r\n", "INFO\t2021-03-14 18:32:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:17\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig116145:3,097\r\n", "INFO\t2021-03-14 18:32:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:19\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig192518:1,762\r\n", "INFO\t2021-03-14 18:32:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:19\tMarkDuplicates\tRead 11370439 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:32:20\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1096868560; totalMemory: 1661992960; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:32:20\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:32:20\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:32:20\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:32:21\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:32:22\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1603773280; totalMemory: 2736783360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:32:22\tMarkDuplicates\tMarking 3163505 records as duplicates.\r\n", "INFO\t2021-03-14 18:32:22\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:32:22\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:32:42\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:32:42\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:32:42\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:32:42\tMarkDuplicates\tBefore output close freeMemory: 700206888; totalMemory: 2736783360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:32:42\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:32:42\tMarkDuplicates\tAfter output close freeMemory: 262954496; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:32:42 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.73 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/291.sorted.bam O=../qc-processing/bowtie/deduplicated/291.dedup.bam M=../qc-processing/bowtie/deduplicated/291.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:32:44\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/292.sorted.bam -O ../qc-processing/bowtie/deduplicated/292.dedup.bam -M ../qc-processing/bowtie/deduplicated/292.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:32:44.365 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:32:44 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/292.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/292.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/292.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:32:44 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:32:44 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:32:44\tMarkDuplicates\tStart of doWork freeMemory: 72061968; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:32:44\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:32:44\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:32:47\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig10923:1,513\r\n", "INFO\t2021-03-14 18:32:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:49\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig27088:5,109\r\n", "INFO\t2021-03-14 18:32:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:54\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 4s. Last read position: Contig37806:33,149\r\n", "INFO\t2021-03-14 18:32:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:56\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig54291:1,050\r\n", "INFO\t2021-03-14 18:32:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:57\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,809\r\n", "INFO\t2021-03-14 18:32:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:32:59\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig89862:1,748\r\n", "INFO\t2021-03-14 18:32:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:01\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig137778:4,144\r\n", "INFO\t2021-03-14 18:33:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:02\tMarkDuplicates\tRead 7689844 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:33:02\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1082121376; totalMemory: 1541406720; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:33:02\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:33:03\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:33:03\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:33:03\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:33:04\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1483185600; totalMemory: 2616197120; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:33:04\tMarkDuplicates\tMarking 2232065 records as duplicates.\r\n", "INFO\t2021-03-14 18:33:04\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:33:04\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:33:17\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:33:17\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:33:17\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:33:17\tMarkDuplicates\tBefore output close freeMemory: 264360216; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:33:17\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:33:17\tMarkDuplicates\tAfter output close freeMemory: 255613152; totalMemory: 363855872; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:33:17 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.55 minutes.\r\n", "Runtime.totalMemory()=363855872\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/292.sorted.bam O=../qc-processing/bowtie/deduplicated/292.dedup.bam M=../qc-processing/bowtie/deduplicated/292.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:33:19\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/293.sorted.bam -O ../qc-processing/bowtie/deduplicated/293.dedup.bam -M ../qc-processing/bowtie/deduplicated/293.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:33:19.226 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:33:19 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/293.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/293.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/293.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:33:19 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:33:19 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:33:19\tMarkDuplicates\tStart of doWork freeMemory: 72061608; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:33:19\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:33:19\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:33:22\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig15654:24,998\r\n", "INFO\t2021-03-14 18:33:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:24\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig27445:16,607\r\n", "INFO\t2021-03-14 18:33:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:25\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig35655:10,905\r\n", "INFO\t2021-03-14 18:33:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:27\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig50479:5,876\r\n", "INFO\t2021-03-14 18:33:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:29\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig59409:16,403\r\n", "INFO\t2021-03-14 18:33:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:30\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig69234:14,487\r\n", "INFO\t2021-03-14 18:33:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:32\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig85279:269\r\n", "INFO\t2021-03-14 18:33:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:33\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig107599:1,003\r\n", "INFO\t2021-03-14 18:33:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:35\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig253642:35\r\n", "INFO\t2021-03-14 18:33:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:35\tMarkDuplicates\tRead 9175577 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:33:35\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 899014408; totalMemory: 1376780288; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:33:35\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:33:36\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:33:36\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:33:37\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:33:37\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1318558800; totalMemory: 2451570688; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:33:37\tMarkDuplicates\tMarking 2446594 records as duplicates.\r\n", "INFO\t2021-03-14 18:33:37\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:33:37\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:33:52\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:33:52\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:33:52\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:33:52\tMarkDuplicates\tBefore output close freeMemory: 1232906080; totalMemory: 2451570688; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:33:52\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:33:53\tMarkDuplicates\tAfter output close freeMemory: 258758904; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:33:53 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.57 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/293.sorted.bam O=../qc-processing/bowtie/deduplicated/293.dedup.bam M=../qc-processing/bowtie/deduplicated/293.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:33:54\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/294.sorted.bam -O ../qc-processing/bowtie/deduplicated/294.dedup.bam -M ../qc-processing/bowtie/deduplicated/294.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:33:54.731 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:33:54 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/294.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/294.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/294.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:33:54 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:33:54 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:33:54\tMarkDuplicates\tStart of doWork freeMemory: 67872448; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:33:54\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:33:54\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:33:58\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3757:12,847\r\n", "INFO\t2021-03-14 18:33:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:33:59\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig19330:89,455\r\n", "INFO\t2021-03-14 18:33:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:01\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig27897:3,122\r\n", "INFO\t2021-03-14 18:34:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:02\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35213:158\r\n", "INFO\t2021-03-14 18:34:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:04\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig42409:10,064\r\n", "INFO\t2021-03-14 18:34:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:06\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig54547:5,869\r\n", "INFO\t2021-03-14 18:34:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:07\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig65875:5,539\r\n", "INFO\t2021-03-14 18:34:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:09\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig73139:247\r\n", "INFO\t2021-03-14 18:34:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:10\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig95984:2,551\r\n", "INFO\t2021-03-14 18:34:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:12\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig130284:6,279\r\n", "INFO\t2021-03-14 18:34:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:14\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig253642:31\r\n", "INFO\t2021-03-14 18:34:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:14\tMarkDuplicates\tRead 11184645 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:34:14\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 946432888; totalMemory: 1539309568; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:34:14\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:34:14\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:34:14\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:34:15\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:34:15\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1481090224; totalMemory: 2614099968; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:34:15\tMarkDuplicates\tMarking 3575239 records as duplicates.\r\n", "INFO\t2021-03-14 18:34:15\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:34:16\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:34:33\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:34:33\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:34:33\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:34:33\tMarkDuplicates\tBefore output close freeMemory: 262191128; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:34:33\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:34:33\tMarkDuplicates\tAfter output close freeMemory: 258760352; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:34:33 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.65 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/294.sorted.bam O=../qc-processing/bowtie/deduplicated/294.dedup.bam M=../qc-processing/bowtie/deduplicated/294.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:34:35\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/295.sorted.bam -O ../qc-processing/bowtie/deduplicated/295.dedup.bam -M ../qc-processing/bowtie/deduplicated/295.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:34:35.519 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:34:35 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/295.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/295.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/295.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:34:35 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:34:35 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:34:35\tMarkDuplicates\tStart of doWork freeMemory: 72064104; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:34:35\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:34:35\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:34:38\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2252:1,684\r\n", "INFO\t2021-03-14 18:34:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:40\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig15378:13,159\r\n", "INFO\t2021-03-14 18:34:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:42\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig21241:6,825\r\n", "INFO\t2021-03-14 18:34:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:43\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig27981:18,747\r\n", "INFO\t2021-03-14 18:34:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:45\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig33004:2,818\r\n", "INFO\t2021-03-14 18:34:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:47\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig38138:16,728\r\n", "INFO\t2021-03-14 18:34:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:48\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig46605:5,982\r\n", "INFO\t2021-03-14 18:34:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:50\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig56033:1,102\r\n", "INFO\t2021-03-14 18:34:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:52\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig58952:6,144\r\n", "INFO\t2021-03-14 18:34:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:53\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig68037:949\r\n", "INFO\t2021-03-14 18:34:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:55\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig69234:14,522\r\n", "INFO\t2021-03-14 18:34:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:57\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig77508:4,218\r\n", "INFO\t2021-03-14 18:34:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:34:59\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig91189:2,415\r\n", "INFO\t2021-03-14 18:34:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:00\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: Contig103849:5,674\r\n", "INFO\t2021-03-14 18:35:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:02\tMarkDuplicates\tRead 15,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: Contig130284:6,254\r\n", "INFO\t2021-03-14 18:35:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:04\tMarkDuplicates\tRead 16,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: Contig198530:2,083\r\n", "INFO\t2021-03-14 18:35:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:05\tMarkDuplicates\tRead 16480928 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:35:05\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 717219280; totalMemory: 1456472064; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:35:05\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:35:05\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:35:05\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:35:07\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:35:07\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1398252688; totalMemory: 2531262464; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:35:07\tMarkDuplicates\tMarking 4956794 records as duplicates.\r\n", "INFO\t2021-03-14 18:35:07\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:35:08\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:35:32\tMarkDuplicates\tWritten 10,000,000 records. Elapsed time: 00:00:23s. Time for last 10,000,000: 23s. Last read position: Contig109675:6,392\r\n", "INFO\t2021-03-14 18:35:35\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:35:35\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:35:35\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:35:35\tMarkDuplicates\tBefore output close freeMemory: 2417635976; totalMemory: 2531262464; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:35:35\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:35:35\tMarkDuplicates\tAfter output close freeMemory: 262954968; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:35:35 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.01 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/295.sorted.bam O=../qc-processing/bowtie/deduplicated/295.dedup.bam M=../qc-processing/bowtie/deduplicated/295.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:35:37\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/296.sorted.bam -O ../qc-processing/bowtie/deduplicated/296.dedup.bam -M ../qc-processing/bowtie/deduplicated/296.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:35:37.723 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:35:37 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/296.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/296.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/296.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:35:38 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:35:38 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:35:38\tMarkDuplicates\tStart of doWork freeMemory: 75209096; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:35:38\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:35:38\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:35:40\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig1476:13,901\r\n", "INFO\t2021-03-14 18:35:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:42\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig5738:10,717\r\n", "INFO\t2021-03-14 18:35:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:44\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig18358:12,982\r\n", "INFO\t2021-03-14 18:35:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:45\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig23690:10,858\r\n", "INFO\t2021-03-14 18:35:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:47\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig28548:12,549\r\n", "INFO\t2021-03-14 18:35:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:48\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig33649:6,790\r\n", "INFO\t2021-03-14 18:35:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:50\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig36557:11,338\r\n", "INFO\t2021-03-14 18:35:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:51\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig42187:43,039\r\n", "INFO\t2021-03-14 18:35:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:53\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig49451:13,755\r\n", "INFO\t2021-03-14 18:35:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:55\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig56693:7,470\r\n", "INFO\t2021-03-14 18:35:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:56\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig63672:13,897\r\n", "INFO\t2021-03-14 18:35:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:58\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig69318:4,434\r\n", "INFO\t2021-03-14 18:35:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:35:59\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig78973:3,817\r\n", "INFO\t2021-03-14 18:35:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:01\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig94256:1,450\r\n", "INFO\t2021-03-14 18:36:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:02\tMarkDuplicates\tRead 15,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: Contig110952:843\r\n", "INFO\t2021-03-14 18:36:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:04\tMarkDuplicates\tRead 16,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: Contig137778:6,413\r\n", "INFO\t2021-03-14 18:36:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:06\tMarkDuplicates\tRead 17,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: Contig194722:1,063\r\n", "INFO\t2021-03-14 18:36:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:07\tMarkDuplicates\tRead 17619461 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:36:07\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 874315864; totalMemory: 1704984576; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:36:07\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:36:07\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:36:07\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:36:09\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:36:09\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1646764872; totalMemory: 2779774976; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:36:09\tMarkDuplicates\tMarking 5650562 records as duplicates.\r\n", "INFO\t2021-03-14 18:36:09\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:36:10\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:36:31\tMarkDuplicates\tWritten 10,000,000 records. Elapsed time: 00:00:21s. Time for last 10,000,000: 21s. Last read position: Contig108753:1,020\r\n", "INFO\t2021-03-14 18:36:35\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:36:35\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:36:35\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:36:35\tMarkDuplicates\tBefore output close freeMemory: 262950280; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:36:36\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:36:36\tMarkDuplicates\tAfter output close freeMemory: 262955144; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:36:36 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.97 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/296.sorted.bam O=../qc-processing/bowtie/deduplicated/296.dedup.bam M=../qc-processing/bowtie/deduplicated/296.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:36:37\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/298.sorted.bam -O ../qc-processing/bowtie/deduplicated/298.dedup.bam -M ../qc-processing/bowtie/deduplicated/298.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:36:37.965 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:36:38 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/298.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/298.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/298.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:36:38 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:36:38 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:36:38\tMarkDuplicates\tStart of doWork freeMemory: 67868808; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:36:38\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:36:38\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:36:41\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5475:1,639\r\n", "INFO\t2021-03-14 18:36:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:42\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig22371:1,107\r\n", "INFO\t2021-03-14 18:36:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:44\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig31099:15,415\r\n", "INFO\t2021-03-14 18:36:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:46\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig39551:6,656\r\n", "INFO\t2021-03-14 18:36:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:47\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig52580:8,092\r\n", "INFO\t2021-03-14 18:36:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:49\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig62261:3,644\r\n", "INFO\t2021-03-14 18:36:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:50\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig70638:19,186\r\n", "INFO\t2021-03-14 18:36:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:52\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig91176:138\r\n", "INFO\t2021-03-14 18:36:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:53\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig125409:134\r\n", "INFO\t2021-03-14 18:36:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:55\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig532034:3,473\r\n", "INFO\t2021-03-14 18:36:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:36:55\tMarkDuplicates\tRead 10080774 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:36:55\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1027160808; totalMemory: 1570766848; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:36:55\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:36:56\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:36:56\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:36:57\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:36:57\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1512547032; totalMemory: 2645557248; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:36:57\tMarkDuplicates\tMarking 2927649 records as duplicates.\r\n", "INFO\t2021-03-14 18:36:57\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:36:57\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:37:13\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:37:13\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:37:13\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:37:14\tMarkDuplicates\tBefore output close freeMemory: 257273256; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:37:14\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:37:14\tMarkDuplicates\tAfter output close freeMemory: 258760480; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:37:14 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.60 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/298.sorted.bam O=../qc-processing/bowtie/deduplicated/298.dedup.bam M=../qc-processing/bowtie/deduplicated/298.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:37:15\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/299.sorted.bam -O ../qc-processing/bowtie/deduplicated/299.dedup.bam -M ../qc-processing/bowtie/deduplicated/299.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:37:15.948 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:37:16 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/299.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/299.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/299.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:37:16 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:37:16 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:37:16\tMarkDuplicates\tStart of doWork freeMemory: 75209704; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:37:16\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:37:16\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:37:19\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2333:3,238\r\n", "INFO\t2021-03-14 18:37:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:20\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig15915:4,117\r\n", "INFO\t2021-03-14 18:37:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:22\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig22606:5,619\r\n", "INFO\t2021-03-14 18:37:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:23\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig29062:15,624\r\n", "INFO\t2021-03-14 18:37:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:25\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig34398:2,822\r\n", "INFO\t2021-03-14 18:37:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:26\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig40465:1,727\r\n", "INFO\t2021-03-14 18:37:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:28\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig48780:13,700\r\n", "INFO\t2021-03-14 18:37:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:30\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig56693:9,310\r\n", "INFO\t2021-03-14 18:37:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:31\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig64157:772\r\n", "INFO\t2021-03-14 18:37:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:33\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig69234:14,811\r\n", "INFO\t2021-03-14 18:37:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:34\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig80308:10,132\r\n", "INFO\t2021-03-14 18:37:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:36\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,706\r\n", "INFO\t2021-03-14 18:37:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:37\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig118978:2,609\r\n", "INFO\t2021-03-14 18:37:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:39\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig167362:627\r\n", "INFO\t2021-03-14 18:37:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:37:40\tMarkDuplicates\tRead 14788657 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:37:41\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 679525208; totalMemory: 1376780288; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:37:41\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:37:41\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:37:41\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:37:42\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:37:42\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1318560656; totalMemory: 2451570688; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:37:42\tMarkDuplicates\tMarking 4313552 records as duplicates.\r\n", "INFO\t2021-03-14 18:37:42\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:37:43\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:38:05\tMarkDuplicates\tWritten 10,000,000 records. Elapsed time: 00:00:21s. Time for last 10,000,000: 21s. Last read position: Contig182947:809\r\n", "INFO\t2021-03-14 18:38:06\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:38:06\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:38:06\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:38:06\tMarkDuplicates\tBefore output close freeMemory: 258389408; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:38:06\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:38:06\tMarkDuplicates\tAfter output close freeMemory: 255613992; totalMemory: 363855872; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:38:06 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.84 minutes.\r\n", "Runtime.totalMemory()=363855872\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/299.sorted.bam O=../qc-processing/bowtie/deduplicated/299.dedup.bam M=../qc-processing/bowtie/deduplicated/299.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:38:08\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/301.sorted.bam -O ../qc-processing/bowtie/deduplicated/301.dedup.bam -M ../qc-processing/bowtie/deduplicated/301.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:38:08.179 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:38:08 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/301.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/301.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/301.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:38:08 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:38:08 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:38:08\tMarkDuplicates\tStart of doWork freeMemory: 67869032; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:38:08\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:38:08\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:38:12\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3692:6,055\r\n", "INFO\t2021-03-14 18:38:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:13\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig20021:7,076\r\n", "INFO\t2021-03-14 18:38:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:15\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig28866:13,366\r\n", "INFO\t2021-03-14 18:38:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:17\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35213:2,558\r\n", "INFO\t2021-03-14 18:38:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:18\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig44579:3,367\r\n", "INFO\t2021-03-14 18:38:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:20\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig56693:7,489\r\n", "INFO\t2021-03-14 18:38:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:21\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig67291:5,964\r\n", "INFO\t2021-03-14 18:38:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:23\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig73139:79\r\n", "INFO\t2021-03-14 18:38:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:24\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig95735:1,519\r\n", "INFO\t2021-03-14 18:38:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:26\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig126307:10,748\r\n", "INFO\t2021-03-14 18:38:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:28\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig276216:4,928\r\n", "INFO\t2021-03-14 18:38:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:28\tMarkDuplicates\tRead 11189722 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:38:28\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1145499856; totalMemory: 1724907520; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:38:28\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:38:29\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:38:29\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:38:29\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:38:30\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1666688016; totalMemory: 2799697920; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:38:30\tMarkDuplicates\tMarking 3251158 records as duplicates.\r\n", "INFO\t2021-03-14 18:38:30\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:38:30\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:38:48\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:38:48\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:38:48\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:38:48\tMarkDuplicates\tBefore output close freeMemory: 1609707920; totalMemory: 2799697920; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:38:48\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:38:48\tMarkDuplicates\tAfter output close freeMemory: 262954752; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:38:48 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.68 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/301.sorted.bam O=../qc-processing/bowtie/deduplicated/301.dedup.bam M=../qc-processing/bowtie/deduplicated/301.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:38:50\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/302.sorted.bam -O ../qc-processing/bowtie/deduplicated/302.dedup.bam -M ../qc-processing/bowtie/deduplicated/302.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:38:50.737 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:38:50 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/302.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/302.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/302.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:38:50 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:38:50 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:38:50\tMarkDuplicates\tStart of doWork freeMemory: 75209040; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:38:50\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:38:50\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:38:53\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig1705:12,981\r\n", "INFO\t2021-03-14 18:38:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:55\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig7126:1,579\r\n", "INFO\t2021-03-14 18:38:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:57\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig19570:5,110\r\n", "INFO\t2021-03-14 18:38:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:38:58\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig25482:7,996\r\n", "INFO\t2021-03-14 18:38:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:00\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig31246:2,376\r\n", "INFO\t2021-03-14 18:39:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:01\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig35290:25,932\r\n", "INFO\t2021-03-14 18:39:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:03\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig41518:3,123\r\n", "INFO\t2021-03-14 18:39:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:05\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig49076:2,430\r\n", "INFO\t2021-03-14 18:39:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:06\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig56693:12,118\r\n", "INFO\t2021-03-14 18:39:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:08\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig65858:13,810\r\n", "INFO\t2021-03-14 18:39:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:09\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig72420:2,499\r\n", "INFO\t2021-03-14 18:39:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:11\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig85537:4,684\r\n", "INFO\t2021-03-14 18:39:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:12\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig104309:3,902\r\n", "INFO\t2021-03-14 18:39:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:14\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig134879:2,027\r\n", "INFO\t2021-03-14 18:39:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:16\tMarkDuplicates\tRead 15,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: Contig189043:2,137\r\n", "INFO\t2021-03-14 18:39:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:17\tMarkDuplicates\tRead 15628981 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:39:17\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 791553144; totalMemory: 1536163840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:39:17\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:39:17\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:39:17\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:39:18\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:39:19\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1477944792; totalMemory: 2610954240; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:39:19\tMarkDuplicates\tMarking 4512368 records as duplicates.\r\n", "INFO\t2021-03-14 18:39:19\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:39:19\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:39:41\tMarkDuplicates\tWritten 10,000,000 records. Elapsed time: 00:00:21s. Time for last 10,000,000: 21s. Last read position: Contig137778:6,941\r\n", "INFO\t2021-03-14 18:39:44\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:39:44\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:39:44\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:39:44\tMarkDuplicates\tBefore output close freeMemory: 266785776; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:39:44\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:39:44\tMarkDuplicates\tAfter output close freeMemory: 258761176; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:39:44 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.90 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/302.sorted.bam O=../qc-processing/bowtie/deduplicated/302.dedup.bam M=../qc-processing/bowtie/deduplicated/302.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:39:46\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/303.sorted.bam -O ../qc-processing/bowtie/deduplicated/303.dedup.bam -M ../qc-processing/bowtie/deduplicated/303.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:39:46.604 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:39:46 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/303.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/303.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/303.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:39:46 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:39:46 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:39:46\tMarkDuplicates\tStart of doWork freeMemory: 67869912; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:39:46\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:39:46\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:39:49\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3667:3,773\r\n", "INFO\t2021-03-14 18:39:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:51\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig19570:3,030\r\n", "INFO\t2021-03-14 18:39:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:53\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig27893:7,742\r\n", "INFO\t2021-03-14 18:39:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:54\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig34928:5,187\r\n", "INFO\t2021-03-14 18:39:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:56\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig42678:1,093\r\n", "INFO\t2021-03-14 18:39:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:58\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig54567:4,674\r\n", "INFO\t2021-03-14 18:39:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:39:59\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig64598:10,514\r\n", "INFO\t2021-03-14 18:39:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:01\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig73139:296\r\n", "INFO\t2021-03-14 18:40:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:02\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig97441:30\r\n", "INFO\t2021-03-14 18:40:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:04\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig132450:8,963\r\n", "INFO\t2021-03-14 18:40:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:06\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig341658:662\r\n", "INFO\t2021-03-14 18:40:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:06\tMarkDuplicates\tRead 11158976 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:40:06\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1105603600; totalMemory: 1716518912; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:40:06\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:40:07\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:40:07\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:40:07\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:40:08\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1658300312; totalMemory: 2791309312; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:40:08\tMarkDuplicates\tMarking 3496227 records as duplicates.\r\n", "INFO\t2021-03-14 18:40:08\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:40:08\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:40:26\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:40:26\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:40:26\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:40:26\tMarkDuplicates\tBefore output close freeMemory: 267477520; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:40:26\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:40:26\tMarkDuplicates\tAfter output close freeMemory: 262955632; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:40:26 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.67 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/303.sorted.bam O=../qc-processing/bowtie/deduplicated/303.dedup.bam M=../qc-processing/bowtie/deduplicated/303.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:40:28\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/304.sorted.bam -O ../qc-processing/bowtie/deduplicated/304.dedup.bam -M ../qc-processing/bowtie/deduplicated/304.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:40:28.467 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:40:28 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/304.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/304.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/304.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:40:28 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:40:28 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:40:28\tMarkDuplicates\tStart of doWork freeMemory: 67872272; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:40:28\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:40:28\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:40:31\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3005:21,657\r\n", "INFO\t2021-03-14 18:40:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:33\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig17943:1,943\r\n", "INFO\t2021-03-14 18:40:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:35\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig25971:16,015\r\n", "INFO\t2021-03-14 18:40:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:36\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig32753:1,496\r\n", "INFO\t2021-03-14 18:40:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:38\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig39210:1,639\r\n", "INFO\t2021-03-14 18:40:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:39\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig48706:8,275\r\n", "INFO\t2021-03-14 18:40:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:41\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig57512:454\r\n", "INFO\t2021-03-14 18:40:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:42\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,780\r\n", "INFO\t2021-03-14 18:40:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:44\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig74622:3,659\r\n", "INFO\t2021-03-14 18:40:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:45\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig96933:2,162\r\n", "INFO\t2021-03-14 18:40:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:47\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig122955:4,964\r\n", "INFO\t2021-03-14 18:40:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:49\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig194710:698\r\n", "INFO\t2021-03-14 18:40:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:40:49\tMarkDuplicates\tRead 12431900 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:40:49\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 839092400; totalMemory: 1485832192; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:40:49\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:40:50\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:40:50\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:40:51\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:40:51\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1427612944; totalMemory: 2560622592; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:40:51\tMarkDuplicates\tMarking 3899163 records as duplicates.\r\n", "INFO\t2021-03-14 18:40:51\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:40:52\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:41:10\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:41:10\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:41:10\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:41:11\tMarkDuplicates\tBefore output close freeMemory: 271266616; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:41:11\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:41:11\tMarkDuplicates\tAfter output close freeMemory: 262955216; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:41:11 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.71 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/304.sorted.bam O=../qc-processing/bowtie/deduplicated/304.dedup.bam M=../qc-processing/bowtie/deduplicated/304.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:41:12\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/305.sorted.bam -O ../qc-processing/bowtie/deduplicated/305.dedup.bam -M ../qc-processing/bowtie/deduplicated/305.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:41:13.017 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:41:13 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/305.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/305.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/305.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:41:13 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:41:13 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:41:13\tMarkDuplicates\tStart of doWork freeMemory: 75207992; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:41:13\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:41:13\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:41:16\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5042:6,316\r\n", "INFO\t2021-03-14 18:41:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:17\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig22036:959\r\n", "INFO\t2021-03-14 18:41:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:19\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,992\r\n", "INFO\t2021-03-14 18:41:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:21\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig39579:29,793\r\n", "INFO\t2021-03-14 18:41:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:22\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig52771:6,422\r\n", "INFO\t2021-03-14 18:41:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:24\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig63317:18,483\r\n", "INFO\t2021-03-14 18:41:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:25\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig70819:7,354\r\n", "INFO\t2021-03-14 18:41:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:27\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig93510:1\r\n", "INFO\t2021-03-14 18:41:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:29\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig123544:583\r\n", "INFO\t2021-03-14 18:41:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:31\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig391966:1,005\r\n", "INFO\t2021-03-14 18:41:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:31\tMarkDuplicates\tRead 10141601 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:41:31\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 966411328; totalMemory: 1470103552; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:41:31\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:41:31\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:41:31\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:41:32\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:41:32\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1411883200; totalMemory: 2544893952; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:41:32\tMarkDuplicates\tMarking 2355711 records as duplicates.\r\n", "INFO\t2021-03-14 18:41:32\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:41:33\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:41:51\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:41:51\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:41:51\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:41:51\tMarkDuplicates\tBefore output close freeMemory: 2433219384; totalMemory: 2544893952; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:41:51\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:41:51\tMarkDuplicates\tAfter output close freeMemory: 262953584; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:41:51 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.64 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/305.sorted.bam O=../qc-processing/bowtie/deduplicated/305.dedup.bam M=../qc-processing/bowtie/deduplicated/305.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:41:53\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/306.sorted.bam -O ../qc-processing/bowtie/deduplicated/306.dedup.bam -M ../qc-processing/bowtie/deduplicated/306.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:41:53.289 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:41:53 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/306.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/306.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/306.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:41:53 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:41:53 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:41:53\tMarkDuplicates\tStart of doWork freeMemory: 72063768; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:41:53\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:41:53\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:41:56\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4151:778\r\n", "INFO\t2021-03-14 18:41:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:58\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig20021:6,825\r\n", "INFO\t2021-03-14 18:41:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:41:59\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig29072:37,233\r\n", "INFO\t2021-03-14 18:41:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:01\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35213:878\r\n", "INFO\t2021-03-14 18:42:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:03\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig44127:2,209\r\n", "INFO\t2021-03-14 18:42:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:04\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig56521:5,240\r\n", "INFO\t2021-03-14 18:42:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:06\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig66871:14,241\r\n", "INFO\t2021-03-14 18:42:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:08\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig73139:255\r\n", "INFO\t2021-03-14 18:42:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:09\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig94817:3,286\r\n", "INFO\t2021-03-14 18:42:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:11\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig117949:512\r\n", "INFO\t2021-03-14 18:42:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:13\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig194722:1,063\r\n", "INFO\t2021-03-14 18:42:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:13\tMarkDuplicates\tRead 11374201 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:42:13\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 889362312; totalMemory: 1482686464; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:42:13\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:42:14\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:42:14\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:42:15\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:42:15\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1424467488; totalMemory: 2557476864; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:42:15\tMarkDuplicates\tMarking 3524830 records as duplicates.\r\n", "INFO\t2021-03-14 18:42:15\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:42:16\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:42:34\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:42:34\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:42:34\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:42:34\tMarkDuplicates\tBefore output close freeMemory: 2443617840; totalMemory: 2557476864; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:42:34\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:42:34\tMarkDuplicates\tAfter output close freeMemory: 266101048; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:42:34 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.69 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/306.sorted.bam O=../qc-processing/bowtie/deduplicated/306.dedup.bam M=../qc-processing/bowtie/deduplicated/306.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:42:36\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/307.sorted.bam -O ../qc-processing/bowtie/deduplicated/307.dedup.bam -M ../qc-processing/bowtie/deduplicated/307.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:42:36.423 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:42:36 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/307.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/307.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/307.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:42:36 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:42:36 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:42:36\tMarkDuplicates\tStart of doWork freeMemory: 75210616; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:42:36\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:42:36\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:42:39\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4035:809\r\n", "INFO\t2021-03-14 18:42:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:41\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig20103:4,160\r\n", "INFO\t2021-03-14 18:42:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:42\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig29276:2,601\r\n", "INFO\t2021-03-14 18:42:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:44\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35461:3,280\r\n", "INFO\t2021-03-14 18:42:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:46\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig45593:3,499\r\n", "INFO\t2021-03-14 18:42:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:47\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig57206:190\r\n", "INFO\t2021-03-14 18:42:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:49\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,809\r\n", "INFO\t2021-03-14 18:42:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:51\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig84270:1,150\r\n", "INFO\t2021-03-14 18:42:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:52\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig105337:8,560\r\n", "INFO\t2021-03-14 18:42:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:54\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig154392:6,495\r\n", "INFO\t2021-03-14 18:42:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:42:55\tMarkDuplicates\tRead 10677350 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:42:55\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1229584120; totalMemory: 1795162112; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:42:55\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:42:56\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:42:56\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:42:57\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:42:57\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1736943024; totalMemory: 2869952512; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:42:57\tMarkDuplicates\tMarking 3068097 records as duplicates.\r\n", "INFO\t2021-03-14 18:42:57\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:42:57\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:43:15\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:43:15\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:43:15\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:43:15\tMarkDuplicates\tBefore output close freeMemory: 263501632; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:43:15\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:43:15\tMarkDuplicates\tAfter output close freeMemory: 258761176; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:43:15 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.65 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/307.sorted.bam O=../qc-processing/bowtie/deduplicated/307.dedup.bam M=../qc-processing/bowtie/deduplicated/307.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:43:17\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/308.sorted.bam -O ../qc-processing/bowtie/deduplicated/308.dedup.bam -M ../qc-processing/bowtie/deduplicated/308.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:43:17.340 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:43:17 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/308.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/308.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/308.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:43:17 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:43:17 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:43:17\tMarkDuplicates\tStart of doWork freeMemory: 72061112; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:43:17\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:43:17\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:43:20\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3005:21,600\r\n", "INFO\t2021-03-14 18:43:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:22\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig17443:17,549\r\n", "INFO\t2021-03-14 18:43:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:23\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig25496:21,631\r\n", "INFO\t2021-03-14 18:43:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:25\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig32730:7,388\r\n", "INFO\t2021-03-14 18:43:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:26\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig37686:4,130\r\n", "INFO\t2021-03-14 18:43:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:28\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig46700:4,617\r\n", "INFO\t2021-03-14 18:43:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:30\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig56693:2,680\r\n", "INFO\t2021-03-14 18:43:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:31\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig64644:275\r\n", "INFO\t2021-03-14 18:43:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:33\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig71412:29,764\r\n", "INFO\t2021-03-14 18:43:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:34\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,944\r\n", "INFO\t2021-03-14 18:43:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:36\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig107599:7,284\r\n", "INFO\t2021-03-14 18:43:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:38\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig147638:757\r\n", "INFO\t2021-03-14 18:43:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:43:39\tMarkDuplicates\tRead 12964605 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:43:39\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 829658464; totalMemory: 1465909248; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:43:39\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:43:40\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:43:40\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:43:41\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:43:41\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1407687672; totalMemory: 2540699648; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:43:41\tMarkDuplicates\tMarking 3980225 records as duplicates.\r\n", "INFO\t2021-03-14 18:43:41\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:43:42\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:44:02\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:44:02\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:44:02\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:44:02\tMarkDuplicates\tBefore output close freeMemory: 267981816; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:44:02\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:44:02\tMarkDuplicates\tAfter output close freeMemory: 262950416; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:44:02 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.75 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/308.sorted.bam O=../qc-processing/bowtie/deduplicated/308.dedup.bam M=../qc-processing/bowtie/deduplicated/308.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:44:04\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/309.sorted.bam -O ../qc-processing/bowtie/deduplicated/309.dedup.bam -M ../qc-processing/bowtie/deduplicated/309.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:44:04.269 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:44:04 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/309.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/309.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/309.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:44:04 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:44:04 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:44:04\tMarkDuplicates\tStart of doWork freeMemory: 72063016; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:44:04\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:44:04\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:44:07\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2750:11,456\r\n", "INFO\t2021-03-14 18:44:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:09\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig16904:4,783\r\n", "INFO\t2021-03-14 18:44:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:11\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig24126:14,157\r\n", "INFO\t2021-03-14 18:44:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:12\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,655\r\n", "INFO\t2021-03-14 18:44:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:14\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig35613:10,283\r\n", "INFO\t2021-03-14 18:44:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:16\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig42980:24,005\r\n", "INFO\t2021-03-14 18:44:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:17\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig52971:1,838\r\n", "INFO\t2021-03-14 18:44:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:19\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig59523:8,321\r\n", "INFO\t2021-03-14 18:44:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:21\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,821\r\n", "INFO\t2021-03-14 18:44:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:22\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig74383:6,496\r\n", "INFO\t2021-03-14 18:44:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:24\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig90311:478\r\n", "INFO\t2021-03-14 18:44:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:25\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig111123:11,150\r\n", "INFO\t2021-03-14 18:44:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:27\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig148303:745\r\n", "INFO\t2021-03-14 18:44:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:44:29\tMarkDuplicates\tRead 13993476 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:44:29\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 906439848; totalMemory: 1569718272; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:44:29\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:44:29\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:44:29\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:44:30\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:44:31\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1511499216; totalMemory: 2644508672; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:44:31\tMarkDuplicates\tMarking 4005909 records as duplicates.\r\n", "INFO\t2021-03-14 18:44:31\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:44:31\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:44:54\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:44:54\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:44:54\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:44:54\tMarkDuplicates\tBefore output close freeMemory: 271011368; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:44:54\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:44:54\tMarkDuplicates\tAfter output close freeMemory: 262954976; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:44:54 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.84 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/309.sorted.bam O=../qc-processing/bowtie/deduplicated/309.dedup.bam M=../qc-processing/bowtie/deduplicated/309.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:44:56\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/311.sorted.bam -O ../qc-processing/bowtie/deduplicated/311.dedup.bam -M ../qc-processing/bowtie/deduplicated/311.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:44:56.704 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:44:56 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/311.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/311.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/311.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:44:56 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:44:56 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:44:56\tMarkDuplicates\tStart of doWork freeMemory: 72063200; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:44:56\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:44:56\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:44:59\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3874:7,263\r\n", "INFO\t2021-03-14 18:44:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:01\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig20004:12,075\r\n", "INFO\t2021-03-14 18:45:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:03\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig28601:21,958\r\n", "INFO\t2021-03-14 18:45:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:04\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35213:870\r\n", "INFO\t2021-03-14 18:45:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:06\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig43353:18,683\r\n", "INFO\t2021-03-14 18:45:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:08\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig56033:1,092\r\n", "INFO\t2021-03-14 18:45:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:09\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig66007:6,443\r\n", "INFO\t2021-03-14 18:45:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:11\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig70638:19,186\r\n", "INFO\t2021-03-14 18:45:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:12\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig87755:1,513\r\n", "INFO\t2021-03-14 18:45:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:14\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig111970:7,422\r\n", "INFO\t2021-03-14 18:45:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:16\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig175154:3,901\r\n", "INFO\t2021-03-14 18:45:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:17\tMarkDuplicates\tRead 11533234 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:45:17\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1001635824; totalMemory: 1576009728; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:45:17\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:45:17\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:45:17\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:45:18\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:45:18\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1517791112; totalMemory: 2650800128; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:45:18\tMarkDuplicates\tMarking 3094631 records as duplicates.\r\n", "INFO\t2021-03-14 18:45:18\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:45:19\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:45:37\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:45:37\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:45:37\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:45:38\tMarkDuplicates\tBefore output close freeMemory: 266926408; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:45:38\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:45:38\tMarkDuplicates\tAfter output close freeMemory: 262955568; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:45:38 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.69 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/311.sorted.bam O=../qc-processing/bowtie/deduplicated/311.dedup.bam M=../qc-processing/bowtie/deduplicated/311.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:45:40\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/312.sorted.bam -O ../qc-processing/bowtie/deduplicated/312.dedup.bam -M ../qc-processing/bowtie/deduplicated/312.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:45:40.294 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:45:40 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/312.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/312.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/312.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:45:40 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:45:40 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:45:40\tMarkDuplicates\tStart of doWork freeMemory: 72063536; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:45:40\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:45:40\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:45:43\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3036:14,200\r\n", "INFO\t2021-03-14 18:45:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:45\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig18125:18,538\r\n", "INFO\t2021-03-14 18:45:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:46\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig26549:5,947\r\n", "INFO\t2021-03-14 18:45:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:48\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig33765:4,506\r\n", "INFO\t2021-03-14 18:45:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:50\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig41930:235\r\n", "INFO\t2021-03-14 18:45:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:51\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig53025:2,316\r\n", "INFO\t2021-03-14 18:45:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:53\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig64723:1,565\r\n", "INFO\t2021-03-14 18:45:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:54\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig74351:646\r\n", "INFO\t2021-03-14 18:45:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:56\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig97360:708\r\n", "INFO\t2021-03-14 18:45:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:58\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig123544:573\r\n", "INFO\t2021-03-14 18:45:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:45:59\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig196361:896\r\n", "INFO\t2021-03-14 18:45:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:00\tMarkDuplicates\tRead 11408430 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:46:00\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1172340304; totalMemory: 1737490432; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:46:00\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:46:00\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:46:00\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:46:01\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:46:02\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1679271008; totalMemory: 2812280832; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:46:02\tMarkDuplicates\tMarking 2991794 records as duplicates.\r\n", "INFO\t2021-03-14 18:46:02\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:46:02\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:46:21\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:46:21\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:46:21\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:46:21\tMarkDuplicates\tBefore output close freeMemory: 263603720; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:46:21\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:46:21\tMarkDuplicates\tAfter output close freeMemory: 262954816; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:46:21 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.69 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/312.sorted.bam O=../qc-processing/bowtie/deduplicated/312.dedup.bam M=../qc-processing/bowtie/deduplicated/312.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:46:23\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/313.sorted.bam -O ../qc-processing/bowtie/deduplicated/313.dedup.bam -M ../qc-processing/bowtie/deduplicated/313.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:46:23.464 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:46:23 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/313.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/313.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/313.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:46:23 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:46:23 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:46:23\tMarkDuplicates\tStart of doWork freeMemory: 75207864; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:46:23\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:46:23\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:46:27\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4608:13,623\r\n", "INFO\t2021-03-14 18:46:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:28\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig20707:12,497\r\n", "INFO\t2021-03-14 18:46:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:30\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig29976:25,827\r\n", "INFO\t2021-03-14 18:46:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:31\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig36186:33,329\r\n", "INFO\t2021-03-14 18:46:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:33\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig45969:18,573\r\n", "INFO\t2021-03-14 18:46:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:35\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig56693:11,961\r\n", "INFO\t2021-03-14 18:46:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:36\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig68253:1,151\r\n", "INFO\t2021-03-14 18:46:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:38\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig74927:534\r\n", "INFO\t2021-03-14 18:46:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:40\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig98616:5,019\r\n", "INFO\t2021-03-14 18:46:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:41\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig133838:606\r\n", "INFO\t2021-03-14 18:46:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:43\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig519002:3,189\r\n", "INFO\t2021-03-14 18:46:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:46:43\tMarkDuplicates\tRead 11112238 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:46:43\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 771321592; totalMemory: 1342177280; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:46:43\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:46:44\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:46:44\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:46:45\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:46:45\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1283956728; totalMemory: 2416967680; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:46:45\tMarkDuplicates\tMarking 3249319 records as duplicates.\r\n", "INFO\t2021-03-14 18:46:45\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:46:46\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:47:03\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:47:03\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:47:03\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:47:04\tMarkDuplicates\tBefore output close freeMemory: 266811864; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:47:04\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:47:04\tMarkDuplicates\tAfter output close freeMemory: 258759384; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:47:04 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.68 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/313.sorted.bam O=../qc-processing/bowtie/deduplicated/313.dedup.bam M=../qc-processing/bowtie/deduplicated/313.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:47:05\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/314.sorted.bam -O ../qc-processing/bowtie/deduplicated/314.dedup.bam -M ../qc-processing/bowtie/deduplicated/314.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:47:06.000 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:47:06 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/314.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/314.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/314.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:47:06 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:47:06 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:47:06\tMarkDuplicates\tStart of doWork freeMemory: 72060736; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:47:06\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:47:06\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:47:09\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig16563:14,119\r\n", "INFO\t2021-03-14 18:47:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:11\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig29213:12,328\r\n", "INFO\t2021-03-14 18:47:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:12\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig38003:16,521\r\n", "INFO\t2021-03-14 18:47:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:14\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig56033:1,106\r\n", "INFO\t2021-03-14 18:47:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:16\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig66297:3,136\r\n", "INFO\t2021-03-14 18:47:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:17\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,925\r\n", "INFO\t2021-03-14 18:47:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:19\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig89106:10,274\r\n", "INFO\t2021-03-14 18:47:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:21\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig112073:1,953\r\n", "INFO\t2021-03-14 18:47:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:22\tMarkDuplicates\tRead 8972206 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:47:23\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1061879600; totalMemory: 1509949440; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:47:23\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:47:23\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:47:23\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:47:24\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:47:24\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1451727880; totalMemory: 2584739840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:47:24\tMarkDuplicates\tMarking 2392794 records as duplicates.\r\n", "INFO\t2021-03-14 18:47:24\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:47:24\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:47:40\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:47:40\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:47:40\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:47:40\tMarkDuplicates\tBefore output close freeMemory: 271142088; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:47:40\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:47:40\tMarkDuplicates\tAfter output close freeMemory: 258758784; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:47:40 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.58 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/314.sorted.bam O=../qc-processing/bowtie/deduplicated/314.dedup.bam M=../qc-processing/bowtie/deduplicated/314.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:47:42\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/315.sorted.bam -O ../qc-processing/bowtie/deduplicated/315.dedup.bam -M ../qc-processing/bowtie/deduplicated/315.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:47:42.593 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:47:42 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/315.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/315.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/315.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:47:42 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:47:42 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:47:42\tMarkDuplicates\tStart of doWork freeMemory: 75210184; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:47:42\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:47:42\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:47:46\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2688:17,828\r\n", "INFO\t2021-03-14 18:47:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:47\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig16435:2,100\r\n", "INFO\t2021-03-14 18:47:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:49\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig23843:36,756\r\n", "INFO\t2021-03-14 18:47:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:50\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig30569:261\r\n", "INFO\t2021-03-14 18:47:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:52\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig35403:41,139\r\n", "INFO\t2021-03-14 18:47:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:54\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig42766:13,552\r\n", "INFO\t2021-03-14 18:47:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:55\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig52605:3,506\r\n", "INFO\t2021-03-14 18:47:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:57\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig59490:14,284\r\n", "INFO\t2021-03-14 18:47:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:47:58\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig69234:9,229\r\n", "INFO\t2021-03-14 18:47:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:00\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig78287:14,880\r\n", "INFO\t2021-03-14 18:48:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:01\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,705\r\n", "INFO\t2021-03-14 18:48:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:03\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig124113:2,808\r\n", "INFO\t2021-03-14 18:48:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:04\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig182192:5,547\r\n", "INFO\t2021-03-14 18:48:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:05\tMarkDuplicates\tRead 13585458 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:48:06\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 870717000; totalMemory: 1534066688; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:48:06\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:48:07\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:48:07\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:48:08\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:48:08\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1475847368; totalMemory: 2608857088; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:48:08\tMarkDuplicates\tMarking 4162565 records as duplicates.\r\n", "INFO\t2021-03-14 18:48:08\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:48:10\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:48:30\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:48:30\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:48:30\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:48:31\tMarkDuplicates\tBefore output close freeMemory: 271053512; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:48:31\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:48:31\tMarkDuplicates\tAfter output close freeMemory: 262954792; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:48:31 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.81 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/315.sorted.bam O=../qc-processing/bowtie/deduplicated/315.dedup.bam M=../qc-processing/bowtie/deduplicated/315.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:48:32\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/316.sorted.bam -O ../qc-processing/bowtie/deduplicated/316.dedup.bam -M ../qc-processing/bowtie/deduplicated/316.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:48:32.922 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:48:33 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/316.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/316.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/316.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:48:33 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:48:33 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:48:33\tMarkDuplicates\tStart of doWork freeMemory: 67871640; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:48:33\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:48:33\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:48:36\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig1927:15,652\r\n", "INFO\t2021-03-14 18:48:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:37\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig8637:2,376\r\n", "INFO\t2021-03-14 18:48:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:39\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig20015:4,524\r\n", "INFO\t2021-03-14 18:48:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:41\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig26025:641\r\n", "INFO\t2021-03-14 18:48:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:42\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig30879:28,594\r\n", "INFO\t2021-03-14 18:48:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:44\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig35776:12,482\r\n", "INFO\t2021-03-14 18:48:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:45\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig42152:3,532\r\n", "INFO\t2021-03-14 18:48:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:47\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig50033:24,901\r\n", "INFO\t2021-03-14 18:48:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:48\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig56693:12,060\r\n", "INFO\t2021-03-14 18:48:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:50\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig64488:2,628\r\n", "INFO\t2021-03-14 18:48:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:51\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig69263:4,710\r\n", "INFO\t2021-03-14 18:48:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:53\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig78322:61\r\n", "INFO\t2021-03-14 18:48:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:55\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig91287:23\r\n", "INFO\t2021-03-14 18:48:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:56\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig107387:6,269\r\n", "INFO\t2021-03-14 18:48:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:58\tMarkDuplicates\tRead 15,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: Contig137778:3,201\r\n", "INFO\t2021-03-14 18:48:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:48:59\tMarkDuplicates\tRead 16,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: Contig206377:598\r\n", "INFO\t2021-03-14 18:48:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:49:00\tMarkDuplicates\tRead 16487174 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:49:00\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 925568544; totalMemory: 1663041536; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:49:00\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:49:01\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:49:01\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:49:02\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:49:02\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1604821976; totalMemory: 2737831936; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:49:02\tMarkDuplicates\tMarking 4746427 records as duplicates.\r\n", "INFO\t2021-03-14 18:49:02\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:49:03\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:49:24\tMarkDuplicates\tWritten 10,000,000 records. Elapsed time: 00:00:21s. Time for last 10,000,000: 21s. Last read position: Contig111110:738\r\n", "INFO\t2021-03-14 18:49:28\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:49:28\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:49:28\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:49:28\tMarkDuplicates\tBefore output close freeMemory: 267230272; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:49:28\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:49:28\tMarkDuplicates\tAfter output close freeMemory: 262954264; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:49:28 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.93 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/316.sorted.bam O=../qc-processing/bowtie/deduplicated/316.dedup.bam M=../qc-processing/bowtie/deduplicated/316.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:49:30\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/317.sorted.bam -O ../qc-processing/bowtie/deduplicated/317.dedup.bam -M ../qc-processing/bowtie/deduplicated/317.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:49:30.592 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:49:30 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/317.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/317.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/317.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:49:30 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:49:30 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:49:30\tMarkDuplicates\tStart of doWork freeMemory: 72062560; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:49:30\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:49:30\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:49:33\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5612:4,135\r\n", "INFO\t2021-03-14 18:49:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:49:35\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig22309:2,660\r\n", "INFO\t2021-03-14 18:49:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:49:37\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig31395:31,151\r\n", "INFO\t2021-03-14 18:49:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:49:38\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig40789:87\r\n", "INFO\t2021-03-14 18:49:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:49:40\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig54239:529\r\n", "INFO\t2021-03-14 18:49:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:49:41\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig66209:9,419\r\n", "INFO\t2021-03-14 18:49:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:49:43\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig77346:3,884\r\n", "INFO\t2021-03-14 18:49:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:49:45\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,264\r\n", "INFO\t2021-03-14 18:49:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:49:46\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig149343:2,185\r\n", "INFO\t2021-03-14 18:49:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:49:47\tMarkDuplicates\tRead 9672371 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:49:48\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 914813424; totalMemory: 1423966208; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:49:48\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:49:48\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:49:48\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:49:49\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:49:49\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1365745632; totalMemory: 2498756608; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:49:49\tMarkDuplicates\tMarking 2376458 records as duplicates.\r\n", "INFO\t2021-03-14 18:49:49\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:49:50\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:50:07\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:50:07\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:50:07\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:50:07\tMarkDuplicates\tBefore output close freeMemory: 2387710192; totalMemory: 2498756608; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:50:07\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:50:07\tMarkDuplicates\tAfter output close freeMemory: 262954104; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:50:07 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.62 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/317.sorted.bam O=../qc-processing/bowtie/deduplicated/317.dedup.bam M=../qc-processing/bowtie/deduplicated/317.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:50:09\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/318.sorted.bam -O ../qc-processing/bowtie/deduplicated/318.dedup.bam -M ../qc-processing/bowtie/deduplicated/318.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:50:09.567 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:50:09 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/318.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/318.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/318.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:50:09 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:50:09 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:50:09\tMarkDuplicates\tStart of doWork freeMemory: 72062096; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:50:09\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:50:09\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:50:13\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: Contig4689:1\r\n", "INFO\t2021-03-14 18:50:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:15\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig21387:3,165\r\n", "INFO\t2021-03-14 18:50:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:17\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,667\r\n", "INFO\t2021-03-14 18:50:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:18\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig38252:19,888\r\n", "INFO\t2021-03-14 18:50:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:20\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig51001:3,157\r\n", "INFO\t2021-03-14 18:50:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:22\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig61804:4,494\r\n", "INFO\t2021-03-14 18:50:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:23\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig73139:80\r\n", "INFO\t2021-03-14 18:50:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:25\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig98642:9,877\r\n", "INFO\t2021-03-14 18:50:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:26\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig137778:4,200\r\n", "INFO\t2021-03-14 18:50:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:28\tMarkDuplicates\tRead 9912254 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:50:28\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1191886000; totalMemory: 1729101824; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:50:28\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:50:29\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:50:29\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:50:30\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:50:30\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1670881864; totalMemory: 2803892224; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:50:30\tMarkDuplicates\tMarking 2849552 records as duplicates.\r\n", "INFO\t2021-03-14 18:50:30\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:50:31\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:50:47\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:50:47\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:50:47\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:50:47\tMarkDuplicates\tBefore output close freeMemory: 265477248; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:50:47\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:50:47\tMarkDuplicates\tAfter output close freeMemory: 262954248; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:50:47 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.63 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/318.sorted.bam O=../qc-processing/bowtie/deduplicated/318.dedup.bam M=../qc-processing/bowtie/deduplicated/318.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:50:49\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/319.sorted.bam -O ../qc-processing/bowtie/deduplicated/319.dedup.bam -M ../qc-processing/bowtie/deduplicated/319.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:50:49.071 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:50:49 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/319.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/319.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/319.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:50:49 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:50:49 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:50:49\tMarkDuplicates\tStart of doWork freeMemory: 72063952; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:50:49\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:50:49\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:50:52\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3671:5,293\r\n", "INFO\t2021-03-14 18:50:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:53\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig19437:7,265\r\n", "INFO\t2021-03-14 18:50:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:55\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig28248:872\r\n", "INFO\t2021-03-14 18:50:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:57\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35213:23\r\n", "INFO\t2021-03-14 18:50:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:50:58\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig43565:1,872\r\n", "INFO\t2021-03-14 18:50:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:00\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig56033:1,103\r\n", "INFO\t2021-03-14 18:51:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:01\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig67512:4,131\r\n", "INFO\t2021-03-14 18:51:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:03\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig75123:6,167\r\n", "INFO\t2021-03-14 18:51:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:05\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig98472:2,165\r\n", "INFO\t2021-03-14 18:51:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:06\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig119450:2,337\r\n", "INFO\t2021-03-14 18:51:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:08\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig192657:2,815\r\n", "INFO\t2021-03-14 18:51:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:08\tMarkDuplicates\tRead 11422505 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:51:09\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 887889128; totalMemory: 1473249280; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:51:09\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:51:09\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:51:09\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:51:10\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:51:10\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1415030608; totalMemory: 2548039680; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:51:10\tMarkDuplicates\tMarking 3882970 records as duplicates.\r\n", "INFO\t2021-03-14 18:51:10\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:51:11\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:51:29\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:51:29\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:51:29\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:51:29\tMarkDuplicates\tBefore output close freeMemory: 271494936; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:51:29\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:51:29\tMarkDuplicates\tAfter output close freeMemory: 258761080; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:51:29 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.67 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/319.sorted.bam O=../qc-processing/bowtie/deduplicated/319.dedup.bam M=../qc-processing/bowtie/deduplicated/319.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:51:31\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/321.sorted.bam -O ../qc-processing/bowtie/deduplicated/321.dedup.bam -M ../qc-processing/bowtie/deduplicated/321.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:51:31.107 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:51:31 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/321.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/321.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/321.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:51:31 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:51:31 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:51:31\tMarkDuplicates\tStart of doWork freeMemory: 72064064; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:51:31\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:51:31\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:51:34\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5118:1,555\r\n", "INFO\t2021-03-14 18:51:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:36\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig22087:36,503\r\n", "INFO\t2021-03-14 18:51:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:37\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,922\r\n", "INFO\t2021-03-14 18:51:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:39\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig39730:51\r\n", "INFO\t2021-03-14 18:51:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:41\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig52672:3,609\r\n", "INFO\t2021-03-14 18:51:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:42\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig63400:5,899\r\n", "INFO\t2021-03-14 18:51:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:44\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig71398:5,251\r\n", "INFO\t2021-03-14 18:51:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:45\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig95550:392\r\n", "INFO\t2021-03-14 18:51:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:47\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig127749:5,129\r\n", "INFO\t2021-03-14 18:51:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:49\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig519002:3,466\r\n", "INFO\t2021-03-14 18:51:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:51:49\tMarkDuplicates\tRead 10083385 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:51:49\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 959952224; totalMemory: 1482686464; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:51:49\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:51:49\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:51:49\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:51:50\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:51:50\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1424467744; totalMemory: 2557476864; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:51:50\tMarkDuplicates\tMarking 2547479 records as duplicates.\r\n", "INFO\t2021-03-14 18:51:50\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:51:51\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:52:08\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:52:08\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:52:08\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:52:08\tMarkDuplicates\tBefore output close freeMemory: 267501160; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:52:08\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:52:08\tMarkDuplicates\tAfter output close freeMemory: 266101096; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:52:08 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.63 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/321.sorted.bam O=../qc-processing/bowtie/deduplicated/321.dedup.bam M=../qc-processing/bowtie/deduplicated/321.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:52:10\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/322.sorted.bam -O ../qc-processing/bowtie/deduplicated/322.dedup.bam -M ../qc-processing/bowtie/deduplicated/322.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:52:10.655 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:52:10 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/322.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/322.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/322.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:52:10 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:52:10 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:52:10\tMarkDuplicates\tStart of doWork freeMemory: 72065120; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:52:10\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:52:10\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:52:13\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3311:9,966\r\n", "INFO\t2021-03-14 18:52:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:52:15\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig19099:1,403\r\n", "INFO\t2021-03-14 18:52:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:52:17\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig27068:7,330\r\n", "INFO\t2021-03-14 18:52:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:52:18\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig34149:10,404\r\n", "INFO\t2021-03-14 18:52:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:52:20\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig41787:13,428\r\n", "INFO\t2021-03-14 18:52:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:52:21\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig52744:6,449\r", "\r\n", "INFO\t2021-03-14 18:52:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:52:23\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig61794:5,520\r\n", "INFO\t2021-03-14 18:52:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:52:25\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,581\r\n", "INFO\t2021-03-14 18:52:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:52:26\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig85486:2,331\r\n", "INFO\t2021-03-14 18:52:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "INFO\t2021-03-14 18:52:28\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig107823:19,404\r\n", "INFO\t2021-03-14 18:52:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:52:29\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig151503:1,505\r\n", "INFO\t2021-03-14 18:52:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:52:31\tMarkDuplicates\tRead 11786078 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:52:31\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1029882048; totalMemory: 1627389952; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:52:31\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:52:31\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:52:31\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:52:32\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:52:33\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1569171152; totalMemory: 2702180352; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:52:33\tMarkDuplicates\tMarking 3431166 records as duplicates.\r\n", "INFO\t2021-03-14 18:52:33\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:52:33\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:52:52\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:52:52\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:52:52\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:52:52\tMarkDuplicates\tBefore output close freeMemory: 261069632; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:52:52\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:52:52\tMarkDuplicates\tAfter output close freeMemory: 258761104; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:52:52 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.70 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/322.sorted.bam O=../qc-processing/bowtie/deduplicated/322.dedup.bam M=../qc-processing/bowtie/deduplicated/322.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:52:54\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/323.sorted.bam -O ../qc-processing/bowtie/deduplicated/323.dedup.bam -M ../qc-processing/bowtie/deduplicated/323.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:52:54.494 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:52:54 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/323.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/323.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/323.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:52:54 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:52:54 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:52:54\tMarkDuplicates\tStart of doWork freeMemory: 72063072; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:52:54\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:52:54\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:52:57\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2021:3,967\r\n", "INFO\t2021-03-14 18:52:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:52:59\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig9322:683\r\n", "INFO\t2021-03-14 18:52:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:01\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig20662:23,925\r\n", "INFO\t2021-03-14 18:53:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:02\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig27036:6,835\r\n", "INFO\t2021-03-14 18:53:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:04\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig32909:11,883\r\n", "INFO\t2021-03-14 18:53:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:05\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig37595:11,517\r\n", "INFO\t2021-03-14 18:53:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:07\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig44916:13,929\r\n", "INFO\t2021-03-14 18:53:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:08\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig53739:11,272\r\n", "INFO\t2021-03-14 18:53:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:10\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig61889:466\r\n", "INFO\t2021-03-14 18:53:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:11\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig70595:996\r\n", "INFO\t2021-03-14 18:53:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:13\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig83174:2,272\r\n", "INFO\t2021-03-14 18:53:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:14\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,208\r\n", "INFO\t2021-03-14 18:53:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:16\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig121487:5,946\r\n", "INFO\t2021-03-14 18:53:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:17\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig165237:1,379\r\n", "INFO\t2021-03-14 18:53:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:19\tMarkDuplicates\tRead 14887252 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:53:19\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1013060728; totalMemory: 1742733312; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:53:19\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:53:19\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:53:19\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:53:20\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:53:21\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1684512528; totalMemory: 2817523712; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:53:21\tMarkDuplicates\tMarking 4633463 records as duplicates.\r\n", "INFO\t2021-03-14 18:53:21\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:53:21\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:53:43\tMarkDuplicates\tWritten 10,000,000 records. Elapsed time: 00:00:21s. Time for last 10,000,000: 21s. Last read position: Contig213225:1,154\r\n", "INFO\t2021-03-14 18:53:43\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:53:43\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:53:43\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:53:44\tMarkDuplicates\tBefore output close freeMemory: 264389488; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:53:44\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:53:44\tMarkDuplicates\tAfter output close freeMemory: 258759096; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:53:44 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.83 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/323.sorted.bam O=../qc-processing/bowtie/deduplicated/323.dedup.bam M=../qc-processing/bowtie/deduplicated/323.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:53:45\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/324.sorted.bam -O ../qc-processing/bowtie/deduplicated/324.dedup.bam -M ../qc-processing/bowtie/deduplicated/324.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:53:45.972 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:53:46 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/324.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/324.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/324.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:53:46 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:53:46 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:53:46\tMarkDuplicates\tStart of doWork freeMemory: 72064800; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:53:46\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:53:46\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:53:49\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2173:15,090\r\n", "INFO\t2021-03-14 18:53:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:50\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig16513:4,654\r\n", "INFO\t2021-03-14 18:53:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:52\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig24235:20,153\r\n", "INFO\t2021-03-14 18:53:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:53\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig31018:21,050\r\n", "INFO\t2021-03-14 18:53:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:55\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig35434:16,987\r\n", "INFO\t2021-03-14 18:53:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:56\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig42783:29,531\r\n", "INFO\t2021-03-14 18:53:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:53:58\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig53025:1,828\r\n", "INFO\t2021-03-14 18:53:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:00\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig62354:4,275\r\n", "INFO\t2021-03-14 18:54:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:01\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,891\r\n", "INFO\t2021-03-14 18:54:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:03\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,669\r\n", "INFO\t2021-03-14 18:54:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:04\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig106749:435\r\n", "INFO\t2021-03-14 18:54:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:06\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig141072:9,286\r\n", "INFO\t2021-03-14 18:54:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:08\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig627027:5,789\r\n", "INFO\t2021-03-14 18:54:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:08\tMarkDuplicates\tRead 13050914 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:54:08\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 890362904; totalMemory: 1548746752; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:54:08\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:54:08\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:54:08\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:54:09\tMarkDuplicates\tSorting list of duplicate records.\r", "\r\n", "INFO\t2021-03-14 18:54:09\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1490527208; totalMemory: 2623537152; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:54:09\tMarkDuplicates\tMarking 4287054 records as duplicates.\r\n", "INFO\t2021-03-14 18:54:09\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:54:10\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:54:29\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:54:29\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:54:29\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:54:30\tMarkDuplicates\tBefore output close freeMemory: 262950384; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:54:30\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:54:30\tMarkDuplicates\tAfter output close freeMemory: 258760584; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:54:30 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.74 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/324.sorted.bam O=../qc-processing/bowtie/deduplicated/324.dedup.bam M=../qc-processing/bowtie/deduplicated/324.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:54:32\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/325.sorted.bam -O ../qc-processing/bowtie/deduplicated/325.dedup.bam -M ../qc-processing/bowtie/deduplicated/325.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:54:32.667 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:54:32 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/325.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/325.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/325.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:54:32 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:54:32 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:54:32\tMarkDuplicates\tStart of doWork freeMemory: 72063672; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:54:32\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:54:32\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:54:36\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2912:405\r\n", "INFO\t2021-03-14 18:54:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:37\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig17606:26,803\r\n", "INFO\t2021-03-14 18:54:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:39\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig25418:13,617\r\n", "INFO\t2021-03-14 18:54:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:41\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig32391:18,330\r\n", "INFO\t2021-03-14 18:54:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:42\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig38258:14,976\r\n", "INFO\t2021-03-14 18:54:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:44\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig47690:2,406\r\n", "INFO\t2021-03-14 18:54:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:46\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig56693:12,114\r\n", "INFO\t2021-03-14 18:54:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:47\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig68037:874\r\n", "INFO\t2021-03-14 18:54:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:49\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig74190:10,817\r\n", "INFO\t2021-03-14 18:54:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:50\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig94856:223\r\n", "INFO\t2021-03-14 18:54:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:52\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig119922:1,495\r\n", "INFO\t2021-03-14 18:54:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:54\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig181070:169\r\n", "INFO\t2021-03-14 18:54:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:54:55\tMarkDuplicates\tRead 12567210 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:54:55\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1035481448; totalMemory: 1653604352; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:54:55\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:54:55\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:54:55\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:54:56\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:54:57\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1595385448; totalMemory: 2728394752; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:54:57\tMarkDuplicates\tMarking 3361738 records as duplicates.\r\n", "INFO\t2021-03-14 18:54:57\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:54:57\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:55:19\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:55:19\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:55:19\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:55:19\tMarkDuplicates\tBefore output close freeMemory: 267198016; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:55:19\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:55:19\tMarkDuplicates\tAfter output close freeMemory: 258761208; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:55:19 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.78 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/325.sorted.bam O=../qc-processing/bowtie/deduplicated/325.dedup.bam M=../qc-processing/bowtie/deduplicated/325.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:55:21\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/326.sorted.bam -O ../qc-processing/bowtie/deduplicated/326.dedup.bam -M ../qc-processing/bowtie/deduplicated/326.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:55:21.164 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:55:21 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/326.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/326.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/326.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:55:21 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:55:21 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:55:21\tMarkDuplicates\tStart of doWork freeMemory: 72062192; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:55:21\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:55:21\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:55:24\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2653:9,933\r\n", "INFO\t2021-03-14 18:55:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:26\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig16586:1,455\r\n", "INFO\t2021-03-14 18:55:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:27\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig24238:9,655\r\n", "INFO\t2021-03-14 18:55:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:29\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig31058:33,223\r\n", "INFO\t2021-03-14 18:55:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:30\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig35720:2,419\r\n", "INFO\t2021-03-14 18:55:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:32\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig42760:2,704\r\n", "INFO\t2021-03-14 18:55:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:34\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig52413:7,853\r\n", "INFO\t2021-03-14 18:55:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:35\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig61298:3,832\r\n", "INFO\t2021-03-14 18:55:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:37\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig69234:14,768\r\n", "INFO\t2021-03-14 18:55:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:38\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig82015:2,365\r\n", "INFO\t2021-03-14 18:55:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:40\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,590\r\n", "INFO\t2021-03-14 18:55:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:42\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig137778:2,754\r\n", "INFO\t2021-03-14 18:55:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:43\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig217221:376\r\n", "INFO\t2021-03-14 18:55:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:55:44\tMarkDuplicates\tRead 13259245 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:55:44\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 737989656; totalMemory: 1427111936; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:55:44\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:55:44\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:55:44\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:55:45\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:55:46\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1368891264; totalMemory: 2501902336; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:55:46\tMarkDuplicates\tMarking 4458033 records as duplicates.\r\n", "INFO\t2021-03-14 18:55:46\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:55:47\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:56:07\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:56:07\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:56:07\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:56:07\tMarkDuplicates\tBefore output close freeMemory: 264443040; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:56:07\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:56:07\tMarkDuplicates\tAfter output close freeMemory: 262953792; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:56:07 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.77 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/326.sorted.bam O=../qc-processing/bowtie/deduplicated/326.dedup.bam M=../qc-processing/bowtie/deduplicated/326.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:56:09\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/327.sorted.bam -O ../qc-processing/bowtie/deduplicated/327.dedup.bam -M ../qc-processing/bowtie/deduplicated/327.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:56:09.083 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:56:09 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/327.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/327.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/327.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:56:09 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:56:09 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:56:09\tMarkDuplicates\tStart of doWork freeMemory: 72062776; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:56:09\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:56:09\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:56:12\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5564:8,770\r\n", "INFO\t2021-03-14 18:56:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:14\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig22725:1,030\r\n", "INFO\t2021-03-14 18:56:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:16\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig32287:12,225\r\n", "INFO\t2021-03-14 18:56:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:17\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig41456:10,446\r\n", "INFO\t2021-03-14 18:56:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:19\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig55012:3,317\r\n", "INFO\t2021-03-14 18:56:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:20\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig66247:2,698\r\n", "INFO\t2021-03-14 18:56:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:22\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig77150:2,677\r\n", "INFO\t2021-03-14 18:56:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:24\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,239\r\n", "INFO\t2021-03-14 18:56:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:25\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig149741:49\r\n", "INFO\t2021-03-14 18:56:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:26\tMarkDuplicates\tRead 9679107 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:56:27\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 968185048; totalMemory: 1487929344; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:56:27\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:56:27\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:56:27\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:56:28\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:56:28\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1429709536; totalMemory: 2562719744; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:56:28\tMarkDuplicates\tMarking 2740089 records as duplicates.\r\n", "INFO\t2021-03-14 18:56:28\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:56:29\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:56:44\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:56:44\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:56:44\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:56:45\tMarkDuplicates\tBefore output close freeMemory: 264067928; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:56:45\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:56:45\tMarkDuplicates\tAfter output close freeMemory: 258760528; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:56:45 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.60 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/327.sorted.bam O=../qc-processing/bowtie/deduplicated/327.dedup.bam M=../qc-processing/bowtie/deduplicated/327.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:56:47\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/328.sorted.bam -O ../qc-processing/bowtie/deduplicated/328.dedup.bam -M ../qc-processing/bowtie/deduplicated/328.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:56:47.119 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:56:47 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/328.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/328.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/328.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:56:47 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:56:47 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:56:47\tMarkDuplicates\tStart of doWork freeMemory: 75209824; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:56:47\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:56:47\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:56:50\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig1267:12,188\r\n", "INFO\t2021-03-14 18:56:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:51\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig4405:11,675\r\n", "INFO\t2021-03-14 18:56:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:53\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig16152:3,109\r\n", "INFO\t2021-03-14 18:56:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:54\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig20906:5,346\r\n", "INFO\t2021-03-14 18:56:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:56\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig25774:8,446\r\n", "INFO\t2021-03-14 18:56:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:57\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig30068:6,481\r\n", "INFO\t2021-03-14 18:56:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:56:59\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig34228:3,120\r\n", "INFO\t2021-03-14 18:56:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:00\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig38213:13,322\r\n", "INFO\t2021-03-14 18:57:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:02\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig43678:16,844\r\n", "INFO\t2021-03-14 18:57:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:03\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig50282:20,155\r\n", "INFO\t2021-03-14 18:57:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:05\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig56693:2,683\r\n", "INFO\t2021-03-14 18:57:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:06\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig62463:2,733\r\n", "INFO\t2021-03-14 18:57:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:08\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig69234:14,487\r\n", "INFO\t2021-03-14 18:57:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:10\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig77337:13,648\r\n", "INFO\t2021-03-14 18:57:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:11\tMarkDuplicates\tRead 15,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: Contig88912:141\r\n", "INFO\t2021-03-14 18:57:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:13\tMarkDuplicates\tRead 16,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: Contig103886:900\r\n", "INFO\t2021-03-14 18:57:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:14\tMarkDuplicates\tRead 17,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: Contig124017:8,941\r\n", "INFO\t2021-03-14 18:57:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:16\tMarkDuplicates\tRead 18,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: Contig150923:994\r\n", "INFO\t2021-03-14 18:57:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:18\tMarkDuplicates\tRead 19,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: Contig218418:1,227\r\n", "INFO\t2021-03-14 18:57:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:18\tMarkDuplicates\tRead 19386217 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:57:18\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 673274584; totalMemory: 1543503872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:57:18\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:57:19\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:57:19\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:57:21\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:57:21\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1485284472; totalMemory: 2618294272; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:57:21\tMarkDuplicates\tMarking 5729855 records as duplicates.\r\n", "INFO\t2021-03-14 18:57:21\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:57:22\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:57:43\tMarkDuplicates\tWritten 10,000,000 records. Elapsed time: 00:00:20s. Time for last 10,000,000: 20s. Last read position: Contig82647:5,663\r\n", "INFO\t2021-03-14 18:57:50\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:57:50\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:57:50\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:57:50\tMarkDuplicates\tBefore output close freeMemory: 274042944; totalMemory: 384827392; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:57:50\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:57:50\tMarkDuplicates\tAfter output close freeMemory: 258760392; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:57:50 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.06 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/328.sorted.bam O=../qc-processing/bowtie/deduplicated/328.dedup.bam M=../qc-processing/bowtie/deduplicated/328.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:57:52\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/329.sorted.bam -O ../qc-processing/bowtie/deduplicated/329.dedup.bam -M ../qc-processing/bowtie/deduplicated/329.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:57:52.723 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:57:52 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/329.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/329.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/329.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:57:53 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:57:53 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:57:53\tMarkDuplicates\tStart of doWork freeMemory: 72065272; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:57:53\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:57:53\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:57:55\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3002:39,955\r\n", "INFO\t2021-03-14 18:57:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:57\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig17443:32,129\r\n", "INFO\t2021-03-14 18:57:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:57:59\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig24722:16,736\r\n", "INFO\t2021-03-14 18:57:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:01\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,919\r\n", "INFO\t2021-03-14 18:58:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:02\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig37004:13,707\r\n", "INFO\t2021-03-14 18:58:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:04\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig46265:4,039\r\n", "INFO\t2021-03-14 18:58:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:05\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig56423:22,387\r\n", "INFO\t2021-03-14 18:58:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:07\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig65290:1\r\n", "INFO\t2021-03-14 18:58:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:09\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,637\r\n", "INFO\t2021-03-14 18:58:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:10\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig84222:2,290\r\n", "INFO\t2021-03-14 18:58:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:12\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig101096:4,576\r\n", "INFO\t2021-03-14 18:58:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:14\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig123987:367\r\n", "INFO\t2021-03-14 18:58:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:15\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig194073:1,437\r\n", "INFO\t2021-03-14 18:58:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:16\tMarkDuplicates\tRead 13466533 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:58:16\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 917677528; totalMemory: 1561329664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:58:16\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:58:17\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:58:17\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:58:18\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:58:18\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1503111264; totalMemory: 2636120064; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:58:18\tMarkDuplicates\tMarking 3925434 records as duplicates.\r\n", "INFO\t2021-03-14 18:58:18\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:58:19\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:58:40\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:58:40\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:58:40\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:58:40\tMarkDuplicates\tBefore output close freeMemory: 271405896; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:58:41\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:58:41\tMarkDuplicates\tAfter output close freeMemory: 262955528; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:58:41 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.81 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/329.sorted.bam O=../qc-processing/bowtie/deduplicated/329.dedup.bam M=../qc-processing/bowtie/deduplicated/329.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:58:42\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/331.sorted.bam -O ../qc-processing/bowtie/deduplicated/331.dedup.bam -M ../qc-processing/bowtie/deduplicated/331.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:58:42.845 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:58:42 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/331.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/331.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/331.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:58:43 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:58:43 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:58:43\tMarkDuplicates\tStart of doWork freeMemory: 72064368; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:58:43\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:58:43\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:58:46\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig13791:2,742\r\n", "INFO\t2021-03-14 18:58:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:47\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig26736:13,010\r\n", "INFO\t2021-03-14 18:58:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:49\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig33631:69,518\r\n", "INFO\t2021-03-14 18:58:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:50\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig44024:2,507\r\n", "INFO\t2021-03-14 18:58:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:52\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56693:7,466\r\n", "INFO\t2021-03-14 18:58:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:54\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig64644:275\r\n", "INFO\t2021-03-14 18:58:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:55\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig69234:11,734\r\n", "INFO\t2021-03-14 18:58:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:57\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig70638:19,290\r\n", "INFO\t2021-03-14 18:58:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:58:58\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig85486:2,602\r\n", "INFO\t2021-03-14 18:58:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:59:00\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,395\r\n", "INFO\t2021-03-14 18:59:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:59:02\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig137005:2,570\r\n", "INFO\t2021-03-14 18:59:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:59:03\tMarkDuplicates\tRead 11773130 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:59:03\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 994592904; totalMemory: 1516240896; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:59:03\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:59:03\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:59:03\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:59:04\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:59:04\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1458022088; totalMemory: 2591031296; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:59:04\tMarkDuplicates\tMarking 3329870 records as duplicates.\r\n", "INFO\t2021-03-14 18:59:04\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:59:05\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:59:24\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:59:24\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:59:24\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:59:25\tMarkDuplicates\tBefore output close freeMemory: 264886040; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:59:25\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:59:25\tMarkDuplicates\tAfter output close freeMemory: 266101536; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:59:25 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.71 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/331.sorted.bam O=../qc-processing/bowtie/deduplicated/331.dedup.bam M=../qc-processing/bowtie/deduplicated/331.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:59:26\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/332.sorted.bam -O ../qc-processing/bowtie/deduplicated/332.dedup.bam -M ../qc-processing/bowtie/deduplicated/332.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:59:26.925 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:59:27 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/332.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/332.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/332.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:59:27 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:59:27 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:59:27\tMarkDuplicates\tStart of doWork freeMemory: 67873840; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:59:27\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:59:27\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 18:59:30\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig9826:4,742\r\n", "INFO\t2021-03-14 18:59:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:59:31\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig27063:3,916\r\n", "INFO\t2021-03-14 18:59:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:59:33\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig36412:566\r\n", "INFO\t2021-03-14 18:59:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:59:35\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig52139:6,683\r\n", "INFO\t2021-03-14 18:59:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:59:36\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig67549:4,154\r\n", "INFO\t2021-03-14 18:59:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:59:38\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig83429:7,741\r\n", "INFO\t2021-03-14 18:59:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:59:40\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig111435:3,659\r\n", "INFO\t2021-03-14 18:59:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:59:41\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig519002:3,179\r\n", "INFO\t2021-03-14 18:59:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 18:59:42\tMarkDuplicates\tRead 8071252 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 18:59:42\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1059719624; totalMemory: 1509949440; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:59:42\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 18:59:42\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:59:42\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 18:59:43\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 18:59:43\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1451730632; totalMemory: 2584739840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:59:43\tMarkDuplicates\tMarking 2109331 records as duplicates.\r\n", "INFO\t2021-03-14 18:59:43\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 18:59:44\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 18:59:57\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 18:59:57\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 18:59:57\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 18:59:57\tMarkDuplicates\tBefore output close freeMemory: 263869760; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:59:57\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 18:59:58\tMarkDuplicates\tAfter output close freeMemory: 262955928; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 18:59:58 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.52 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/332.sorted.bam O=../qc-processing/bowtie/deduplicated/332.dedup.bam M=../qc-processing/bowtie/deduplicated/332.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 18:59:59\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/333.sorted.bam -O ../qc-processing/bowtie/deduplicated/333.dedup.bam -M ../qc-processing/bowtie/deduplicated/333.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "17:59:59.761 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 18:59:59 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/333.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/333.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/333.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 6:59:59 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 18:59:59 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 18:59:59\tMarkDuplicates\tStart of doWork freeMemory: 67872448; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 18:59:59\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 18:59:59\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:00:03\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: Contig15441:4,178\r\n", "INFO\t2021-03-14 19:00:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:05\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig28748:5,682\r\n", "INFO\t2021-03-14 19:00:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:07\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig37981:582\r\n", "INFO\t2021-03-14 19:00:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:08\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig54291:841\r\n", "INFO\t2021-03-14 19:00:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:10\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig68908:704\r\n", "INFO\t2021-03-14 19:00:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:12\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig85291:7,988\r\n", "INFO\t2021-03-14 19:00:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:13\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig123544:573\r\n", "INFO\t2021-03-14 19:00:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:15\tMarkDuplicates\tRead 7938296 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:00:15\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1119354040; totalMemory: 1593835520; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:00:15\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:00:15\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:00:15\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:00:16\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:00:16\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1535617824; totalMemory: 2668625920; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:00:16\tMarkDuplicates\tMarking 2418757 records as duplicates.\r\n", "INFO\t2021-03-14 19:00:16\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:00:17\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:00:30\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:00:30\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:00:30\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:00:30\tMarkDuplicates\tBefore output close freeMemory: 271598384; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:00:30\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:00:30\tMarkDuplicates\tAfter output close freeMemory: 258762560; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:00:30 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.51 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/333.sorted.bam O=../qc-processing/bowtie/deduplicated/333.dedup.bam M=../qc-processing/bowtie/deduplicated/333.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:00:32\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/334.sorted.bam -O ../qc-processing/bowtie/deduplicated/334.dedup.bam -M ../qc-processing/bowtie/deduplicated/334.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:00:32.320 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:00:32 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/334.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/334.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/334.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:00:32 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:00:32 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:00:32\tMarkDuplicates\tStart of doWork freeMemory: 75208936; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:00:32\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:00:32\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:00:35\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig12011:1,177\r\n", "INFO\t2021-03-14 19:00:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:37\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig26383:9,123\r\n", "INFO\t2021-03-14 19:00:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:38\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig34438:2,014\r\n", "INFO\t2021-03-14 19:00:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:40\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig47434:99\r\n", "INFO\t2021-03-14 19:00:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:42\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56693:12,102\r\n", "INFO\t2021-03-14 19:00:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:43\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig68908:1,051\r\n", "INFO\t2021-03-14 19:00:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:45\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig76034:996\r\n", "INFO\t2021-03-14 19:00:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:47\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,745\r\n", "INFO\t2021-03-14 19:00:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:48\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig121681:3,679\r\n", "INFO\t2021-03-14 19:00:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:00:50\tMarkDuplicates\tRead 9992160 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:00:50\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1089436912; totalMemory: 1558183936; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:00:50\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:00:51\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:00:51\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:00:51\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:00:51\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1499965104; totalMemory: 2632974336; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:00:51\tMarkDuplicates\tMarking 2504699 records as duplicates.\r\n", "INFO\t2021-03-14 19:00:51\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:00:52\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:01:09\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:01:09\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:01:09\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:01:10\tMarkDuplicates\tBefore output close freeMemory: 266994512; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:01:10\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:01:10\tMarkDuplicates\tAfter output close freeMemory: 258761104; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:01:10 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.63 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/334.sorted.bam O=../qc-processing/bowtie/deduplicated/334.dedup.bam M=../qc-processing/bowtie/deduplicated/334.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:01:12\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/335.sorted.bam -O ../qc-processing/bowtie/deduplicated/335.dedup.bam -M ../qc-processing/bowtie/deduplicated/335.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:01:12.081 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:01:12 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/335.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/335.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/335.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:01:12 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:01:12 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:01:12\tMarkDuplicates\tStart of doWork freeMemory: 67868296; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:01:12\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:01:12\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:01:15\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig15609:2,433\r\n", "INFO\t2021-03-14 19:01:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:17\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig28652:3,681\r\n", "INFO\t2021-03-14 19:01:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:18\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig37656:21,265\r\n", "INFO\t2021-03-14 19:01:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:20\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig54936:592\r\n", "INFO\t2021-03-14 19:01:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:22\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,784\r\n", "INFO\t2021-03-14 19:01:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:23\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,944\r\n", "INFO\t2021-03-14 19:01:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:25\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig130572:7\r\n", "INFO\t2021-03-14 19:01:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:26\tMarkDuplicates\tRead 7774286 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:01:27\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1116295736; totalMemory: 1587544064; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:01:27\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:01:27\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:01:27\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:01:28\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:01:28\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1529324696; totalMemory: 2662334464; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:01:28\tMarkDuplicates\tMarking 2325035 records as duplicates.\r\n", "INFO\t2021-03-14 19:01:28\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:01:29\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:01:41\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:01:41\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:01:41\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:01:41\tMarkDuplicates\tBefore output close freeMemory: 272358648; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:01:41\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:01:41\tMarkDuplicates\tAfter output close freeMemory: 258759792; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:01:41 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.50 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/335.sorted.bam O=../qc-processing/bowtie/deduplicated/335.dedup.bam M=../qc-processing/bowtie/deduplicated/335.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:01:43\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/336.sorted.bam -O ../qc-processing/bowtie/deduplicated/336.dedup.bam -M ../qc-processing/bowtie/deduplicated/336.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:01:43.487 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:01:43 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/336.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/336.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/336.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:01:43 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:01:43 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:01:43\tMarkDuplicates\tStart of doWork freeMemory: 72065440; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:01:43\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:01:43\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:01:46\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4198:13,228\r\n", "INFO\t2021-03-14 19:01:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:48\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig20601:4,530\r\n", "INFO\t2021-03-14 19:01:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:50\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30130:1,252\r\n", "INFO\t2021-03-14 19:01:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:51\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35774:1,112\r\n", "INFO\t2021-03-14 19:01:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:53\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig46328:8,937\r\n", "INFO\t2021-03-14 19:01:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:54\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig57779:4,170\r\n", "INFO\t2021-03-14 19:01:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:56\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig69234:11,734\r\n", "INFO\t2021-03-14 19:01:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:01:58\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig85156:27,318\r\n", "INFO\t2021-03-14 19:01:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:00\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig104373:1,317\r\n", "INFO\t2021-03-14 19:02:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:01\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig149299:9,260\r\n", "INFO\t2021-03-14 19:02:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:02\tMarkDuplicates\tRead 10709147 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:02:02\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1003333224; totalMemory: 1545601024; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:02:02\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:02:03\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:02:03\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:02:04\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:02:04\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1487379392; totalMemory: 2620391424; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:02:04\tMarkDuplicates\tMarking 2982703 records as duplicates.\r\n", "INFO\t2021-03-14 19:02:04\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:02:05\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:02:22\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:02:22\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:02:22\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:02:23\tMarkDuplicates\tBefore output close freeMemory: 270990824; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:02:23\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:02:23\tMarkDuplicates\tAfter output close freeMemory: 262952576; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:02:23 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.66 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/336.sorted.bam O=../qc-processing/bowtie/deduplicated/336.dedup.bam M=../qc-processing/bowtie/deduplicated/336.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:02:25\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/337.sorted.bam -O ../qc-processing/bowtie/deduplicated/337.dedup.bam -M ../qc-processing/bowtie/deduplicated/337.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:02:25.041 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:02:25 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/337.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/337.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/337.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:02:25 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:02:25 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:02:25\tMarkDuplicates\tStart of doWork freeMemory: 72063224; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:02:25\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:02:25\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:02:28\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2268:9,193\r\n", "INFO\t2021-03-14 19:02:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:29\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig10742:9,617\r\n", "INFO\t2021-03-14 19:02:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:31\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig21438:15,911\r\n", "INFO\t2021-03-14 19:02:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:33\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig28264:10,588\r\n", "INFO\t2021-03-14 19:02:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:34\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig33739:575\r\n", "INFO\t2021-03-14 19:02:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:36\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig37588:13,721\r\n", "INFO\t2021-03-14 19:02:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:37\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig45152:5,695\r\n", "INFO\t2021-03-14 19:02:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:39\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig54565:4,382\r\n", "INFO\t2021-03-14 19:02:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:40\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig61796:10,932\r\n", "INFO\t2021-03-14 19:02:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:42\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig68908:744\r\n", "INFO\t2021-03-14 19:02:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:44\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig74454:3,329\r\n", "INFO\t2021-03-14 19:02:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:45\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig90977:7,694\r\n", "INFO\t2021-03-14 19:02:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:47\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig111970:3,500\r\n", "INFO\t2021-03-14 19:02:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:49\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: Contig147865:1,622\r\n", "INFO\t2021-03-14 19:02:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:50\tMarkDuplicates\tRead 15,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: Contig568337:1,178\r\n", "INFO\t2021-03-14 19:02:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:02:50\tMarkDuplicates\tRead 15087210 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:02:51\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 703574168; totalMemory: 1460666368; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:02:51\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:02:51\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:02:51\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:02:52\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:02:53\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1402446360; totalMemory: 2535456768; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:02:53\tMarkDuplicates\tMarking 5440155 records as duplicates.\r\n", "INFO\t2021-03-14 19:02:53\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:02:54\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:03:16\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:03:16\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:03:16\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:03:16\tMarkDuplicates\tBefore output close freeMemory: 264843376; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:03:16\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:03:16\tMarkDuplicates\tAfter output close freeMemory: 258760288; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:03:16 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.86 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/337.sorted.bam O=../qc-processing/bowtie/deduplicated/337.dedup.bam M=../qc-processing/bowtie/deduplicated/337.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:03:19\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/338.sorted.bam -O ../qc-processing/bowtie/deduplicated/338.dedup.bam -M ../qc-processing/bowtie/deduplicated/338.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:03:19.039 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:03:19 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/338.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/338.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/338.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:03:19 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:03:19 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:03:19\tMarkDuplicates\tStart of doWork freeMemory: 75208648; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:03:19\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:03:19\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:03:22\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4522:6,868\r\n", "INFO\t2021-03-14 19:03:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:03:24\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig21128:6,809\r\n", "INFO\t2021-03-14 19:03:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:03:25\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30643:3,175\r\n", "INFO\t2021-03-14 19:03:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:03:27\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig37346:5,301\r\n", "INFO\t2021-03-14 19:03:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:03:29\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig48506:4,790\r\n", "INFO\t2021-03-14 19:03:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:03:30\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig56693:13,894\r\n", "INFO\t2021-03-14 19:03:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:03:32\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,790\r\n", "INFO\t2021-03-14 19:03:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:03:33\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig78855:5,070\r\n", "INFO\t2021-03-14 19:03:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:03:35\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig103849:2,598\r\n", "INFO\t2021-03-14 19:03:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:03:37\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig141397:7,560\r\n", "INFO\t2021-03-14 19:03:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:03:38\tMarkDuplicates\tRead 10872680 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:03:38\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1207798896; totalMemory: 1735393280; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:03:38\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:03:39\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:03:39\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:03:40\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:03:41\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1677173264; totalMemory: 2810183680; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:03:41\tMarkDuplicates\tMarking 2652536 records as duplicates.\r\n", "INFO\t2021-03-14 19:03:41\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:03:42\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:04:00\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:04:00\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:04:00\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:04:00\tMarkDuplicates\tBefore output close freeMemory: 257904400; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:04:00\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:04:00\tMarkDuplicates\tAfter output close freeMemory: 255614112; totalMemory: 363855872; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:04:00 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.70 minutes.\r\n", "Runtime.totalMemory()=363855872\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/338.sorted.bam O=../qc-processing/bowtie/deduplicated/338.dedup.bam M=../qc-processing/bowtie/deduplicated/338.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:04:02\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/339.sorted.bam -O ../qc-processing/bowtie/deduplicated/339.dedup.bam -M ../qc-processing/bowtie/deduplicated/339.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:04:02.598 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:04:02 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/339.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/339.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/339.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:04:02 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:04:02 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:04:02\tMarkDuplicates\tStart of doWork freeMemory: 72063264; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:04:02\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:04:02\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:04:06\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3541:386\r\n", "INFO\t2021-03-14 19:04:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:07\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig19099:1,618\r\n", "INFO\t2021-03-14 19:04:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:09\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig27538:26,222\r\n", "INFO\t2021-03-14 19:04:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:10\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35213:220\r\n", "INFO\t2021-03-14 19:04:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:12\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig42669:5,728\r\n", "INFO\t2021-03-14 19:04:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:13\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig54957:22,764\r\n", "INFO\t2021-03-14 19:04:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:15\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig63443:2,571\r\n", "INFO\t2021-03-14 19:04:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:17\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,891\r\n", "INFO\t2021-03-14 19:04:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:18\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig86737:11,547\r\n", "INFO\t2021-03-14 19:04:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:20\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig109801:8,426\r\n", "INFO\t2021-03-14 19:04:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:21\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig163120:116\r\n", "INFO\t2021-03-14 19:04:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:22\tMarkDuplicates\tRead 11666925 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:04:23\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 912457992; totalMemory: 1488977920; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:04:23\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:04:23\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:04:23\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:04:24\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:04:24\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1430757368; totalMemory: 2563768320; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:04:24\tMarkDuplicates\tMarking 3304830 records as duplicates.\r\n", "INFO\t2021-03-14 19:04:24\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:04:25\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:04:43\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:04:43\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:04:43\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:04:43\tMarkDuplicates\tBefore output close freeMemory: 271568320; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:04:43\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:04:43\tMarkDuplicates\tAfter output close freeMemory: 258759264; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:04:43 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.69 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/339.sorted.bam O=../qc-processing/bowtie/deduplicated/339.dedup.bam M=../qc-processing/bowtie/deduplicated/339.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:04:45\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/34.sorted.bam -O ../qc-processing/bowtie/deduplicated/34..dedup.bam -M ../qc-processing/bowtie/deduplicated/34..dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:04:45.639 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:04:45 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/34.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/34..dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/34..dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:04:45 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:04:45 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:04:45\tMarkDuplicates\tStart of doWork freeMemory: 67868312; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:04:45\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:04:45\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:04:49\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: Contig16118:39,828\r\n", "INFO\t2021-03-14 19:04:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:51\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig22200:3,529\r\n", "INFO\t2021-03-14 19:04:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:53\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,735\r\n", "INFO\t2021-03-14 19:04:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:54\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35487:29,237\r\n", "INFO\t2021-03-14 19:04:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:56\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig49089:16,038\r\n", "INFO\t2021-03-14 19:04:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:57\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig56693:7,301\r\n", "INFO\t2021-03-14 19:04:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:04:59\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig56910:792\r\n", "INFO\t2021-03-14 19:04:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:00\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig68037:820\r\n", "INFO\t2021-03-14 19:05:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:02\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,639\r\n", "INFO\t2021-03-14 19:05:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:04\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig83174:2,419\r\n", "INFO\t2021-03-14 19:05:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:06\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig88342:3,464\r\n", "INFO\t2021-03-14 19:05:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:07\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,477\r\n", "INFO\t2021-03-14 19:05:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:09\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig137636:6,616\r\n", "INFO\t2021-03-14 19:05:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:10\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: Contig686969:1,564\r\n", "INFO\t2021-03-14 19:05:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:10\tMarkDuplicates\tRead 14027016 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:05:11\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 887629656; totalMemory: 1440743424; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:05:11\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:05:11\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:05:11\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:05:12\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:05:12\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1382523632; totalMemory: 2515533824; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:05:12\tMarkDuplicates\tMarking 4339647 records as duplicates.\r\n", "INFO\t2021-03-14 19:05:12\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:05:13\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:05:35\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:05:35\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:05:35\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:05:36\tMarkDuplicates\tBefore output close freeMemory: 264191760; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:05:36\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:05:36\tMarkDuplicates\tAfter output close freeMemory: 258760376; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:05:36 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.84 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/34.sorted.bam O=../qc-processing/bowtie/deduplicated/34..dedup.bam M=../qc-processing/bowtie/deduplicated/34..dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:05:37\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/341.sorted.bam -O ../qc-processing/bowtie/deduplicated/341.dedup.bam -M ../qc-processing/bowtie/deduplicated/341.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:05:37.886 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:05:38 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/341.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/341.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/341.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:05:38 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:05:38 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:05:38\tMarkDuplicates\tStart of doWork freeMemory: 75212504; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:05:38\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:05:38\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:05:41\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig8839:1,517\r\n", "INFO\t2021-03-14 19:05:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:43\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig27044:9,626\r\n", "INFO\t2021-03-14 19:05:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:44\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig35213:2,490\r\n", "INFO\t2021-03-14 19:05:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:46\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig48729:2,828\r\n", "INFO\t2021-03-14 19:05:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:47\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig63927:1,155\r\n", "INFO\t2021-03-14 19:05:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:49\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig75617:1,510\r\n", "INFO\t2021-03-14 19:05:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:50\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig103886:807\r\n", "INFO\t2021-03-14 19:05:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:52\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig171609:1,761\r\n", "INFO\t2021-03-14 19:05:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:05:53\tMarkDuplicates\tRead 8398656 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:05:53\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1125705768; totalMemory: 1604321280; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:05:53\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:05:53\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:05:53\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:05:54\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:05:54\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1546102344; totalMemory: 2679111680; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:05:54\tMarkDuplicates\tMarking 2296026 records as duplicates.\r\n", "INFO\t2021-03-14 19:05:54\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:05:55\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:06:11\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:06:11\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:06:11\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:06:12\tMarkDuplicates\tBefore output close freeMemory: 266096808; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:06:12\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:06:12\tMarkDuplicates\tAfter output close freeMemory: 258761640; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:06:12 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.57 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/341.sorted.bam O=../qc-processing/bowtie/deduplicated/341.dedup.bam M=../qc-processing/bowtie/deduplicated/341.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:06:14\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/342.sorted.bam -O ../qc-processing/bowtie/deduplicated/342.dedup.bam -M ../qc-processing/bowtie/deduplicated/342.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:06:14.074 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:06:14 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/342.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/342.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/342.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:06:14 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:06:14 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:06:14\tMarkDuplicates\tStart of doWork freeMemory: 75207888; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:06:14\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:06:14\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:06:17\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2870:6,266\r\n", "INFO\t2021-03-14 19:06:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:19\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig16972:8,967\r\n", "INFO\t2021-03-14 19:06:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:20\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig24377:29,697\r\n", "INFO\t2021-03-14 19:06:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:22\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,671\r\n", "INFO\t2021-03-14 19:06:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:23\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig35849:9,012\r\n", "INFO\t2021-03-14 19:06:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:25\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig42785:5,344\r\n", "INFO\t2021-03-14 19:06:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:26\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig52854:16,045\r\n", "INFO\t2021-03-14 19:06:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:28\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig60992:1,575\r\n", "INFO\t2021-03-14 19:06:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:30\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,921\r\n", "INFO\t2021-03-14 19:06:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:31\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig78849:13,991\r\n", "INFO\t2021-03-14 19:06:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:33\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,750\r\n", "INFO\t2021-03-14 19:06:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:34\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig124836:2,052\r\n", "INFO\t2021-03-14 19:06:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:36\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig181638:2,112\r\n", "INFO\t2021-03-14 19:06:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:06:37\tMarkDuplicates\tRead 13558049 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:06:37\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 886071896; totalMemory: 1560281088; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:06:37\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:06:37\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:06:37\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:06:38\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:06:39\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1502060072; totalMemory: 2635071488; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:06:39\tMarkDuplicates\tMarking 4429135 records as duplicates.\r\n", "INFO\t2021-03-14 19:06:39\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:06:39\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:06:59\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:06:59\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:06:59\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:07:00\tMarkDuplicates\tBefore output close freeMemory: 264690256; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:07:00\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:07:00\tMarkDuplicates\tAfter output close freeMemory: 266099080; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:07:00 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.77 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/342.sorted.bam O=../qc-processing/bowtie/deduplicated/342.dedup.bam M=../qc-processing/bowtie/deduplicated/342.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:07:01\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/343.sorted.bam -O ../qc-processing/bowtie/deduplicated/343.dedup.bam -M ../qc-processing/bowtie/deduplicated/343.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "18:07:01.969 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:07:02 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/343.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/343.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/343.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:07:02 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:07:02 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:07:02\tMarkDuplicates\tStart of doWork freeMemory: 72062992; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:07:02\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:07:02\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:07:05\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3112:1,249\r\n", "INFO\t2021-03-14 19:07:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:06\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig18609:16,597\r\n", "INFO\t2021-03-14 19:07:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:08\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig26808:20,746\r\n", "INFO\t2021-03-14 19:07:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:10\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig34501:5,667\r\n", "INFO\t2021-03-14 19:07:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:11\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig41518:3,084\r\n", "INFO\t2021-03-14 19:07:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:13\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig52503:7,310\r\n", "INFO\t2021-03-14 19:07:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:14\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig64198:1,271\r\n", "INFO\t2021-03-14 19:07:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:16\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig76529:556\r\n", "INFO\t2021-03-14 19:07:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:18\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig101000:5,412\r\n", "INFO\t2021-03-14 19:07:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:19\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig103886:900\r\n", "INFO\t2021-03-14 19:07:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:21\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig145734:2,268\r\n", "INFO\t2021-03-14 19:07:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:22\tMarkDuplicates\tRead 11884225 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:07:22\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1008765944; totalMemory: 1605369856; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:07:22\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:07:23\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:07:23\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:07:24\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:07:24\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1547150856; totalMemory: 2680160256; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:07:24\tMarkDuplicates\tMarking 3050107 records as duplicates.\r\n", "INFO\t2021-03-14 19:07:24\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:07:25\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:07:44\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:07:44\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:07:44\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:07:44\tMarkDuplicates\tBefore output close freeMemory: 261412144; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:07:44\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:07:44\tMarkDuplicates\tAfter output close freeMemory: 262955248; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:07:44 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.72 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/343.sorted.bam O=../qc-processing/bowtie/deduplicated/343.dedup.bam M=../qc-processing/bowtie/deduplicated/343.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:07:46\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/344.sorted.bam -O ../qc-processing/bowtie/deduplicated/344.dedup.bam -M ../qc-processing/bowtie/deduplicated/344.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:07:46.713 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:07:46 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/344.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/344.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/344.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:07:47 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:07:47 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:07:47\tMarkDuplicates\tStart of doWork freeMemory: 72061680; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:07:47\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:07:47\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:07:50\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig2891:2,342\r\n", "INFO\t2021-03-14 19:07:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:52\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig18486:16,022\r\n", "INFO\t2021-03-14 19:07:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:53\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig26204:23,722\r\n", "INFO\t2021-03-14 19:07:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:55\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,720\r\n", "INFO\t2021-03-14 19:07:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:56\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig36557:12,137\r\n", "INFO\t2021-03-14 19:07:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:07:58\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig44640:3,717\r\n", "INFO\t2021-03-14 19:07:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:00\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig56693:2,649\r\n", "INFO\t2021-03-14 19:08:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:01\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig56693:16,401\r\n", "INFO\t2021-03-14 19:08:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:03\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig66255:1,482\r\n", "INFO\t2021-03-14 19:08:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:04\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig69234:11,761\r\n", "INFO\t2021-03-14 19:08:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:06\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig70638:19,186\r\n", "INFO\t2021-03-14 19:08:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:07\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig81563:3,618\r\n", "INFO\t2021-03-14 19:08:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:08\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig98935:2,018\r\n", "INFO\t2021-03-14 19:08:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:10\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig109802:560\r\n", "INFO\t2021-03-14 19:08:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:12\tMarkDuplicates\tRead 15,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: Contig149236:96\r\n", "INFO\t2021-03-14 19:08:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:13\tMarkDuplicates\tRead 15876307 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:08:13\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 703387256; totalMemory: 1390411776; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:08:13\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:08:14\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:08:14\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:08:15\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:08:15\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1332189856; totalMemory: 2465202176; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:08:15\tMarkDuplicates\tMarking 4709300 records as duplicates.\r\n", "INFO\t2021-03-14 19:08:15\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:08:16\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:08:37\tMarkDuplicates\tWritten 10,000,000 records. Elapsed time: 00:00:21s. Time for last 10,000,000: 21s. Last read position: Contig123544:573\r\n", "INFO\t2021-03-14 19:08:40\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:08:40\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:08:40\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:08:40\tMarkDuplicates\tBefore output close freeMemory: 265471328; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:08:40\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:08:40\tMarkDuplicates\tAfter output close freeMemory: 262952064; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:08:40 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.90 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/344.sorted.bam O=../qc-processing/bowtie/deduplicated/344.dedup.bam M=../qc-processing/bowtie/deduplicated/344.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:08:42\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r", "\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/345.sorted.bam -O ../qc-processing/bowtie/deduplicated/345.dedup.bam -M ../qc-processing/bowtie/deduplicated/345.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:08:42.483 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:08:42 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/345.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/345.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/345.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:08:42 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:08:42 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:08:42\tMarkDuplicates\tStart of doWork freeMemory: 75210904; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:08:42\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:08:42\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:08:45\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig7085:163\r\n", "INFO\t2021-03-14 19:08:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:47\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig25068:12,662\r\n", "INFO\t2021-03-14 19:08:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:48\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig35213:854\r\n", "INFO\t2021-03-14 19:08:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:50\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig47067:8,692\r\n", "INFO\t2021-03-14 19:08:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:52\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig61796:10,932\r\n", "INFO\t2021-03-14 19:08:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:53\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig77522:6,757\r\n", "INFO\t2021-03-14 19:08:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:55\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig111954:463\r\n", "INFO\t2021-03-14 19:08:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:56\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig211325:446\r\n", "INFO\t2021-03-14 19:08:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:08:57\tMarkDuplicates\tRead 8198694 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:08:57\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1160393168; totalMemory: 1650458624; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:08:57\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:08:57\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:08:57\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:08:58\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:08:58\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1592240624; totalMemory: 2725249024; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:08:58\tMarkDuplicates\tMarking 2298868 records as duplicates.\r\n", "INFO\t2021-03-14 19:08:58\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:08:59\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:09:12\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:09:12\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:09:12\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:09:13\tMarkDuplicates\tBefore output close freeMemory: 262181984; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:09:13\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:09:13\tMarkDuplicates\tAfter output close freeMemory: 258762048; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:09:13 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.51 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/345.sorted.bam O=../qc-processing/bowtie/deduplicated/345.dedup.bam M=../qc-processing/bowtie/deduplicated/345.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:09:14\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/346.sorted.bam -O ../qc-processing/bowtie/deduplicated/346.dedup.bam -M ../qc-processing/bowtie/deduplicated/346.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:09:14.894 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:09:14 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/346.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/346.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/346.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:09:15 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:09:15 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:09:15\tMarkDuplicates\tStart of doWork freeMemory: 72062032; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:09:15\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:09:15\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:09:18\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5628:2,433\r\n", "INFO\t2021-03-14 19:09:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:09:19\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig23182:22,794\r\n", "INFO\t2021-03-14 19:09:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:09:21\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig33124:3,757\r\n", "INFO\t2021-03-14 19:09:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:09:23\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig42187:42,959\r\n", "INFO\t2021-03-14 19:09:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:09:24\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56152:920\r\n", "INFO\t2021-03-14 19:09:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:09:26\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig68037:506\r\n", "INFO\t2021-03-14 19:09:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:09:27\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig78298:4,973\r\n", "INFO\t2021-03-14 19:09:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:09:29\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig103886:807\r\n", "INFO\t2021-03-14 19:09:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:09:30\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig149666:3,390\r\n", "INFO\t2021-03-14 19:09:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:09:32\tMarkDuplicates\tRead 9633922 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:09:32\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1058808968; totalMemory: 1569718272; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:09:32\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:09:32\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:09:32\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:09:33\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:09:33\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1511497760; totalMemory: 2644508672; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:09:33\tMarkDuplicates\tMarking 2450085 records as duplicates.\r\n", "INFO\t2021-03-14 19:09:33\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:09:34\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:09:50\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:09:50\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:09:50\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:09:50\tMarkDuplicates\tBefore output close freeMemory: 2531845664; totalMemory: 2644508672; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:09:50\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:09:50\tMarkDuplicates\tAfter output close freeMemory: 262954344; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:09:50 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.59 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/346.sorted.bam O=../qc-processing/bowtie/deduplicated/346.dedup.bam M=../qc-processing/bowtie/deduplicated/346.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:09:52\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/347.sorted.bam -O ../qc-processing/bowtie/deduplicated/347.dedup.bam -M ../qc-processing/bowtie/deduplicated/347.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:09:52.227 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:09:52 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/347.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/347.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/347.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:09:52 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:09:52 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:09:52\tMarkDuplicates\tStart of doWork freeMemory: 75209480; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:09:52\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:09:52\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:09:55\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5475:1,646\r\n", "INFO\t2021-03-14 19:09:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:09:57\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig22598:1,468\r\n", "INFO\t2021-03-14 19:09:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:09:59\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig32497:7,675\r\n", "INFO\t2021-03-14 19:09:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:00\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig40564:1,249\r\n", "INFO\t2021-03-14 19:10:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:02\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig54243:26,029\r\n", "INFO\t2021-03-14 19:10:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:03\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig68037:802\r\n", "INFO\t2021-03-14 19:10:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:05\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig81791:23,527\r\n", "INFO\t2021-03-14 19:10:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:07\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig105282:2,949\r\n", "INFO\t2021-03-14 19:10:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:08\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig171204:3,385\r\n", "INFO\t2021-03-14 19:10:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:09\tMarkDuplicates\tRead 9472397 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:10:09\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 798784824; totalMemory: 1345323008; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:10:09\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:10:10\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:10:10\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:10:11\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:10:11\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1287103680; totalMemory: 2420113408; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:10:11\tMarkDuplicates\tMarking 3067496 records as duplicates.\r\n", "INFO\t2021-03-14 19:10:11\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:10:12\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:10:27\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:10:27\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:10:27\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:10:27\tMarkDuplicates\tBefore output close freeMemory: 715648704; totalMemory: 2420113408; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:10:27\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:10:27\tMarkDuplicates\tAfter output close freeMemory: 262954912; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:10:27 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.59 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/347.sorted.bam O=../qc-processing/bowtie/deduplicated/347.dedup.bam M=../qc-processing/bowtie/deduplicated/347.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:10:29\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/348.sorted.bam -O ../qc-processing/bowtie/deduplicated/348.dedup.bam -M ../qc-processing/bowtie/deduplicated/348.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:10:29.066 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:10:29 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/348.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/348.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/348.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:10:29 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:10:29 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:10:29\tMarkDuplicates\tStart of doWork freeMemory: 75211600; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:10:29\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:10:29\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:10:32\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3849:6,634\r\n", "INFO\t2021-03-14 19:10:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:34\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig20021:7,008\r\n", "INFO\t2021-03-14 19:10:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:35\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig28839:522\r\n", "INFO\t2021-03-14 19:10:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:37\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35213:861\r\n", "INFO\t2021-03-14 19:10:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:38\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig42679:23,804\r\n", "INFO\t2021-03-14 19:10:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:40\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig55181:5,897\r\n", "INFO\t2021-03-14 19:10:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:42\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig61245:2,268\r\n", "INFO\t2021-03-14 19:10:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:43\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig69234:11,777\r\n", "INFO\t2021-03-14 19:10:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:45\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig80162:3,345\r\n", "INFO\t2021-03-14 19:10:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:46\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig101302:2,438\r\n", "INFO\t2021-03-14 19:10:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:48\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig130956:12,390\r\n", "INFO\t2021-03-14 19:10:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:50\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig269830:105\r\n", "INFO\t2021-03-14 19:10:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:10:50\tMarkDuplicates\tRead 12212793 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:10:50\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1300395568; totalMemory: 1886388224; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:10:50\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:10:51\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:10:51\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:10:51\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:10:52\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1828168120; totalMemory: 2961178624; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:10:52\tMarkDuplicates\tMarking 3430130 records as duplicates.\r\n", "INFO\t2021-03-14 19:10:52\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:10:52\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:11:12\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:11:12\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:11:12\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:11:12\tMarkDuplicates\tBefore output close freeMemory: 268165272; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:11:12\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:11:12\tMarkDuplicates\tAfter output close freeMemory: 262954400; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:11:12 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.73 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/348.sorted.bam O=../qc-processing/bowtie/deduplicated/348.dedup.bam M=../qc-processing/bowtie/deduplicated/348.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:11:14\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/349.sorted.bam -O ../qc-processing/bowtie/deduplicated/349.dedup.bam -M ../qc-processing/bowtie/deduplicated/349.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:11:14.607 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:11:14 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/349.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/349.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/349.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:11:14 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:11:14 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:11:14\tMarkDuplicates\tStart of doWork freeMemory: 75209832; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:11:14\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:11:14\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:11:17\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig7517:6,298\r\n", "INFO\t2021-03-14 19:11:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:19\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig25175:9,283\r\n", "INFO\t2021-03-14 19:11:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:21\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig34897:6,022\r\n", "INFO\t2021-03-14 19:11:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:22\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig46478:7,244\r\n", "INFO\t2021-03-14 19:11:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:24\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig57693:20,359\r\n", "INFO\t2021-03-14 19:11:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:25\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig69525:5,325\r\n", "INFO\t2021-03-14 19:11:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:27\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig89106:10,211\r\n", "INFO\t2021-03-14 19:11:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:29\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig131920:3,931\r\n", "INFO\t2021-03-14 19:11:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:30\tMarkDuplicates\tRead 8897134 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:11:30\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1168837504; totalMemory: 1664090112; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:11:30\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:11:31\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:11:31\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:11:31\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:11:31\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1605869968; totalMemory: 2738880512; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:11:31\tMarkDuplicates\tMarking 2519877 records as duplicates.\r\n", "INFO\t2021-03-14 19:11:31\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:11:32\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:11:46\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:11:46\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:11:46\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:11:46\tMarkDuplicates\tBefore output close freeMemory: 265055072; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:11:46\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:11:46\tMarkDuplicates\tAfter output close freeMemory: 258760304; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:11:46 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.54 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/349.sorted.bam O=../qc-processing/bowtie/deduplicated/349.dedup.bam M=../qc-processing/bowtie/deduplicated/349.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:11:48\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/35.sorted.bam -O ../qc-processing/bowtie/deduplicated/35..dedup.bam -M ../qc-processing/bowtie/deduplicated/35..dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:11:48.481 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:11:48 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/35.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/35..dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/35..dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:11:48 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:11:48 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:11:48\tMarkDuplicates\tStart of doWork freeMemory: 72060416; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:11:48\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:11:48\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:11:51\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig42187:43,034\r\n", "INFO\t2021-03-14 19:11:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:53\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig70638:19,331\r\n", "INFO\t2021-03-14 19:11:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:54\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig103886:807\r\n", "INFO\t2021-03-14 19:11:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:55\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig686969:1,573\r\n", "INFO\t2021-03-14 19:11:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:11:55\tMarkDuplicates\tRead 4008896 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:11:56\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 698867232; totalMemory: 993001472; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:11:56\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:11:56\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:11:56\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:11:56\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:11:57\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 934778984; totalMemory: 2067791872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:11:57\tMarkDuplicates\tMarking 1350158 records as duplicates.\r\n", "INFO\t2021-03-14 19:11:57\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:11:57\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:12:04\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:12:04\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:12:04\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:12:04\tMarkDuplicates\tBefore output close freeMemory: 271488712; totalMemory: 381681664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:12:04\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:12:04\tMarkDuplicates\tAfter output close freeMemory: 262951768; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:12:04 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.26 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/35.sorted.bam O=../qc-processing/bowtie/deduplicated/35..dedup.bam M=../qc-processing/bowtie/deduplicated/35..dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:12:05\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/37.sorted.bam -O ../qc-processing/bowtie/deduplicated/37..dedup.bam -M ../qc-processing/bowtie/deduplicated/37..dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:12:05.902 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:12:06 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/37.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/37..dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/37..dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:12:06 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:12:06 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:12:06\tMarkDuplicates\tStart of doWork freeMemory: 67870616; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:12:06\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:12:06\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:12:09\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig18167:41,612\r\n", "INFO\t2021-03-14 19:12:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:10\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,216\r\n", "INFO\t2021-03-14 19:12:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:12\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig35213:853\r\n", "INFO\t2021-03-14 19:12:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:13\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig42289:563\r\n", "INFO\t2021-03-14 19:12:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:15\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56693:7,502\r\n", "INFO\t2021-03-14 19:12:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:16\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig56693:13,888\r\n", "INFO\t2021-03-14 19:12:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:18\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig68037:348\r\n", "INFO\t2021-03-14 19:12:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:20\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,637\r\n", "INFO\t2021-03-14 19:12:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:21\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,537\r\n", "INFO\t2021-03-14 19:12:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:23\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig98184:1,973\r\n", "INFO\t2021-03-14 19:12:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:25\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig103886:807\r\n", "INFO\t2021-03-14 19:12:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:26\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig686969:632\r\n", "INFO\t2021-03-14 19:12:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:27\tMarkDuplicates\tRead 12522185 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:12:27\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1055673088; totalMemory: 1560281088; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:12:27\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:12:27\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:12:27\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:12:28\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:12:28\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1502063400; totalMemory: 2635071488; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:12:28\tMarkDuplicates\tMarking 3999771 records as duplicates.\r\n", "INFO\t2021-03-14 19:12:28\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:12:29\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:12:49\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:12:49\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:12:49\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:12:49\tMarkDuplicates\tBefore output close freeMemory: 654532512; totalMemory: 2635071488; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:12:49\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:12:49\tMarkDuplicates\tAfter output close freeMemory: 262956424; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:12:49 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.73 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/37.sorted.bam O=../qc-processing/bowtie/deduplicated/37..dedup.bam M=../qc-processing/bowtie/deduplicated/37..dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:12:51\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/39.sorted.bam -O ../qc-processing/bowtie/deduplicated/39..dedup.bam -M ../qc-processing/bowtie/deduplicated/39..dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:12:51.310 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:12:51 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/39.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/39..dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/39..dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:12:51 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:12:51 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:12:51\tMarkDuplicates\tStart of doWork freeMemory: 67870840; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:12:51\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:12:51\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:12:54\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig16189:8,795\r\n", "INFO\t2021-03-14 19:12:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:56\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig30144:2,661\r\n", "INFO\t2021-03-14 19:12:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:57\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig39846:4,370\r\n", "INFO\t2021-03-14 19:12:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:12:59\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig56598:3,113\r\n", "INFO\t2021-03-14 19:12:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:01\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig67826:3,318\r\n", "INFO\t2021-03-14 19:13:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:02\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig80484:1,529\r\n", "INFO\t2021-03-14 19:13:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:04\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig106636:5,951\r\n", "INFO\t2021-03-14 19:13:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:05\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig686969:1,319\r\n", "INFO\t2021-03-14 19:13:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:05\tMarkDuplicates\tRead 8028351 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:13:06\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 999117976; totalMemory: 1471152128; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:13:06\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:13:06\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:13:06\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:13:07\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:13:07\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1412933112; totalMemory: 2545942528; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:13:07\tMarkDuplicates\tMarking 2443042 records as duplicates.\r\n", "INFO\t2021-03-14 19:13:07\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:13:08\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:13:21\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:13:21\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:13:21\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:13:21\tMarkDuplicates\tBefore output close freeMemory: 264858440; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:13:21\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:13:21\tMarkDuplicates\tAfter output close freeMemory: 262955696; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:13:21 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.50 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/39.sorted.bam O=../qc-processing/bowtie/deduplicated/39..dedup.bam M=../qc-processing/bowtie/deduplicated/39..dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:13:23\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/401.sorted.bam -O ../qc-processing/bowtie/deduplicated/401.dedup.bam -M ../qc-processing/bowtie/deduplicated/401.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:13:23.234 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:13:23 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/401.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/401.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/401.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:13:23 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:13:23 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:13:23\tMarkDuplicates\tStart of doWork freeMemory: 72064312; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:13:23\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:13:23\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:13:26\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig24892:4,131\r\n", "INFO\t2021-03-14 19:13:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:28\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig42187:43,004\r\n", "INFO\t2021-03-14 19:13:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:29\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig56693:12,071\r\n", "INFO\t2021-03-14 19:13:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:31\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig68777:4,032\r\n", "INFO\t2021-03-14 19:13:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:32\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,936\r\n", "INFO\t2021-03-14 19:13:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:34\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,750\r\n", "INFO\t2021-03-14 19:13:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:36\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig148303:704\r\n", "INFO\t2021-03-14 19:13:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:36\tMarkDuplicates\tRead 7308746 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:13:36\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 926028712; totalMemory: 1318060032; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:13:36\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:13:37\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:13:37\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:13:37\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:13:38\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1259839536; totalMemory: 2392850432; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:13:38\tMarkDuplicates\tMarking 2256756 records as duplicates.\r\n", "INFO\t2021-03-14 19:13:38\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:13:38\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:13:50\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:13:50\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:13:50\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:13:50\tMarkDuplicates\tBefore output close freeMemory: 266094912; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:13:51\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:13:51\tMarkDuplicates\tAfter output close freeMemory: 262954048; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:13:51 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.46 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/401.sorted.bam O=../qc-processing/bowtie/deduplicated/401.dedup.bam M=../qc-processing/bowtie/deduplicated/401.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:13:52\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/402.sorted.bam -O ../qc-processing/bowtie/deduplicated/402.dedup.bam -M ../qc-processing/bowtie/deduplicated/402.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:13:52.766 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:13:52 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/402.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/402.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/402.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:13:52 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:13:52 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:13:52\tMarkDuplicates\tStart of doWork freeMemory: 72063888; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:13:52\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:13:52\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:13:56\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: Contig15959:44,961\r\n", "INFO\t2021-03-14 19:13:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:13:58\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig28042:3,696\r\n", "INFO\t2021-03-14 19:13:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:00\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig37726:25,023\r\n", "INFO\t2021-03-14 19:14:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:01\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig53348:4,541\r\n", "INFO\t2021-03-14 19:14:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:03\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig66247:2,670\r\n", "INFO\t2021-03-14 19:14:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:04\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig70819:7,358\r\n", "INFO\t2021-03-14 19:14:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:06\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig101302:2,343\r\n", "INFO\t2021-03-14 19:14:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:07\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig174154:6,402\r\n", "INFO\t2021-03-14 19:14:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:08\tMarkDuplicates\tRead 8371875 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:14:08\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 824309880; totalMemory: 1309671424; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:14:08\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:14:09\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:14:09\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:14:09\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:14:10\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1251451192; totalMemory: 2384461824; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:14:10\tMarkDuplicates\tMarking 2605655 records as duplicates.\r\n", "INFO\t2021-03-14 19:14:10\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:14:10\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:14:23\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:14:23\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:14:23\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:14:24\tMarkDuplicates\tBefore output close freeMemory: 261640976; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:14:24\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:14:24\tMarkDuplicates\tAfter output close freeMemory: 262954304; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:14:24 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.52 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/402.sorted.bam O=../qc-processing/bowtie/deduplicated/402.dedup.bam M=../qc-processing/bowtie/deduplicated/402.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:14:25\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/403.sorted.bam -O ../qc-processing/bowtie/deduplicated/403.dedup.bam -M ../qc-processing/bowtie/deduplicated/403.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:14:25.955 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:14:26 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/403.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/403.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/403.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:14:26 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:14:26 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:14:26\tMarkDuplicates\tStart of doWork freeMemory: 75209776; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:14:26\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:14:26\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:14:29\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5482:1,682\r\n", "INFO\t2021-03-14 19:14:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:31\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig23485:22,261\r\n", "INFO\t2021-03-14 19:14:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:32\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig33895:2,123\r\n", "INFO\t2021-03-14 19:14:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:34\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig42719:4,137\r\n", "INFO\t2021-03-14 19:14:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:35\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56693:2,649\r\n", "INFO\t2021-03-14 19:14:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:37\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,794\r\n", "INFO\t2021-03-14 19:14:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:39\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig90849:8,040\r\n", "INFO\t2021-03-14 19:14:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:40\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig133490:1,930\r\n", "INFO\t2021-03-14 19:14:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:14:42\tMarkDuplicates\tRead 8843600 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:14:42\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1097442568; totalMemory: 1643118592; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:14:42\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:14:42\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:14:42\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:14:43\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:14:43\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1584899016; totalMemory: 2717908992; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:14:43\tMarkDuplicates\tMarking 2958023 records as duplicates.\r\n", "INFO\t2021-03-14 19:14:43\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:14:44\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:14:58\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:14:58\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:14:58\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:14:59\tMarkDuplicates\tBefore output close freeMemory: 264203712; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:14:59\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:14:59\tMarkDuplicates\tAfter output close freeMemory: 262954696; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:14:59 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.55 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/403.sorted.bam O=../qc-processing/bowtie/deduplicated/403.dedup.bam M=../qc-processing/bowtie/deduplicated/403.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:15:01\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/404.sorted.bam -O ../qc-processing/bowtie/deduplicated/404.dedup.bam -M ../qc-processing/bowtie/deduplicated/404.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:15:01.113 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:15:01 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/404.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/404.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/404.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:15:01 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:15:01 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:15:01\tMarkDuplicates\tStart of doWork freeMemory: 64726928; totalMemory: 91226112; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:15:01\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:15:01\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:15:04\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig15298:857\r\n", "INFO\t2021-03-14 19:15:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:06\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig29038:10,845\r\n", "INFO\t2021-03-14 19:15:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:08\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig39636:2,918\r\n", "INFO\t2021-03-14 19:15:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:09\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig55763:2,206\r\n", "INFO\t2021-03-14 19:15:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:11\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig67389:9,966\r\n", "INFO\t2021-03-14 19:15:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:12\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig80410:1,869\r\n", "INFO\t2021-03-14 19:15:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:14\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig103849:2,735\r\n", "INFO\t2021-03-14 19:15:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:16\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig174154:7,169\r\n", "INFO\t2021-03-14 19:15:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:16\tMarkDuplicates\tRead 8359296 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:15:16\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 826235112; totalMemory: 1361051648; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:15:16\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:15:17\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:15:17\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:15:18\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:15:18\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1302833160; totalMemory: 2435842048; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:15:18\tMarkDuplicates\tMarking 3562318 records as duplicates.\r\n", "INFO\t2021-03-14 19:15:18\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:15:19\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:15:32\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:15:32\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:15:32\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:15:32\tMarkDuplicates\tBefore output close freeMemory: 266096592; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:15:32\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:15:32\tMarkDuplicates\tAfter output close freeMemory: 262955728; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:15:32 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.52 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/404.sorted.bam O=../qc-processing/bowtie/deduplicated/404.dedup.bam M=../qc-processing/bowtie/deduplicated/404.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:15:33\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/41.sorted.bam -O ../qc-processing/bowtie/deduplicated/41..dedup.bam -M ../qc-processing/bowtie/deduplicated/41..dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:15:33.995 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:15:34 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/41.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/41..dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/41..dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:15:34 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:15:34 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:15:34\tMarkDuplicates\tStart of doWork freeMemory: 72061680; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:15:34\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:15:34\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:15:37\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig15836:31,933\r\n", "INFO\t2021-03-14 19:15:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:38\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig21019:6,270\r\n", "INFO\t2021-03-14 19:15:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:40\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,659\r\n", "INFO\t2021-03-14 19:15:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:41\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig32900:15,019\r\n", "INFO\t2021-03-14 19:15:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:43\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig42187:43,004\r\n", "INFO\t2021-03-14 19:15:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:44\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig56033:1,117\r\n", "INFO\t2021-03-14 19:15:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:46\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig56693:11,741\r\n", "INFO\t2021-03-14 19:15:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:48\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig62580:2,530\r\n", "INFO\t2021-03-14 19:15:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:50\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig68037:873\r\n", "INFO\t2021-03-14 19:15:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:51\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,603\r\n", "INFO\t2021-03-14 19:15:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:53\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig71494:3,713\r\n", "INFO\t2021-03-14 19:15:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:55\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,669\r\n", "INFO\t2021-03-14 19:15:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:56\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig103849:2,598\r\n", "INFO\t2021-03-14 19:15:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:58\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,511\r\n", "INFO\t2021-03-14 19:15:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:15:59\tMarkDuplicates\tRead 15,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: Contig148184:614\r\n", "INFO\t2021-03-14 19:15:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:16:01\tMarkDuplicates\tRead 15914293 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:16:01\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 894912848; totalMemory: 1521483776; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:16:01\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:16:01\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:16:01\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:16:02\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:16:03\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1463262376; totalMemory: 2596274176; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:16:03\tMarkDuplicates\tMarking 5224154 records as duplicates.\r\n", "INFO\t2021-03-14 19:16:03\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:16:03\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:16:28\tMarkDuplicates\tWritten 10,000,000 records. Elapsed time: 00:00:24s. Time for last 10,000,000: 24s. Last read position: Contig137778:6,438\r\n", "INFO\t2021-03-14 19:16:29\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:16:29\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:16:29\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:16:29\tMarkDuplicates\tBefore output close freeMemory: 2485635240; totalMemory: 2596274176; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:16:29\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:16:29\tMarkDuplicates\tAfter output close freeMemory: 262952856; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:16:29 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.93 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/41.sorted.bam O=../qc-processing/bowtie/deduplicated/41..dedup.bam M=../qc-processing/bowtie/deduplicated/41..dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:16:31\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/411.sorted.bam -O ../qc-processing/bowtie/deduplicated/411.dedup.bam -M ../qc-processing/bowtie/deduplicated/411.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:16:31.710 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:16:32 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/411.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/411.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/411.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:16:32 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:16:32 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:16:32\tMarkDuplicates\tStart of doWork freeMemory: 72061656; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:16:32\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:16:32\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:16:35\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig7297:1,954\r\n", "INFO\t2021-03-14 19:16:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:16:36\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig25638:4,795\r\n", "INFO\t2021-03-14 19:16:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:16:38\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig35213:877\r\n", "INFO\t2021-03-14 19:16:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:16:40\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig46083:7,960\r\n", "INFO\t2021-03-14 19:16:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:16:41\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig57693:20,365\r\n", "INFO\t2021-03-14 19:16:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:16:43\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig69234:11,734\r\n", "INFO\t2021-03-14 19:16:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:16:44\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig85851:5,624\r\n", "INFO\t2021-03-14 19:16:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:16:46\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig121105:2,537\r\n", "INFO\t2021-03-14 19:16:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:16:47\tMarkDuplicates\tRead 8939401 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:16:48\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1127202176; totalMemory: 1650458624; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:16:48\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:16:48\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:16:48\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:16:49\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:16:49\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1592238544; totalMemory: 2725249024; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:16:49\tMarkDuplicates\tMarking 3029121 records as duplicates.\r\n", "INFO\t2021-03-14 19:16:49\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:16:50\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:17:04\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:17:04\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:17:04\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:17:04\tMarkDuplicates\tBefore output close freeMemory: 267486320; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:17:04\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:17:04\tMarkDuplicates\tAfter output close freeMemory: 258759808; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:17:04 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.54 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/411.sorted.bam O=../qc-processing/bowtie/deduplicated/411.dedup.bam M=../qc-processing/bowtie/deduplicated/411.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:17:06\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/412.sorted.bam -O ../qc-processing/bowtie/deduplicated/412.dedup.bam -M ../qc-processing/bowtie/deduplicated/412.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:17:06.076 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:17:06 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/412.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/412.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/412.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:17:06 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:17:06 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:17:06\tMarkDuplicates\tStart of doWork freeMemory: 72063640; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:17:06\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:17:06\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:17:09\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig35213:853\r\n", "INFO\t2021-03-14 19:17:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:17:10\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig68133:6,494\r\n", "INFO\t2021-03-14 19:17:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:17:12\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig103886:807\r\n", "INFO\t2021-03-14 19:17:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:17:13\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig103886:900\r\n", "INFO\t2021-03-14 19:17:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:17:14\tMarkDuplicates\tRead 4784064 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:17:15\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 839900552; totalMemory: 1192230912; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:17:15\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:17:15\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:17:15\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:17:16\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:17:16\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1134010576; totalMemory: 2267021312; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:17:16\tMarkDuplicates\tMarking 2225608 records as duplicates.\r\n", "INFO\t2021-03-14 19:17:16\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:17:17\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:17:23\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:17:23\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:17:23\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:17:24\tMarkDuplicates\tBefore output close freeMemory: 266095112; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:17:24\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:17:24\tMarkDuplicates\tAfter output close freeMemory: 262954248; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:17:24 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.30 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/412.sorted.bam O=../qc-processing/bowtie/deduplicated/412.dedup.bam M=../qc-processing/bowtie/deduplicated/412.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:17:25\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/413.sorted.bam -O ../qc-processing/bowtie/deduplicated/413.dedup.bam -M ../qc-processing/bowtie/deduplicated/413.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:17:25.905 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:17:25 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/413.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/413.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/413.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:17:26 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:17:26 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:17:26\tMarkDuplicates\tStart of doWork freeMemory: 72061184; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:17:26\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:17:26\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:17:29\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig6483:6,175\r\n", "INFO\t2021-03-14 19:17:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:17:30\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig25603:6,380\r\n", "INFO\t2021-03-14 19:17:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:17:32\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig35967:93\r\n", "INFO\t2021-03-14 19:17:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:17:34\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig47617:5,006\r\n", "INFO\t2021-03-14 19:17:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:17:35\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig64789:2,789\r\n", "INFO\t2021-03-14 19:17:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:17:37\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,944\r\n", "INFO\t2021-03-14 19:17:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:17:38\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig134210:619\r\n", "INFO\t2021-03-14 19:17:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:17:40\tMarkDuplicates\tRead 7749399 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:17:40\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1236907056; totalMemory: 1761607680; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:17:40\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:17:40\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:17:40\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:17:41\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:17:41\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1703385856; totalMemory: 2836398080; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:17:41\tMarkDuplicates\tMarking 3139760 records as duplicates.\r\n", "INFO\t2021-03-14 19:17:41\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:17:42\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:17:53\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:17:53\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:17:53\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:17:53\tMarkDuplicates\tBefore output close freeMemory: 262115264; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:17:53\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:17:53\tMarkDuplicates\tAfter output close freeMemory: 258758112; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:17:53 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.47 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/413.sorted.bam O=../qc-processing/bowtie/deduplicated/413.dedup.bam M=../qc-processing/bowtie/deduplicated/413.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:17:55\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/414.sorted.bam -O ../qc-processing/bowtie/deduplicated/414.dedup.bam -M ../qc-processing/bowtie/deduplicated/414.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:17:55.611 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:17:55 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/414.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/414.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/414.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:17:55 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:17:55 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:17:55\tMarkDuplicates\tStart of doWork freeMemory: 75210264; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:17:55\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:17:55\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:17:58\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig18183:3,156\r\n", "INFO\t2021-03-14 19:17:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:00\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig32665:6,351\r\n", "INFO\t2021-03-14 19:18:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:01\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig48580:5,666\r\n", "INFO\t2021-03-14 19:18:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:03\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig68716:4,703\r\n", "INFO\t2021-03-14 19:18:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:04\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig89303:7,448\r\n", "INFO\t2021-03-14 19:18:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:06\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig170266:2,396\r\n", "INFO\t2021-03-14 19:18:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:06\tMarkDuplicates\tRead 6324460 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:18:06\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1010900888; totalMemory: 1440743424; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:18:06\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:18:07\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:18:07\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:18:08\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:18:08\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1382524376; totalMemory: 2515533824; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:18:08\tMarkDuplicates\tMarking 2021644 records as duplicates.\r\n", "INFO\t2021-03-14 19:18:08\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:18:08\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:18:18\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:18:18\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:18:18\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:18:18\tMarkDuplicates\tBefore output close freeMemory: 257789608; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:18:18\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:18:18\tMarkDuplicates\tAfter output close freeMemory: 255615312; totalMemory: 363855872; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:18:18 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.38 minutes.\r\n", "Runtime.totalMemory()=363855872\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/414.sorted.bam O=../qc-processing/bowtie/deduplicated/414.dedup.bam M=../qc-processing/bowtie/deduplicated/414.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:18:20\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/421.sorted.bam -O ../qc-processing/bowtie/deduplicated/421.dedup.bam -M ../qc-processing/bowtie/deduplicated/421.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:18:20.121 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:18:20 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/421.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/421.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/421.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:18:20 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:18:20 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:18:20\tMarkDuplicates\tStart of doWork freeMemory: 72061352; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:18:20\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:18:20\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:18:23\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4583:2,684\r\n", "INFO\t2021-03-14 19:18:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:25\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig20021:7,076\r\n", "INFO\t2021-03-14 19:18:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:26\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig29369:25,118\r\n", "INFO\t2021-03-14 19:18:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:28\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig36186:33,309\r\n", "INFO\t2021-03-14 19:18:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:29\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig45529:8,300\r\n", "INFO\t2021-03-14 19:18:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:31\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig56693:7,480\r\n", "INFO\t2021-03-14 19:18:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:33\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig64644:333\r\n", "INFO\t2021-03-14 19:18:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:34\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig69234:14,487\r\n", "INFO\t2021-03-14 19:18:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:36\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig82614:3,298\r\n", "INFO\t2021-03-14 19:18:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:37\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig103849:2,681\r\n", "INFO\t2021-03-14 19:18:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:39\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig136973:1,666\r\n", "INFO\t2021-03-14 19:18:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:41\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig686969:1,537\r\n", "INFO\t2021-03-14 19:18:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:18:41\tMarkDuplicates\tRead 12014744 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:18:41\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1041307320; totalMemory: 1632632832; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:18:41\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:18:41\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:18:41\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:18:42\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:18:42\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1574411088; totalMemory: 2707423232; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:18:42\tMarkDuplicates\tMarking 3287648 records as duplicates.\r\n", "INFO\t2021-03-14 19:18:42\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:18:43\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:19:03\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:19:03\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:19:03\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:19:03\tMarkDuplicates\tBefore output close freeMemory: 267205608; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:19:03\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:19:03\tMarkDuplicates\tAfter output close freeMemory: 258758592; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:19:03 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.72 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/421.sorted.bam O=../qc-processing/bowtie/deduplicated/421.dedup.bam M=../qc-processing/bowtie/deduplicated/421.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:19:05\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/43.sorted.bam -O ../qc-processing/bowtie/deduplicated/43..dedup.bam -M ../qc-processing/bowtie/deduplicated/43..dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:19:05.157 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:19:05 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/43.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/43..dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/43..dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:19:05 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:19:05 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:19:05\tMarkDuplicates\tStart of doWork freeMemory: 72062008; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:19:05\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:19:05\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:19:08\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5148:760\r\n", "INFO\t2021-03-14 19:19:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:10\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig21438:15,911\r\n", "INFO\t2021-03-14 19:19:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:11\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30879:28,000\r\n", "INFO\t2021-03-14 19:19:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:13\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig38357:21,416\r\n", "INFO\t2021-03-14 19:19:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:14\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig49969:18,826\r\n", "INFO\t2021-03-14 19:19:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:16\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig59806:2,737\r\n", "INFO\t2021-03-14 19:19:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:18\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig69234:11,734\r\n", "INFO\t2021-03-14 19:19:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:19\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig84841:4,235\r\n", "INFO\t2021-03-14 19:19:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:21\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig107599:7,345\r\n", "INFO\t2021-03-14 19:19:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:22\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig187982:4,099\r\n", "INFO\t2021-03-14 19:19:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:23\tMarkDuplicates\tRead 10392878 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:19:23\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 995424280; totalMemory: 1556086784; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:19:23\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:19:23\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:19:23\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:19:24\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:19:25\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1497866808; totalMemory: 2630877184; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:19:25\tMarkDuplicates\tMarking 3195288 records as duplicates.\r\n", "INFO\t2021-03-14 19:19:25\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:19:25\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:19:41\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:19:41\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:19:41\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:19:41\tMarkDuplicates\tBefore output close freeMemory: 267649096; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:19:41\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:19:41\tMarkDuplicates\tAfter output close freeMemory: 266100064; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:19:41 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.61 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/43.sorted.bam O=../qc-processing/bowtie/deduplicated/43..dedup.bam M=../qc-processing/bowtie/deduplicated/43..dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:19:43\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/431b.sorted.bam -O ../qc-processing/bowtie/deduplicated/431.dedup.bam -M ../qc-processing/bowtie/deduplicated/431.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:19:43.942 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:19:44 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/431b.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/431.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/431.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r", "\r\n", "Mar 14, 2021 7:19:44 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:19:44 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:19:44\tMarkDuplicates\tStart of doWork freeMemory: 72064616; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:19:44\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:19:44\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:19:47\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig15994:7,628\r\n", "INFO\t2021-03-14 19:19:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:48\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig29931:21,345\r\n", "INFO\t2021-03-14 19:19:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:50\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig38003:16,521\r\n", "INFO\t2021-03-14 19:19:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:51\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig53225:768\r\n", "INFO\t2021-03-14 19:19:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:53\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56693:12,071\r\n", "INFO\t2021-03-14 19:19:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:55\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig66871:14,215\r\n", "INFO\t2021-03-14 19:19:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:56\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig69234:17,340\r\n", "INFO\t2021-03-14 19:19:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:19:58\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,537\r\n", "INFO\t2021-03-14 19:19:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:00\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,406\r\n", "INFO\t2021-03-14 19:20:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:01\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig147865:530\r\n", "INFO\t2021-03-14 19:20:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:02\tMarkDuplicates\tRead 10561880 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:20:02\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1048684296; totalMemory: 1576009728; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:20:02\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:20:03\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:20:03\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:20:04\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:20:04\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1517788584; totalMemory: 2650800128; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:20:04\tMarkDuplicates\tMarking 3480826 records as duplicates.\r\n", "INFO\t2021-03-14 19:20:04\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:20:04\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:20:23\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:20:23\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:20:23\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:20:23\tMarkDuplicates\tBefore output close freeMemory: 255608528; totalMemory: 363855872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:20:23\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:20:23\tMarkDuplicates\tAfter output close freeMemory: 255613392; totalMemory: 363855872; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:20:23 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.66 minutes.\r\n", "Runtime.totalMemory()=363855872\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/431b.sorted.bam O=../qc-processing/bowtie/deduplicated/431.dedup.bam M=../qc-processing/bowtie/deduplicated/431.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:20:25\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r", "\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/432.sorted.bam -O ../qc-processing/bowtie/deduplicated/432.dedup.bam -M ../qc-processing/bowtie/deduplicated/432.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:20:25.321 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:20:25 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/432.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/432.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/432.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:20:25 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:20:25 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:20:25\tMarkDuplicates\tStart of doWork freeMemory: 67868672; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:20:25\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:20:25\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:20:28\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig20021:6,825\r\n", "INFO\t2021-03-14 19:20:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:30\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,671\r\n", "INFO\t2021-03-14 19:20:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:31\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30879:28,010\r\n", "INFO\t2021-03-14 19:20:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:32\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig42187:43,019\r\n", "INFO\t2021-03-14 19:20:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:34\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig56693:2,649\r\n", "INFO\t2021-03-14 19:20:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:35\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig56693:11,741\r\n", "INFO\t2021-03-14 19:20:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:37\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig64644:488\r\n", "INFO\t2021-03-14 19:20:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:39\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig68037:873\r\n", "INFO\t2021-03-14 19:20:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:40\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,510\r\n", "INFO\t2021-03-14 19:20:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:42\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,891\r\n", "INFO\t2021-03-14 19:20:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:44\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig83174:2,161\r\n", "INFO\t2021-03-14 19:20:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:45\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,537\r\n", "INFO\t2021-03-14 19:20:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:47\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,944\r\n", "INFO\t2021-03-14 19:20:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:48\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,229\r\n", "INFO\t2021-03-14 19:20:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:50\tMarkDuplicates\tRead 15,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,346\r\n", "INFO\t2021-03-14 19:20:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:51\tMarkDuplicates\tRead 16,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: Contig146366:3,809\r\n", "INFO\t2021-03-14 19:20:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:53\tMarkDuplicates\tRead 17,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: Contig686969:1,563\r\n", "INFO\t2021-03-14 19:20:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:20:53\tMarkDuplicates\tRead 17208981 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:20:53\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 997578304; totalMemory: 1529872384; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:20:53\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:20:54\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:20:54\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:20:55\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:20:55\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1471651872; totalMemory: 2604662784; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:20:55\tMarkDuplicates\tMarking 4727429 records as duplicates.\r\n", "INFO\t2021-03-14 19:20:55\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:20:56\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:21:18\tMarkDuplicates\tWritten 10,000,000 records. Elapsed time: 00:00:22s. Time for last 10,000,000: 22s. Last read position: Contig85486:1,944\r\n", "INFO\t2021-03-14 19:21:24\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:21:24\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:21:24\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:21:25\tMarkDuplicates\tBefore output close freeMemory: 264878216; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:21:25\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:21:25\tMarkDuplicates\tAfter output close freeMemory: 262953792; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:21:25 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.00 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/432.sorted.bam O=../qc-processing/bowtie/deduplicated/432.dedup.bam M=../qc-processing/bowtie/deduplicated/432.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:21:26\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/434.sorted.bam -O ../qc-processing/bowtie/deduplicated/434.dedup.bam -M ../qc-processing/bowtie/deduplicated/434.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:21:26.829 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:21:27 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/434.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/434.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/434.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:21:27 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:21:27 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:21:27\tMarkDuplicates\tStart of doWork freeMemory: 67868656; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:21:27\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:21:27\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:21:30\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig15298:865\r\n", "INFO\t2021-03-14 19:21:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:21:31\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig31265:2,720\r\n", "INFO\t2021-03-14 19:21:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:21:33\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig40873:4,380\r\n", "INFO\t2021-03-14 19:21:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:21:34\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig57718:12,557\r\n", "INFO\t2021-03-14 19:21:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:21:36\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig74387:2,042\r\n", "INFO\t2021-03-14 19:21:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:21:38\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig108137:164\r\n", "INFO\t2021-03-14 19:21:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:21:39\tMarkDuplicates\tRead 6914225 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:21:39\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 959427760; totalMemory: 1469054976; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:21:39\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:21:40\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:21:40\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:21:41\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:21:41\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1410835312; totalMemory: 2543845376; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:21:41\tMarkDuplicates\tMarking 3423588 records as duplicates.\r\n", "INFO\t2021-03-14 19:21:41\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:21:42\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:21:52\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:21:52\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:21:52\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:21:52\tMarkDuplicates\tBefore output close freeMemory: 262949608; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:21:52\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:21:52\tMarkDuplicates\tAfter output close freeMemory: 258760168; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:21:52 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.43 minutes.\r\n", "Runtime.totalMemory()=367001600\r", "\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/434.sorted.bam O=../qc-processing/bowtie/deduplicated/434.dedup.bam M=../qc-processing/bowtie/deduplicated/434.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:21:54\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/44.sorted.bam -O ../qc-processing/bowtie/deduplicated/44..dedup.bam -M ../qc-processing/bowtie/deduplicated/44..dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:21:54.480 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:21:54 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/44.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/44..dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/44..dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:21:54 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:21:54 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:21:54\tMarkDuplicates\tStart of doWork freeMemory: 67874104; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:21:54\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:21:54\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:21:57\tMarkDuplicates\tRead 915416 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:21:57\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 514973576; totalMemory: 727711744; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:21:57\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:21:57\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:21:57\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:21:58\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:21:58\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 761767992; totalMemory: 1894776832; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:21:58\tMarkDuplicates\tMarking 343899 records as duplicates.\r\n", "INFO\t2021-03-14 19:21:58\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:21:58\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:22:00\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:22:00\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:22:00\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:22:00\tMarkDuplicates\tBefore output close freeMemory: 264637504; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:22:00\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:22:00\tMarkDuplicates\tAfter output close freeMemory: 258761568; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:22:00 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.11 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/44.sorted.bam O=../qc-processing/bowtie/deduplicated/44..dedup.bam M=../qc-processing/bowtie/deduplicated/44..dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:22:02\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/441.sorted.bam -O ../qc-processing/bowtie/deduplicated/441.dedup.bam -M ../qc-processing/bowtie/deduplicated/441.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:22:02.552 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:22:02 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/441.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/441.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/441.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:22:02 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:22:02 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:22:02\tMarkDuplicates\tStart of doWork freeMemory: 72063552; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:22:02\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:22:02\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:22:05\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig20043:18,889\r\n", "INFO\t2021-03-14 19:22:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:07\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig36186:16,958\r\n", "INFO\t2021-03-14 19:22:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:08\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig53881:929\r\n", "INFO\t2021-03-14 19:22:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:10\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig76256:34\r\n", "INFO\t2021-03-14 19:22:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:12\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig103886:807\r\n", "INFO\t2021-03-14 19:22:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:13\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig103886:807\r\n", "INFO\t2021-03-14 19:22:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:14\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig103886:807\r\n", "INFO\t2021-03-14 19:22:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:16\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig103886:900\r\n", "INFO\t2021-03-14 19:22:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:17\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig103886:900\r\n", "INFO\t2021-03-14 19:22:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:18\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig103886:900\r\n", "INFO\t2021-03-14 19:22:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:20\tMarkDuplicates\tRead 10826756 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:22:20\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 973945552; totalMemory: 1624244224; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:22:20\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:22:20\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:22:20\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:22:22\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:22:22\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1566024696; totalMemory: 2699034624; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:22:22\tMarkDuplicates\tMarking 6401934 records as duplicates.\r\n", "INFO\t2021-03-14 19:22:22\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:22:23\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:22:36\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:22:36\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:22:36\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:22:36\tMarkDuplicates\tBefore output close freeMemory: 262551680; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:22:36\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:22:36\tMarkDuplicates\tAfter output close freeMemory: 262954992; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:22:36 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.57 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/441.sorted.bam O=../qc-processing/bowtie/deduplicated/441.dedup.bam M=../qc-processing/bowtie/deduplicated/441.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:22:38\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/442b.sorted.bam -O ../qc-processing/bowtie/deduplicated/442.dedup.bam -M ../qc-processing/bowtie/deduplicated/442.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:22:38.151 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:22:38 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/442b.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/442.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/442.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:22:38 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:22:38 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:22:38\tMarkDuplicates\tStart of doWork freeMemory: 67873296; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:22:38\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:22:38\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:22:41\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig20021:6,825\r\n", "INFO\t2021-03-14 19:22:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:42\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig30879:28,089\r\n", "INFO\t2021-03-14 19:22:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:44\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig50339:20,905\r\n", "INFO\t2021-03-14 19:22:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:46\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig66349:6,445\r\n", "INFO\t2021-03-14 19:22:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:47\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,891\r\n", "INFO\t2021-03-14 19:22:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:49\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig85486:2,335\r\n", "INFO\t2021-03-14 19:22:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:51\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig105506:8,199\r\n", "INFO\t2021-03-14 19:22:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:22:52\tMarkDuplicates\tRead 7815845 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:22:52\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1033005496; totalMemory: 1472200704; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:22:52\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:22:52\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:22:52\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:22:53\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:22:53\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1413982368; totalMemory: 2546991104; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:22:53\tMarkDuplicates\tMarking 2611210 records as duplicates.\r\n", "INFO\t2021-03-14 19:22:53\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:22:54\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:23:06\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:23:06\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:23:06\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:23:07\tMarkDuplicates\tBefore output close freeMemory: 262950816; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:23:07\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:23:07\tMarkDuplicates\tAfter output close freeMemory: 258761376; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:23:07 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.49 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/442b.sorted.bam O=../qc-processing/bowtie/deduplicated/442.dedup.bam M=../qc-processing/bowtie/deduplicated/442.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:23:08\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/443.sorted.bam -O ../qc-processing/bowtie/deduplicated/443.dedup.bam -M ../qc-processing/bowtie/deduplicated/443.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:23:08.973 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:23:09 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/443.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/443.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/443.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:23:09 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:23:09 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:23:09\tMarkDuplicates\tStart of doWork freeMemory: 64722568; totalMemory: 91226112; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:23:09\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:23:09\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:23:12\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig15439:47,440\r\n", "INFO\t2021-03-14 19:23:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:13\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,639\r\n", "INFO\t2021-03-14 19:23:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:15\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig42375:3,433\r\n", "INFO\t2021-03-14 19:23:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:17\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig59424:1,399\r\n", "INFO\t2021-03-14 19:23:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:18\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig81792:4,920\r\n", "INFO\t2021-03-14 19:23:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:20\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig135300:18,411\r\n", "INFO\t2021-03-14 19:23:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:21\tMarkDuplicates\tRead 6616242 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:23:21\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1155898248; totalMemory: 1646264320; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:23:21\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:23:21\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:23:21\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:23:22\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:23:22\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1588044144; totalMemory: 2721054720; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:23:22\tMarkDuplicates\tMarking 3012328 records as duplicates.\r\n", "INFO\t2021-03-14 19:23:22\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:23:23\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:23:32\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:23:32\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:23:32\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:23:32\tMarkDuplicates\tBefore output close freeMemory: 262649512; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:23:32\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:23:32\tMarkDuplicates\tAfter output close freeMemory: 262954256; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:23:32 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.40 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/443.sorted.bam O=../qc-processing/bowtie/deduplicated/443.dedup.bam M=../qc-processing/bowtie/deduplicated/443.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:23:34\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/444.sorted.bam -O ../qc-processing/bowtie/deduplicated/444.dedup.bam -M ../qc-processing/bowtie/deduplicated/444.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:23:34.349 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:23:34 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/444.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/444.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/444.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:23:34 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:23:34 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:23:34\tMarkDuplicates\tStart of doWork freeMemory: 72062296; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:23:34\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:23:34\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:23:37\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5115:4,519\r\n", "INFO\t2021-03-14 19:23:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:39\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig24129:4,034\r\n", "INFO\t2021-03-14 19:23:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:40\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig35213:855\r\n", "INFO\t2021-03-14 19:23:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:42\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig45006:159\r\n", "INFO\t2021-03-14 19:23:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:43\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig58498:3,665\r\n", "INFO\t2021-03-14 19:23:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:45\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig75533:15,480\r\n", "INFO\t2021-03-14 19:23:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:47\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig104654:5,377\r\n", "INFO\t2021-03-14 19:23:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:48\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig205407:2,693\r\n", "INFO\t2021-03-14 19:23:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:23:48\tMarkDuplicates\tRead 8199010 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:23:49\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 844507688; totalMemory: 1428160512; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:23:49\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:23:49\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:23:49\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:23:50\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:23:50\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1369940168; totalMemory: 2502950912; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:23:50\tMarkDuplicates\tMarking 4252788 records as duplicates.\r\n", "INFO\t2021-03-14 19:23:50\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:23:51\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:24:03\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:24:03\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:24:03\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:24:03\tMarkDuplicates\tBefore output close freeMemory: 258754680; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:24:03\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:24:03\tMarkDuplicates\tAfter output close freeMemory: 258759544; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:24:03 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.48 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/444.sorted.bam O=../qc-processing/bowtie/deduplicated/444.dedup.bam M=../qc-processing/bowtie/deduplicated/444.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:24:05\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/445.sorted.bam -O ../qc-processing/bowtie/deduplicated/445.dedup.bam -M ../qc-processing/bowtie/deduplicated/445.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:24:05.148 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:24:05 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/445.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/445.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/445.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:24:05 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:24:05 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:24:05\tMarkDuplicates\tStart of doWork freeMemory: 67868752; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:24:05\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:24:05\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:24:08\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5705:6,465\r\n", "INFO\t2021-03-14 19:24:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:10\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig23498:20,136\r\n", "INFO\t2021-03-14 19:24:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:11\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig33765:9,163\r\n", "INFO\t2021-03-14 19:24:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:13\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig42936:6,885\r\n", "INFO\t2021-03-14 19:24:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:14\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56693:4,516\r\n", "INFO\t2021-03-14 19:24:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:16\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig68908:739\r\n", "INFO\t2021-03-14 19:24:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:18\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig85426:2,226\r\n", "INFO\t2021-03-14 19:24:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:19\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig110898:6,083\r\n", "INFO\t2021-03-14 19:24:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:21\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig313765:1,651\r\n", "INFO\t2021-03-14 19:24:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:21\tMarkDuplicates\tRead 9154329 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:24:21\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 958662080; totalMemory: 1504706560; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:24:21\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:24:22\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:24:22\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:24:22\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:24:23\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1446486368; totalMemory: 2579496960; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:24:23\tMarkDuplicates\tMarking 3045674 records as duplicates.\r\n", "INFO\t2021-03-14 19:24:23\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:24:23\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:24:37\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:24:37\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:24:37\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:24:38\tMarkDuplicates\tBefore output close freeMemory: 264594496; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:24:38\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:24:38\tMarkDuplicates\tAfter output close freeMemory: 258760344; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:24:38 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.55 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/445.sorted.bam O=../qc-processing/bowtie/deduplicated/445.dedup.bam M=../qc-processing/bowtie/deduplicated/445.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:24:39\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/45.sorted.bam -O ../qc-processing/bowtie/deduplicated/45..dedup.bam -M ../qc-processing/bowtie/deduplicated/45..dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:24:39.940 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:24:40 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/45.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/45..dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/45..dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:24:40 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:24:40 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:24:40\tMarkDuplicates\tStart of doWork freeMemory: 64725560; totalMemory: 91226112; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:24:40\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:24:40\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:24:43\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5839:2,047\r\n", "INFO\t2021-03-14 19:24:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:44\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig22359:2,556\r\n", "INFO\t2021-03-14 19:24:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:46\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig31928:6,944\r\n", "INFO\t2021-03-14 19:24:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:47\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig41537:1,221\r\n", "INFO\t2021-03-14 19:24:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:49\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig55040:6,345\r\n", "INFO\t2021-03-14 19:24:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:50\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig66450:1,167\r\n", "INFO\t2021-03-14 19:24:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:52\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig70882:7,693\r\n", "INFO\t2021-03-14 19:24:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:54\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig92992:14,808\r\n", "INFO\t2021-03-14 19:24:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:56\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig123992:1,952\r\n", "INFO\t2021-03-14 19:24:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:57\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig492755:82\r\n", "INFO\t2021-03-14 19:24:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:24:57\tMarkDuplicates\tRead 10126095 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:24:57\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 869769680; totalMemory: 1379926016; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:24:57\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:24:58\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:24:58\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:24:59\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:24:59\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1321706008; totalMemory: 2454716416; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:24:59\tMarkDuplicates\tMarking 3430318 records as duplicates.\r\n", "INFO\t2021-03-14 19:24:59\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:25:00\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:25:15\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:25:15\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:25:15\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:25:15\tMarkDuplicates\tBefore output close freeMemory: 375217864; totalMemory: 2454716416; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:25:15\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:25:15\tMarkDuplicates\tAfter output close freeMemory: 262954320; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:25:15 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.59 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/45.sorted.bam O=../qc-processing/bowtie/deduplicated/45..dedup.bam M=../qc-processing/bowtie/deduplicated/45..dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:25:17\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/451.sorted.bam -O ../qc-processing/bowtie/deduplicated/451.dedup.bam -M ../qc-processing/bowtie/deduplicated/451.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:25:17.071 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:25:17 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/451.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/451.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/451.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:25:17 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:25:17 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:25:17\tMarkDuplicates\tStart of doWork freeMemory: 67868464; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:25:17\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:25:17\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:25:20\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3255:600\r\n", "INFO\t2021-03-14 19:25:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:25:22\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig20015:3,210\r\n", "INFO\t2021-03-14 19:25:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:25:23\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig29566:785\r\n", "INFO\t2021-03-14 19:25:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:25:25\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig36557:11,314\r\n", "INFO\t2021-03-14 19:25:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:25:26\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig45811:6,132\r\n", "INFO\t2021-03-14 19:25:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:25:28\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig56910:900\r\n", "INFO\t2021-03-14 19:25:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:25:29\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,805\r\n", "INFO\t2021-03-14 19:25:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:25:31\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig89302:1,507\r\n", "INFO\t2021-03-14 19:25:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:25:33\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig115433:3,440\r\n", "INFO\t2021-03-14 19:25:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:25:34\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig206328:1,420\r\n", "INFO\t2021-03-14 19:25:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:25:35\tMarkDuplicates\tRead 10291693 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:25:35\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 936725688; totalMemory: 1577058304; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:25:35\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:25:35\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:25:35\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:25:37\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:25:37\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1518838448; totalMemory: 2651848704; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:25:37\tMarkDuplicates\tMarking 4258107 records as duplicates.\r\n", "INFO\t2021-03-14 19:25:37\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:25:37\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:25:52\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:25:52\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:25:52\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:25:52\tMarkDuplicates\tBefore output close freeMemory: 267630192; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:25:52\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:25:52\tMarkDuplicates\tAfter output close freeMemory: 262954528; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:25:52 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.60 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/451.sorted.bam O=../qc-processing/bowtie/deduplicated/451.dedup.bam M=../qc-processing/bowtie/deduplicated/451.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:25:54\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/452b.sorted.bam -O ../qc-processing/bowtie/deduplicated/452.dedup.bam -M ../qc-processing/bowtie/deduplicated/452.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:25:54.561 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:25:54 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/452b.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/452.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/452.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:25:54 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:25:54 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:25:54\tMarkDuplicates\tStart of doWork freeMemory: 72067080; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:25:54\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:25:54\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:25:57\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig17782:9,886\r\n", "INFO\t2021-03-14 19:25:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:25:59\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,672\r\n", "INFO\t2021-03-14 19:25:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:01\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig43103:377\r\n", "INFO\t2021-03-14 19:26:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:02\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig56693:12,060\r\n", "INFO\t2021-03-14 19:26:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:04\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig68908:704\r\n", "INFO\t2021-03-14 19:26:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:06\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig73535:1,225\r\n", "INFO\t2021-03-14 19:26:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:07\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,334\r\n", "INFO\t2021-03-14 19:26:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:09\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig189001:5,385\r\n", "INFO\t2021-03-14 19:26:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:10\tMarkDuplicates\tRead 8281261 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:26:10\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1118778832; totalMemory: 1590689792; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:26:10\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:26:10\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:26:10\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:26:11\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:26:11\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1532472640; totalMemory: 2665480192; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:26:11\tMarkDuplicates\tMarking 2686431 records as duplicates.\r\n", "INFO\t2021-03-14 19:26:11\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:26:12\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:26:24\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:26:24\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:26:24\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:26:24\tMarkDuplicates\tBefore output close freeMemory: 258757760; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:26:24\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:26:25\tMarkDuplicates\tAfter output close freeMemory: 258762624; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:26:25 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.51 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/452b.sorted.bam O=../qc-processing/bowtie/deduplicated/452.dedup.bam M=../qc-processing/bowtie/deduplicated/452.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:26:26\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/453.sorted.bam -O ../qc-processing/bowtie/deduplicated/453.dedup.bam -M ../qc-processing/bowtie/deduplicated/453.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:26:26.711 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:26:26 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/453.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/453.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/453.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:26:26 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:26:26 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:26:26\tMarkDuplicates\tStart of doWork freeMemory: 75209784; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:26:26\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:26:26\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:26:30\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: Contig15978:2,686\r\n", "INFO\t2021-03-14 19:26:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:32\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: Contig29882:20,225\r\n", "INFO\t2021-03-14 19:26:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:34\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig40873:4,349\r\n", "INFO\t2021-03-14 19:26:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:36\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig57009:2,287\r\n", "INFO\t2021-03-14 19:26:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:37\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig71579:4,565\r\n", "INFO\t2021-03-14 19:26:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:39\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig107599:7,355\r\n", "INFO\t2021-03-14 19:26:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:26:41\tMarkDuplicates\tRead 6936824 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:26:41\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1113340328; totalMemory: 1583349760; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:26:41\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:26:41\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:26:41\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:26:42\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:26:42\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1525130376; totalMemory: 2658140160; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:26:42\tMarkDuplicates\tMarking 2420412 records as duplicates.\r\n", "INFO\t2021-03-14 19:26:42\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:26:43\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:26:53\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:26:53\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:26:53\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:26:53\tMarkDuplicates\tBefore output close freeMemory: 1471128712; totalMemory: 2658140160; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:26:53\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:26:54\tMarkDuplicates\tAfter output close freeMemory: 262954920; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:26:54 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.46 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/453.sorted.bam O=../qc-processing/bowtie/deduplicated/453.dedup.bam M=../qc-processing/bowtie/deduplicated/453.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:26:55\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/46.sorted.bam -O ../qc-processing/bowtie/deduplicated/46..dedup.bam -M ../qc-processing/bowtie/deduplicated/46..dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:26:55.779 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:26:55 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/46.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/46..dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/46..dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:26:56 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:26:56 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:26:56\tMarkDuplicates\tStart of doWork freeMemory: 67869344; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:26:56\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:26:56\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:26:58\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig16202:1,865\r\n", "INFO\t2021-03-14 19:26:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:00\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig25496:5,545\r\n", "INFO\t2021-03-14 19:27:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:02\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30879:28,098\r\n", "INFO\t2021-03-14 19:27:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:03\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig43261:14,832\r\n", "INFO\t2021-03-14 19:27:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:05\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56693:2,649\r\n", "INFO\t2021-03-14 19:27:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:06\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig63193:15,275\r\n", "INFO\t2021-03-14 19:27:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:08\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig69234:14,487\r\n", "INFO\t2021-03-14 19:27:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:10\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig77069:9,020\r\n", "INFO\t2021-03-14 19:27:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:11\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig95501:1,591\r\n", "INFO\t2021-03-14 19:27:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:13\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,495\r\n", "INFO\t2021-03-14 19:27:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:15\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig186382:383\r\n", "INFO\t2021-03-14 19:27:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:15\tMarkDuplicates\tRead 11459236 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:27:16\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1142263264; totalMemory: 1699741696; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:27:16\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:27:16\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:27:16\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:27:17\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:27:17\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1641522880; totalMemory: 2774532096; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:27:17\tMarkDuplicates\tMarking 4365146 records as duplicates.\r\n", "INFO\t2021-03-14 19:27:17\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:27:18\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:27:35\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:27:35\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:27:35\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:27:36\tMarkDuplicates\tBefore output close freeMemory: 265584600; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:27:36\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:27:36\tMarkDuplicates\tAfter output close freeMemory: 266101624; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:27:36 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.67 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/46.sorted.bam O=../qc-processing/bowtie/deduplicated/46..dedup.bam M=../qc-processing/bowtie/deduplicated/46..dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:27:38\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/461b.sorted.bam -O ../qc-processing/bowtie/deduplicated/461.dedup.bam -M ../qc-processing/bowtie/deduplicated/461.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:27:38.203 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:27:38 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/461b.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/461.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/461.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:27:38 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:27:38 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:27:38\tMarkDuplicates\tStart of doWork freeMemory: 72062608; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:27:38\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:27:38\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:27:41\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig21665:33,329\r\n", "INFO\t2021-03-14 19:27:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:43\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig38227:6,038\r\n", "INFO\t2021-03-14 19:27:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:45\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig56693:9,308\r\n", "INFO\t2021-03-14 19:27:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:46\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig70595:999\r\n", "INFO\t2021-03-14 19:27:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:48\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig101783:541\r\n", "INFO\t2021-03-14 19:27:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:27:50\tMarkDuplicates\tRead 5982926 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:27:50\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 999495200; totalMemory: 1422917632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:27:50\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:27:50\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:27:50\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:27:51\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:27:51\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1364697656; totalMemory: 2497708032; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:27:51\tMarkDuplicates\tMarking 2253446 records as duplicates.\r\n", "INFO\t2021-03-14 19:27:51\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:27:52\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:28:01\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:28:01\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:28:01\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:28:01\tMarkDuplicates\tBefore output close freeMemory: 262949600; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:28:01\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:28:01\tMarkDuplicates\tAfter output close freeMemory: 258760032; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:28:01 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.40 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/461b.sorted.bam O=../qc-processing/bowtie/deduplicated/461.dedup.bam M=../qc-processing/bowtie/deduplicated/461.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:28:03\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/462b.sorted.bam -O ../qc-processing/bowtie/deduplicated/462.dedup.bam -M ../qc-processing/bowtie/deduplicated/462.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:28:03.580 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:28:03 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/462b.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/462.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/462.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:28:03 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:28:03 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:28:03\tMarkDuplicates\tStart of doWork freeMemory: 75209184; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:28:03\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:28:03\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:28:06\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5738:10,717\r\n", "INFO\t2021-03-14 19:28:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:08\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig24129:3,965\r\n", "INFO\t2021-03-14 19:28:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:10\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig32730:7,350\r\n", "INFO\t2021-03-14 19:28:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:11\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig42187:43,004\r\n", "INFO\t2021-03-14 19:28:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:13\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56598:3,105\r\n", "INFO\t2021-03-14 19:28:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:14\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig68037:876\r\n", "INFO\t2021-03-14 19:28:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:16\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig81479:1,748\r\n", "INFO\t2021-03-14 19:28:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:18\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,705\r\n", "INFO\t2021-03-14 19:28:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:19\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig109966:244\r\n", "INFO\t2021-03-14 19:28:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:21\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig492138:5,850\r\n", "INFO\t2021-03-14 19:28:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:21\tMarkDuplicates\tRead 10143015 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:28:21\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1003491312; totalMemory: 1659895808; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:28:21\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:28:22\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:28:22\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:28:23\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:28:23\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1601676120; totalMemory: 2734686208; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:28:23\tMarkDuplicates\tMarking 5251407 records as duplicates.\r\n", "INFO\t2021-03-14 19:28:23\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:28:24\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:28:37\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:28:37\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:28:37\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:28:38\tMarkDuplicates\tBefore output close freeMemory: 262949192; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:28:38\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:28:38\tMarkDuplicates\tAfter output close freeMemory: 258759752; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:28:38 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.58 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/462b.sorted.bam O=../qc-processing/bowtie/deduplicated/462.dedup.bam M=../qc-processing/bowtie/deduplicated/462.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:28:39\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/47.sorted.bam -O ../qc-processing/bowtie/deduplicated/47..dedup.bam -M ../qc-processing/bowtie/deduplicated/47..dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:28:39.918 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:28:40 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/47.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/47..dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/47..dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:28:40 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:28:40 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:28:40\tMarkDuplicates\tStart of doWork freeMemory: 67875296; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:28:40\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:28:40\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:28:43\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig16373:12,206\r\n", "INFO\t2021-03-14 19:28:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:45\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig29931:28,092\r\n", "INFO\t2021-03-14 19:28:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:46\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig39679:11,238\r\n", "INFO\t2021-03-14 19:28:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:48\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig56693:7,500\r\n", "INFO\t2021-03-14 19:28:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:49\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,805\r\n", "INFO\t2021-03-14 19:28:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:51\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig92992:19,305\r\n", "INFO\t2021-03-14 19:28:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:53\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig139531:5,444\r\n", "INFO\t2021-03-14 19:28:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:28:54\tMarkDuplicates\tRead 7591272 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:28:54\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1087722016; totalMemory: 1548746752; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:28:54\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:28:54\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:28:54\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:28:55\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:28:55\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1490528128; totalMemory: 2623537152; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:28:55\tMarkDuplicates\tMarking 2432924 records as duplicates.\r\n", "INFO\t2021-03-14 19:28:55\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:28:56\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:29:08\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:29:08\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:29:08\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:29:08\tMarkDuplicates\tBefore output close freeMemory: 267430896; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:29:08\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:29:08\tMarkDuplicates\tAfter output close freeMemory: 258761320; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:29:08 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.48 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/47.sorted.bam O=../qc-processing/bowtie/deduplicated/47..dedup.bam M=../qc-processing/bowtie/deduplicated/47..dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:29:10\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/471b.sorted.bam -O ../qc-processing/bowtie/deduplicated/471.dedup.bam -M ../qc-processing/bowtie/deduplicated/471.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:29:10.437 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:29:10 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/471b.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/471.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/471.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:29:10 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:29:10 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:29:10\tMarkDuplicates\tStart of doWork freeMemory: 67871112; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:29:10\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:29:10\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:29:13\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig16668:7,094\r\n", "INFO\t2021-03-14 19:29:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:15\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,420\r\n", "INFO\t2021-03-14 19:29:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:17\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig40873:2,646\r\n", "INFO\t2021-03-14 19:29:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:18\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig56693:2,649\r\n", "INFO\t2021-03-14 19:29:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:20\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig66871:14,257\r\n", "INFO\t2021-03-14 19:29:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:21\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig71414:3,444\r\n", "INFO\t2021-03-14 19:29:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:23\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,738\r\n", "INFO\t2021-03-14 19:29:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:25\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig138882:2,496\r\n", "INFO\t2021-03-14 19:29:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:26\tMarkDuplicates\tRead 8581233 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:29:26\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 875142040; totalMemory: 1390411776; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:29:26\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:29:26\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:29:26\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:29:27\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:29:27\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1332192672; totalMemory: 2465202176; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:29:27\tMarkDuplicates\tMarking 3150487 records as duplicates.\r\n", "INFO\t2021-03-14 19:29:27\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:29:28\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:29:41\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:29:41\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:29:41\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:29:42\tMarkDuplicates\tBefore output close freeMemory: 258756224; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:29:42\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:29:42\tMarkDuplicates\tAfter output close freeMemory: 258761088; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:29:42 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.53 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/471b.sorted.bam O=../qc-processing/bowtie/deduplicated/471.dedup.bam M=../qc-processing/bowtie/deduplicated/471.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:29:44\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r", "\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/472b.sorted.bam -O ../qc-processing/bowtie/deduplicated/472.dedup.bam -M ../qc-processing/bowtie/deduplicated/472.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:29:44.044 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:29:44 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/472b.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/472.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/472.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:29:44 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:29:44 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:29:44\tMarkDuplicates\tStart of doWork freeMemory: 67874360; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:29:44\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:29:44\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:29:47\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig16509:24,097\r\n", "INFO\t2021-03-14 19:29:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:49\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,413\r\n", "INFO\t2021-03-14 19:29:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:51\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig41407:5,826\r\n", "INFO\t2021-03-14 19:29:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:52\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig56693:5,048\r\n", "INFO\t2021-03-14 19:29:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:54\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig68908:700\r\n", "INFO\t2021-03-14 19:29:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:56\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig79944:2,798\r\n", "INFO\t2021-03-14 19:29:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:57\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig104005:11,137\r\n", "INFO\t2021-03-14 19:29:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:59\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig673102:167\r\n", "INFO\t2021-03-14 19:29:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:29:59\tMarkDuplicates\tRead 8047176 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:29:59\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1171049136; totalMemory: 1678770176; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:29:59\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:29:59\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:29:59\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:30:00\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:30:01\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1620551064; totalMemory: 2753560576; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:30:01\tMarkDuplicates\tMarking 3092587 records as duplicates.\r\n", "INFO\t2021-03-14 19:30:01\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:30:01\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:30:14\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:30:14\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:30:14\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:30:14\tMarkDuplicates\tBefore output close freeMemory: 262950648; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:30:14\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:30:14\tMarkDuplicates\tAfter output close freeMemory: 258761208; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:30:14 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.51 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/472b.sorted.bam O=../qc-processing/bowtie/deduplicated/472.dedup.bam M=../qc-processing/bowtie/deduplicated/472.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:30:16\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/473.sorted.bam -O ../qc-processing/bowtie/deduplicated/473.dedup.bam -M ../qc-processing/bowtie/deduplicated/473.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:30:16.562 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:30:16 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/473.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/473.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/473.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:30:16 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:30:16 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:30:16\tMarkDuplicates\tStart of doWork freeMemory: 72064600; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:30:16\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:30:16\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:30:20\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig7085:2,274\r\n", "INFO\t2021-03-14 19:30:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:21\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig25713:11,312\r\n", "INFO\t2021-03-14 19:30:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:23\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig35774:1,112\r\n", "INFO\t2021-03-14 19:30:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:25\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig47617:8,854\r\n", "INFO\t2021-03-14 19:30:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:26\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig62744:3,367\r\n", "INFO\t2021-03-14 19:30:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:28\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig77734:588\r\n", "INFO\t2021-03-14 19:30:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:30\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig103849:5,739\r\n", "INFO\t2021-03-14 19:30:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:31\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig205580:2,117\r\n", "INFO\t2021-03-14 19:30:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:31\tMarkDuplicates\tRead 8219914 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:30:32\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 856754704; totalMemory: 1390411776; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:30:32\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:30:32\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:30:32\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:30:33\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:30:33\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1332192904; totalMemory: 2465202176; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:30:33\tMarkDuplicates\tMarking 3188510 records as duplicates.\r\n", "INFO\t2021-03-14 19:30:33\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:30:34\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:30:46\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:30:46\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:30:46\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:30:47\tMarkDuplicates\tBefore output close freeMemory: 265097432; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:30:47\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:30:47\tMarkDuplicates\tAfter output close freeMemory: 258760600; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:30:47 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.51 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/473.sorted.bam O=../qc-processing/bowtie/deduplicated/473.dedup.bam M=../qc-processing/bowtie/deduplicated/473.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:30:48\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/474.sorted.bam -O ../qc-processing/bowtie/deduplicated/474.dedup.bam -M ../qc-processing/bowtie/deduplicated/474.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:30:48.882 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:30:48 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/474.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/474.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/474.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:30:49 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:30:49 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:30:49\tMarkDuplicates\tStart of doWork freeMemory: 75208320; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:30:49\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:30:49\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:30:52\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3058:2,096\r\n", "INFO\t2021-03-14 19:30:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:53\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig20453:9,506\r\n", "INFO\t2021-03-14 19:30:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:55\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30266:21,848\r\n", "INFO\t2021-03-14 19:30:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:57\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig37186:10,622\r\n", "INFO\t2021-03-14 19:30:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:30:58\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig47544:1,295\r\n", "INFO\t2021-03-14 19:30:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:00\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig59424:2,860\r\n", "INFO\t2021-03-14 19:31:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:01\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig73878:4,356\r\n", "INFO\t2021-03-14 19:31:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:03\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,750\r\n", "INFO\t2021-03-14 19:31:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:05\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig145172:932\r\n", "INFO\t2021-03-14 19:31:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:06\tMarkDuplicates\tRead 9698119 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:31:06\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 996001384; totalMemory: 1619001344; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:31:06\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:31:06\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:31:06\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:31:07\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:31:07\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1560780288; totalMemory: 2693791744; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:31:07\tMarkDuplicates\tMarking 4192238 records as duplicates.\r\n", "INFO\t2021-03-14 19:31:07\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:31:08\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:31:22\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:31:22\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:31:22\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:31:22\tMarkDuplicates\tBefore output close freeMemory: 258753944; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:31:22\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:31:22\tMarkDuplicates\tAfter output close freeMemory: 258758808; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:31:22 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.56 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/474.sorted.bam O=../qc-processing/bowtie/deduplicated/474.dedup.bam M=../qc-processing/bowtie/deduplicated/474.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:31:24\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/475.sorted.bam -O ../qc-processing/bowtie/deduplicated/475.dedup.bam -M ../qc-processing/bowtie/deduplicated/475.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:31:24.207 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:31:24 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/475.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/475.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/475.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:31:24 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:31:24 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:31:24\tMarkDuplicates\tStart of doWork freeMemory: 67872704; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:31:24\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:31:24\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:31:27\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3894:418\r\n", "INFO\t2021-03-14 19:31:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:29\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig22282:19,521\r\n", "INFO\t2021-03-14 19:31:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:30\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig33224:2,648\r\n", "INFO\t2021-03-14 19:31:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:32\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig41196:1,682\r\n", "INFO\t2021-03-14 19:31:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:33\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig54227:13,730\r\n", "INFO\t2021-03-14 19:31:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:35\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig68908:739\r\n", "INFO\t2021-03-14 19:31:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:36\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig94163:7,985\r\n", "INFO\t2021-03-14 19:31:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:38\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig137890:7,842\r\n", "INFO\t2021-03-14 19:31:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:31:39\tMarkDuplicates\tRead 8713997 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:31:39\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 956256912; totalMemory: 1541406720; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:31:39\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:31:40\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:31:40\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:31:41\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:31:41\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1483185624; totalMemory: 2616197120; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:31:41\tMarkDuplicates\tMarking 3806886 records as duplicates.\r\n", "INFO\t2021-03-14 19:31:41\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:31:42\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:31:54\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:31:54\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:31:54\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:31:54\tMarkDuplicates\tBefore output close freeMemory: 258754016; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:31:54\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:31:54\tMarkDuplicates\tAfter output close freeMemory: 258758752; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:31:54 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.51 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/475.sorted.bam O=../qc-processing/bowtie/deduplicated/475.dedup.bam M=../qc-processing/bowtie/deduplicated/475.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:31:56\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/476.sorted.bam -O ../qc-processing/bowtie/deduplicated/476.dedup.bam -M ../qc-processing/bowtie/deduplicated/476.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:31:56.371 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:31:56 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/476.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/476.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/476.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:31:56 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:31:56 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:31:56\tMarkDuplicates\tStart of doWork freeMemory: 72063472; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:31:56\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:31:56\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:31:59\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig19245:31,067\r\n", "INFO\t2021-03-14 19:31:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:01\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig35611:2,642\r\n", "INFO\t2021-03-14 19:32:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:02\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig54868:3,474\r\n", "INFO\t2021-03-14 19:32:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:04\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig81594:9,315\r\n", "INFO\t2021-03-14 19:32:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:06\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig171746:500\r\n", "INFO\t2021-03-14 19:32:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:06\tMarkDuplicates\tRead 5228074 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:32:06\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1036697328; totalMemory: 1475346432; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:32:06\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:32:07\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:32:07\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:32:07\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:32:07\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1417126560; totalMemory: 2550136832; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:32:07\tMarkDuplicates\tMarking 2588387 records as duplicates.\r\n", "INFO\t2021-03-14 19:32:07\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:32:08\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:32:15\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:32:15\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:32:15\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:32:16\tMarkDuplicates\tBefore output close freeMemory: 258755248; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:32:16\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:32:16\tMarkDuplicates\tAfter output close freeMemory: 258760112; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:32:16 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.33 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/476.sorted.bam O=../qc-processing/bowtie/deduplicated/476.dedup.bam M=../qc-processing/bowtie/deduplicated/476.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:32:17\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/477.sorted.bam -O ../qc-processing/bowtie/deduplicated/477.dedup.bam -M ../qc-processing/bowtie/deduplicated/477.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:32:17.886 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:32:17 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/477.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/477.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/477.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:32:18 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:32:18 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:32:18\tMarkDuplicates\tStart of doWork freeMemory: 75209112; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:32:18\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:32:18\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:32:21\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5738:10,531\r\n", "INFO\t2021-03-14 19:32:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:22\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig23145:17,026\r\n", "INFO\t2021-03-14 19:32:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:24\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig32979:8,232\r\n", "INFO\t2021-03-14 19:32:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:25\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig42901:13,574\r\n", "INFO\t2021-03-14 19:32:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:27\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56693:2,567\r\n", "INFO\t2021-03-14 19:32:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:29\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig67725:7,957\r\n", "INFO\t2021-03-14 19:32:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:30\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig70819:7,362\r\n", "INFO\t2021-03-14 19:32:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:32\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig96963:44\r\n", "INFO\t2021-03-14 19:32:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:34\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig130752:1,764\r\n", "INFO\t2021-03-14 19:32:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:32:35\tMarkDuplicates\tRead 9914264 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:32:35\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 964600328; totalMemory: 1506803712; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:32:35\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:32:36\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:32:36\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:32:37\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:32:37\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1448583488; totalMemory: 2581594112; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:32:37\tMarkDuplicates\tMarking 3025760 records as duplicates.\r\n", "INFO\t2021-03-14 19:32:37\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:32:37\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:32:53\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:32:53\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:32:53\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:32:53\tMarkDuplicates\tBefore output close freeMemory: 608302224; totalMemory: 2581594112; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:32:53\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:32:54\tMarkDuplicates\tAfter output close freeMemory: 262953888; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:32:54 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.60 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/477.sorted.bam O=../qc-processing/bowtie/deduplicated/477.dedup.bam M=../qc-processing/bowtie/deduplicated/477.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:32:55\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/481.sorted.bam -O ../qc-processing/bowtie/deduplicated/481.dedup.bam -M ../qc-processing/bowtie/deduplicated/481.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:32:55.845 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:32:55 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/481.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/481.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/481.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:32:56 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:32:56 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:32:56\tMarkDuplicates\tStart of doWork freeMemory: 72061800; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:32:56\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:32:56\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:32:59\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig9588:937\r\n", "INFO\t2021-03-14 19:32:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:00\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig26849:3,199\r\n", "INFO\t2021-03-14 19:33:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:02\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig35213:857\r\n", "INFO\t2021-03-14 19:33:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:04\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig47071:3,297\r\n", "INFO\t2021-03-14 19:33:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:05\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig61691:10,621\r\n", "INFO\t2021-03-14 19:33:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:07\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig70638:19,280\r\n", "INFO\t2021-03-14 19:33:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:08\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,703\r\n", "INFO\t2021-03-14 19:33:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:10\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig127092:1,360\r\n", "INFO\t2021-03-14 19:33:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:11\tMarkDuplicates\tRead 8841925 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:33:11\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1048113824; totalMemory: 1580204032; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:33:11\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:33:12\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:33:12\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:33:13\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:33:13\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1521983632; totalMemory: 2654994432; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:33:13\tMarkDuplicates\tMarking 3276199 records as duplicates.\r\n", "INFO\t2021-03-14 19:33:13\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:33:14\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:33:27\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:33:27\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:33:27\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:33:27\tMarkDuplicates\tBefore output close freeMemory: 258754544; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:33:27\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:33:27\tMarkDuplicates\tAfter output close freeMemory: 258759408; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:33:27 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.53 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/481.sorted.bam O=../qc-processing/bowtie/deduplicated/481.dedup.bam M=../qc-processing/bowtie/deduplicated/481.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:33:29\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/482.sorted.bam -O ../qc-processing/bowtie/deduplicated/482.dedup.bam -M ../qc-processing/bowtie/deduplicated/482.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:33:29.156 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:33:29 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/482.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/482.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/482.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:33:29 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:33:29 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:33:29\tMarkDuplicates\tStart of doWork freeMemory: 78354624; totalMemory: 104857600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:33:29\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:33:29\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:33:32\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig17598:27,552\r\n", "INFO\t2021-03-14 19:33:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:34\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig34828:35,108\r\n", "INFO\t2021-03-14 19:33:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:35\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig47617:7,008\r\n", "INFO\t2021-03-14 19:33:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:37\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig68908:721\r\n", "INFO\t2021-03-14 19:33:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:38\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig107026:2,482\r\n", "INFO\t2021-03-14 19:33:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:40\tMarkDuplicates\tRead 5814560 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:33:40\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 829146888; totalMemory: 1291845632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:33:40\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:33:40\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:33:40\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:33:41\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:33:41\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1233625136; totalMemory: 2366636032; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:33:41\tMarkDuplicates\tMarking 2852549 records as duplicates.\r\n", "INFO\t2021-03-14 19:33:41\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:33:42\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:33:50\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:33:50\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:33:50\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:33:50\tMarkDuplicates\tBefore output close freeMemory: 258754896; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:33:50\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:33:50\tMarkDuplicates\tAfter output close freeMemory: 258759760; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:33:50 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.36 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/482.sorted.bam O=../qc-processing/bowtie/deduplicated/482.dedup.bam M=../qc-processing/bowtie/deduplicated/482.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:33:52\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/483.sorted.bam -O ../qc-processing/bowtie/deduplicated/483.dedup.bam -M ../qc-processing/bowtie/deduplicated/483.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:33:52.451 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:33:52 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/483.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/483.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/483.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:33:52 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:33:52 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:33:52\tMarkDuplicates\tStart of doWork freeMemory: 72063480; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:33:52\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:33:52\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:33:55\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig18494:2,867\r\n", "INFO\t2021-03-14 19:33:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:57\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig33873:45,317\r\n", "INFO\t2021-03-14 19:33:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:33:58\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig48849:2,416\r\n", "INFO\t2021-03-14 19:33:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:00\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig61379:9,375\r\n", "INFO\t2021-03-14 19:34:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:01\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig72108:728\r\n", "INFO\t2021-03-14 19:34:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:03\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig103849:4,264\r\n", "INFO\t2021-03-14 19:34:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:04\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig686969:1,541\r\n", "INFO\t2021-03-14 19:34:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:04\tMarkDuplicates\tRead 7022197 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:34:05\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 861859400; totalMemory: 1317011456; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:34:05\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:34:05\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:34:05\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:34:06\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:34:06\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1258790440; totalMemory: 2391801856; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:34:06\tMarkDuplicates\tMarking 2684548 records as duplicates.\r\n", "INFO\t2021-03-14 19:34:06\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:34:07\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:34:17\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:34:17\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:34:17\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:34:17\tMarkDuplicates\tBefore output close freeMemory: 266094800; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:34:17\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:34:17\tMarkDuplicates\tAfter output close freeMemory: 258759632; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:34:17 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.42 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/483.sorted.bam O=../qc-processing/bowtie/deduplicated/483.dedup.bam M=../qc-processing/bowtie/deduplicated/483.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:34:19\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/484.sorted.bam -O ../qc-processing/bowtie/deduplicated/484.dedup.bam -M ../qc-processing/bowtie/deduplicated/484.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:34:19.487 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:34:19 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/484.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/484.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/484.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:34:19 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:34:19 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:34:19\tMarkDuplicates\tStart of doWork freeMemory: 75209624; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:34:19\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:34:19\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:34:22\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig17421:16,748\r\n", "INFO\t2021-03-14 19:34:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:24\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,400\r\n", "INFO\t2021-03-14 19:34:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:26\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig42185:16,551\r\n", "INFO\t2021-03-14 19:34:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:27\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig56693:7,510\r\n", "INFO\t2021-03-14 19:34:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:29\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig68226:1,172\r\n", "INFO\t2021-03-14 19:34:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:31\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig76179:5,879\r\n", "INFO\t2021-03-14 19:34:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:32\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,590\r\n", "INFO\t2021-03-14 19:34:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:34\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig216445:3,168\r\n", "INFO\t2021-03-14 19:34:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:34\tMarkDuplicates\tRead 8210507 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:34:34\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 939329536; totalMemory: 1394606080; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:34:34\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:34:35\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:34:35\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:34:36\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:34:36\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1336385944; totalMemory: 2469396480; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:34:36\tMarkDuplicates\tMarking 2315855 records as duplicates.\r\n", "INFO\t2021-03-14 19:34:36\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:34:36\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:34:50\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:34:50\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:34:50\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:34:50\tMarkDuplicates\tBefore output close freeMemory: 268316432; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:34:50\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:34:50\tMarkDuplicates\tAfter output close freeMemory: 262954520; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:34:50 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.52 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/484.sorted.bam O=../qc-processing/bowtie/deduplicated/484.dedup.bam M=../qc-processing/bowtie/deduplicated/484.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:34:52\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/485.sorted.bam -O ../qc-processing/bowtie/deduplicated/485.dedup.bam -M ../qc-processing/bowtie/deduplicated/485.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:34:52.533 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:34:52 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/485.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/485.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/485.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:34:52 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:34:52 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:34:52\tMarkDuplicates\tStart of doWork freeMemory: 72063160; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:34:52\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:34:52\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:34:56\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4875:1,914\r\n", "INFO\t2021-03-14 19:34:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:57\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig22210:6,986\r\n", "INFO\t2021-03-14 19:34:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:34:59\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig32285:3,690\r\n", "INFO\t2021-03-14 19:34:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:01\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig40564:1,249\r\n", "INFO\t2021-03-14 19:35:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:02\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig53186:14,305\r\n", "INFO\t2021-03-14 19:35:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:04\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig66753:649\r\n", "INFO\t2021-03-14 19:35:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:06\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig79286:172\r\n", "INFO\t2021-03-14 19:35:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:07\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig103849:5,693\r\n", "INFO\t2021-03-14 19:35:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:09\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig170943:2,048\r\n", "INFO\t2021-03-14 19:35:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:10\tMarkDuplicates\tRead 9461956 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:35:10\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 885281456; totalMemory: 1447034880; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:35:10\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:35:11\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:35:11\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:35:12\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:35:12\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1388814352; totalMemory: 2521825280; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:35:12\tMarkDuplicates\tMarking 3254875 records as duplicates.\r\n", "INFO\t2021-03-14 19:35:12\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:35:13\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:35:28\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:35:28\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:35:28\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:35:28\tMarkDuplicates\tBefore output close freeMemory: 268501840; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:35:28\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:35:28\tMarkDuplicates\tAfter output close freeMemory: 258759472; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:35:28 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.60 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/485.sorted.bam O=../qc-processing/bowtie/deduplicated/485.dedup.bam M=../qc-processing/bowtie/deduplicated/485.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:35:30\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/487.sorted.bam -O ../qc-processing/bowtie/deduplicated/487.dedup.bam -M ../qc-processing/bowtie/deduplicated/487.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:35:30.087 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:35:30 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/487.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/487.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/487.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:35:30 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:35:30 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:35:30\tMarkDuplicates\tStart of doWork freeMemory: 72063992; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:35:30\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:35:30\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:35:33\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4039:2,328\r\n", "INFO\t2021-03-14 19:35:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:34\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig20807:15,474\r\n", "INFO\t2021-03-14 19:35:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:36\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30354:336\r\n", "INFO\t2021-03-14 19:35:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:38\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig37352:9,663\r\n", "INFO\t2021-03-14 19:35:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:39\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig47662:11,151\r\n", "INFO\t2021-03-14 19:35:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:41\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig58365:4,740\r\n", "INFO\t2021-03-14 19:35:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:42\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig69925:5,140\r\n", "INFO\t2021-03-14 19:35:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:44\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig90554:2,739\r\n", "INFO\t2021-03-14 19:35:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:45\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig130284:6,300\r\n", "INFO\t2021-03-14 19:35:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:47\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig686969:942\r\n", "INFO\t2021-03-14 19:35:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:35:47\tMarkDuplicates\tRead 10023321 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:35:47\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 878890176; totalMemory: 1462763520; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:35:47\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:35:48\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:35:48\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:35:49\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:35:49\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1404544480; totalMemory: 2537553920; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:35:49\tMarkDuplicates\tMarking 3669196 records as duplicates.\r\n", "INFO\t2021-03-14 19:35:49\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:35:50\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:36:10\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:36:10\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:36:10\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:36:10\tMarkDuplicates\tBefore output close freeMemory: 262949768; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:36:11\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:36:11\tMarkDuplicates\tAfter output close freeMemory: 262954632; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:36:11 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.68 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/487.sorted.bam O=../qc-processing/bowtie/deduplicated/487.dedup.bam M=../qc-processing/bowtie/deduplicated/487.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:36:13\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/488.sorted.bam -O ../qc-processing/bowtie/deduplicated/488.dedup.bam -M ../qc-processing/bowtie/deduplicated/488.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:36:13.187 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:36:13 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/488.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/488.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/488.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:36:13 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:36:13 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:36:13\tMarkDuplicates\tStart of doWork freeMemory: 72063320; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:36:13\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:36:13\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:36:16\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5705:6,477\r\n", "INFO\t2021-03-14 19:36:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:18\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig25135:13,109\r\n", "INFO\t2021-03-14 19:36:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:20\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig35897:1,267\r\n", "INFO\t2021-03-14 19:36:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:22\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig46998:5,895\r\n", "INFO\t2021-03-14 19:36:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:23\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig63531:4,723\r\n", "INFO\t2021-03-14 19:36:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:25\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig84462:3,128\r\n", "INFO\t2021-03-14 19:36:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:27\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig131913:3,111\r\n", "INFO\t2021-03-14 19:36:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:28\tMarkDuplicates\tRead 7690308 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:36:28\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1082453320; totalMemory: 1639972864; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:36:28\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:36:29\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:36:29\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:36:29\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:36:30\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1581754120; totalMemory: 2714763264; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:36:30\tMarkDuplicates\tMarking 3934291 records as duplicates.\r\n", "INFO\t2021-03-14 19:36:30\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:36:30\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:36:41\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:36:41\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:36:41\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:36:42\tMarkDuplicates\tBefore output close freeMemory: 262951064; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:36:42\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:36:42\tMarkDuplicates\tAfter output close freeMemory: 262955928; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:36:42 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.48 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/488.sorted.bam O=../qc-processing/bowtie/deduplicated/488.dedup.bam M=../qc-processing/bowtie/deduplicated/488.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:36:43\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/489.sorted.bam -O ../qc-processing/bowtie/deduplicated/489.dedup.bam -M ../qc-processing/bowtie/deduplicated/489.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:36:44.000 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:36:44 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/489.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/489.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/489.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:36:44 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:36:44 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:36:44\tMarkDuplicates\tStart of doWork freeMemory: 72063232; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:36:44\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:36:44\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:36:47\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5117:2,581\r\n", "INFO\t2021-03-14 19:36:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:49\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig21309:39,060\r\n", "INFO\t2021-03-14 19:36:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:51\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,647\r\n", "INFO\t2021-03-14 19:36:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:52\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig37707:7,419\r\n", "INFO\t2021-03-14 19:36:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:54\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig48737:5,387\r\n", "INFO\t2021-03-14 19:36:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:56\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig56693:16,400\r\n", "INFO\t2021-03-14 19:36:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:57\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig68037:397\r\n", "INFO\t2021-03-14 19:36:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:36:59\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig69234:14,487\r\n", "INFO\t2021-03-14 19:36:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:00\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig80528:7,130\r\n", "INFO\t2021-03-14 19:37:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:02\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig102196:3,221\r\n", "INFO\t2021-03-14 19:37:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:04\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig124730:2,506\r\n", "INFO\t2021-03-14 19:37:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:05\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: Contig686969:920\r\n", "INFO\t2021-03-14 19:37:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:05\tMarkDuplicates\tRead 12071698 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:37:06\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 857598720; totalMemory: 1448083456; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:37:06\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:37:06\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:37:06\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:37:07\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:37:07\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1389863720; totalMemory: 2522873856; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:37:07\tMarkDuplicates\tMarking 3518731 records as duplicates.\r\n", "INFO\t2021-03-14 19:37:07\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:37:08\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:37:28\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:37:28\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:37:28\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:37:28\tMarkDuplicates\tBefore output close freeMemory: 261526072; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:37:28\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:37:28\tMarkDuplicates\tAfter output close freeMemory: 258760216; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:37:28 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.74 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/489.sorted.bam O=../qc-processing/bowtie/deduplicated/489.dedup.bam M=../qc-processing/bowtie/deduplicated/489.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:37:30\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/490.sorted.bam -O ../qc-processing/bowtie/deduplicated/490.dedup.bam -M ../qc-processing/bowtie/deduplicated/490.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:37:30.323 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:37:30 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/490.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/490.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/490.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:37:30 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:37:30 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:37:30\tMarkDuplicates\tStart of doWork freeMemory: 75211472; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:37:30\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:37:30\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:37:33\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig9662:3,258\r\n", "INFO\t2021-03-14 19:37:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:35\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig27262:3,772\r\n", "INFO\t2021-03-14 19:37:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:37\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig37777:9,221\r\n", "INFO\t2021-03-14 19:37:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:38\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig53624:3,055\r\n", "INFO\t2021-03-14 19:37:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:40\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,780\r\n", "INFO\t2021-03-14 19:37:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:42\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig95784:8,907\r\n", "INFO\t2021-03-14 19:37:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:43\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig149651:1,566\r\n", "INFO\t2021-03-14 19:37:43\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:37:44\tMarkDuplicates\tRead 7472616 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:37:44\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 953443192; totalMemory: 1442840576; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:37:44\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:37:45\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:37:45\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:37:46\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:37:46\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1384621560; totalMemory: 2517630976; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:37:46\tMarkDuplicates\tMarking 2462323 records as duplicates.\r\n", "INFO\t2021-03-14 19:37:46\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:37:46\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:37:58\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:37:58\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:37:58\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:37:58\tMarkDuplicates\tBefore output close freeMemory: 320572408; totalMemory: 2517630976; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:37:58\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:37:58\tMarkDuplicates\tAfter output close freeMemory: 266100864; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:37:58 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.48 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/490.sorted.bam O=../qc-processing/bowtie/deduplicated/490.dedup.bam M=../qc-processing/bowtie/deduplicated/490.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:38:00\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/491.sorted.bam -O ../qc-processing/bowtie/deduplicated/491.dedup.bam -M ../qc-processing/bowtie/deduplicated/491.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:38:00.575 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:38:00 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/491.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/491.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/491.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:38:00 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:38:00 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:38:00\tMarkDuplicates\tStart of doWork freeMemory: 75209008; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:38:00\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:38:00\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:38:03\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig17195:10,948\r\n", "INFO\t2021-03-14 19:38:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:05\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig33914:6,873\r\n", "INFO\t2021-03-14 19:38:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:07\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig45737:5,029\r\n", "INFO\t2021-03-14 19:38:07\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:08\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig68037:867\r\n", "INFO\t2021-03-14 19:38:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:10\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,705\r\n", "INFO\t2021-03-14 19:38:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:11\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig194027:711\r\n", "INFO\t2021-03-14 19:38:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:12\tMarkDuplicates\tRead 6206096 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:38:12\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1129904288; totalMemory: 1611661312; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:38:12\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:38:12\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:38:12\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:38:13\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:38:13\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1553441224; totalMemory: 2686451712; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:38:13\tMarkDuplicates\tMarking 3066255 records as duplicates.\r\n", "INFO\t2021-03-14 19:38:13\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:38:14\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:38:23\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:38:23\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:38:23\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:38:23\tMarkDuplicates\tBefore output close freeMemory: 255609624; totalMemory: 363855872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:38:23\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:38:23\tMarkDuplicates\tAfter output close freeMemory: 255614488; totalMemory: 363855872; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:38:23 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.38 minutes.\r\n", "Runtime.totalMemory()=363855872\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/491.sorted.bam O=../qc-processing/bowtie/deduplicated/491.dedup.bam M=../qc-processing/bowtie/deduplicated/491.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:38:25\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/492.sorted.bam -O ../qc-processing/bowtie/deduplicated/492.dedup.bam -M ../qc-processing/bowtie/deduplicated/492.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:38:25.559 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:38:25 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/492.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/492.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/492.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:38:25 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:38:25 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:38:25\tMarkDuplicates\tStart of doWork freeMemory: 67871328; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:38:25\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:38:25\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:38:28\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5559:6,533\r\n", "INFO\t2021-03-14 19:38:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:30\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig23936:31,994\r\n", "INFO\t2021-03-14 19:38:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:31\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig34828:35,116\r\n", "INFO\t2021-03-14 19:38:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:33\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig42633:5,779\r\n", "INFO\t2021-03-14 19:38:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:35\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56693:7,466\r\n", "INFO\t2021-03-14 19:38:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:36\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,805\r\n", "INFO\t2021-03-14 19:38:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:38\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig97708:7,857\r\n", "INFO\t2021-03-14 19:38:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:39\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig144152:1,020\r\n", "INFO\t2021-03-14 19:38:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:38:40\tMarkDuplicates\tRead 8632452 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:38:40\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 929927048; totalMemory: 1517289472; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:38:40\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:38:41\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:38:41\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:38:42\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:38:42\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1459069040; totalMemory: 2592079872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:38:42\tMarkDuplicates\tMarking 4153952 records as duplicates.\r\n", "INFO\t2021-03-14 19:38:42\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:38:43\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:38:54\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:38:54\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:38:54\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:38:55\tMarkDuplicates\tBefore output close freeMemory: 269239976; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:38:55\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:38:55\tMarkDuplicates\tAfter output close freeMemory: 262953256; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:38:55 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.49 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/492.sorted.bam O=../qc-processing/bowtie/deduplicated/492.dedup.bam M=../qc-processing/bowtie/deduplicated/492.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:38:56\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/506.sorted.bam -O ../qc-processing/bowtie/deduplicated/506.dedup.bam -M ../qc-processing/bowtie/deduplicated/506.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:38:56.843 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:38:56 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/506.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/506.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/506.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:38:57 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:38:57 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:38:57\tMarkDuplicates\tStart of doWork freeMemory: 72061904; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:38:57\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:38:57\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:39:00\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig23487:5,041\r\n", "INFO\t2021-03-14 19:39:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:01\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig36557:11,339\r\n", "INFO\t2021-03-14 19:39:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:03\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig58273:4,648\r\n", "INFO\t2021-03-14 19:39:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:04\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig83649:2,416\r\n", "INFO\t2021-03-14 19:39:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:06\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig244871:164\r\n", "INFO\t2021-03-14 19:39:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:06\tMarkDuplicates\tRead 5059600 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:39:06\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 986795048; totalMemory: 1405091840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:39:06\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:39:07\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:39:07\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:39:07\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:39:08\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1346871888; totalMemory: 2479882240; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:39:08\tMarkDuplicates\tMarking 2413267 records as duplicates.\r\n", "INFO\t2021-03-14 19:39:08\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:39:08\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:39:16\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:39:16\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:39:16\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:39:16\tMarkDuplicates\tBefore output close freeMemory: 266095424; totalMemory: 374341632; maxMemory: 4294967296\r", "\r\n", "INFO\t2021-03-14 19:39:16\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:39:16\tMarkDuplicates\tAfter output close freeMemory: 258760128; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:39:16 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.33 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/506.sorted.bam O=../qc-processing/bowtie/deduplicated/506.dedup.bam M=../qc-processing/bowtie/deduplicated/506.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:39:18\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/513.sorted.bam -O ../qc-processing/bowtie/deduplicated/513.dedup.bam -M ../qc-processing/bowtie/deduplicated/513.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:39:18.231 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:39:18 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/513.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/513.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/513.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:39:18 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:39:18 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:39:18\tMarkDuplicates\tStart of doWork freeMemory: 75211216; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:39:18\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:39:18\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:39:21\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig7070:4,091\r\n", "INFO\t2021-03-14 19:39:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:23\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig25623:6,867\r\n", "INFO\t2021-03-14 19:39:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:24\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig35422:217\r\n", "INFO\t2021-03-14 19:39:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:26\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig47071:3,296\r\n", "INFO\t2021-03-14 19:39:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:27\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig62580:2,530\r\n", "INFO\t2021-03-14 19:39:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:29\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig77522:6,730\r\n", "INFO\t2021-03-14 19:39:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:31\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig109779:8,288\r\n", "INFO\t2021-03-14 19:39:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:32\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig464614:3,320\r\n", "INFO\t2021-03-14 19:39:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:32\tMarkDuplicates\tRead 8095344 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:39:32\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1018064072; totalMemory: 1526726656; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:39:32\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:39:33\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:39:33\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:39:34\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:39:34\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1468507688; totalMemory: 2601517056; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:39:34\tMarkDuplicates\tMarking 2671834 records as duplicates.\r\n", "INFO\t2021-03-14 19:39:34\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:39:35\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:39:47\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:39:47\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:39:47\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:39:47\tMarkDuplicates\tBefore output close freeMemory: 1074788392; totalMemory: 2601517056; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:39:47\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:39:47\tMarkDuplicates\tAfter output close freeMemory: 266101576; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:39:47 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.49 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/513.sorted.bam O=../qc-processing/bowtie/deduplicated/513.dedup.bam M=../qc-processing/bowtie/deduplicated/513.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:39:49\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/521.sorted.bam -O ../qc-processing/bowtie/deduplicated/521.dedup.bam -M ../qc-processing/bowtie/deduplicated/521.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:39:49.433 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:39:49 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/521.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/521.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/521.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:39:49 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:39:49 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:39:49\tMarkDuplicates\tStart of doWork freeMemory: 64723368; totalMemory: 91226112; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:39:49\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:39:49\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:39:52\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig5738:10,717\r\n", "INFO\t2021-03-14 19:39:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:54\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig22619:184\r\n", "INFO\t2021-03-14 19:39:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:55\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,671\r\n", "INFO\t2021-03-14 19:39:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:57\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig35213:849\r\n", "INFO\t2021-03-14 19:39:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:39:58\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig43834:3,625\r\n", "INFO\t2021-03-14 19:39:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:00\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig56693:2,649\r\n", "INFO\t2021-03-14 19:40:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:01\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig59424:1,399\r\n", "INFO\t2021-03-14 19:40:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:03\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig68037:874\r\n", "INFO\t2021-03-14 19:40:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:05\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,891\r\n", "INFO\t2021-03-14 19:40:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:06\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig81807:6,003\r\n", "INFO\t2021-03-14 19:40:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:08\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,944\r\n", "INFO\t2021-03-14 19:40:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:10\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,216\r\n", "INFO\t2021-03-14 19:40:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:11\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig104701:4,801\r\n", "INFO\t2021-03-14 19:40:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:12\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: Contig189029:2,207\r\n", "INFO\t2021-03-14 19:40:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:13\tMarkDuplicates\tRead 14567238 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:40:14\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 756731480; totalMemory: 1447034880; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:40:14\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:40:14\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:40:14\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:40:15\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:40:16\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1388814896; totalMemory: 2521825280; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:40:16\tMarkDuplicates\tMarking 5999263 records as duplicates.\r\n", "INFO\t2021-03-14 19:40:16\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:40:17\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:40:38\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:40:38\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:40:38\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:40:38\tMarkDuplicates\tBefore output close freeMemory: 262948984; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:40:38\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:40:38\tMarkDuplicates\tAfter output close freeMemory: 262953760; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:40:38 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.83 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/521.sorted.bam O=../qc-processing/bowtie/deduplicated/521.dedup.bam M=../qc-processing/bowtie/deduplicated/521.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:40:40\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/522.sorted.bam -O ../qc-processing/bowtie/deduplicated/522.dedup.bam -M ../qc-processing/bowtie/deduplicated/522.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:40:41.029 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:40:41 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/522.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/522.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/522.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:40:41 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:40:41 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:40:41\tMarkDuplicates\tStart of doWork freeMemory: 72067024; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:40:41\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:40:41\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:40:44\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig17677:6,479\r\n", "INFO\t2021-03-14 19:40:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:45\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig34544:16,924\r\n", "INFO\t2021-03-14 19:40:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:47\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig48849:4,658\r\n", "INFO\t2021-03-14 19:40:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:49\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,795\r\n", "INFO\t2021-03-14 19:40:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:50\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig104701:4,801\r\n", "INFO\t2021-03-14 19:40:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:40:52\tMarkDuplicates\tRead 5936529 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:40:52\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1063852136; totalMemory: 1514143744; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:40:52\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:40:52\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:40:52\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:40:53\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:40:53\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1455923912; totalMemory: 2588934144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:40:53\tMarkDuplicates\tMarking 2563826 records as duplicates.\r\n", "INFO\t2021-03-14 19:40:53\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:40:54\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:41:03\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:41:03\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:41:03\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:41:03\tMarkDuplicates\tBefore output close freeMemory: 2477761224; totalMemory: 2588934144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:41:03\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:41:03\tMarkDuplicates\tAfter output close freeMemory: 266100072; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:41:03 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.37 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/522.sorted.bam O=../qc-processing/bowtie/deduplicated/522.dedup.bam M=../qc-processing/bowtie/deduplicated/522.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:41:04\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/523.sorted.bam -O ../qc-processing/bowtie/deduplicated/523.dedup.bam -M ../qc-processing/bowtie/deduplicated/523.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:41:04.972 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:41:05 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/523.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/523.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/523.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:41:05 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:41:05 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:41:05\tMarkDuplicates\tStart of doWork freeMemory: 72062848; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:41:05\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:41:05\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:41:08\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig15994:7,626\r\n", "INFO\t2021-03-14 19:41:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:09\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig28498:8,653\r\n", "INFO\t2021-03-14 19:41:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:11\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig37163:7,513\r\n", "INFO\t2021-03-14 19:41:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:12\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig51055:23,495\r\n", "INFO\t2021-03-14 19:41:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:14\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig56693:12,116\r\n", "INFO\t2021-03-14 19:41:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:16\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig68037:457\r\n", "INFO\t2021-03-14 19:41:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:17\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,594\r\n", "INFO\t2021-03-14 19:41:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:19\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,673\r\n", "INFO\t2021-03-14 19:41:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:21\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig103849:5,732\r\n", "INFO\t2021-03-14 19:41:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:22\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig377195:7,036\r\n", "INFO\t2021-03-14 19:41:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:23\tMarkDuplicates\tRead 10277262 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:41:23\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 880220848; totalMemory: 1421869056; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:41:23\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:41:23\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:41:23\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:41:24\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:41:24\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1363648672; totalMemory: 2496659456; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:41:24\tMarkDuplicates\tMarking 3740353 records as duplicates.\r\n", "INFO\t2021-03-14 19:41:24\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:41:25\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:41:41\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:41:41\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:41:41\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:41:41\tMarkDuplicates\tBefore output close freeMemory: 258755128; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:41:41\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:41:41\tMarkDuplicates\tAfter output close freeMemory: 258759992; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:41:41 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.61 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/523.sorted.bam O=../qc-processing/bowtie/deduplicated/523.dedup.bam M=../qc-processing/bowtie/deduplicated/523.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:41:43\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/524.sorted.bam -O ../qc-processing/bowtie/deduplicated/524.dedup.bam -M ../qc-processing/bowtie/deduplicated/524.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:41:43.310 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:41:43 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/524.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/524.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/524.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:41:43 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:41:43 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:41:43\tMarkDuplicates\tStart of doWork freeMemory: 72062536; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:41:43\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:41:43\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:41:46\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig8780:3,008\r\n", "INFO\t2021-03-14 19:41:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:48\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig29072:5,189\r\n", "INFO\t2021-03-14 19:41:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:49\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig40107:5,359\r\n", "INFO\t2021-03-14 19:41:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:51\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig56878:5,805\r\n", "INFO\t2021-03-14 19:41:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:53\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig76520:6,511\r\n", "INFO\t2021-03-14 19:41:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:54\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig112919:3,766\r\n", "INFO\t2021-03-14 19:41:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:41:56\tMarkDuplicates\tRead 6859685 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:41:56\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1175702504; totalMemory: 1674575872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:41:56\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:41:56\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:41:56\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:41:57\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:41:57\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1616356648; totalMemory: 2749366272; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:41:57\tMarkDuplicates\tMarking 3041510 records as duplicates.\r\n", "INFO\t2021-03-14 19:41:57\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:41:58\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:42:08\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:42:08\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:42:08\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:42:08\tMarkDuplicates\tBefore output close freeMemory: 262950104; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:42:08\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:42:08\tMarkDuplicates\tAfter output close freeMemory: 262954968; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:42:08 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.42 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/524.sorted.bam O=../qc-processing/bowtie/deduplicated/524.dedup.bam M=../qc-processing/bowtie/deduplicated/524.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:42:10\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/525.sorted.bam -O ../qc-processing/bowtie/deduplicated/525.dedup.bam -M ../qc-processing/bowtie/deduplicated/525.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:42:10.110 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:42:10 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/525.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/525.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/525.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:42:10 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:42:10 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:42:10\tMarkDuplicates\tStart of doWork freeMemory: 67869904; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:42:10\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:42:10\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:42:13\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig15297:4,755\r\n", "INFO\t2021-03-14 19:42:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:14\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig27493:40,061\r\n", "INFO\t2021-03-14 19:42:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:16\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig37495:4,255\r\n", "INFO\t2021-03-14 19:42:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:18\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig52773:8,956\r\n", "INFO\t2021-03-14 19:42:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:19\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig66871:14,256\r\n", "INFO\t2021-03-14 19:42:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:21\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig77508:4,185\r\n", "INFO\t2021-03-14 19:42:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:23\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig104654:5,353\r\n", "INFO\t2021-03-14 19:42:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:24\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig350376:931\r\n", "INFO\t2021-03-14 19:42:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:24\tMarkDuplicates\tRead 8136272 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:42:25\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 910256072; totalMemory: 1394606080; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:42:25\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:42:25\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:42:25\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:42:26\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:42:26\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1336387160; totalMemory: 2469396480; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:42:26\tMarkDuplicates\tMarking 2365706 records as duplicates.\r\n", "INFO\t2021-03-14 19:42:26\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:42:27\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:42:40\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:42:40\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:42:40\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:42:40\tMarkDuplicates\tBefore output close freeMemory: 263810496; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:42:40\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:42:40\tMarkDuplicates\tAfter output close freeMemory: 258760800; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:42:40 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.51 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/525.sorted.bam O=../qc-processing/bowtie/deduplicated/525.dedup.bam M=../qc-processing/bowtie/deduplicated/525.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:42:42\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/526.sorted.bam -O ../qc-processing/bowtie/deduplicated/526.dedup.bam -M ../qc-processing/bowtie/deduplicated/526.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:42:42.794 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:42:42 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/526.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/526.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/526.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:42:43 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:42:43 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:42:43\tMarkDuplicates\tStart of doWork freeMemory: 75207672; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:42:43\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:42:43\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:42:45\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig16408:90\r\n", "INFO\t2021-03-14 19:42:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:47\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig30392:16,014\r\n", "INFO\t2021-03-14 19:42:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:49\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig42187:43,004\r\n", "INFO\t2021-03-14 19:42:49\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:51\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig57693:20,418\r\n", "INFO\t2021-03-14 19:42:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:52\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig72311:9,116\r\n", "INFO\t2021-03-14 19:42:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:54\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig106614:2,363\r\n", "INFO\t2021-03-14 19:42:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:42:55\tMarkDuplicates\tRead 6971456 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:42:56\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1067266448; totalMemory: 1520435200; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:42:56\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:42:56\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:42:56\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:42:57\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:42:57\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1462215200; totalMemory: 2595225600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:42:57\tMarkDuplicates\tMarking 2039137 records as duplicates.\r\n", "INFO\t2021-03-14 19:42:57\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:42:57\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:43:09\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:43:09\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:43:09\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:43:09\tMarkDuplicates\tBefore output close freeMemory: 262949648; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:43:09\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:43:09\tMarkDuplicates\tAfter output close freeMemory: 258760080; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:43:09 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.45 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/526.sorted.bam O=../qc-processing/bowtie/deduplicated/526.dedup.bam M=../qc-processing/bowtie/deduplicated/526.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:43:11\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/527.sorted.bam -O ../qc-processing/bowtie/deduplicated/527.dedup.bam -M ../qc-processing/bowtie/deduplicated/527.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:43:11.329 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:43:11 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/527.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/527.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/527.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:43:11 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:43:11 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:43:11\tMarkDuplicates\tStart of doWork freeMemory: 67866032; totalMemory: 94371840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:43:11\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:43:11\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:43:14\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4963:3,727\r\n", "INFO\t2021-03-14 19:43:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:16\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig21655:48,522\r\n", "INFO\t2021-03-14 19:43:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:17\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig31694:9,160\r\n", "INFO\t2021-03-14 19:43:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:19\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig38003:36,047\r\n", "INFO\t2021-03-14 19:43:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:20\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig48415:702\r\n", "INFO\t2021-03-14 19:43:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:22\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig62449:8,893\r\n", "INFO\t2021-03-14 19:43:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:24\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig74232:7,680\r\n", "INFO\t2021-03-14 19:43:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:25\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig100843:1,750\r\n", "INFO\t2021-03-14 19:43:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:27\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig147865:528\r\n", "INFO\t2021-03-14 19:43:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:28\tMarkDuplicates\tRead 9691585 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:43:29\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 927788072; totalMemory: 1536163840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:43:29\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:43:29\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:43:29\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:43:30\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:43:30\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1477941832; totalMemory: 2610954240; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:43:30\tMarkDuplicates\tMarking 4248363 records as duplicates.\r\n", "INFO\t2021-03-14 19:43:30\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:43:31\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:43:44\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:43:44\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:43:44\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:43:45\tMarkDuplicates\tBefore output close freeMemory: 265940696; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:43:45\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:43:45\tMarkDuplicates\tAfter output close freeMemory: 255611680; totalMemory: 363855872; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:43:45 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.57 minutes.\r\n", "Runtime.totalMemory()=363855872\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/527.sorted.bam O=../qc-processing/bowtie/deduplicated/527.dedup.bam M=../qc-processing/bowtie/deduplicated/527.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:43:46\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/528.sorted.bam -O ../qc-processing/bowtie/deduplicated/528.dedup.bam -M ../qc-processing/bowtie/deduplicated/528.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:43:46.997 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:43:47 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/528.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/528.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/528.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:43:47 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:43:47 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:43:47\tMarkDuplicates\tStart of doWork freeMemory: 72066856; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:43:47\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:43:47\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:43:51\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: Contig3033:32,612\r\n", "INFO\t2021-03-14 19:43:51\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:52\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig19473:29,368\r\n", "INFO\t2021-03-14 19:43:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:54\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig28449:44,557\r\n", "INFO\t2021-03-14 19:43:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:56\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig35611:2,642\r\n", "INFO\t2021-03-14 19:43:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:57\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig44034:8,556\r\n", "INFO\t2021-03-14 19:43:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:43:59\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig56205:4,740\r\n", "INFO\t2021-03-14 19:43:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:00\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig68908:720\r\n", "INFO\t2021-03-14 19:44:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:02\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig86903:2,595\r\n", "INFO\t2021-03-14 19:44:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:04\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig113539:2,903\r\n", "INFO\t2021-03-14 19:44:04\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:05\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: Contig199624:4,427\r\n", "INFO\t2021-03-14 19:44:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:06\tMarkDuplicates\tRead 10311803 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:44:06\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 715378688; totalMemory: 1355808768; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:44:06\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:44:06\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:44:06\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:44:08\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:44:08\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1297591448; totalMemory: 2430599168; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:44:08\tMarkDuplicates\tMarking 4262114 records as duplicates.\r\n", "INFO\t2021-03-14 19:44:08\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:44:09\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:44:23\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:44:23\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:44:23\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:44:24\tMarkDuplicates\tBefore output close freeMemory: 262891456; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:44:24\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:44:24\tMarkDuplicates\tAfter output close freeMemory: 262956864; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:44:24 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.62 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/528.sorted.bam O=../qc-processing/bowtie/deduplicated/528.dedup.bam M=../qc-processing/bowtie/deduplicated/528.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:44:25\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/529.sorted.bam -O ../qc-processing/bowtie/deduplicated/529.dedup.bam -M ../qc-processing/bowtie/deduplicated/529.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:44:25.905 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:44:26 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/529.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/529.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/529.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:44:26 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:44:26 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:44:26\tMarkDuplicates\tStart of doWork freeMemory: 75209896; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:44:26\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:44:26\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:44:29\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig15296:92\r\n", "INFO\t2021-03-14 19:44:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:30\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig30824:4,544\r\n", "INFO\t2021-03-14 19:44:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:32\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig41405:3,231\r\n", "INFO\t2021-03-14 19:44:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:33\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig56910:832\r\n", "INFO\t2021-03-14 19:44:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:35\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig77027:2,901\r\n", "INFO\t2021-03-14 19:44:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:37\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig110969:6,329\r\n", "INFO\t2021-03-14 19:44:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:38\tMarkDuplicates\tRead 6828865 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:44:38\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 909367136; totalMemory: 1428160512; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:44:38\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:44:38\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:44:38\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:44:39\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:44:40\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1369941080; totalMemory: 2502950912; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:44:40\tMarkDuplicates\tMarking 3660497 records as duplicates.\r\n", "INFO\t2021-03-14 19:44:40\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:44:40\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:44:50\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:44:50\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:44:50\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:44:50\tMarkDuplicates\tBefore output close freeMemory: 262949928; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:44:50\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:44:50\tMarkDuplicates\tAfter output close freeMemory: 262954792; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:44:50 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.41 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/529.sorted.bam O=../qc-processing/bowtie/deduplicated/529.dedup.bam M=../qc-processing/bowtie/deduplicated/529.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:44:52\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/531.sorted.bam -O ../qc-processing/bowtie/deduplicated/531.dedup.bam -M ../qc-processing/bowtie/deduplicated/531.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:44:52.080 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:44:52 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/531.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/531.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/531.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:44:52 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:44:52 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:44:52\tMarkDuplicates\tStart of doWork freeMemory: 75211040; totalMemory: 101711872; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:44:52\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:44:52\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:44:55\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig17280:32,422\r\n", "INFO\t2021-03-14 19:44:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:57\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig30702:6,241\r\n", "INFO\t2021-03-14 19:44:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:44:58\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig42187:42,961\r\n", "INFO\t2021-03-14 19:44:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:00\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig56693:16,402\r\n", "INFO\t2021-03-14 19:45:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:01\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig69234:11,758\r\n", "INFO\t2021-03-14 19:45:01\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:03\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig89106:10,211\r\n", "INFO\t2021-03-14 19:45:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:05\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig142345:5,341\r\n", "INFO\t2021-03-14 19:45:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:06\tMarkDuplicates\tRead 7531668 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:45:06\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1049901792; totalMemory: 1498415104; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:45:06\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:45:06\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:45:06\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:45:07\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:45:07\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1440196544; totalMemory: 2573205504; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:45:07\tMarkDuplicates\tMarking 2058927 records as duplicates.\r\n", "INFO\t2021-03-14 19:45:07\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:45:08\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:45:20\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:45:20\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:45:20\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:45:20\tMarkDuplicates\tBefore output close freeMemory: 267371208; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:45:20\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:45:20\tMarkDuplicates\tAfter output close freeMemory: 262955200; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:45:20 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.48 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/531.sorted.bam O=../qc-processing/bowtie/deduplicated/531.dedup.bam M=../qc-processing/bowtie/deduplicated/531.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:45:22\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/532.sorted.bam -O ../qc-processing/bowtie/deduplicated/532.dedup.bam -M ../qc-processing/bowtie/deduplicated/532.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:45:22.637 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:45:22 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/532.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/532.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/532.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:45:22 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:45:22 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:45:22\tMarkDuplicates\tStart of doWork freeMemory: 64726040; totalMemory: 91226112; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:45:22\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:45:22\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:45:26\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig17971:12,287\r\n", "INFO\t2021-03-14 19:45:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:28\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig34828:35,158\r\n", "INFO\t2021-03-14 19:45:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:29\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig48546:1,559\r\n", "INFO\t2021-03-14 19:45:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:31\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,805\r\n", "INFO\t2021-03-14 19:45:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:33\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig106636:3,219\r\n", "INFO\t2021-03-14 19:45:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:34\tMarkDuplicates\tRead 5853149 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:45:35\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1043488136; totalMemory: 1485832192; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:45:35\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:45:35\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:45:35\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:45:36\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:45:36\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1427612984; totalMemory: 2560622592; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:45:36\tMarkDuplicates\tMarking 2396922 records as duplicates.\r\n", "INFO\t2021-03-14 19:45:36\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:45:37\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:45:45\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:45:45\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:45:45\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:45:45\tMarkDuplicates\tBefore output close freeMemory: 262439720; totalMemory: 371195904; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:45:45\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:45:45\tMarkDuplicates\tAfter output close freeMemory: 258761192; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:45:45 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.39 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/532.sorted.bam O=../qc-processing/bowtie/deduplicated/532.dedup.bam M=../qc-processing/bowtie/deduplicated/532.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:45:47\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/533.sorted.bam -O ../qc-processing/bowtie/deduplicated/533.dedup.bam -M ../qc-processing/bowtie/deduplicated/533.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:45:47.582 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:45:47 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/533.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/533.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/533.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:45:47 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:45:47 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:45:47\tMarkDuplicates\tStart of doWork freeMemory: 72063656; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:45:47\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:45:47\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:45:50\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig17423:1,904\r\n", "INFO\t2021-03-14 19:45:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:52\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,623\r\n", "INFO\t2021-03-14 19:45:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:54\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig42187:43,004\r\n", "INFO\t2021-03-14 19:45:54\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:55\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig56914:3,015\r\n", "INFO\t2021-03-14 19:45:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:57\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig69234:14,487\r\n", "INFO\t2021-03-14 19:45:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:45:59\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,944\r\n", "INFO\t2021-03-14 19:45:59\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:00\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig105506:8,208\r\n", "INFO\t2021-03-14 19:46:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:02\tMarkDuplicates\tRead 7945481 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:46:02\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1101950312; totalMemory: 1566572544; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:46:02\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:46:03\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:46:03\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:46:03\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:46:03\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1508352888; totalMemory: 2641362944; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:46:03\tMarkDuplicates\tMarking 2653991 records as duplicates.\r\n", "INFO\t2021-03-14 19:46:03\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:46:04\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:46:16\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:46:16\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:46:16\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:46:17\tMarkDuplicates\tBefore output close freeMemory: 264182944; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:46:17\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:46:17\tMarkDuplicates\tAfter output close freeMemory: 258760136; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:46:17 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.49 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/533.sorted.bam O=../qc-processing/bowtie/deduplicated/533.dedup.bam M=../qc-processing/bowtie/deduplicated/533.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:46:18\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/541.sorted.bam -O ../qc-processing/bowtie/deduplicated/541.dedup.bam -M ../qc-processing/bowtie/deduplicated/541.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:46:18.920 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:46:18 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/541.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/541.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/541.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:46:19 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:46:19 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:46:19\tMarkDuplicates\tStart of doWork freeMemory: 72063160; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:46:19\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:46:19\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:46:22\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig7365:3,399\r\n", "INFO\t2021-03-14 19:46:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:23\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig26524:20,789\r\n", "INFO\t2021-03-14 19:46:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:25\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig36557:11,314\r\n", "INFO\t2021-03-14 19:46:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:26\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig49166:6,379\r\n", "INFO\t2021-03-14 19:46:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:28\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig64626:2,316\r\n", "INFO\t2021-03-14 19:46:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:30\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig80528:5,723\r\n", "INFO\t2021-03-14 19:46:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:31\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig108457:1,295\r\n", "INFO\t2021-03-14 19:46:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:33\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig519002:3,294\r\n", "INFO\t2021-03-14 19:46:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:33\tMarkDuplicates\tRead 8077792 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:46:33\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1175975472; totalMemory: 1703936000; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:46:33\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:46:33\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:46:33\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:46:34\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:46:34\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1645716968; totalMemory: 2778726400; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:46:34\tMarkDuplicates\tMarking 3317152 records as duplicates.\r\n", "INFO\t2021-03-14 19:46:34\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:46:35\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:46:46\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:46:46\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:46:46\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:46:47\tMarkDuplicates\tBefore output close freeMemory: 264727344; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:46:47\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:46:47\tMarkDuplicates\tAfter output close freeMemory: 258760848; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:46:47 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.47 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/541.sorted.bam O=../qc-processing/bowtie/deduplicated/541.dedup.bam M=../qc-processing/bowtie/deduplicated/541.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:46:49\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/542.sorted.bam -O ../qc-processing/bowtie/deduplicated/542.dedup.bam -M ../qc-processing/bowtie/deduplicated/542.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:46:49.063 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:46:49 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/542.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/542.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/542.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:46:49 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "[Sun Mar 14 19:46:49 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:46:49\tMarkDuplicates\tStart of doWork freeMemory: 72061744; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:46:49\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:46:49\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:46:52\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig21157:3,497\r\n", "INFO\t2021-03-14 19:46:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:53\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig36439:1,862\r\n", "INFO\t2021-03-14 19:46:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:55\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig56320:792\r\n", "INFO\t2021-03-14 19:46:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:57\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig75494:648\r\n", "INFO\t2021-03-14 19:46:57\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:58\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig138833:1,679\r\n", "INFO\t2021-03-14 19:46:58\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:46:59\tMarkDuplicates\tRead 5408988 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:46:59\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 971684304; totalMemory: 1384120320; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:46:59\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:46:59\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:46:59\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:47:00\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:47:00\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1325899632; totalMemory: 2458910720; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:47:00\tMarkDuplicates\tMarking 2196611 records as duplicates.\r\n", "INFO\t2021-03-14 19:47:00\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:47:01\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:47:09\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:47:09\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:47:09\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:47:10\tMarkDuplicates\tBefore output close freeMemory: 263833704; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:47:10\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:47:10\tMarkDuplicates\tAfter output close freeMemory: 258760008; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:47:10 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.35 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/542.sorted.bam O=../qc-processing/bowtie/deduplicated/542.dedup.bam M=../qc-processing/bowtie/deduplicated/542.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:47:11\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/543.sorted.bam -O ../qc-processing/bowtie/deduplicated/543.dedup.bam -M ../qc-processing/bowtie/deduplicated/543.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:47:11.847 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:47:11 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/543.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/543.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/543.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:47:12 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:47:12 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:47:12\tMarkDuplicates\tStart of doWork freeMemory: 72063848; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:47:12\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:47:12\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:47:15\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig21789:3,523\r\n", "INFO\t2021-03-14 19:47:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:16\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig39991:25,645\r\n", "INFO\t2021-03-14 19:47:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:18\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig68040:2,113\r\n", "INFO\t2021-03-14 19:47:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:20\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig121360:1,120\r\n", "INFO\t2021-03-14 19:47:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:21\tMarkDuplicates\tRead 4536531 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:47:21\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 911915584; totalMemory: 1300234240; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:47:21\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:47:21\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:47:21\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:47:22\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:47:22\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1242014952; totalMemory: 2375024640; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:47:22\tMarkDuplicates\tMarking 1678199 records as duplicates.\r\n", "INFO\t2021-03-14 19:47:22\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:47:23\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:47:30\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:47:30\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:47:30\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:47:30\tMarkDuplicates\tBefore output close freeMemory: 264429440; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:47:30\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:47:30\tMarkDuplicates\tAfter output close freeMemory: 255614256; totalMemory: 363855872; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:47:30 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.31 minutes.\r\n", "Runtime.totalMemory()=363855872\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/543.sorted.bam O=../qc-processing/bowtie/deduplicated/543.dedup.bam M=../qc-processing/bowtie/deduplicated/543.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:47:32\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/551.sorted.bam -O ../qc-processing/bowtie/deduplicated/551.dedup.bam -M ../qc-processing/bowtie/deduplicated/551.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:47:32.305 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:47:32 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/551.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/551.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/551.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:47:32 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:47:32 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:47:32\tMarkDuplicates\tStart of doWork freeMemory: 72065912; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:47:32\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:47:32\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:47:36\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: Contig5240:2,172\r\n", "INFO\t2021-03-14 19:47:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:38\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig23691:9,001\r\n", "INFO\t2021-03-14 19:47:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:39\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig34634:538\r\n", "INFO\t2021-03-14 19:47:39\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:41\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig43024:7,290\r\n", "INFO\t2021-03-14 19:47:41\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:42\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: Contig56693:18,541\r\n", "INFO\t2021-03-14 19:47:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:44\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,842\r\n", "INFO\t2021-03-14 19:47:44\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:46\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig97936:72\r\n", "INFO\t2021-03-14 19:47:46\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:47\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: Contig137674:181\r\n", "INFO\t2021-03-14 19:47:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:47:49\tMarkDuplicates\tRead 8767880 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:47:49\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 941298480; totalMemory: 1515192320; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:47:49\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:47:49\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:47:49\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:47:50\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:47:51\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1456972424; totalMemory: 2589982720; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:47:51\tMarkDuplicates\tMarking 3670108 records as duplicates.\r\n", "INFO\t2021-03-14 19:47:51\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:47:51\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:48:04\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:48:04\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:48:04\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:48:04\tMarkDuplicates\tBefore output close freeMemory: 266095368; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:48:04\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:48:04\tMarkDuplicates\tAfter output close freeMemory: 262954376; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:48:04 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.54 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/551.sorted.bam O=../qc-processing/bowtie/deduplicated/551.dedup.bam M=../qc-processing/bowtie/deduplicated/551.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:48:06\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/552b.sorted.bam -O ../qc-processing/bowtie/deduplicated/552.dedup.bam -M ../qc-processing/bowtie/deduplicated/552.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:48:06.378 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:48:06 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/552b.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/552.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/552.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:48:06 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:48:06 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:48:06\tMarkDuplicates\tStart of doWork freeMemory: 72064160; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:48:06\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:48:06\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:48:09\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig23081:7,479\r\n", "INFO\t2021-03-14 19:48:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:48:11\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig41246:5,505\r\n", "INFO\t2021-03-14 19:48:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:48:12\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig63634:12,888\r\n", "INFO\t2021-03-14 19:48:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:48:14\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig95451:4,647\r\n", "INFO\t2021-03-14 19:48:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:48:16\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig328985:1,525\r\n", "INFO\t2021-03-14 19:48:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:48:16\tMarkDuplicates\tRead 5084900 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:48:16\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 932566936; totalMemory: 1325400064; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:48:16\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:48:16\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:48:16\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:48:17\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:48:17\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1267180128; totalMemory: 2400190464; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:48:17\tMarkDuplicates\tMarking 1927245 records as duplicates.\r\n", "INFO\t2021-03-14 19:48:17\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:48:18\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:48:26\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:48:26\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:48:26\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:48:26\tMarkDuplicates\tBefore output close freeMemory: 266095344; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:48:26\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:48:27\tMarkDuplicates\tAfter output close freeMemory: 266100080; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:48:27 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.34 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/552b.sorted.bam O=../qc-processing/bowtie/deduplicated/552.dedup.bam M=../qc-processing/bowtie/deduplicated/552.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:48:28\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/553.sorted.bam -O ../qc-processing/bowtie/deduplicated/553.dedup.bam -M ../qc-processing/bowtie/deduplicated/553.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:48:28.689 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:48:28 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/553.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/553.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/553.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:48:28 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:48:28 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:48:28\tMarkDuplicates\tStart of doWork freeMemory: 72065608; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:48:28\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:48:28\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:48:31\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig16674:48,304\r\n", "INFO\t2021-03-14 19:48:31\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:48:33\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,367\r\n", "INFO\t2021-03-14 19:48:33\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:48:35\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig43398:15,272\r\n", "INFO\t2021-03-14 19:48:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:48:36\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig59179:6,387\r\n", "INFO\t2021-03-14 19:48:36\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:48:38\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig77227:5,921\r\n", "INFO\t2021-03-14 19:48:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:48:40\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig112678:1,107\r\n", "INFO\t2021-03-14 19:48:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:48:41\tMarkDuplicates\tRead 6836851 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:48:41\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1060942640; totalMemory: 1509949440; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:48:41\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:48:42\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:48:42\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:48:42\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:48:43\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1451728504; totalMemory: 2584739840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:48:43\tMarkDuplicates\tMarking 1978470 records as duplicates.\r\n", "INFO\t2021-03-14 19:48:43\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:48:43\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:48:55\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:48:55\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:48:55\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:48:55\tMarkDuplicates\tBefore output close freeMemory: 1099596920; totalMemory: 2584739840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:48:55\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:48:55\tMarkDuplicates\tAfter output close freeMemory: 266098984; totalMemory: 374341632; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:48:55 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.45 minutes.\r\n", "Runtime.totalMemory()=374341632\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/553.sorted.bam O=../qc-processing/bowtie/deduplicated/553.dedup.bam M=../qc-processing/bowtie/deduplicated/553.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:48:57\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/554.sorted.bam -O ../qc-processing/bowtie/deduplicated/554.dedup.bam -M ../qc-processing/bowtie/deduplicated/554.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:48:57.142 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:48:57 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/554.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/554.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/554.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:48:57 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:48:57 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:48:57\tMarkDuplicates\tStart of doWork freeMemory: 72063040; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:48:57\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:48:57\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:49:00\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig3374:5,260\r\n", "INFO\t2021-03-14 19:49:00\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:02\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: Contig19567:313\r\n", "INFO\t2021-03-14 19:49:02\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:03\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig28227:13,555\r\n", "INFO\t2021-03-14 19:49:03\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:05\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig35213:853\r\n", "INFO\t2021-03-14 19:49:05\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:06\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig43340:17,694\r\n", "INFO\t2021-03-14 19:49:06\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:08\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig55470:2,632\r\n", "INFO\t2021-03-14 19:49:08\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:10\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: Contig60316:8,758\r\n", "INFO\t2021-03-14 19:49:10\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:11\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig69234:9,024\r\n", "INFO\t2021-03-14 19:49:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:13\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig75641:16,987\r\n", "INFO\t2021-03-14 19:49:13\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:14\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig97129:507\r\n", "INFO\t2021-03-14 19:49:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:16\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig118770:6,331\r\n", "INFO\t2021-03-14 19:49:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:18\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig206328:1,384\r\n", "INFO\t2021-03-14 19:49:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:18\tMarkDuplicates\tRead 12330905 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:49:18\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 882899224; totalMemory: 1509949440; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:49:18\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:49:19\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:49:19\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:49:20\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:49:20\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1451729408; totalMemory: 2584739840; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:49:20\tMarkDuplicates\tMarking 3764674 records as duplicates.\r\n", "INFO\t2021-03-14 19:49:20\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:49:21\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:49:40\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:49:40\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:49:40\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:49:40\tMarkDuplicates\tBefore output close freeMemory: 267132624; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:49:40\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:49:40\tMarkDuplicates\tAfter output close freeMemory: 262954888; totalMemory: 371195904; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:49:40 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.73 minutes.\r\n", "Runtime.totalMemory()=371195904\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/554.sorted.bam O=../qc-processing/bowtie/deduplicated/554.dedup.bam M=../qc-processing/bowtie/deduplicated/554.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:49:42\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/561.sorted.bam -O ../qc-processing/bowtie/deduplicated/561.dedup.bam -M ../qc-processing/bowtie/deduplicated/561.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:49:42.549 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:49:42 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/561.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/561.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/561.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:49:42 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:49:42 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:49:42\tMarkDuplicates\tStart of doWork freeMemory: 72059032; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:49:42\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:49:42\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:49:45\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig18306:4,271\r\n", "INFO\t2021-03-14 19:49:45\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:47\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig35176:38,138\r\n", "INFO\t2021-03-14 19:49:47\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:48\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig47182:16,906\r\n", "INFO\t2021-03-14 19:49:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:50\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig68908:722\r\n", "INFO\t2021-03-14 19:49:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:52\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,750\r\n", "INFO\t2021-03-14 19:49:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:53\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig208931:6,140\r\n", "INFO\t2021-03-14 19:49:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:49:53\tMarkDuplicates\tRead 6112441 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:49:53\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1104628744; totalMemory: 1579155456; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:49:53\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:49:54\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:49:54\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:49:55\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:49:55\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1520931088; totalMemory: 2653945856; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:49:55\tMarkDuplicates\tMarking 3655331 records as duplicates.\r\n", "INFO\t2021-03-14 19:49:55\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:49:55\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:50:04\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:50:04\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:50:04\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:50:04\tMarkDuplicates\tBefore output close freeMemory: 258380848; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:50:04\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:50:04\tMarkDuplicates\tAfter output close freeMemory: 258755880; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:50:04 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.37 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/561.sorted.bam O=../qc-processing/bowtie/deduplicated/561.dedup.bam M=../qc-processing/bowtie/deduplicated/561.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:50:06\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/562.sorted.bam -O ../qc-processing/bowtie/deduplicated/562.dedup.bam -M ../qc-processing/bowtie/deduplicated/562.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:50:06.443 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:50:06 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/562.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/562.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/562.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:50:06 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:50:06 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:50:06\tMarkDuplicates\tStart of doWork freeMemory: 72059880; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:50:06\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:50:06\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:50:09\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig4449:10,529\r\n", "INFO\t2021-03-14 19:50:09\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:11\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig19099:1,315\r", "\r\n", "INFO\t2021-03-14 19:50:11\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:12\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig27102:353\r\n", "INFO\t2021-03-14 19:50:12\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:14\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,671\r\n", "INFO\t2021-03-14 19:50:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:15\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig33895:2,039\r\n", "INFO\t2021-03-14 19:50:15\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:17\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig41285:7,002\r\n", "INFO\t2021-03-14 19:50:17\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:19\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig48849:2,198\r\n", "INFO\t2021-03-14 19:50:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:20\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig56693:7,512\r\n", "INFO\t2021-03-14 19:50:20\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:22\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig56910:920\r\n", "INFO\t2021-03-14 19:50:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:23\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig68037:746\r\n", "INFO\t2021-03-14 19:50:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:25\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,784\r\n", "INFO\t2021-03-14 19:50:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:27\tMarkDuplicates\tRead 12,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,891\r\n", "INFO\t2021-03-14 19:50:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:29\tMarkDuplicates\tRead 13,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: Contig80528:7,151\r\n", "INFO\t2021-03-14 19:50:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:30\tMarkDuplicates\tRead 14,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: Contig85486:1,944\r\n", "INFO\t2021-03-14 19:50:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:32\tMarkDuplicates\tRead 15,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: Contig98047:1,310\r\n", "INFO\t2021-03-14 19:50:32\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:34\tMarkDuplicates\tRead 16,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,231\r\n", "INFO\t2021-03-14 19:50:34\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:35\tMarkDuplicates\tRead 17,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: Contig103886:807\r\n", "INFO\t2021-03-14 19:50:35\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:37\tMarkDuplicates\tRead 18,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: Contig103886:807\r\n", "INFO\t2021-03-14 19:50:37\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:38\tMarkDuplicates\tRead 19,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: Contig103886:900\r\n", "INFO\t2021-03-14 19:50:38\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:40\tMarkDuplicates\tRead 20,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: Contig144382:1,153\r\n", "INFO\t2021-03-14 19:50:40\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:42\tMarkDuplicates\tRead 21,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: Contig686969:1,553\r\n", "INFO\t2021-03-14 19:50:42\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:50:42\tMarkDuplicates\tRead 21195148 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:50:42\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 658930704; totalMemory: 1561329664; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:50:42\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:50:43\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:50:43\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:50:45\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:50:45\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1503106608; totalMemory: 2636120064; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:50:45\tMarkDuplicates\tMarking 8814091 records as duplicates.\r\n", "INFO\t2021-03-14 19:50:45\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:50:46\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:51:11\tMarkDuplicates\tWritten 10,000,000 records. Elapsed time: 00:00:24s. Time for last 10,000,000: 24s. Last read position: Contig103849:3,274\r\n", "INFO\t2021-03-14 19:51:16\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:51:16\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:51:16\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:51:17\tMarkDuplicates\tBefore output close freeMemory: 267424936; totalMemory: 377487360; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:51:17\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:51:17\tMarkDuplicates\tAfter output close freeMemory: 258757000; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:51:17 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.18 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/562.sorted.bam O=../qc-processing/bowtie/deduplicated/562.dedup.bam M=../qc-processing/bowtie/deduplicated/562.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:51:18\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/563.sorted.bam -O ../qc-processing/bowtie/deduplicated/563.dedup.bam -M ../qc-processing/bowtie/deduplicated/563.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:51:18.876 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:51:19 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/563.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/563.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/563.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:51:19 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:51:19 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:51:19\tMarkDuplicates\tStart of doWork freeMemory: 72063624; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:51:19\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:51:19\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:51:22\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig15963:2,716\r\n", "INFO\t2021-03-14 19:51:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:23\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig31901:3,022\r\n", "INFO\t2021-03-14 19:51:23\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:25\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig41518:3,079\r\n", "INFO\t2021-03-14 19:51:25\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:26\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig58345:594\r\n", "INFO\t2021-03-14 19:51:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:28\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig77299:5,429\r\n", "INFO\t2021-03-14 19:51:28\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:30\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig116145:3,044\r\n", "INFO\t2021-03-14 19:51:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:31\tMarkDuplicates\tRead 6763523 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:51:31\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1185592592; totalMemory: 1697644544; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:51:31\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:51:32\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:51:32\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:51:33\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:51:33\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1639425256; totalMemory: 2772434944; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:51:33\tMarkDuplicates\tMarking 3422885 records as duplicates.\r\n", "INFO\t2021-03-14 19:51:33\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:51:34\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:51:43\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:51:43\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:51:43\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:51:43\tMarkDuplicates\tBefore output close freeMemory: 258756336; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:51:43\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:51:43\tMarkDuplicates\tAfter output close freeMemory: 258761200; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:51:43 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.42 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/563.sorted.bam O=../qc-processing/bowtie/deduplicated/563.dedup.bam M=../qc-processing/bowtie/deduplicated/563.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:51:45\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/564.sorted.bam -O ../qc-processing/bowtie/deduplicated/564.dedup.bam -M ../qc-processing/bowtie/deduplicated/564.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:51:45.472 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:51:45 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/564.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/564.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/564.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:51:45 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:51:45 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:51:45\tMarkDuplicates\tStart of doWork freeMemory: 72064864; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:51:45\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:51:45\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:51:48\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig18799:2,181\r\n", "INFO\t2021-03-14 19:51:48\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:50\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig34117:26,367\r\n", "INFO\t2021-03-14 19:51:50\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:52\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig50592:2,032\r\n", "INFO\t2021-03-14 19:51:52\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:53\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: Contig68908:2,780\r\n", "INFO\t2021-03-14 19:51:53\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:55\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig98974:6,007\r\n", "INFO\t2021-03-14 19:51:55\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:56\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig213985:2,816\r\n", "INFO\t2021-03-14 19:51:56\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:51:57\tMarkDuplicates\tRead 6128374 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:51:57\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 991234648; totalMemory: 1409286144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:51:57\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:51:57\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:51:57\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:51:58\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:51:58\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1351067920; totalMemory: 2484076544; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:51:58\tMarkDuplicates\tMarking 1780947 records as duplicates.\r\n", "INFO\t2021-03-14 19:51:58\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:51:59\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:52:09\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:52:09\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:52:09\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:52:09\tMarkDuplicates\tBefore output close freeMemory: 258229080; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:52:09\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:52:09\tMarkDuplicates\tAfter output close freeMemory: 258760912; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:52:09 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.41 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/564.sorted.bam O=../qc-processing/bowtie/deduplicated/564.dedup.bam M=../qc-processing/bowtie/deduplicated/564.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:52:11\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/565.sorted.bam -O ../qc-processing/bowtie/deduplicated/565.dedup.bam -M ../qc-processing/bowtie/deduplicated/565.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:52:11.688 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:52:11 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/565.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/565.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/565.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:52:11 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:52:11 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:52:11\tMarkDuplicates\tStart of doWork freeMemory: 64724848; totalMemory: 91226112; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:52:11\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:52:11\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:52:14\tMarkDuplicates\tRead 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: Contig19099:2,138\r\n", "INFO\t2021-03-14 19:52:14\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:52:16\tMarkDuplicates\tRead 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: Contig30879:27,427\r\n", "INFO\t2021-03-14 19:52:16\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:52:18\tMarkDuplicates\tRead 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: Contig36557:11,341\r\n", "INFO\t2021-03-14 19:52:18\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:52:19\tMarkDuplicates\tRead 4,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: Contig56693:2,539\r\n", "INFO\t2021-03-14 19:52:19\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:52:21\tMarkDuplicates\tRead 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: Contig61521:7,844\r\n", "INFO\t2021-03-14 19:52:21\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:52:22\tMarkDuplicates\tRead 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: Contig68037:1,092\r\n", "INFO\t2021-03-14 19:52:22\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:52:24\tMarkDuplicates\tRead 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: Contig70638:18,891\r\n", "INFO\t2021-03-14 19:52:24\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:52:26\tMarkDuplicates\tRead 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: Contig82803:4,335\r\n", "INFO\t2021-03-14 19:52:26\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:52:27\tMarkDuplicates\tRead 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: Contig96898:5,336\r\n", "INFO\t2021-03-14 19:52:27\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:52:29\tMarkDuplicates\tRead 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: Contig103849:3,489\r\n", "INFO\t2021-03-14 19:52:29\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:52:30\tMarkDuplicates\tRead 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: Contig206781:4,052\r\n", "INFO\t2021-03-14 19:52:30\tMarkDuplicates\tTracking 0 as yet unmatched pairs. 0 records in RAM.\r\n", "INFO\t2021-03-14 19:52:31\tMarkDuplicates\tRead 11393656 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:52:31\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 1017065280; totalMemory: 1481637888; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:52:31\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:52:31\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:52:31\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:52:32\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:52:32\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 1423418832; totalMemory: 2556428288; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:52:32\tMarkDuplicates\tMarking 3348207 records as duplicates.\r\n", "INFO\t2021-03-14 19:52:32\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:52:33\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:52:52\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:52:52\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:52:52\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:52:52\tMarkDuplicates\tBefore output close freeMemory: 264352560; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:52:52\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:52:52\tMarkDuplicates\tAfter output close freeMemory: 258760424; totalMemory: 367001600; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:52:52 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.68 minutes.\r\n", "Runtime.totalMemory()=367001600\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/565.sorted.bam O=../qc-processing/bowtie/deduplicated/565.dedup.bam M=../qc-processing/bowtie/deduplicated/565.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:52:54\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/571.sorted.bam -O ../qc-processing/bowtie/deduplicated/571.dedup.bam -M ../qc-processing/bowtie/deduplicated/571.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:52:54.324 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:52:54 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/571.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/571.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/571.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:52:54 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:52:54 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:52:54\tMarkDuplicates\tStart of doWork freeMemory: 72065608; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:52:54\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:52:54\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:52:57\tMarkDuplicates\tRead 611951 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:52:57\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 480866520; totalMemory: 681574400; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:52:57\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:52:57\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:52:57\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:52:57\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:52:57\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 761768440; totalMemory: 1894776832; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:52:57\tMarkDuplicates\tMarking 204170 records as duplicates.\r\n", "INFO\t2021-03-14 19:52:57\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:52:58\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:52:59\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:52:59\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:52:59\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:53:00\tMarkDuplicates\tBefore output close freeMemory: 257578576; totalMemory: 367001600; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:53:00\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:53:00\tMarkDuplicates\tAfter output close freeMemory: 255616104; totalMemory: 363855872; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:53:00 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes.\r\n", "Runtime.totalMemory()=363855872\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/571.sorted.bam O=../qc-processing/bowtie/deduplicated/571.dedup.bam M=../qc-processing/bowtie/deduplicated/571.dup_metrics.txt REMOVE_DUPLICATES=true\r\n", "INFO\t2021-03-14 19:53:01\tMarkDuplicates\t\r\n", "\r\n", "********** NOTE: Picard's command line syntax is changing.\r\n", "**********\r\n", "********** For more information, please see:\r\n", "********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)\r\n", "**********\r\n", "********** The command line looks like this in the new syntax:\r\n", "**********\r\n", "********** MarkDuplicates -I ../qc-processing/bowtie/mapped-sorted/Undetermined.sorted.bam -O ../qc-processing/bowtie/deduplicated/Und.dedup.bam -M ../qc-processing/bowtie/deduplicated/Und.dup_metrics.txt -REMOVE_DUPLICATES true\r\n", "**********\r\n", "\r\n", "\r\n", "18:53:01.865 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib\r\n", "[Sun Mar 14 19:53:01 PDT 2021] MarkDuplicates INPUT=[../qc-processing/bowtie/mapped-sorted/Undetermined.sorted.bam] OUTPUT=../qc-processing/bowtie/deduplicated/Und.dedup.bam METRICS_FILE=../qc-processing/bowtie/deduplicated/Und.dup_metrics.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\r\n", "Mar 14, 2021 7:53:02 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine\r\n", "INFO: Failed to detect whether we are running on Google Compute Engine.\r\n", "[Sun Mar 14 19:53:02 PDT 2021] Executing as laura@lauras-MacBook-Pro-2.local on Mac OS X 10.15.7 x86_64; Java HotSpot(TM) 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: 4.1.9.0\r\n", "INFO\t2021-03-14 19:53:02\tMarkDuplicates\tStart of doWork freeMemory: 72062944; totalMemory: 98566144; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:53:02\tMarkDuplicates\tReading input file and constructing read end information.\r\n", "INFO\t2021-03-14 19:53:02\tMarkDuplicates\tWill retain up to 15561475 data points before spilling to disk.\r\n", "INFO\t2021-03-14 19:53:03\tMarkDuplicates\tRead 209837 records. 0 pairs never matched.\r\n", "INFO\t2021-03-14 19:53:03\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 462475616; totalMemory: 654311424; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:53:03\tMarkDuplicates\tWill retain up to 134217728 duplicate indices before spilling to disk.\r\n", "INFO\t2021-03-14 19:53:04\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:53:04\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\r\n", "INFO\t2021-03-14 19:53:04\tMarkDuplicates\tSorting list of duplicate records.\r\n", "INFO\t2021-03-14 19:53:04\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 759669224; totalMemory: 1892679680; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:53:04\tMarkDuplicates\tMarking 33979 records as duplicates.\r\n", "INFO\t2021-03-14 19:53:04\tMarkDuplicates\tFound 0 optical duplicate clusters.\r\n", "INFO\t2021-03-14 19:53:05\tMarkDuplicates\tReads are assumed to be ordered by: coordinate\r\n", "INFO\t2021-03-14 19:53:05\tMarkDuplicates\tWriting complete. Closing input iterator.\r\n", "INFO\t2021-03-14 19:53:05\tMarkDuplicates\tDuplicate Index cleanup.\r\n", "INFO\t2021-03-14 19:53:05\tMarkDuplicates\tGetting Memory Stats.\r\n", "INFO\t2021-03-14 19:53:06\tMarkDuplicates\tBefore output close freeMemory: 264266392; totalMemory: 374341632; maxMemory: 4294967296\r\n", "INFO\t2021-03-14 19:53:06\tMarkDuplicates\tClosed outputs. Getting more Memory Stats.\r\n", "INFO\t2021-03-14 19:53:06\tMarkDuplicates\tAfter output close freeMemory: 140924104; totalMemory: 199229440; maxMemory: 4294967296\r\n", "[Sun Mar 14 19:53:06 PDT 2021] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes.\r\n", "Runtime.totalMemory()=199229440\r\n", "Tool returned:\r\n", "0\r\n", "Using GATK jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar\r\n", "Running:\r\n", " java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /Applications/bioinformatics/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar MarkDuplicates I=../qc-processing/bowtie/mapped-sorted/Undetermined.sorted.bam O=../qc-processing/bowtie/deduplicated/Und.dedup.bam M=../qc-processing/bowtie/deduplicated/Und.dup_metrics.txt REMOVE_DUPLICATES=true\r\n" ] } ], "source": [ "! cat ../qc-processing/bowtie/deduplicated/dedup_stout.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Create bam indices " ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [], "source": [ "%%bash\n", "# create .bam indexes\n", "for file in ../qc-processing/bowtie/deduplicated/*.bam\n", "do\n", "samtools index $file\n", "done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# 5. Generate counts \n", "\n", " - Use `featureCounts` on aligned reads (from Bowtie2) to count the number of reads that uniquely map to each gene. Works on BAM/SAM alignmment files. " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## featureCounts \n", "\n", "Using [this tutorial](https://hbctraining.github.io/Intro-to-rnaseq-hpc-O2/lessons/05_counting_reads.html) as a guide to generate counts using `featureCounts` \n", "\n", "#### Notes: \n", "First I need to install the `subread` package which contains `featureCounts`. Following [these installation directions](http://bioinf.wehi.edu.au/subread-package/) I downloaded the subread vs. 2.0.0 binary for MacOS fron [SourceForge](The executables can be found in the bin diretory of the binary packages.), then unptarred the contents into my Applications/bioinformatics directory on my laptop, and renamed the folder to \"subread\" (from \"subread-2.0.0-MacOS-x86_64\"). The executables are in the bin/ diretory. \n", "\n", "Multi-overlapping genes: A multi-mapping read is a read that maps to more than one location in the reference genome. By default featureCounts does not count these, and recommends that RNASeq experiments do not count them. However, I could try to specify `-M -fraction` to count each alignment fractionally (each alignment carries 1/x count where x is the total number of alignments reported for the read). \n", "\n", "Options \n", "\n", "`-T`: Specify # of threads. \n", "`-t`: Specify the feature type. Only rows which have the matched\n", "feature type in the provided GTF annotation file will be included for read counting. ‘exon’ by default. \n", "`-g`: Specify the attribute type used to group features (eg. exons)\n", "into meta-features (eg. genes) when GTF annotation is provided. ‘gene id’ by default. This attribute type is usually the\n", "gene identifier. This argument is useful for the meta-feature\n", "level summarization. \n", "`-a`: Provide name of an annotation file \n", "`-o`: Give the name of the output file. The output file contains\n", "the number of reads assigned to each meta-feature (or each\n", "feature if -f is specified). Note that the featureCounts function\n", "in Rsubread does not use this parameter. It returns a list\n", "object including read summarization results and other data. " ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "# create path variable for featureCounts program\n", "featureCounts = \"/Applications/bioinformatics/subread/bin/featureCounts\"" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\r\n", "featureCounts v2.0.0\r\n", "\r\n" ] } ], "source": [ "# test path and path variable \n", "! {featureCounts} -v" ] }, { "cell_type": "code", "execution_count": 125, "metadata": {}, "outputs": [], "source": [ "# create directory for featureCounts output \n", "! mkdir {workingdir}qc-processing/featureCounts/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Generate gene annotation file with +2kb on 3' end \n", "\n", "In [this issue](https://github.com/z0on/tag-based_RNAseq/issues/3) Mikhail Matz recommended the following when using featureCounts: \"adjust your genome’s GFF file extend gene regions 1-2kb towards 3’ ; otherwise gene annotations are often missing the non-coding 3’regions where our reads are mapping\". featureCounts using GFF/GTF files as input. I therefore need to generate a GFF file that includes the expanded gene regions. \n", "\n", "### Use bedtools `slop` to include 2kb regions on either side of gene regions \n", "\n", "I want to identify methylated loci that are within genes but also 2kb downstream (aka on the 3' ends) of gene regions. Therefore, before intersecting methylated loci with genes, I need to create a gene region + 2kb file. I will do this using `slopBed`.\n", "\n", "First, generate a \"genome file\", which defines size of each chromosome. This is so the `slop` function restricts results to within a contig. I can use the indexed FASTA file that I created for a blast. " ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Bumblebee/O.lurida_QuantSeq-2020\n" ] } ], "source": [ "cd {workingdir}" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[31m015UG009V0251_QuantSeq_Illumina.pdf\u001b[m\u001b[m \u001b[31mOlurida_v081.fa\u001b[m\u001b[m\r\n", "\u001b[31m20190709-Olurida_v081.stringtie.gtf\u001b[m\u001b[m \u001b[31mOlurida_v081.fa.fai\u001b[m\u001b[m\r\n", "\u001b[31mOlurida_chrom.sizes\u001b[m\u001b[m \u001b[31mOlurida_v081_CG-motif.gff\u001b[m\u001b[m\r\n", "\u001b[31mOlurida_gene_uniprot\u001b[m\u001b[m \u001b[31mOlurida_v081_concat.fa\u001b[m\u001b[m\r\n", "\u001b[31mOlurida_gentrome.fa\u001b[m\u001b[m \u001b[31mOlurida_v081_concat_rehead.fa\u001b[m\u001b[m\r\n", "\u001b[31mOlurida_transcriptome_v3.fasta\u001b[m\u001b[m \u001b[31mOlurida_v081_concat_rehead.fa.bak\u001b[m\u001b[m\r\n", "\u001b[31mOlurida_transcriptome_v3_blastx.tab\u001b[m\u001b[m \u001b[31mOlurida_v081_concat_rehead.fa.fai\u001b[m\u001b[m\r\n", "\u001b[31mOlurida_v081-20190709-UniprotID.gff\u001b[m\u001b[m \u001b[31mSTARmanual.pdf\u001b[m\u001b[m\r\n", "\u001b[31mOlurida_v081-20190709.exon.gff\u001b[m\u001b[m \u001b[31mbiostats.R\u001b[m\u001b[m\r\n", "\u001b[31mOlurida_v081-20190709.gene.2kbdown.gff\u001b[m\u001b[m \u001b[30m\u001b[43mblastdb\u001b[m\u001b[m\r\n", "\u001b[31mOlurida_v081-20190709.gene.2kbslop.gff\u001b[m\u001b[m \u001b[31mmerge_contigs.awk.txt\u001b[m\u001b[m\r\n", "\u001b[31mOlurida_v081-20190709.gene.gff\u001b[m\u001b[m \u001b[31mvcf2genepop.pl\u001b[m\u001b[m\r\n", "\u001b[31mOlurida_v081.dict\u001b[m\u001b[m\r\n" ] } ], "source": [ "# Extract column 1 (contig name) and column 2 (# bases in the contig)\n", "\n", "! cut -f 1,2 references/Olurida_v081.fa.fai > references/Olurida_chrom.sizes\n", "! ls references/" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Contig0\t116746\r\n", "Contig1\t87411\r\n" ] } ], "source": [ "#check out format of resulting chromosome size file \n", "! head -n 2 references/Olurida_chrom.sizes" ] }, { "cell_type": "code", "execution_count": 129, "metadata": {}, "outputs": [], "source": [ "# Run slopBed with gene feature file to create gene+2kb \n", "! slopBed \\\n", "-i {workingdir}references/Olurida_v081-20190709.gene.gff \\\n", "-g {workingdir}references/Olurida_chrom.sizes \\\n", "-r 2000 \\\n", "-l 0 \\\n", "> {workingdir}references/Olurida_v081-20190709.gene.2kbdown.gff" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "##gff-version 3\r\n", "Contig61093\tmaker\tgene\t7493\t7946\t.\t+\t.\tID=OLUR_00020575;Name=OLUR_00020575;Alias=maker-Contig61093-snap-gene-0.2;Note=Protein of unknown function;\r\n", "Contig1111\tmaker\tgene\t24968\t28696\t.\t-\t.\tID=OLUR_00006628;Name=OLUR_00006628;Alias=maker-Contig1111-snap-gene-0.1;Note=Similar to Spag6: Sperm-associated antigen 6 (Mus musculus OX%3D10090);Dbxref=Gene3D:G3DSA:1.25.10.10,InterPro:IPR000225,InterPro:IPR000357,InterPro:IPR011989,InterPro:IPR016024,Pfam:PF02985,SMART:SM00185,SUPERFAMILY:SSF48371;Ontology_term=GO:0005515;\r\n", "Contig214118\tmaker\tgene\t201\t926\t.\t+\t.\tID=OLUR_00032161;Name=OLUR_00032161;Alias=maker-Contig214118-snap-gene-0.0;Note=Protein of unknown function;Dbxref=Gene3D:G3DSA:3.10.450.10;\r\n", "Contig58217\tmaker\tgene\t9736\t11541\t.\t-\t.\tID=OLUR_00019127;Name=OLUR_00019127;Alias=snap_masked-Contig58217-processed-gene-0.2;Note=Protein of unknown function;Dbxref=MobiDBLite:mobidb-lite;\r\n" ] } ], "source": [ "### Check out sequence of pre-extended first couple genes \n", "! head -n 5 {workingdir}references/Olurida_v081-20190709.gene.gff" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Contig61093\tmaker\tgene\t7493\t9946\t.\t+\t.\tID=OLUR_00020575;Name=OLUR_00020575;Alias=maker-Contig61093-snap-gene-0.2;Note=Protein of unknown function;\r\n", "Contig1111\tmaker\tgene\t24968\t28792\t.\t-\t.\tID=OLUR_00006628;Name=OLUR_00006628;Alias=maker-Contig1111-snap-gene-0.1;Note=Similar to Spag6: Sperm-associated antigen 6 (Mus musculus OX%3D10090);Dbxref=Gene3D:G3DSA:1.25.10.10,InterPro:IPR000225,InterPro:IPR000357,InterPro:IPR011989,InterPro:IPR016024,Pfam:PF02985,SMART:SM00185,SUPERFAMILY:SSF48371;Ontology_term=GO:0005515;\r\n", "Contig214118\tmaker\tgene\t201\t1068\t.\t+\t.\tID=OLUR_00032161;Name=OLUR_00032161;Alias=maker-Contig214118-snap-gene-0.0;Note=Protein of unknown function;Dbxref=Gene3D:G3DSA:3.10.450.10;\r\n", "Contig58217\tmaker\tgene\t9736\t11618\t.\t-\t.\tID=OLUR_00019127;Name=OLUR_00019127;Alias=snap_masked-Contig58217-processed-gene-0.2;Note=Protein of unknown function;Dbxref=MobiDBLite:mobidb-lite;\r\n" ] } ], "source": [ "### Check out sequnce of first couple genes+2kb \n", "! head -n 4 {workingdir}references/Olurida_v081-20190709.gene.2kbdown.gff" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Generate counts using `featureCounts` \n", "\n", "Using gene GFF that HAS been extended by 2kb past the 3' end \n", " \n", "featureCounts options\n", "`-T 5` - 5 threads \n", "`-s 1` these data are \"forward\"ly stranded \n", "`-t exon` \n", "`-g gene_id` \n", "`-a [annotation file]`\n", "`-o [output file]` \n", "\n", "featureCounts can also take into account whether your data are stranded or not. If strandedness is specified, then in addition to considering the genomic coordinates it will also take the strand into account for counting. If your data are stranded always specify it." ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", " \u001b[44;37m ========== \u001b[0m\u001b[36m _____ _ _ ____ _____ ______ _____ \n", " \u001b[44;37m ===== \u001b[0m\u001b[36m / ____| | | | _ \\| __ \\| ____| /\\ | __ \\ \n", " \u001b[44;37m ===== \u001b[0m\u001b[36m | (___ | | | | |_) | |__) | |__ / \\ | | | |\n", " \u001b[44;37m ==== \u001b[0m\u001b[36m \\___ \\| | | | _ <| _ /| __| / /\\ \\ | | | |\n", " \u001b[44;37m ==== \u001b[0m\u001b[36m ____) | |__| | |_) | | \\ \\| |____ / ____ \\| |__| |\n", " \u001b[44;37m ========== \u001b[0m\u001b[36m |_____/ \\____/|____/|_| \\_\\______/_/ \\_\\_____/\u001b[0m\n", "\t v2.0.0\n", "\n", "//==========================\u001b[36m featureCounts setting \u001b[0m===========================\\\\\n", "|| \u001b[0m ||\n", "|| Input files : \u001b[36m147 BAM files \u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 137.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 139.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 140.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 141.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 156.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 159.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 161.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 162.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 168.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 169.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 171.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 172.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 181.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 183.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 184.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 185.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 291.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 292.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 293.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 294.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 295.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 296.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 298.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 299.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 301.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 302.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 303.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 304.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 305.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 306.dedup.bam\u001b[0m \u001b[0m ||\n", "|| 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"stdout", "output_type": "stream", "text": [ "|| \u001b[32mo\u001b[36m 403.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 404.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 41..dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 411.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 412.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 413.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 414.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 421.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 43..dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 431.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 432.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 434.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 44..dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 441.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 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542.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 543.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 551.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 552.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 553.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 554.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 561.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 562.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 563.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 564.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 565.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m 571.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[32mo\u001b[36m Und.dedup.bam\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Output file : \u001b[36mfeaturecounts-gene2kbdown-deduplicated.txt\u001b[0m \u001b[0m ||\n", "|| Summary : \u001b[36mfeaturecounts-gene2kbdown-deduplicated.txt.s\u001b[0m ...\u001b[0m \u001b[0m||\n", "|| Annotation : \u001b[36mOlurida_v081-20190709.gene.2kbdown.gff (GTF)\u001b[0m \u001b[0m ||\n", "|| Dir for temp files : \u001b[36m/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc\u001b[0m ...\u001b[0m \u001b[0m||\n", "|| \u001b[0m ||\n", "|| Threads : \u001b[36m5\u001b[0m \u001b[0m ||\n", "|| Level : \u001b[36mmeta-feature level\u001b[0m \u001b[0m ||\n", "|| Paired-end : \u001b[36mno\u001b[0m \u001b[0m ||\n", "|| Multimapping reads : \u001b[36mnot counted\u001b[0m \u001b[0m ||\n", "|| Multi-overlapping reads : \u001b[36mnot counted\u001b[0m \u001b[0m ||\n", "|| Min overlapping bases : \u001b[36m1\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "\\\\============================================================================//\n", "\n", "//=================================\u001b[36m Running \u001b[0m==================================\\\\\n", "|| \u001b[0m ||\n", "|| Load annotation file Olurida_v081-20190709.gene.2kbdown.gff \u001b[0m... \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Features : \u001b[36m32210\u001b[0m \u001b[0m ||\n", "|| Meta-features : \u001b[36m32210\u001b[0m \u001b[0m ||\n", "|| Chromosomes/contigs : \u001b[36m26218\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 137.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5214327\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1474354 (28.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 139.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m2065570\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m638045 (30.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 140.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4024124\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1317988 (32.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 141.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m1755386\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m566723 (32.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 156.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m2997323\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1031170 (34.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 159.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5351565\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1641679 (30.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 161.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5085856\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1409314 (27.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 162.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4132151\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1157742 (28.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 168.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m2067342\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m674811 (32.6%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 169.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8276298\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2197047 (26.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 171.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5397062\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1711459 (31.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 172.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3912107\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1193532 (30.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 181.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m1804748\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m537925 (29.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.01 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Process BAM file 183.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7538035\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2064387 (27.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 184.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m2832399\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m874831 (30.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 185.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m1489561\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m500978 (33.6%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.01 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 291.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8206934\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1865440 (22.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 292.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5457779\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1362574 (25.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 293.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6728983\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1434660 (21.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 294.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7609406\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1971995 (25.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 295.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m11524134\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2521269 (21.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.08 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 296.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m11968899\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2953278 (24.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.08 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 298.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7153125\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1767033 (24.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 299.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m10475105\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2429500 (23.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.07 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 301.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7938564\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1863500 (23.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 302.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m11116613\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2780206 (25.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.08 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Process BAM file 303.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7662749\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2173066 (28.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 304.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8532737\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2119571 (24.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 305.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7785890\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1700000 (21.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 306.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7849371\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1975761 (25.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 307.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7609253\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1861543 (24.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 308.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8984380\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2260372 (25.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 309.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m9987567\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2354037 (23.6%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.07 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 311.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8438603\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1979301 (23.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 312.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8416636\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1981430 (23.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 313.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7862919\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1984566 (25.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 314.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6579412\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1181531 (18.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 315.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m9422893\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2237806 (23.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 316.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m11740747\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2693225 (22.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.08 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Process BAM file 317.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7295913\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1803960 (24.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 318.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7062702\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1832641 (25.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 319.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7539535\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1739061 (23.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 321.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7535906\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1779528 (23.6%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 322.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8354912\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2020410 (24.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 323.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m10253789\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2634172 (25.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.07 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 324.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8763860\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2282236 (26.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 325.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m9205472\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2218500 (24.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 326.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8801212\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2441004 (27.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 327.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6939018\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1759884 (25.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 328.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m13656362\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m3296961 (24.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.09 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 329.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m9541099\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2204520 (23.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.07 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 331.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8443260\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1205133 (14.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Process BAM file 332.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5961921\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1288754 (21.6%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 333.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5519539\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1458236 (26.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 334.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7487461\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1212871 (16.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 335.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5449251\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1498292 (27.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 336.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7726444\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1727964 (22.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 337.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m9647055\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2562272 (26.6%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 338.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8220144\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1732716 (21.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 339.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8362095\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1889705 (22.6%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 34..dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m9687369\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m753533 (7.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 341.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6102630\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1568472 (25.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 342.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m9128914\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2314837 (25.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 343.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8834118\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2133005 (24.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 344.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m11167007\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1907570 (17.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.07 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Process BAM file 345.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5899826\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1579237 (26.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 346.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7183837\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1760374 (24.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 347.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6404901\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1920025 (30.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 348.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8782663\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1904560 (21.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 349.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6377257\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1519775 (23.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 35..dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m2658738\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m150053 (5.6%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 37..dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8522414\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m614501 (7.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 39..dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5585309\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1301356 (23.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 401.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5051990\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m654927 (13.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 402.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5766220\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1340804 (23.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 403.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5885577\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1738945 (29.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 404.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4796978\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1279987 (26.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 41..dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m10690139\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m962092 (9.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.07 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Process BAM file 411.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5910280\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1483789 (25.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 412.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m2558456\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m393253 (15.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 413.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4609639\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1485295 (32.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 414.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4302816\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1012073 (23.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 421.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8727096\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1967544 (22.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 43..dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7197590\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1760257 (24.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 431.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7081054\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1223207 (17.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 432.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m12481552\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m374382 (3.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.08 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 434.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3490637\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1082107 (31.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 44..dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m571517\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m40483 (7.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.01 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 441.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4424822\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m484850 (11.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 442.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5204635\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m818209 (15.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 443.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3603914\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1201608 (33.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Process BAM file 444.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3946222\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1271770 (32.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 445.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6108655\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1741612 (28.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 45..dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6695777\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1100863 (16.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 451.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6033586\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1920411 (31.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 452.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5594830\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1217152 (21.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 453.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4516412\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1370563 (30.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 46..dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m7094090\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m855474 (12.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 461.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3729480\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m895971 (24.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 462.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4891608\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1213954 (24.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 47..dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5158348\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1189795 (23.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 471.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5430746\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1291579 (23.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 472.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4954589\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1198323 (24.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 473.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5031404\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1504898 (29.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Process BAM file 474.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5505881\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1774697 (32.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 475.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4907111\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1663122 (33.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 476.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m2639687\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m880721 (33.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 477.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6888504\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1757320 (25.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 481.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5565726\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1317017 (23.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 482.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m2962011\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m964092 (32.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 483.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4337649\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m919240 (21.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 484.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5894652\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1230543 (20.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 485.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6207081\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1795217 (28.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 487.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6354125\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1798062 (28.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 488.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3756017\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1229962 (32.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 489.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8552967\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1881350 (22.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 490.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5010293\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1509931 (30.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Process BAM file 491.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3139841\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m989466 (31.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 492.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4478500\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1421128 (31.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 506.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m2646333\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m767112 (29.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 513.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5423510\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1501272 (27.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 521.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8567975\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1159654 (13.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 522.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3372703\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1069226 (31.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 523.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6536909\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1049736 (16.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 524.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3818175\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1218248 (31.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 525.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5770566\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1521287 (26.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 526.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4932319\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1383142 (28.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 527.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5443222\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1636747 (30.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 528.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m6049689\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1831528 (30.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 529.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3168368\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1050650 (33.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Process BAM file 531.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5472741\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1298997 (23.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 532.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3456227\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1072218 (31.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 533.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5291490\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1173177 (22.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 541.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4760640\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1384211 (29.1%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 542.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3212377\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m925714 (28.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 543.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m2858332\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m933477 (32.7%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 551.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m5097772\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1569386 (30.8%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.04 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 552.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3157655\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m867822 (27.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 553.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4858381\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1411092 (29.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 554.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8566231\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m2052116 (24.0%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.06 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 561.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m2457110\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m649023 (26.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 562.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m12381057\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1313631 (10.6%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.07 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 563.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m3340638\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1100092 (32.9%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.02 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "|| Process BAM file 564.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m4347427\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m1193560 (27.5%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.03 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 565.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m8045449\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m665149 (8.3%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.05 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file 571.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m407781\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m46381 (11.4%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.01 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Process BAM file Und.dedup.bam... \u001b[0m ||\n", "|| Strand specific : \u001b[36mstranded\u001b[0m \u001b[0m ||\n", "|| Single-end reads are included. \u001b[0m ||\n", "|| Total alignments : \u001b[36m175858\u001b[0m \u001b[0m ||\n", "|| Successfully assigned alignments : \u001b[36m51425 (29.2%)\u001b[0m \u001b[0m ||\n", "|| Running time : \u001b[36m0.01 minutes\u001b[0m \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| \u001b[0m ||\n", "|| Summary of counting results can be found in file \"/Volumes/Bumblebee/O.lu \u001b[0m ||\n", "|| rida_QuantSeq-2020/qc-processing/featureCounts/featurecounts-gene2kbdown- \u001b[0m ||\n", "|| deduplicated.txt.summary\" \u001b[0m ||\n", "|| \u001b[0m ||\n", "\\\\============================================================================//\n", "\n" ] } ], "source": [ "# 1) gene GFF with 2kb 3' extention \n", "! {featureCounts} \\\n", "-T 5 \\\n", "-s 1 \\\n", "-t gene \\\n", "-g ID \\\n", "-a {workingdir}references/Olurida_v081-20190709.gene.2kbdown.gff \\\n", "-o {workingdir}qc-processing/featureCounts/featurecounts-gene2kbdown-deduplicated.txt \\\n", "{workingdir}qc-processing/bowtie/deduplicated/*.bam" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[31mfeaturecounts-gene2kbdown-deduplicated.txt\u001b[m\u001b[m*\r\n", "\u001b[31mfeaturecounts-gene2kbdown-deduplicated.txt.summary\u001b[m\u001b[m*\r\n", "\u001b[31mfeaturecounts-gene2kbdown.Rmatrix.txt\u001b[m\u001b[m*\r\n", "\u001b[31mfeaturecounts-gene2kbdown.txt\u001b[m\u001b[m*\r\n", "\u001b[31mfeaturecounts-gene2kbdown.txt.summary\u001b[m\u001b[m*\r\n", "\u001b[31mfilenames.txt\u001b[m\u001b[m*\r\n" ] } ], "source": [ "ls {workingdir}qc-processing/featureCounts/" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ 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] } ], "source": [ "! cat {workingdir}qc-processing/featureCounts/featurecounts-gene2kbdown-deduplicated.txt.summary" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Clean up the featureCounts matrix\n", "\n", "There is information about the genomic coordinates and the length of the gene, we don’t need this for the next step, so we are going to extract the columns that we are interested in." ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "# Program:featureCounts v2.0.0; Command:\"/Applications/bioinformatics/subread/bin/featureCounts\" \"-T\" \"5\" \"-s\" \"1\" \"-t\" \"gene\" \"-g\" \"ID\" \"-a\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/references/Olurida_v081-20190709.gene.2kbdown.gff\" \"-o\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/featureCounts/featurecounts-gene2kbdown-deduplicated.txt\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/137.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/139.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/140.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/141.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/156.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/159.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/161.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/162.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/168.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/169.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/171.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/172.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/181.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/183.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/184.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/185.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/291.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/292.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/293.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/294.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/295.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/296.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/298.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/299.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/301.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/302.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/303.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/304.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/305.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/306.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/307.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/308.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/309.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/311.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/312.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/313.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/314.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/315.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/316.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/317.dedup.bam\" 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\"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/329.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/331.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/332.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/333.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/334.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/335.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/336.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/337.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/338.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/339.dedup.bam\" 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\"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/413.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/414.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/421.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/43..dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/431.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/432.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/434.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/44..dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/441.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/442.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/443.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/444.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/445.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/45..dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/451.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/452.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/453.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/46..dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/461.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/462.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/47..dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/471.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/472.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/473.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/474.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/475.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/476.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/477.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/481.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/482.dedup.bam\" 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\"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/513.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/521.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/522.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/523.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/524.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/525.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/526.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/527.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/528.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/529.dedup.bam\" 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"OLUR_00019127\tContig58217\t9736\t11618\t-\t1883\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t2\t0\t0\t0\t1\t0\t0\t1\t2\t1\t0\t0\t2\t0\t0\t0\t1\t2\t1\t1\t4\t1\t0\t1\t1\t1\t0\t0\t1\t1\t3\t0\t0\t1\t0\t0\t1\t2\t1\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t3\t0\t1\t1\t1\t0\t0\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n", "OLUR_00011450\tContig2046\t2295\t19920\t+\t17626\t19\t8\t16\t14\t25\t25\t23\t13\t16\t38\t38\t24\t3\t27\t12\t9\t52\t9\t11\t25\t49\t39\t19\t18\t25\t30\t14\t16\t16\t53\t37\t34\t31\t30\t10\t23\t14\t25\t21\t21\t27\t32\t19\t25\t19\t32\t30\t45\t14\t46\t41\t18\t13\t22\t28\t8\t16\t60\t26\t30\t6\t23\t41\t19\t18\t13\t14\t47\t34\t9\t0\t8\t25\t12\t11\t53\t35\t18\t18\t0\t21\t8\t21\t27\t23\t15\t16\t0\t0\t6\t25\t27\t30\t2\t38\t17\t27\t14\t28\t24\t17\t16\t25\t32\t42\t30\t22\t20\t19\t17\t20\t14\t38\t31\t46\t34\t11\t39\t43\t16\t14\t7\t19\t29\t31\t26\t22\t35\t33\t30\t17\t27\t20\t18\t13\t21\t44\t18\t28\t28\t5\t20\t26\t24\t6\t0\t3\r\n", "OLUR_00018391\tContig9540\t4303\t12179\t-\t7877\t3\t1\t4\t1\t2\t4\t6\t4\t1\t9\t5\t1\t0\t9\t4\t0\t11\t7\t9\t10\t17\t20\t17\t12\t24\t12\t10\t8\t20\t23\t5\t5\t15\t17\t13\t15\t13\t27\t14\t11\t10\t16\t10\t9\t8\t18\t7\t9\t8\t28\t21\t0\t10\t5\t13\t13\t4\t5\t6\t7\t1\t13\t19\t17\t19\t7\t15\t5\t25\t9\t0\t0\t1\t0\t2\t3\t1\t4\t5\t5\t2\t1\t2\t1\t1\t0\t2\t0\t0\t0\t1\t4\t1\t12\t1\t1\t2\t1\t1\t2\t9\t1\t1\t1\t3\t0\t2\t2\t6\t3\t0\t1\t1\t4\t1\t3\t0\t1\t5\t5\t2\t3\t1\t1\t1\t7\t2\t4\t6\t0\t4\t3\t2\t3\t4\t2\t1\t1\t2\t6\t0\t2\t0\t2\t0\t0\t0\r\n", "OLUR_00011614\tContig52254\t8908\t13733\t+\t4826\t3\t2\t5\t6\t0\t0\t9\t1\t0\t4\t0\t6\t1\t13\t2\t0\t40\t36\t14\t31\t31\t97\t21\t90\t52\t102\t39\t42\t46\t25\t22\t44\t46\t43\t44\t23\t22\t78\t67\t29\t48\t22\t36\t33\t86\t30\t40\t37\t57\t118\t27\t33\t26\t20\t26\t18\t28\t24\t42\t44\t12\t43\t18\t66\t62\t38\t35\t13\t39\t36\t9\t2\t15\t0\t14\t14\t5\t4\t15\t0\t11\t17\t37\t31\t7\t0\t3\t0\t0\t4\t10\t2\t19\t15\t24\t5\t8\t1\t5\t6\t6\t4\t10\t7\t7\t8\t1\t11\t16\t3\t15\t24\t11\t26\t2\t20\t17\t13\t7\t5\t11\t4\t4\t8\t10\t14\t11\t16\t22\t0\t20\t3\t4\t15\t12\t11\t6\t4\t18\t31\t0\t1\t0\t12\t16\t0\t0\r\n", "OLUR_00022996\tContig36645\t2185\t5340\t+\t3156\t0\t0\t2\t1\t0\t2\t0\t2\t2\t3\t2\t0\t1\t29\t2\t0\t1\t4\t7\t3\t2\t18\t3\t6\t6\t11\t3\t4\t4\t2\t7\t0\t6\t16\t7\t2\t6\t5\t8\t7\t6\t9\t4\t3\t5\t0\t24\t4\t2\t13\t6\t7\t3\t0\t4\t6\t0\t1\t28\t4\t5\t3\t2\t7\t6\t13\t6\t2\t15\t4\t0\t0\t6\t0\t1\t6\t1\t2\t3\t0\t2\t1\t3\t8\t3\t0\t0\t0\t0\t1\t1\t0\t3\t9\t3\t4\t2\t0\t0\t3\t4\t3\t2\t5\t3\t1\t0\t8\t8\t1\t2\t2\t2\t2\t0\t6\t6\t1\t3\t0\t7\t1\t2\t2\t1\t3\t2\t3\t5\t0\t5\t0\t4\t1\t2\t1\t0\t1\t5\t8\t0\t1\t0\t2\t6\t0\t0\r\n" ] } ], "source": [ "! head {workingdir}qc-processing/featureCounts/featurecounts-gene2kbdown-deduplicated.txt" ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [], "source": [ "# remove columns 2-6, which contain merged contig info \n", "! cut -f-1,7- {workingdir}qc-processing/featureCounts/featurecounts-gene2kbdown-deduplicated.txt \\\n", "> {workingdir}qc-processing/featureCounts/featurecounts-gene2kbdown-deduplicated.Rmatrix.txt" ] }, { "cell_type": "code", "execution_count": 27, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "# Program:featureCounts v2.0.0; Command:\"/Applications/bioinformatics/subread/bin/featureCounts\" \"-T\" \"5\" \"-s\" \"1\" \"-t\" \"gene\" \"-g\" \"ID\" \"-a\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/references/Olurida_v081-20190709.gene.2kbdown.gff\" \"-o\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/featureCounts/featurecounts-gene2kbdown-deduplicated.txt\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/137.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/139.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/140.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/141.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/156.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/159.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/161.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/162.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/168.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/169.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/171.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/172.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/181.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/183.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/184.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/185.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/291.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/292.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/293.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/294.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/295.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/296.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/298.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/299.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/301.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/302.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/303.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/304.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/305.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/306.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/307.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/308.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/309.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/311.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/312.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/313.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/314.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/315.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/316.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/317.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/318.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/319.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/321.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/322.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/323.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/324.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/325.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/326.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/327.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/328.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/329.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/331.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/332.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/333.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/334.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/335.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/336.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/337.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/338.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/339.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/34..dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/341.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/342.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/343.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/344.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/345.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/346.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/347.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/348.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/349.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/35..dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/37..dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/39..dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/401.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/402.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/403.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/404.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/41..dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/411.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/412.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/413.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/414.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/421.dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/43..dedup.bam\" \"/Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/bowtie/deduplicated/431.dedup.bam\" 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"OLUR_00022996\t0\t0\t2\t1\t0\t2\t0\t2\t2\t3\t2\t0\t1\t29\t2\t0\t1\t4\t7\t3\t2\t18\t3\t6\t6\t11\t3\t4\t4\t2\t7\t0\t6\t16\t7\t2\t6\t5\t8\t7\t6\t9\t4\t3\t5\t0\t24\t4\t2\t13\t6\t7\t3\t0\t4\t6\t0\t1\t28\t4\t5\t3\t2\t7\t6\t13\t6\t2\t15\t4\t0\t0\t6\t0\t1\t6\t1\t2\t3\t0\t2\t1\t3\t8\t3\t0\t0\t0\t0\t1\t1\t0\t3\t9\t3\t4\t2\t0\t0\t3\t4\t3\t2\t5\t3\t1\t0\t8\t8\t1\t2\t2\t2\t2\t0\t6\t6\t1\t3\t0\t7\t1\t2\t2\t1\t3\t2\t3\t5\t0\t5\t0\t4\t1\t2\t1\t0\t1\t5\t8\t0\t1\t0\t2\t6\t0\t0\r\n" ] } ], "source": [ "! head {workingdir}qc-processing/featureCounts/featurecounts-gene2kbdown-deduplicated.Rmatrix.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Create a .txt file that lists file names in order of run " ] }, { "cell_type": "code", "execution_count": 36, "metadata": {}, "outputs": [], "source": [ "%%bash \n", "\n", "for file in qc-processing/bowtie/deduplicated/*.bam\n", "do\n", "sample=\"$(basename -a $file | cut -d \".\" -f 1)\"\n", "echo $sample >> qc-processing/featureCounts/filenames-deduplicated.txt\n", "done" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "137\r\n", "139\r\n", "140\r\n", "141\r\n", "156\r\n", "159\r\n", "161\r\n", "162\r\n", "168\r\n", "169\r\n" ] } ], "source": [ "! head {workingdir}qc-processing/featureCounts/filenames-deduplicated.txt" ] }, { "cell_type": "code", "execution_count": 38, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 32212 /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/featureCounts/featurecounts-gene2kbdown-deduplicated.Rmatrix.txt\r\n" ] } ], "source": [ "# No. genes identified \n", "! wc -l {workingdir}qc-processing/featureCounts/featurecounts-gene2kbdown-deduplicated.Rmatrix.txt" ] }, { "cell_type": "code", "execution_count": 39, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 147 /Volumes/Bumblebee/O.lurida_QuantSeq-2020/qc-processing/featureCounts/filenames-deduplicated.txt\r\n" ] } ], "source": [ "# No. samples \n", "! wc -l {workingdir}qc-processing/featureCounts/filenames-deduplicated.txt " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## RESULT: the Bowtie --> featureCounts pipeline resulted in counts for 32,212 genes \n", "\n", "Counts can now be read in to R and manipulated there. Location of resulting count matrix file: {workingdir}qc-processing/featureCounts/test-out_featurecounts.Rmatrix.txt\n", "\n", "I pulled count dataframe into R and generated some initial summary stats: \n", "\n", "- Number of samples files (including \"Undetermined\": 147 \n", "- Total number of genes in dataframe: 110,784 " ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.7.7" } }, "nbformat": 4, "nbformat_minor": 2 }