{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Tue Mar 8 13:05:43 PST 2016\r\n" ] } ], "source": [ "!date" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Print system info" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Software:\n", "\n", " System Software Overview:\n", "\n", " System Version: OS X 10.9.5 (13F34)\n", " Kernel Version: Darwin 13.4.0\n", " Boot Volume: Hummingbird\n", " Boot Mode: Normal\n", " Computer Name: hummingbird\n", " User Name: Sam (Sam)\n", " Secure Virtual Memory: Enabled\n", " Time since boot: 108 days 22:56\n", "\n" ] } ], "source": [ "%%bash\n", "system_profiler SPSoftwareDataType" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/owl_home/Project_BS1511196_R2_02/ftp2.genewiz.com/Project_BS1511196_R2\n" ] } ], "source": [ "cd /Volumes/owl_home/Project_BS1511196_R2_02/ftp2.genewiz.com/Project_BS1511196_R2/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Find all FASTQ files with \"Undetermined\" in file name" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "./151217_SN1123_0455_AHCTVKBCXX/Unaligned6/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/Unaligned6/Undetermined_indices/Sample_lane2/lane2_Undetermined_L002_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual5/Undetermined_indices/Sample_lane2/lane2_Undetermined_L002_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual7/Undetermined_indices/Sample_lane2/lane2_Undetermined_L002_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual8/Undetermined_indices/Sample_lane2/lane2_Undetermined_L002_R1_001.fastq.gz\n", "./151218_SN1123_0456_AHFYH7BCXX/Unaligned6/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151218_SN1123_0456_AHFYH7BCXX/Unaligned6/Undetermined_indices/Sample_lane2/lane2_Undetermined_L002_R1_001.fastq.gz\n", "./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual6/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz\n" ] } ], "source": [ "%%bash\n", "find . -name '*Undetermined*.gz'" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Rename each undetermined file to contain specific sequencing info" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151217_SN1123_0455_AHCTVKBCXX/Unaligned6/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151217_SN1123_0455_AHCTVKBCXX/Unaligned6/Undetermined_indices/Sample_lane1/AHCTVKBCXX_Unaligned6_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "mv ./151217_SN1123_0455_AHCTVKBCXX/Unaligned6/Undetermined_indices/Sample_lane2/lane2_Undetermined_L002_R1_001.fastq.gz ./151217_SN1123_0455_AHCTVKBCXX/Unaligned6/Undetermined_indices/Sample_lane2/AHCTVKBCXX_Unaligned6_lane2_Undetermined_L002_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/AHCTVKBCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual5/Undetermined_indices/Sample_lane2/lane2_Undetermined_L002_R1_001.fastq.gz ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual5/Undetermined_indices/Sample_lane2/AHCTVKBCXX_UnalignedDual5_lane2_Undetermined_L002_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/AHCTVKBCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual7/Undetermined_indices/Sample_lane2/lane2_Undetermined_L002_R1_001.fastq.gz ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual7/Undetermined_indices/Sample_lane2/AHCTVKBCXX_UnalignedDual7_lane2_Undetermined_L002_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/AHCTVKBCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual8/Undetermined_indices/Sample_lane2/lane2_Undetermined_L002_R1_001.fastq.gz ./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual8/Undetermined_indices/Sample_lane2/AHCTVKBCXX_UnalignedDual8_lane2_Undetermined_L002_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151218_SN1123_0456_AHFYH7BCXX/Unaligned6/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151218_SN1123_0456_AHFYH7BCXX/Unaligned6/Undetermined_indices/Sample_lane1/AHFYH7BCXX_Unaligned6_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151218_SN1123_0456_AHFYH7BCXX/Unaligned6/Undetermined_indices/Sample_lane2/lane2_Undetermined_L002_R1_001.fastq.gz ./151218_SN1123_0456_AHFYH7BCXX/Unaligned6/Undetermined_indices/Sample_lane2/AHFYH7BCXX_Unaligned6_lane2_Undetermined_L002_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/AHFYH7BCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/AHFYH7BCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/AHFYH7BCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/AHCTV7BCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual6/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual6/Undetermined_indices/Sample_lane1/AHCTV7BCXX_UnalignedDual6_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/AHCTV7BCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv ./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/lane1_Undetermined_L001_R1_001.fastq.gz ./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/AHCTV7BCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Search for FASTQ files beginning with \"lane\" (i.e. the old filenames)" ] }, { "cell_type": "code", "execution_count": 25, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "find . -name 'lane*.gz'" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Verify new file names" ] }, { "cell_type": "code", "execution_count": 26, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "./151217_SN1123_0455_AHCTVKBCXX/Unaligned6/Undetermined_indices/Sample_lane1/AHCTVKBCXX_Unaligned6_lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/Unaligned6/Undetermined_indices/Sample_lane2/AHCTVKBCXX_Unaligned6_lane2_Undetermined_L002_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/AHCTVKBCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual5/Undetermined_indices/Sample_lane2/AHCTVKBCXX_UnalignedDual5_lane2_Undetermined_L002_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/AHCTVKBCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual7/Undetermined_indices/Sample_lane2/AHCTVKBCXX_UnalignedDual7_lane2_Undetermined_L002_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/AHCTVKBCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151217_SN1123_0455_AHCTVKBCXX/UnalignedDual8/Undetermined_indices/Sample_lane2/AHCTVKBCXX_UnalignedDual8_lane2_Undetermined_L002_R1_001.fastq.gz\n", "./151218_SN1123_0456_AHFYH7BCXX/Unaligned6/Undetermined_indices/Sample_lane1/AHFYH7BCXX_Unaligned6_lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151218_SN1123_0456_AHFYH7BCXX/Unaligned6/Undetermined_indices/Sample_lane2/AHFYH7BCXX_Unaligned6_lane2_Undetermined_L002_R1_001.fastq.gz\n", "./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/AHFYH7BCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/AHFYH7BCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151218_SN1123_0456_AHFYH7BCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/AHFYH7BCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual5/Undetermined_indices/Sample_lane1/AHCTV7BCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual6/Undetermined_indices/Sample_lane1/AHCTV7BCXX_UnalignedDual6_lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual7/Undetermined_indices/Sample_lane1/AHCTV7BCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz\n", "./151221_SN1123_0457_AHCTV7BCXX/UnalignedDual8/Undetermined_indices/Sample_lane1/AHCTV7BCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz\n" ] } ], "source": [ "%%bash\n", "find . -name '*Undetermined*.gz'" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Copy files to Owl/nightingales/O_lurida/2bRAD_Dec2015" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "find . -name '*Undetermined*.gz' -exec cp '{}' /Volumes/nightingales/O_lurida/2bRAD_Dec2015/ \\;" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Verify files copied" ] }, { "cell_type": "code", "execution_count": 29, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTV7BCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTV7BCXX_UnalignedDual6_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTV7BCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTV7BCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTVKBCXX_Unaligned6_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTVKBCXX_Unaligned6_lane2_Undetermined_L002_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTVKBCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTVKBCXX_UnalignedDual5_lane2_Undetermined_L002_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTVKBCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTVKBCXX_UnalignedDual7_lane2_Undetermined_L002_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTVKBCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHCTVKBCXX_UnalignedDual8_lane2_Undetermined_L002_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHFYH7BCXX_Unaligned6_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHFYH7BCXX_Unaligned6_lane2_Undetermined_L002_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHFYH7BCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHFYH7BCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/AHFYH7BCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/lane2_Undetermined_L002_R1_001.fastq.gz\n" ] } ], "source": [ "%%bash\n", "ls /Volumes/nightingales/O_lurida/2bRAD_Dec2015/*Undetermined*.gz" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Check for old \"Undetermined\" FASTQ files in Owl/nightingales/O_lurida/2bRAD_Dec2015" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/lane1_Undetermined_L001_R1_001.fastq.gz\n", "/Volumes/nightingales/O_lurida/2bRAD_Dec2015/lane2_Undetermined_L002_R1_001.fastq.gz\n" ] } ], "source": [ "%%bash\n", "ls /Volumes/nightingales/O_lurida/2bRAD_Dec2015/lane*.gz" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Delete old \"Undetermined\" FASTQ files" ] }, { "cell_type": "code", "execution_count": 31, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "rm /Volumes/nightingales/O_lurida/2bRAD_Dec2015/lane*.gz" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Verify deletion" ] }, { "cell_type": "code", "execution_count": 32, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "ls: /Volumes/nightingales/O_lurida/2bRAD_Dec2015/lane*.gz: No such file or directory\n" ] } ], "source": [ "%%bash\n", "ls /Volumes/nightingales/O_lurida/2bRAD_Dec2015/lane*.gz" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Generate checksums." ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t52m51.012s\n", "user\t5m48.627s\n", "sys\t1m38.324s\n" ] } ], "source": [ "%%bash\n", "\n", "#For loop generates a md5 checksum hash value for each file\n", "#and appends the output to the checksums.md5 file.\n", "time for file in /Volumes/nightingales/O_lurida/2bRAD_Dec2015/*Undetermined*.gz\n", " do\n", " md5 \"$file\" >>/Volumes/nightingales/O_lurida/2bRAD_Dec2015/checksums.md5\n", " done" ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "##### Calculate number of reads per file and, append filename and corresponding number of reads to readme file" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "AHCTV7BCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz\t155722611\n", "\n", "AHCTV7BCXX_UnalignedDual6_lane1_Undetermined_L001_R1_001.fastq.gz\t161584091\n", "\n", "AHCTV7BCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz\t144750481\n", "\n", "AHCTV7BCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz\t175267582\n", "\n", "AHCTVKBCXX_Unaligned6_lane1_Undetermined_L001_R1_001.fastq.gz\t115549984\n", "\n", "AHCTVKBCXX_Unaligned6_lane2_Undetermined_L002_R1_001.fastq.gz\t141164573\n", "\n", "AHCTVKBCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz\t135581455\n", "\n", "AHCTVKBCXX_UnalignedDual5_lane2_Undetermined_L002_R1_001.fastq.gz\t156456924\n", "\n", "AHCTVKBCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz\t138863398\n", "\n", "AHCTVKBCXX_UnalignedDual7_lane2_Undetermined_L002_R1_001.fastq.gz\t152625882\n", "\n", "AHCTVKBCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz\t156527984\n", "\n", "AHCTVKBCXX_UnalignedDual8_lane2_Undetermined_L002_R1_001.fastq.gz\t183575566\n", "\n", "AHFYH7BCXX_Unaligned6_lane1_Undetermined_L001_R1_001.fastq.gz\t123225782\n", "\n", "AHFYH7BCXX_Unaligned6_lane2_Undetermined_L002_R1_001.fastq.gz\t175194657\n", "\n", "AHFYH7BCXX_UnalignedDual5_lane1_Undetermined_L001_R1_001.fastq.gz\t139242901\n", "\n", "AHFYH7BCXX_UnalignedDual7_lane1_Undetermined_L001_R1_001.fastq.gz\t125091422\n", "\n", "AHFYH7BCXX_UnalignedDual8_lane1_Undetermined_L001_R1_001.fastq.gz\t146618279\n", "\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t122m33.043s\n", "user\t58m13.020s\n", "sys\t6m29.226s\n" ] } ], "source": [ "%%bash\n", "\n", "#For loop counts the lines in each file and divides them by four. This is performed because\n", "#Illumina sequencing files are composed of four lines per read.\n", "#Format the output (printf) to print the filename, followed by a tab, followed by the readcount.\n", "#The command \"tee -a\" is used to both print the output to the screen and append the output to the readme.md file.\n", "time for file in /Volumes/nightingales/O_lurida/2bRAD_Dec2015/*Undetermined*.gz\n", " do linecount=`gunzip -c \"$file\" | wc -l`\n", " readcount=$(($linecount/4))\n", " printf \"%s\\t%s\\n\\n\" \"${file##*/}\" \"$readcount\" | tee -a /Volumes/nightingales/O_lurida/2bRAD_Dec2015/readme.md\n", "done" ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "##### Compress raw data folder provided by Genewiz & put in nightingales project folder" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "tar: Removing leading '/' from member names\n", "a 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