{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "### Running in Docker container on Swoose\n", "\n", "Started Docker container with the following command:\n", "\n", "```docker run -p 8888:8888 -v /home/sam/data/pacbio_oly/:/home/data -v /mnt/owl/:/home/owl -it bioinformatics/bioinformatics:v0 /bin/bash```\n", "\n", "The command allows ```/home/sam/data/``` and ```mnt/owl``` (our server Owl) to be accessible to the Docker container.\n", "\n", "Once access to Jupyter Notebook over port 8888 and makes my Jupyter Notebook GitHub repo and my data files the container was started, started Jupyter Notebook with the following command inside the Docker container:\n", "\n", "```jupyter notebook --allow-root```\n", "\n", "This is configured in the Docker container to launch a Jupyter Notebook without a browser on port 8888.\n", "The Docker container is running on an image created from this [Dockerfile (Git commit 4f0d2ff](https://github.com/RobertsLab/code/commit/4f0d2ffb3e1596bd3a267095a01d0b6fcabb2e73)" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "TODAY'S DATE\n", "Wed Oct 18 14:28:20 UTC 2017\n", "------------\n", "\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "bash: line 15: unexpected EOF while looking for matching `\"'\n", "bash: line 17: syntax error: unexpected end of file\n" ] } ], "source": [ "%%bash\n", "echo \"TODAY'S DATE\"\n", "date\n", "echo \"------------\"\n", "echo \"\"\n", "echo \"HOSTNAME: $hostname\"\"\n", "echo \"\"\n", "echo \"------------\"\n", "echo \"Computer Specs:\"\n", "echo \"\"\n", "lscpu\n", "echo \"\"\n", "echo \"------------\"\n", "echo \"\"\n", "echo \"Memory Specs\"\n", "echo \"\"\n", "free -mh" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "TODAY'S DATE\n", "Wed Oct 18 14:28:44 UTC 2017\n", "------------\n", "\n", "HOSTNAME: \n", "\n", "------------\n", "Computer Specs:\n", "\n", "Architecture: x86_64\n", "CPU op-mode(s): 32-bit, 64-bit\n", "Byte Order: Little Endian\n", "CPU(s): 24\n", "On-line CPU(s) list: 0-23\n", "Thread(s) per core: 2\n", "Core(s) per socket: 6\n", "Socket(s): 2\n", "NUMA node(s): 1\n", "Vendor ID: GenuineIntel\n", "CPU family: 6\n", "Model: 44\n", "Model name: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz\n", "Stepping: 2\n", "CPU MHz: 2925.850\n", "BogoMIPS: 5851.96\n", "Virtualization: VT-x\n", "L1d cache: 32K\n", "L1i cache: 32K\n", "L2 cache: 256K\n", "L3 cache: 12288K\n", "NUMA node0 CPU(s): 0-23\n", "\n", "------------\n", "\n", "Memory Specs\n", "\n", " total used free shared buffers cached\n", "Mem: 70G 5.7G 65G 120M 596M 1.6G\n", "-/+ buffers/cache: 3.6G 67G\n", "Swap: 4.7G 0B 4.7G\n" ] } ], "source": [ "%%bash\n", "echo \"TODAY'S DATE\"\n", "date\n", "echo \"------------\"\n", "echo \"\"\n", "echo \"HOSTNAME: $hostname\"\n", "echo \"\"\n", "echo \"------------\"\n", "echo \"Computer Specs:\"\n", "echo \"\"\n", "lscpu\n", "echo \"\"\n", "echo \"------------\"\n", "echo \"\"\n", "echo \"Memory Specs\"\n", "echo \"\"\n", "free -mh" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "473812ccc24f\n" ] } ], "source": [ "%%bash\n", "hostname" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/home/data\n" ] } ], "source": [ "%%bash\n", "pwd" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Assemble PacBio data with [Canu v1.6](https://github.com/marbl/canu/releases)" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/canu\n" ] } ], "source": [ "%%bash\n", "which canu" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "%%bash\n", "mkdir 20171018_oly_pacbio_canu" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [], "source": [ "%%bash\n", "ls 20171018_oly_pacbio_canu/" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "ls 20171018_oly_pacbio_canu/" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq\n", "m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz\n", "m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz\n", "m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz\n", "m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz\n", "m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz\n", "m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz\n", "m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz\n", "m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz\n", "m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz\n", "m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz\n" ] } ], "source": [ "%%bash\n", "ls m*" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "usage: canu [-version] [-citation] \\\n", " [-correct | -trim | -assemble | -trim-assemble] \\\n", " [-s ] \\\n", " -p \\\n", " -d \\\n", " genomeSize=[g|m|k] \\\n", " [other-options] \\\n", " [-pacbio-raw |\n", " -pacbio-corrected |\n", " -nanopore-raw |\n", " -nanopore-corrected] file1 file2 ...\n", "\n", "example: canu -d run1 -p godzilla genomeSize=1g -nanopore-raw reads/*.fasta.gz \n", "\n", "\n", " To restrict canu to only a specific stage, use:\n", " -correct - generate corrected reads\n", " -trim - generate trimmed reads\n", " -assemble - generate an assembly\n", " -trim-assemble - generate trimmed reads and then assemble them\n", "\n", " The assembly is computed in the -d , with output files named\n", " using the -p . This directory is created if needed. It is not\n", " possible to run multiple assemblies in the same directory.\n", "\n", " The genome size should be your best guess of the haploid genome size of what is being\n", " assembled. It is used primarily to estimate coverage in reads, NOT as the desired\n", " assembly size. Fractional values are allowed: '4.7m' equals '4700k' equals '4700000'\n", "\n", " Some common options:\n", " useGrid=string\n", " - Run under grid control (true), locally (false), or set up for grid control\n", " but don't submit any jobs (remote)\n", " rawErrorRate=fraction-error\n", " - The allowed difference in an overlap between two raw uncorrected reads. For lower\n", " quality reads, use a higher number. The defaults are 0.300 for PacBio reads and\n", " 0.500 for Nanopore reads.\n", " correctedErrorRate=fraction-error\n", " - The allowed difference in an overlap between two corrected reads. Assemblies of\n", " low coverage or data with biological differences will benefit from a slight increase\n", " in this. Defaults are 0.045 for PacBio reads and 0.144 for Nanopore reads.\n", " gridOptions=string\n", " - Pass string to the command used to submit jobs to the grid. Can be used to set\n", " maximum run time limits. Should NOT be used to set memory limits; Canu will do\n", " that for you.\n", " minReadLength=number\n", " - Ignore reads shorter than 'number' bases long. Default: 1000.\n", " minOverlapLength=number\n", " - Ignore read-to-read overlaps shorter than 'number' bases long. Default: 500.\n", " A full list of options can be printed with '-options'. All options can be supplied in\n", " an optional sepc file with the -s option.\n", "\n", " Reads can be either FASTA or FASTQ format, uncompressed, or compressed with gz, bz2 or xz.\n", " Reads are specified by the technology they were generated with:\n", " -pacbio-raw \n", " -pacbio-corrected \n", " -nanopore-raw \n", " -nanopore-corrected \n", "\n", "Complete documentation at http://canu.readthedocs.org/en/latest/\n", "\n", "ERROR: mhap overlapper requires java version at least 1.8.0; you have 1.7.0_151 (from 'java').\n", "ERROR: 'java -showversion' reports:\n", "ERROR: 'java version \"1.7.0_151\"'\n", "ERROR: 'OpenJDK Runtime Environment (IcedTea 2.6.11) (7u151-2.6.11-1~deb8u1)'\n", "ERROR: 'OpenJDK 64-Bit Server VM (build 24.151-b01, mixed mode)'\n", "ERROR: ''\n", "ERROR: 'Usage: java [-options] class [args...]'\n", "ERROR: ' (to execute a class)'\n", "ERROR: ' or java [-options] -jar jarfile [args...]'\n", "ERROR: ' (to execute a jar file)'\n", "ERROR: 'where options include:'\n", "ERROR: ' -d32\t use a 32-bit data model if available'\n", "ERROR: ' -d64\t use a 64-bit data model if available'\n", "ERROR: ' -server\t to select the \"server\" VM'\n", "ERROR: ' -zero\t to select the \"zero\" VM'\n", "ERROR: ' -jamvm\t to select the \"jamvm\" VM'\n", "ERROR: ' -avian\t to select the \"avian\" VM'\n", "ERROR: ' -dcevm\t to select the \"dcevm\" VM'\n", "ERROR: ' The default VM is server,'\n", "ERROR: ' because you are running on a server-class machine.'\n", "ERROR: ''\n", "ERROR: ''\n", "ERROR: ' -cp '\n", "ERROR: ' -classpath '\n", "ERROR: ' A : separated list of directories, JAR archives,'\n", "ERROR: ' and ZIP archives to search for class files.'\n", "ERROR: ' -D='\n", "ERROR: ' set a system property'\n", "ERROR: ' -verbose:[class|gc|jni]'\n", "ERROR: ' enable verbose output'\n", "ERROR: ' -version print product version and exit'\n", "ERROR: ' -version:'\n", "ERROR: ' require the specified version to run'\n", "ERROR: ' -showversion print product version and continue'\n", "ERROR: ' -jre-restrict-search | -no-jre-restrict-search'\n", "ERROR: ' include/exclude user private JREs in the version search'\n", "ERROR: ' -? -help print this help message'\n", "ERROR: ' -X print help on non-standard options'\n", "ERROR: ' -ea[:...|:]'\n", "ERROR: ' -enableassertions[:...|:]'\n", "ERROR: ' enable assertions with specified granularity'\n", "ERROR: ' -da[:...|:]'\n", "ERROR: ' -disableassertions[:...|:]'\n", "ERROR: ' disable assertions with specified granularity'\n", "ERROR: ' -esa | -enablesystemassertions'\n", "ERROR: ' enable system assertions'\n", "ERROR: ' -dsa | -disablesystemassertions'\n", "ERROR: ' disable system assertions'\n", "ERROR: ' -agentlib:[=]'\n", "ERROR: ' load native agent library , e.g. -agentlib:hprof'\n", "ERROR: ' see also, -agentlib:jdwp=help and -agentlib:hprof=help'\n", "ERROR: ' -agentpath:[=]'\n", "ERROR: ' load native agent library by full pathname'\n", "ERROR: ' -javaagent:[=]'\n", "ERROR: ' load Java programming language agent, see java.lang.instrument'\n", "ERROR: ' -splash:'\n", "ERROR: ' show splash screen with specified image'\n", "ERROR: 'See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details.'\n", "ERROR: Failed to run gnuplot from 'gnuplot'.ERROR: Set option gnuplot= or gnuplotTested=true to skip this test and not generate plots.\n", "\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "-- Canu 1.6\n", "--\n", "-- CITATIONS\n", "--\n", "-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.\n", "-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.\n", "-- Genome Res. 2017 May;27(5):722-736.\n", "-- http://doi.org/10.1101/gr.215087.116\n", "-- \n", "-- Read and contig alignments during correction, consensus and GFA building use:\n", "-- Šošic M, Šikic M.\n", "-- Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.\n", "-- Bioinformatics. 2017 May 1;33(9):1394-1395.\n", "-- http://doi.org/10.1093/bioinformatics/btw753\n", "-- \n", "-- Overlaps are generated using:\n", "-- Berlin K, et al.\n", "-- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.\n", "-- Nat Biotechnol. 2015 Jun;33(6):623-30.\n", "-- http://doi.org/10.1038/nbt.3238\n", "-- \n", "-- Myers EW, et al.\n", "-- A Whole-Genome Assembly of Drosophila.\n", "-- Science. 2000 Mar 24;287(5461):2196-204.\n", "-- http://doi.org/10.1126/science.287.5461.2196\n", "-- \n", "-- Li H.\n", "-- Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.\n", "-- Bioinformatics. 2016 Jul 15;32(14):2103-10.\n", "-- http://doi.org/10.1093/bioinformatics/btw152\n", "-- \n", "-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:\n", "-- Chin CS, et al.\n", "-- Phased diploid genome assembly with single-molecule real-time sequencing.\n", "-- Nat Methods. 2016 Dec;13(12):1050-1054.\n", "-- http://doi.org/10.1038/nmeth.4035\n", "-- \n", "-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:\n", "-- Chin CS, et al.\n", "-- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.\n", "-- Nat Methods. 2013 Jun;10(6):563-9\n", "-- http://doi.org/10.1038/nmeth.2474\n", "-- \n", "-- CONFIGURE CANU\n", "--\n", "\n", "real\t0m2.252s\n", "user\t0m0.304s\n", "sys\t0m0.076s\n" ] } ], "source": [ "%%bash\n", "time canu \\\n", "useGrid=false \\\n", "-p 20171009_oly_pacbio \\\n", "-d /home/data/20171018_oly_pacbio_canu/ \\\n", "genomeSize=1.9g \\\n", "correctedErrorRate=0.075 \\\n", "-pacbio-raw m*" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Hmmmm, java version isn't current. In theory, the Dockerfile should pull the most current version. Will fix..." ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "java version \"1.7.0_151\"\n", "OpenJDK Runtime Environment (IcedTea 2.6.11) (7u151-2.6.11-1~deb8u1)\n", "OpenJDK 64-Bit Server VM (build 24.151-b01, mixed mode)\n", "\n", "Usage: java [-options] class [args...]\n", " (to execute a class)\n", " or java [-options] -jar jarfile [args...]\n", " (to execute a jar file)\n", "where options include:\n", " -d32\t use a 32-bit data model if available\n", " -d64\t use a 64-bit data model if available\n", " -server\t to select the \"server\" VM\n", " -zero\t to select the \"zero\" VM\n", " -jamvm\t to select the \"jamvm\" VM\n", " -avian\t to select the \"avian\" VM\n", " -dcevm\t to select the \"dcevm\" VM\n", " The default VM is server,\n", " because you are running on a server-class machine.\n", "\n", "\n", " -cp \n", " -classpath \n", " A : separated list of directories, JAR archives,\n", " and ZIP archives to search for class files.\n", " -D=\n", " set a system property\n", " -verbose:[class|gc|jni]\n", " enable verbose output\n", " -version print product version and exit\n", " -version:\n", " require the specified version to run\n", " -showversion print product version and continue\n", " -jre-restrict-search | -no-jre-restrict-search\n", " include/exclude user private JREs in the version search\n", " -? -help print this help message\n", " -X print help on non-standard options\n", " -ea[:...|:]\n", " -enableassertions[:...|:]\n", " enable assertions with specified granularity\n", " -da[:...|:]\n", " -disableassertions[:...|:]\n", " disable assertions with specified granularity\n", " -esa | -enablesystemassertions\n", " enable system assertions\n", " -dsa | -disablesystemassertions\n", " disable system assertions\n", " -agentlib:[=]\n", " load native agent library , e.g. -agentlib:hprof\n", " see also, -agentlib:jdwp=help and -agentlib:hprof=help\n", " -agentpath:[=]\n", " load native agent library by full pathname\n", " -javaagent:[=]\n", " load Java programming language agent, see java.lang.instrument\n", " -splash:\n", " show splash screen with specified image\n", "See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details.\n" ] } ], "source": [ "%%bash\n", "java -showversion" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Wed Oct 18 16:48:11 UTC 2017\n" ] } ], "source": [ "%%bash\n", "date" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "bash: line 1: fg: no job control\n", "openjdk version \"1.8.0_131\"\n", "OpenJDK Runtime Environment (build 1.8.0_131-8u131-b11-1~bpo8+1-b11)\n", "OpenJDK 64-Bit Server VM (build 25.131-b11, mixed mode)\n", "\n", "Usage: java [-options] class [args...]\n", " (to execute a class)\n", " or java [-options] -jar jarfile [args...]\n", " (to execute a jar file)\n", "where options include:\n", " -d32\t use a 32-bit data model if available\n", " -d64\t use a 64-bit data model if available\n", " -server\t to select the \"server\" VM\n", " -zero\t to select the \"zero\" VM\n", " -dcevm\t to select the \"dcevm\" VM\n", " The default VM is server,\n", " because you are running on a server-class machine.\n", "\n", "\n", " -cp \n", " -classpath \n", " A : separated list of directories, JAR archives,\n", " and ZIP archives to search for class files.\n", " -D=\n", " set a system property\n", " -verbose:[class|gc|jni]\n", " enable verbose output\n", " -version print product version and exit\n", " -version:\n", " Warning: this feature is deprecated and will be removed\n", " in a future release.\n", " require the specified version to run\n", " -showversion print product version and continue\n", " -jre-restrict-search | -no-jre-restrict-search\n", " Warning: this feature is deprecated and will be removed\n", " in a future release.\n", " include/exclude user private JREs in the version search\n", " -? -help print this help message\n", " -X print help on non-standard options\n", " -ea[:...|:]\n", " -enableassertions[:...|:]\n", " enable assertions with specified granularity\n", " -da[:...|:]\n", " -disableassertions[:...|:]\n", " disable assertions with specified granularity\n", " -esa | -enablesystemassertions\n", " enable system assertions\n", " -dsa | -disablesystemassertions\n", " disable system assertions\n", " -agentlib:[=]\n", " load native agent library , e.g. -agentlib:hprof\n", " see also, -agentlib:jdwp=help and -agentlib:hprof=help\n", " -agentpath:[=]\n", " load native agent library by full pathname\n", " -javaagent:[=]\n", " load Java programming language agent, see java.lang.instrument\n", " -splash:\n", " show splash screen with specified image\n", "See http://www.oracle.com/technetwork/java/javase/documentation/index.html for more details.\n" ] } ], "source": [ "%%bash\n", "%%bash\n", "java -showversion" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "usage: canu [-version] [-citation] \\\n", " [-correct | -trim | -assemble | -trim-assemble] \\\n", " [-s ] \\\n", " -p \\\n", " -d \\\n", " genomeSize=[g|m|k] \\\n", " [other-options] \\\n", " [-pacbio-raw |\n", " -pacbio-corrected |\n", " -nanopore-raw |\n", " -nanopore-corrected] file1 file2 ...\n", "\n", "example: canu -d run1 -p godzilla genomeSize=1g -nanopore-raw reads/*.fasta.gz \n", "\n", "\n", " To restrict canu to only a specific stage, use:\n", " -correct - generate corrected reads\n", " -trim - generate trimmed reads\n", " -assemble - generate an assembly\n", " -trim-assemble - generate trimmed reads and then assemble them\n", "\n", " The assembly is computed in the -d , with output files named\n", " using the -p . This directory is created if needed. It is not\n", " possible to run multiple assemblies in the same directory.\n", "\n", " The genome size should be your best guess of the haploid genome size of what is being\n", " assembled. It is used primarily to estimate coverage in reads, NOT as the desired\n", " assembly size. Fractional values are allowed: '4.7m' equals '4700k' equals '4700000'\n", "\n", " Some common options:\n", " useGrid=string\n", " - Run under grid control (true), locally (false), or set up for grid control\n", " but don't submit any jobs (remote)\n", " rawErrorRate=fraction-error\n", " - The allowed difference in an overlap between two raw uncorrected reads. For lower\n", " quality reads, use a higher number. The defaults are 0.300 for PacBio reads and\n", " 0.500 for Nanopore reads.\n", " correctedErrorRate=fraction-error\n", " - The allowed difference in an overlap between two corrected reads. Assemblies of\n", " low coverage or data with biological differences will benefit from a slight increase\n", " in this. Defaults are 0.045 for PacBio reads and 0.144 for Nanopore reads.\n", " gridOptions=string\n", " - Pass string to the command used to submit jobs to the grid. Can be used to set\n", " maximum run time limits. Should NOT be used to set memory limits; Canu will do\n", " that for you.\n", " minReadLength=number\n", " - Ignore reads shorter than 'number' bases long. Default: 1000.\n", " minOverlapLength=number\n", " - Ignore read-to-read overlaps shorter than 'number' bases long. Default: 500.\n", " A full list of options can be printed with '-options'. All options can be supplied in\n", " an optional sepc file with the -s option.\n", "\n", " Reads can be either FASTA or FASTQ format, uncompressed, or compressed with gz, bz2 or xz.\n", " Reads are specified by the technology they were generated with:\n", " -pacbio-raw \n", " -pacbio-corrected \n", " -nanopore-raw \n", " -nanopore-corrected \n", "\n", "Complete documentation at http://canu.readthedocs.org/en/latest/\n", "\n", "ERROR: Failed to run gnuplot from 'gnuplot'.ERROR: Set option gnuplot= or gnuplotTested=true to skip this test and not generate plots.\n", "\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "-- Canu 1.6\n", "--\n", "-- CITATIONS\n", "--\n", "-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.\n", "-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.\n", "-- Genome Res. 2017 May;27(5):722-736.\n", "-- http://doi.org/10.1101/gr.215087.116\n", "-- \n", "-- Read and contig alignments during correction, consensus and GFA building use:\n", "-- Šošic M, Šikic M.\n", "-- Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.\n", "-- Bioinformatics. 2017 May 1;33(9):1394-1395.\n", "-- http://doi.org/10.1093/bioinformatics/btw753\n", "-- \n", "-- Overlaps are generated using:\n", "-- Berlin K, et al.\n", "-- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.\n", "-- Nat Biotechnol. 2015 Jun;33(6):623-30.\n", "-- http://doi.org/10.1038/nbt.3238\n", "-- \n", "-- Myers EW, et al.\n", "-- A Whole-Genome Assembly of Drosophila.\n", "-- Science. 2000 Mar 24;287(5461):2196-204.\n", "-- http://doi.org/10.1126/science.287.5461.2196\n", "-- \n", "-- Li H.\n", "-- Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.\n", "-- Bioinformatics. 2016 Jul 15;32(14):2103-10.\n", "-- http://doi.org/10.1093/bioinformatics/btw152\n", "-- \n", "-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:\n", "-- Chin CS, et al.\n", "-- Phased diploid genome assembly with single-molecule real-time sequencing.\n", "-- Nat Methods. 2016 Dec;13(12):1050-1054.\n", "-- http://doi.org/10.1038/nmeth.4035\n", "-- \n", "-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:\n", "-- Chin CS, et al.\n", "-- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.\n", "-- Nat Methods. 2013 Jun;10(6):563-9\n", "-- http://doi.org/10.1038/nmeth.2474\n", "-- \n", "-- CONFIGURE CANU\n", "--\n", "-- Detected Java(TM) Runtime Environment '1.8.0_131' (from 'java').\n", "\n", "real\t0m0.234s\n", "user\t0m0.184s\n", "sys\t0m0.064s\n" ] } ], "source": [ "%%bash\n", "time canu \\\n", "useGrid=false \\\n", "-p 20171009_oly_pacbio \\\n", "-d /home/data/20171018_oly_pacbio_canu/ \\\n", "genomeSize=1.9g \\\n", "correctedErrorRate=0.075 \\\n", "-pacbio-raw m*" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Error message says it can't find gnuplot. Will update Docker file to install gnuplot. BRB..." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Wed Oct 18 17:05:55 UTC 2017\n" ] } ], "source": [ "%%bash\n", "date" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "usage: canu [-version] [-citation] \\\n", " [-correct | -trim | -assemble | -trim-assemble] \\\n", " [-s ] \\\n", " -p \\\n", " -d \\\n", " genomeSize=[g|m|k] \\\n", " [other-options] \\\n", " [-pacbio-raw |\n", " -pacbio-corrected |\n", " -nanopore-raw |\n", " -nanopore-corrected] file1 file2 ...\n", "\n", "example: canu -d run1 -p godzilla genomeSize=1g -nanopore-raw reads/*.fasta.gz \n", "\n", "\n", " To restrict canu to only a specific stage, use:\n", " -correct - generate corrected reads\n", " -trim - generate trimmed reads\n", " -assemble - generate an assembly\n", " -trim-assemble - generate trimmed reads and then assemble them\n", "\n", " The assembly is computed in the -d , with output files named\n", " using the -p . This directory is created if needed. It is not\n", " possible to run multiple assemblies in the same directory.\n", "\n", " The genome size should be your best guess of the haploid genome size of what is being\n", " assembled. It is used primarily to estimate coverage in reads, NOT as the desired\n", " assembly size. Fractional values are allowed: '4.7m' equals '4700k' equals '4700000'\n", "\n", " Some common options:\n", " useGrid=string\n", " - Run under grid control (true), locally (false), or set up for grid control\n", " but don't submit any jobs (remote)\n", " rawErrorRate=fraction-error\n", " - The allowed difference in an overlap between two raw uncorrected reads. For lower\n", " quality reads, use a higher number. The defaults are 0.300 for PacBio reads and\n", " 0.500 for Nanopore reads.\n", " correctedErrorRate=fraction-error\n", " - The allowed difference in an overlap between two corrected reads. Assemblies of\n", " low coverage or data with biological differences will benefit from a slight increase\n", " in this. Defaults are 0.045 for PacBio reads and 0.144 for Nanopore reads.\n", " gridOptions=string\n", " - Pass string to the command used to submit jobs to the grid. Can be used to set\n", " maximum run time limits. Should NOT be used to set memory limits; Canu will do\n", " that for you.\n", " minReadLength=number\n", " - Ignore reads shorter than 'number' bases long. Default: 1000.\n", " minOverlapLength=number\n", " - Ignore read-to-read overlaps shorter than 'number' bases long. Default: 500.\n", " A full list of options can be printed with '-options'. All options can be supplied in\n", " an optional sepc file with the -s option.\n", "\n", " Reads can be either FASTA or FASTQ format, uncompressed, or compressed with gz, bz2 or xz.\n", " Reads are specified by the technology they were generated with:\n", " -pacbio-raw \n", " -pacbio-corrected \n", " -nanopore-raw \n", " -nanopore-corrected \n", "\n", "Complete documentation at http://canu.readthedocs.org/en/latest/\n", "\n", "ERROR: ovsMethod=parallel requires useGrid=true or useGrid=remote. Set ovsMethod=sequential if no grid is available\n", "\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "-- Canu 1.6\n", "--\n", "-- CITATIONS\n", "--\n", "-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.\n", "-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.\n", "-- Genome Res. 2017 May;27(5):722-736.\n", "-- http://doi.org/10.1101/gr.215087.116\n", "-- \n", "-- Read and contig alignments during correction, consensus and GFA building use:\n", "-- Šošic M, Šikic M.\n", "-- Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.\n", "-- Bioinformatics. 2017 May 1;33(9):1394-1395.\n", "-- http://doi.org/10.1093/bioinformatics/btw753\n", "-- \n", "-- Overlaps are generated using:\n", "-- Berlin K, et al.\n", "-- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.\n", "-- Nat Biotechnol. 2015 Jun;33(6):623-30.\n", "-- http://doi.org/10.1038/nbt.3238\n", "-- \n", "-- Myers EW, et al.\n", "-- A Whole-Genome Assembly of Drosophila.\n", "-- Science. 2000 Mar 24;287(5461):2196-204.\n", "-- http://doi.org/10.1126/science.287.5461.2196\n", "-- \n", "-- Li H.\n", "-- Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.\n", "-- Bioinformatics. 2016 Jul 15;32(14):2103-10.\n", "-- http://doi.org/10.1093/bioinformatics/btw152\n", "-- \n", "-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:\n", "-- Chin CS, et al.\n", "-- Phased diploid genome assembly with single-molecule real-time sequencing.\n", "-- Nat Methods. 2016 Dec;13(12):1050-1054.\n", "-- http://doi.org/10.1038/nmeth.4035\n", "-- \n", "-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:\n", "-- Chin CS, et al.\n", "-- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.\n", "-- Nat Methods. 2013 Jun;10(6):563-9\n", "-- http://doi.org/10.1038/nmeth.2474\n", "-- \n", "-- CONFIGURE CANU\n", "--\n", "-- Detected Java(TM) Runtime Environment '1.8.0_131' (from 'java').\n", "-- Detected gnuplot version '5.2 patchlevel 0' (from 'gnuplot') and image format 'svg'.\n", "-- Detected 24 CPUs and 71 gigabytes of memory.\n", "-- No grid engine detected, grid disabled.\n", "--\n", "-- (tag)Concurrency\n", "-- (tag)Threads |\n", "-- (tag)Memory | |\n", "-- (tag) | | | algorithm\n", "-- ------- ------ -------- -------- -----------------------------\n", "-- Local: meryl 71 GB 24 CPUs x 1 job (k-mer counting)\n", "-- Local: cormhap 32 GB 12 CPUs x 2 jobs (overlap detection with mhap)\n", "-- Local: obtovl 12 GB 8 CPUs x 3 jobs (overlap detection)\n", "-- Local: utgovl 12 GB 8 CPUs x 3 jobs (overlap detection)\n", "-- Local: cor 11 GB 4 CPUs x 6 jobs (read correction)\n", "-- Local: ovb 2 GB 1 CPU x 24 jobs (overlap store bucketizer)\n", "-- Local: ovs 32 GB 1 CPU x 24 jobs (overlap store sorting)\n", "-- Local: red 8 GB 8 CPUs x 3 jobs (read error detection)\n", "-- Local: oea 2 GB 1 CPU x 24 jobs (overlap error adjustment)\n", "-- Local: bat 35 GB 12 CPUs x 2 jobs (contig construction)\n", "-- Local: cns 71 GB 8 CPUs x 3 jobs (consensus)\n", "-- Local: gfa 16 GB 12 CPUs x 2 jobs (GFA alignment and processing)\n", "--\n", "-- Found PacBio uncorrected reads in the input files.\n", "\n", "real\t0m0.297s\n", "user\t0m0.232s\n", "sys\t0m0.056s\n" ] } ], "source": [ "%%bash\n", "time canu \\\n", "useGrid=false \\\n", "-p 20171009_oly_pacbio \\\n", "-d /home/data/20171018_oly_pacbio_canu/ \\\n", "genomeSize=1.9g \\\n", "correctedErrorRate=0.075 \\\n", "-pacbio-raw m*" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Error message says I need to change ```ovsMethod=``` to sequentila if no grid available. Figured that'd be adjusted when I specified ```useGrid=false```... Will change command." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Code overview:\n", "\n", "- ```useGrid=false```: Needed to disable Canu's parallel computing scheduler thingy (on by default)\n", "- ```ovsMethod=sequential```: Same as above.\n", "- ```-p```: The assembly prefix string. Screwed this up; leftover from copy/paste of earlier attempt.\n", "- ```-d```: Destination folder for output.\n", "- ```genomeSize=```: Needs estimated genome size. Used 1.9g [based on BGI k-mer estimate](http://owl.fish.washington.edu/O_lurida_genome_assemblies_BGI/20160512/20160512_F15FTSUSAT0327_genome_survey.pdf).\n", "- ```correctedErrorRate=```: Expecting low coverage, so increased this from the default (4.5% to 7.5%)." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Process is interrupted.\n" ] } ], "source": [ "%%bash\n", "time canu \\\n", "useGrid=false \\\n", "ovsMethod=sequential \\\n", "-p 20171009_oly_pacbio \\\n", "-d /home/data/20171018_oly_pacbio_canu/ \\\n", "genomeSize=1.9g \\\n", "correctedErrorRate=0.075 \\\n", "-pacbio-raw m*" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "ename": "OSError", "evalue": "\"sh\" shell not found", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mOSError\u001b[0m Traceback (most recent call last)", "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmagic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mu'ls -l'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mmagic\u001b[0;34m(self, arg_s)\u001b[0m\n\u001b[1;32m 2158\u001b[0m \u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0marg_s\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpartition\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m' '\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2159\u001b[0m \u001b[0mmagic_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmagic_name\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlstrip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprefilter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mESC_MAGIC\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2160\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_line_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmagic_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2161\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2162\u001b[0m \u001b[0;31m#-------------------------------------------------------------------------\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36mrun_line_magic\u001b[0;34m(self, magic_name, line)\u001b[0m\n\u001b[1;32m 2079\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'local_ns'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getframe\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstack_depth\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf_locals\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2080\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2081\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2082\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2083\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/alias.pyc\u001b[0m in \u001b[0;36m__call__\u001b[0;34m(self, rest)\u001b[0m\n\u001b[1;32m 185\u001b[0m \u001b[0mcmd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'%s %s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mcmd\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mtuple\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0mnargs\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m' '\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mnargs\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 186\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 187\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshell\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msystem\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcmd\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 188\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 189\u001b[0m \u001b[0;31m#-----------------------------------------------------------------------------\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc\u001b[0m in \u001b[0;36msystem_piped\u001b[0;34m(self, cmd)\u001b[0m\n\u001b[1;32m 2209\u001b[0m \u001b[0;31m# a non-None value would trigger :func:`sys.displayhook` calls.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2210\u001b[0m \u001b[0;31m# Instead, we store the exit_code in user_ns.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2211\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0muser_ns\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'_exit_code'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msystem\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvar_expand\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcmd\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdepth\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2212\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2213\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0msystem_raw\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcmd\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/utils/_process_posix.pyc\u001b[0m in \u001b[0;36msystem\u001b[0;34m(self, cmd)\u001b[0m\n\u001b[1;32m 155\u001b[0m \u001b[0mchild\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpexpect\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mspawnb\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msh\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'-c'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcmd\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# Pexpect-U\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 156\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 157\u001b[0;31m \u001b[0mchild\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpexpect\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mspawn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msh\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'-c'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcmd\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# Vanilla Pexpect\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 158\u001b[0m \u001b[0mflush\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstdout\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mflush\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 159\u001b[0m \u001b[0;32mwhile\u001b[0m \u001b[0mTrue\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;32m/root/miniconda2/lib/python2.7/site-packages/IPython/utils/_process_posix.pyc\u001b[0m in \u001b[0;36msh\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 64\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_sh\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpexpect\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwhich\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'sh'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 65\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_sh\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 66\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mOSError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'\"sh\" shell not found'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 67\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 68\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_sh\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;31mOSError\u001b[0m: \"sh\" shell not found" ] } ], "source": [ "ls -l" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Couldn't find program: 'bash'\n" ] } ], "source": [ "%%bash\n", "ls -l" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This was crazy! It turns out the entire working directory's contents were deleted!!! Very scary. Going to re-copy the FASTQ files and try again..." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Wed Oct 18 22:36:30 UTC 2017\n", "a56217b83023\n" ] } ], "source": [ "%%bash\n", "date\n", "hostname" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 11249952\r\n", "-rw-r--r-- 1 root root 52177 Oct 18 22:09 20171018_docker_oly_canu.ipynb\r\n", "-rw-rw-r-- 1 1000 1000 389254888 Oct 18 22:25 m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq\r\n", "-rwxrwxr-x 1 1000 1000 1243634577 Oct 18 22:25 \u001b[0m\u001b[01;32mm170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "-rwxrwxr-x 1 1000 1000 1388585547 Oct 18 22:26 \u001b[01;32mm170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "-rwxrwxr-x 1 1000 1000 1258960377 Oct 18 22:26 \u001b[01;32mm170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "-rwxrwxr-x 1 1000 1000 1384102715 Oct 18 22:26 \u001b[01;32mm170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "-rwxrwxr-x 1 1000 1000 1305285460 Oct 18 22:27 \u001b[01;32mm170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "-rwxrwxr-x 1 1000 1000 1321354256 Oct 18 22:27 \u001b[01;32mm170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "-rwxrwxr-x 1 1000 1000 910321803 Oct 18 22:27 \u001b[01;32mm170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "-rwxrwxr-x 1 1000 1000 798040545 Oct 18 22:28 \u001b[01;32mm170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "-rwxrwxr-x 1 1000 1000 724173972 Oct 18 22:28 \u001b[01;32mm170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "-rwxrwxr-x 1 1000 1000 796112682 Oct 18 22:28 \u001b[01;32mm170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n" ] } ], "source": [ "ls -l" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "%%bash\n", "mkdir /home/data/20171018_oly_pacbio_canu" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "20171018_docker_oly_canu.ipynb\r\n", "\u001b[0m\u001b[01;34m20171018_oly_pacbio_canu\u001b[0m/\r\n", "m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq\r\n", "\u001b[01;32mm170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "\u001b[01;32mm170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "\u001b[01;32mm170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "\u001b[01;32mm170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "\u001b[01;32mm170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "\u001b[01;32mm170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "\u001b[01;32mm170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "\u001b[01;32mm170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "\u001b[01;32mm170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n", "\u001b[01;32mm170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz\u001b[0m\u001b[K*\r\n" ] } ], "source": [ "ls -F" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "-- Canu 1.6\n", "--\n", "-- CITATIONS\n", "--\n", "-- Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM.\n", "-- Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.\n", "-- Genome Res. 2017 May;27(5):722-736.\n", "-- http://doi.org/10.1101/gr.215087.116\n", "-- \n", "-- Read and contig alignments during correction, consensus and GFA building use:\n", "-- Šošic M, Šikic M.\n", "-- Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.\n", "-- Bioinformatics. 2017 May 1;33(9):1394-1395.\n", "-- http://doi.org/10.1093/bioinformatics/btw753\n", "-- \n", "-- Overlaps are generated using:\n", "-- Berlin K, et al.\n", "-- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.\n", "-- Nat Biotechnol. 2015 Jun;33(6):623-30.\n", "-- http://doi.org/10.1038/nbt.3238\n", "-- \n", "-- Myers EW, et al.\n", "-- A Whole-Genome Assembly of Drosophila.\n", "-- Science. 2000 Mar 24;287(5461):2196-204.\n", "-- http://doi.org/10.1126/science.287.5461.2196\n", "-- \n", "-- Li H.\n", "-- Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.\n", "-- Bioinformatics. 2016 Jul 15;32(14):2103-10.\n", "-- http://doi.org/10.1093/bioinformatics/btw152\n", "-- \n", "-- Corrected read consensus sequences are generated using an algorithm derived from FALCON-sense:\n", "-- Chin CS, et al.\n", "-- Phased diploid genome assembly with single-molecule real-time sequencing.\n", "-- Nat Methods. 2016 Dec;13(12):1050-1054.\n", "-- http://doi.org/10.1038/nmeth.4035\n", "-- \n", "-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:\n", "-- Chin CS, et al.\n", "-- Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.\n", "-- Nat Methods. 2013 Jun;10(6):563-9\n", "-- http://doi.org/10.1038/nmeth.2474\n", "-- \n", "-- CONFIGURE CANU\n", "--\n", "-- Detected Java(TM) Runtime Environment '1.8.0_131' (from 'java').\n", "-- Detected gnuplot version '5.2 patchlevel 0' (from 'gnuplot') and image format 'svg'.\n", "-- Detected 24 CPUs and 71 gigabytes of memory.\n", "-- No grid engine detected, grid disabled.\n", "--\n", "-- (tag)Concurrency\n", "-- (tag)Threads |\n", "-- (tag)Memory | |\n", "-- (tag) | | | algorithm\n", "-- ------- ------ -------- -------- -----------------------------\n", "-- Local: meryl 71 GB 24 CPUs x 1 job (k-mer counting)\n", "-- Local: cormhap 32 GB 12 CPUs x 2 jobs (overlap detection with mhap)\n", "-- Local: obtovl 12 GB 8 CPUs x 3 jobs (overlap detection)\n", "-- Local: utgovl 12 GB 8 CPUs x 3 jobs (overlap detection)\n", "-- Local: cor 11 GB 4 CPUs x 6 jobs (read correction)\n", "-- Local: ovb 2 GB 1 CPU x 24 jobs (overlap store bucketizer)\n", "-- Local: ovs 32 GB 1 CPU x 24 jobs (overlap store sorting)\n", "-- Local: red 8 GB 8 CPUs x 3 jobs (read error detection)\n", "-- Local: oea 2 GB 1 CPU x 24 jobs (overlap error adjustment)\n", "-- Local: bat 35 GB 12 CPUs x 2 jobs (contig construction)\n", "-- Local: cns 71 GB 8 CPUs x 3 jobs (consensus)\n", "-- Local: gfa 16 GB 12 CPUs x 2 jobs (GFA alignment and processing)\n", "--\n", "-- Found PacBio uncorrected reads in the input files.\n", "--\n", "-- Generating assembly '20171018_oly_pacbio' in '/home/data/20171018_oly_pacbio_canu'\n", "--\n", "-- Parameters:\n", "--\n", "-- genomeSize 1900000000\n", "--\n", "-- Overlap Generation Limits:\n", "-- corOvlErrorRate 0.2400 ( 24.00%)\n", "-- obtOvlErrorRate 0.0750 ( 7.50%)\n", "-- utgOvlErrorRate 0.0750 ( 7.50%)\n", "--\n", "-- Overlap Processing Limits:\n", "-- corErrorRate 0.3000 ( 30.00%)\n", "-- obtErrorRate 0.0750 ( 7.50%)\n", "-- utgErrorRate 0.0750 ( 7.50%)\n", "-- cnsErrorRate 0.0750 ( 7.50%)\n", "--\n", "--\n", "-- BEGIN CORRECTION\n", "--\n", "----------------------------------------\n", "-- Starting command on Wed Oct 18 22:37:54 2017 with 849.001 GB free disk space\n", "\n", " cd correction\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/gatekeeperCreate \\\n", " -minlength 1000 \\\n", " -o ./20171018_oly_pacbio.gkpStore.BUILDING \\\n", " ./20171018_oly_pacbio.gkpStore.gkp \\\n", " > ./20171018_oly_pacbio.gkpStore.BUILDING.err 2>&1\n", "\n", "-- Finished on Wed Oct 18 22:41:44 2017 (230 seconds) with 845.607 GB free disk space\n", "----------------------------------------\n", "--\n", "-- In gatekeeper store 'correction/20171018_oly_pacbio.gkpStore':\n", "-- Found 1738852 reads.\n", "-- Found 12725659496 bases (6.69 times coverage).\n", "--\n", "-- Read length histogram (one '*' equals 3616.75 reads):\n", "-- 0 999 0 \n", "-- 1000 1999 132777 ************************************\n", "-- 2000 2999 143827 ***************************************\n", "-- 3000 3999 138184 **************************************\n", "-- 4000 4999 130729 ************************************\n", "-- 5000 5999 168299 **********************************************\n", "-- 6000 6999 253173 **********************************************************************\n", "-- 7000 7999 189248 ****************************************************\n", "-- 8000 8999 135856 *************************************\n", "-- 9000 9999 98310 ***************************\n", "-- 10000 10999 74004 ********************\n", "-- 11000 11999 56563 ***************\n", "-- 12000 12999 44400 ************\n", "-- 13000 13999 35095 *********\n", "-- 14000 14999 27878 *******\n", "-- 15000 15999 21885 ******\n", "-- 16000 16999 17635 ****\n", "-- 17000 17999 14000 ***\n", "-- 18000 18999 11258 ***\n", "-- 19000 19999 9067 **\n", "-- 20000 20999 7244 **\n", "-- 21000 21999 5867 *\n", "-- 22000 22999 4521 *\n", "-- 23000 23999 3708 *\n", "-- 24000 24999 2892 \n", "-- 25000 25999 2245 \n", "-- 26000 26999 1894 \n", "-- 27000 27999 1551 \n", "-- 28000 28999 1257 \n", "-- 29000 29999 1005 \n", "-- 30000 30999 794 \n", "-- 31000 31999 704 \n", "-- 32000 32999 542 \n", "-- 33000 33999 422 \n", "-- 34000 34999 338 \n", "-- 35000 35999 273 \n", "-- 36000 36999 258 \n", "-- 37000 37999 213 \n", "-- 38000 38999 165 \n", "-- 39000 39999 140 \n", "-- 40000 40999 127 \n", "-- 41000 41999 97 \n", "-- 42000 42999 76 \n", "-- 43000 43999 59 \n", "-- 44000 44999 49 \n", "-- 45000 45999 42 \n", "-- 46000 46999 36 \n", "-- 47000 47999 29 \n", "-- 48000 48999 27 \n", "-- 49000 49999 21 \n", "-- 50000 50999 11 \n", "-- 51000 51999 10 \n", "-- 52000 52999 8 \n", "-- 53000 53999 7 \n", "-- 54000 54999 4 \n", "-- 55000 55999 6 \n", "-- 56000 56999 5 \n", "-- 57000 57999 3 \n", "-- 58000 58999 6 \n", "-- 59000 59999 0 \n", "-- 60000 60999 3 \n", "-- 61000 61999 0 \n", "-- 62000 62999 1 \n", "-- 63000 63999 2 \n", "-- 64000 64999 0 \n", "-- 65000 65999 1 \n", "-- 66000 66999 0 \n", "-- 67000 67999 0 \n", "-- 68000 68999 1 \n", "-- Finished stage 'cor-gatekeeper', reset canuIteration.\n", "-- Finished stage 'merylConfigure', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'meryl' concurrent execution on Wed Oct 18 22:42:07 2017 with 845.554 GB free disk space (1 processes; 1 concurrently)\n", "\n", " cd correction/0-mercounts\n", " ./meryl.sh 1 > ./meryl.000001.out 2>&1\n", "\n", "-- Finished on Wed Oct 18 23:15:25 2017 (1998 seconds) with 837.703 GB free disk space\n", "----------------------------------------\n", "-- Meryl finished successfully.\n", "-- Finished stage 'merylCheck', reset canuIteration.\n", "--\n", "-- 16-mers Fraction\n", "-- Occurrences NumMers Unique Total\n", "-- 1- 1 385488671 **************************************************************** 0.2091 0.0304\n", "-- 2- 2 324564045 ****************************************************** 0.3852 0.0815\n", "-- 3- 4 418987507 ********************************************************************** 0.5166 0.1387\n", "-- 5- 7 303655603 ************************************************** 0.6831 0.2457\n", "-- 8- 11 175681884 ***************************** 0.8092 0.3707\n", "-- 12- 16 96333136 **************** 0.8866 0.4859\n", "-- 17- 22 53526300 ******** 0.9312 0.5811\n", "-- 23- 29 30754739 ***** 0.9569 0.6563\n", "-- 30- 37 18389991 *** 0.9721 0.7149\n", "-- 38- 46 11388024 * 0.9813 0.7606\n", "-- 47- 56 7298685 * 0.9871 0.7964\n", "-- 57- 67 4830492 0.9909 0.8248\n", "-- 68- 79 3287983 0.9934 0.8476\n", "-- 80- 92 2276997 0.9951 0.8660\n", "-- 93- 106 1616821 0.9963 0.8810\n", "-- 107- 121 1168529 0.9971 0.8934\n", "-- 122- 137 861132 0.9977 0.9037\n", "-- 138- 154 644741 0.9982 0.9123\n", "-- 155- 172 494164 0.9985 0.9196\n", "-- 173- 191 385159 0.9988 0.9259\n", "-- 192- 211 303250 0.9990 0.9313\n", "-- 212- 232 241440 0.9992 0.9361\n", "-- 233- 254 192941 0.9993 0.9403\n", "-- 255- 277 156500 0.9994 0.9439\n", "-- 278- 301 127545 0.9995 0.9472\n", "-- 302- 326 105904 0.9996 0.9501\n", "-- 327- 352 87888 0.9996 0.9526\n", "-- 353- 379 72868 0.9997 0.9550\n", "-- 380- 407 61693 0.9997 0.9571\n", "-- 408- 436 52543 0.9997 0.9590\n", "-- 437- 466 44553 0.9998 0.9607\n", "-- 467- 497 38393 0.9998 0.9623\n", "-- 498- 529 33193 0.9998 0.9637\n", "-- 530- 562 29162 0.9998 0.9651\n", "-- 563- 596 25892 0.9998 0.9663\n", "-- 597- 631 22484 0.9999 0.9675\n", "-- 632- 667 20132 0.9999 0.9686\n", "-- 668- 704 17937 0.9999 0.9696\n", "-- 705- 742 15848 0.9999 0.9706\n", "-- 743- 781 14105 0.9999 0.9715\n", "-- 782- 821 12734 0.9999 0.9723\n", "--\n", "-- 4763892 (max occurrences)\n", "-- 12314088045 (total mers, non-unique)\n", "-- 1457976283 (distinct mers, non-unique)\n", "-- 385488671 (unique mers)\n", "-- For mhap overlapping, set repeat k-mer threshold to 126995.\n", "--\n", "-- Found 12699576716 16-mers; 1843464954 distinct and 385488671 unique. Largest count 4763892.\n", "-- Finished stage 'cor-meryl', reset canuIteration.\n", "--\n", "-- OVERLAPPER (mhap) (correction)\n", "--\n", "-- Set corMhapSensitivity=high based on read coverage of 6.\n", "--\n", "-- PARAMETERS: hashes=768, minMatches=2, threshold=0.73\n", "--\n", "-- Given 32 GB, can fit 48000 reads per block.\n", "-- For 38 blocks, set stride to 9 blocks.\n", "-- Logging partitioning to 'correction/1-overlapper/partitioning.log'.\n", "-- Configured 37 mhap precompute jobs.\n", "-- Configured 91 mhap overlap jobs.\n", "-- Finished stage 'cor-mhapConfigure', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'cormhap' concurrent execution on Wed Oct 18 23:16:40 2017 with 845.581 GB free disk space (37 processes; 2 concurrently)\n", "\n", " cd correction/1-overlapper\n", " ./precompute.sh 1 > ./precompute.000001.out 2>&1\n", " ./precompute.sh 2 > ./precompute.000002.out 2>&1\n", " ./precompute.sh 3 > ./precompute.000003.out 2>&1\n", " ./precompute.sh 4 > ./precompute.000004.out 2>&1\n", " ./precompute.sh 5 > ./precompute.000005.out 2>&1\n", " ./precompute.sh 6 > ./precompute.000006.out 2>&1\n", " ./precompute.sh 7 > ./precompute.000007.out 2>&1\n", " ./precompute.sh 8 > ./precompute.000008.out 2>&1\n", " ./precompute.sh 9 > ./precompute.000009.out 2>&1\n", " ./precompute.sh 10 > ./precompute.000010.out 2>&1\n", " ./precompute.sh 11 > ./precompute.000011.out 2>&1\n", " ./precompute.sh 12 > ./precompute.000012.out 2>&1\n", " ./precompute.sh 13 > ./precompute.000013.out 2>&1\n", " ./precompute.sh 14 > ./precompute.000014.out 2>&1\n", " ./precompute.sh 15 > ./precompute.000015.out 2>&1\n", " ./precompute.sh 16 > ./precompute.000016.out 2>&1\n", " ./precompute.sh 17 > ./precompute.000017.out 2>&1\n", " ./precompute.sh 18 > ./precompute.000018.out 2>&1\n", " ./precompute.sh 19 > ./precompute.000019.out 2>&1\n", " ./precompute.sh 20 > ./precompute.000020.out 2>&1\n", " ./precompute.sh 21 > ./precompute.000021.out 2>&1\n", " ./precompute.sh 22 > ./precompute.000022.out 2>&1\n", " ./precompute.sh 23 > ./precompute.000023.out 2>&1\n", " ./precompute.sh 24 > ./precompute.000024.out 2>&1\n", " ./precompute.sh 25 > ./precompute.000025.out 2>&1\n", " ./precompute.sh 26 > ./precompute.000026.out 2>&1\n", " ./precompute.sh 27 > ./precompute.000027.out 2>&1\n", " ./precompute.sh 28 > ./precompute.000028.out 2>&1\n", " ./precompute.sh 29 > ./precompute.000029.out 2>&1\n", " ./precompute.sh 30 > ./precompute.000030.out 2>&1\n", " ./precompute.sh 31 > ./precompute.000031.out 2>&1\n", " ./precompute.sh 32 > ./precompute.000032.out 2>&1\n", " ./precompute.sh 33 > ./precompute.000033.out 2>&1\n", " ./precompute.sh 34 > ./precompute.000034.out 2>&1\n", " ./precompute.sh 35 > ./precompute.000035.out 2>&1\n", " ./precompute.sh 36 > ./precompute.000036.out 2>&1\n", " ./precompute.sh 37 > ./precompute.000037.out 2>&1\n", "\n", "-- Finished on Thu Oct 19 08:16:20 2017 (32380 seconds) with 796 GB free disk space\n", "----------------------------------------\n", "-- All 37 mhap precompute jobs finished successfully.\n", "-- Finished stage 'cor-mhapPrecomputeCheck', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'cormhap' concurrent execution on Thu Oct 19 08:16:20 2017 with 796 GB free disk space (91 processes; 2 concurrently)\n", "\n", " cd correction/1-overlapper\n", " ./mhap.sh 1 > ./mhap.000001.out 2>&1\n", " ./mhap.sh 2 > ./mhap.000002.out 2>&1\n", " ./mhap.sh 3 > ./mhap.000003.out 2>&1\n", " ./mhap.sh 4 > ./mhap.000004.out 2>&1\n", " ./mhap.sh 5 > ./mhap.000005.out 2>&1\n", " ./mhap.sh 6 > ./mhap.000006.out 2>&1\n", " ./mhap.sh 7 > ./mhap.000007.out 2>&1\n", " ./mhap.sh 8 > ./mhap.000008.out 2>&1\n", " ./mhap.sh 9 > ./mhap.000009.out 2>&1\n", " ./mhap.sh 10 > ./mhap.000010.out 2>&1\n", " ./mhap.sh 11 > ./mhap.000011.out 2>&1\n", " ./mhap.sh 12 > ./mhap.000012.out 2>&1\n", " ./mhap.sh 13 > ./mhap.000013.out 2>&1\n", " ./mhap.sh 14 > ./mhap.000014.out 2>&1\n", " ./mhap.sh 15 > ./mhap.000015.out 2>&1\n", " ./mhap.sh 16 > ./mhap.000016.out 2>&1\n", " ./mhap.sh 17 > ./mhap.000017.out 2>&1\n", " ./mhap.sh 18 > ./mhap.000018.out 2>&1\n", " ./mhap.sh 19 > ./mhap.000019.out 2>&1\n", " ./mhap.sh 20 > ./mhap.000020.out 2>&1\n", " ./mhap.sh 21 > ./mhap.000021.out 2>&1\n", " ./mhap.sh 22 > ./mhap.000022.out 2>&1\n", " ./mhap.sh 23 > ./mhap.000023.out 2>&1\n", " ./mhap.sh 24 > ./mhap.000024.out 2>&1\n", " ./mhap.sh 25 > ./mhap.000025.out 2>&1\n", " ./mhap.sh 26 > ./mhap.000026.out 2>&1\n", " ./mhap.sh 27 > ./mhap.000027.out 2>&1\n", " ./mhap.sh 28 > ./mhap.000028.out 2>&1\n", " ./mhap.sh 29 > ./mhap.000029.out 2>&1\n", " ./mhap.sh 30 > ./mhap.000030.out 2>&1\n", " ./mhap.sh 31 > ./mhap.000031.out 2>&1\n", " ./mhap.sh 32 > ./mhap.000032.out 2>&1\n", " ./mhap.sh 33 > ./mhap.000033.out 2>&1\n", " ./mhap.sh 34 > ./mhap.000034.out 2>&1\n", " ./mhap.sh 35 > ./mhap.000035.out 2>&1\n", " ./mhap.sh 36 > ./mhap.000036.out 2>&1\n", " ./mhap.sh 37 > ./mhap.000037.out 2>&1\n", " ./mhap.sh 38 > ./mhap.000038.out 2>&1\n", " ./mhap.sh 39 > ./mhap.000039.out 2>&1\n", " ./mhap.sh 40 > ./mhap.000040.out 2>&1\n", " ./mhap.sh 41 > ./mhap.000041.out 2>&1\n", " ./mhap.sh 42 > ./mhap.000042.out 2>&1\n", " ./mhap.sh 43 > ./mhap.000043.out 2>&1\n", " ./mhap.sh 44 > ./mhap.000044.out 2>&1\n", " ./mhap.sh 45 > ./mhap.000045.out 2>&1\n", " ./mhap.sh 46 > ./mhap.000046.out 2>&1\n", " ./mhap.sh 47 > ./mhap.000047.out 2>&1\n", " ./mhap.sh 48 > ./mhap.000048.out 2>&1\n", " ./mhap.sh 49 > ./mhap.000049.out 2>&1\n", " ./mhap.sh 50 > ./mhap.000050.out 2>&1\n", " ./mhap.sh 51 > ./mhap.000051.out 2>&1\n", " ./mhap.sh 52 > ./mhap.000052.out 2>&1\n", " ./mhap.sh 53 > ./mhap.000053.out 2>&1\n", " ./mhap.sh 54 > ./mhap.000054.out 2>&1\n", " ./mhap.sh 55 > ./mhap.000055.out 2>&1\n", " ./mhap.sh 56 > ./mhap.000056.out 2>&1\n", " ./mhap.sh 57 > ./mhap.000057.out 2>&1\n", " ./mhap.sh 58 > ./mhap.000058.out 2>&1\n", " ./mhap.sh 59 > ./mhap.000059.out 2>&1\n", " ./mhap.sh 60 > ./mhap.000060.out 2>&1\n", " ./mhap.sh 61 > ./mhap.000061.out 2>&1\n", " ./mhap.sh 62 > ./mhap.000062.out 2>&1\n", " ./mhap.sh 63 > ./mhap.000063.out 2>&1\n", " ./mhap.sh 64 > ./mhap.000064.out 2>&1\n", " ./mhap.sh 65 > ./mhap.000065.out 2>&1\n", " ./mhap.sh 66 > ./mhap.000066.out 2>&1\n", " ./mhap.sh 67 > ./mhap.000067.out 2>&1\n", " ./mhap.sh 68 > ./mhap.000068.out 2>&1\n", " ./mhap.sh 69 > ./mhap.000069.out 2>&1\n", " ./mhap.sh 70 > ./mhap.000070.out 2>&1\n", " ./mhap.sh 71 > ./mhap.000071.out 2>&1\n", " ./mhap.sh 72 > ./mhap.000072.out 2>&1\n", " ./mhap.sh 73 > ./mhap.000073.out 2>&1\n", " ./mhap.sh 74 > ./mhap.000074.out 2>&1\n", " ./mhap.sh 75 > ./mhap.000075.out 2>&1\n", " ./mhap.sh 76 > ./mhap.000076.out 2>&1\n", " ./mhap.sh 77 > ./mhap.000077.out 2>&1\n", " ./mhap.sh 78 > ./mhap.000078.out 2>&1\n", " ./mhap.sh 79 > ./mhap.000079.out 2>&1\n", " ./mhap.sh 80 > ./mhap.000080.out 2>&1\n", " ./mhap.sh 81 > ./mhap.000081.out 2>&1\n", " ./mhap.sh 82 > ./mhap.000082.out 2>&1\n", " ./mhap.sh 83 > ./mhap.000083.out 2>&1\n", " ./mhap.sh 84 > ./mhap.000084.out 2>&1\n", " ./mhap.sh 85 > ./mhap.000085.out 2>&1\n", " ./mhap.sh 86 > ./mhap.000086.out 2>&1\n", " ./mhap.sh 87 > ./mhap.000087.out 2>&1\n", " ./mhap.sh 88 > ./mhap.000088.out 2>&1\n", " ./mhap.sh 89 > ./mhap.000089.out 2>&1\n", " ./mhap.sh 90 > ./mhap.000090.out 2>&1\n", " ./mhap.sh 91 > ./mhap.000091.out 2>&1\n", "\n", "-- Finished on Fri Oct 20 03:15:18 2017 (68338 seconds) with 709.861 GB free disk space\n", "----------------------------------------\n", "-- Found 91 mhap overlap output files.\n", "-- Finished stage 'cor-mhapCheck', reset canuIteration.\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 03:15:20 2017 with 709.861 GB free disk space\n", "\n", " cd correction\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/ovStoreBuild \\\n", " -O ./20171018_oly_pacbio.ovlStore.BUILDING \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -M 4-32 \\\n", " -L ./1-overlapper/ovljob.files \\\n", " > ./20171018_oly_pacbio.ovlStore.err 2>&1\n", "\n", "-- Finished on Fri Oct 20 06:04:35 2017 (10155 seconds) with 540.286 GB free disk space\n", "----------------------------------------\n", "-- Checking store.\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 06:04:35 2017 with 540.286 GB free disk space\n", "\n", " cd correction\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/ovStoreDump \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -O ./20171018_oly_pacbio.ovlStore \\\n", " -d -counts \\\n", " > ./20171018_oly_pacbio.ovlStore/counts.dat 2> ./20171018_oly_pacbio.ovlStore/counts.err\n", "\n", "-- Finished on Fri Oct 20 06:04:38 2017 (3 seconds) with 540.267 GB free disk space\n", "----------------------------------------\n", "--\n", "-- Overlap store 'correction/20171018_oly_pacbio.ovlStore' successfully constructed.\n", "-- Found 9101620838 overlaps for 1737978 reads; 874 reads have no overlaps.\n", "--\n", "FILE correction/1-overlapper/results/000001.ovb\n", "FILE correction/1-overlapper/results/000002.ovb\n", "FILE correction/1-overlapper/results/000003.ovb\n", "FILE correction/1-overlapper/results/000004.ovb\n", "FILE correction/1-overlapper/results/000005.ovb\n", "FILE correction/1-overlapper/results/000006.ovb\n", "FILE correction/1-overlapper/results/000007.ovb\n", "FILE correction/1-overlapper/results/000008.ovb\n", "FILE correction/1-overlapper/results/000009.ovb\n", "FILE correction/1-overlapper/results/000010.ovb\n", "FILE correction/1-overlapper/results/000011.ovb\n", "FILE correction/1-overlapper/results/000012.ovb\n", "FILE correction/1-overlapper/results/000013.ovb\n", "FILE correction/1-overlapper/results/000014.ovb\n", "FILE correction/1-overlapper/results/000015.ovb\n", "FILE correction/1-overlapper/results/000016.ovb\n", "FILE correction/1-overlapper/results/000017.ovb\n", "FILE correction/1-overlapper/results/000018.ovb\n", "FILE correction/1-overlapper/results/000019.ovb\n", "FILE correction/1-overlapper/results/000020.ovb\n", "FILE correction/1-overlapper/results/000021.ovb\n", "FILE correction/1-overlapper/results/000022.ovb\n", "FILE correction/1-overlapper/results/000023.ovb\n", "FILE correction/1-overlapper/results/000024.ovb\n", "FILE correction/1-overlapper/results/000025.ovb\n", "FILE correction/1-overlapper/results/000026.ovb\n", "FILE correction/1-overlapper/results/000027.ovb\n", "FILE correction/1-overlapper/results/000028.ovb\n", "FILE correction/1-overlapper/results/000029.ovb\n", "FILE correction/1-overlapper/results/000030.ovb\n", "FILE correction/1-overlapper/results/000031.ovb\n", "FILE correction/1-overlapper/results/000032.ovb\n", "FILE correction/1-overlapper/results/000033.ovb\n", "FILE correction/1-overlapper/results/000034.ovb\n", "FILE correction/1-overlapper/results/000035.ovb\n", "FILE correction/1-overlapper/results/000036.ovb\n", "FILE correction/1-overlapper/results/000037.ovb\n", "FILE correction/1-overlapper/results/000038.ovb\n", "FILE correction/1-overlapper/results/000039.ovb\n", "FILE correction/1-overlapper/results/000040.ovb\n", "FILE correction/1-overlapper/results/000041.ovb\n", "FILE correction/1-overlapper/results/000042.ovb\n", "FILE correction/1-overlapper/results/000043.ovb\n", "FILE correction/1-overlapper/results/000044.ovb\n", "FILE correction/1-overlapper/results/000045.ovb\n", "FILE correction/1-overlapper/results/000046.ovb\n", "FILE correction/1-overlapper/results/000047.ovb\n", "FILE correction/1-overlapper/results/000048.ovb\n", "FILE correction/1-overlapper/results/000049.ovb\n", "FILE correction/1-overlapper/results/000050.ovb\n", "FILE correction/1-overlapper/results/000051.ovb\n", "FILE correction/1-overlapper/results/000052.ovb\n", "FILE correction/1-overlapper/results/000053.ovb\n", "FILE correction/1-overlapper/results/000054.ovb\n", "FILE correction/1-overlapper/results/000055.ovb\n", "FILE correction/1-overlapper/results/000056.ovb\n", "FILE correction/1-overlapper/results/000057.ovb\n", "FILE correction/1-overlapper/results/000058.ovb\n", "FILE correction/1-overlapper/results/000059.ovb\n", "FILE correction/1-overlapper/results/000060.ovb\n", "FILE correction/1-overlapper/results/000061.ovb\n", "FILE correction/1-overlapper/results/000062.ovb\n", "FILE correction/1-overlapper/results/000063.ovb\n", "FILE correction/1-overlapper/results/000064.ovb\n", "FILE correction/1-overlapper/results/000065.ovb\n", "FILE correction/1-overlapper/results/000066.ovb\n", "FILE correction/1-overlapper/results/000067.ovb\n", "FILE correction/1-overlapper/results/000068.ovb\n", "FILE correction/1-overlapper/results/000069.ovb\n", "FILE correction/1-overlapper/results/000070.ovb\n", "FILE correction/1-overlapper/results/000071.ovb\n", "FILE correction/1-overlapper/results/000072.ovb\n", "FILE correction/1-overlapper/results/000073.ovb\n", "FILE correction/1-overlapper/results/000074.ovb\n", "FILE correction/1-overlapper/results/000075.ovb\n", "FILE correction/1-overlapper/results/000076.ovb\n", "FILE correction/1-overlapper/results/000077.ovb\n", "FILE correction/1-overlapper/results/000078.ovb\n", "FILE correction/1-overlapper/results/000079.ovb\n", "FILE correction/1-overlapper/results/000080.ovb\n", "FILE correction/1-overlapper/results/000081.ovb\n", "FILE correction/1-overlapper/results/000082.ovb\n", "FILE correction/1-overlapper/results/000083.ovb\n", "FILE correction/1-overlapper/results/000084.ovb\n", "FILE correction/1-overlapper/results/000085.ovb\n", "FILE correction/1-overlapper/results/000086.ovb\n", "FILE correction/1-overlapper/results/000087.ovb\n", "FILE correction/1-overlapper/results/000088.ovb\n", "FILE correction/1-overlapper/results/000089.ovb\n", "FILE correction/1-overlapper/results/000090.ovb\n", "FILE correction/1-overlapper/results/000091.ovb\n", "FILE correction/1-overlapper/results/000001.counts\n", "FILE correction/1-overlapper/results/000002.counts\n", "FILE correction/1-overlapper/results/000003.counts\n", "FILE correction/1-overlapper/results/000004.counts\n", "FILE correction/1-overlapper/results/000005.counts\n", "FILE correction/1-overlapper/results/000006.counts\n", "FILE correction/1-overlapper/results/000007.counts\n", "FILE correction/1-overlapper/results/000008.counts\n", "FILE correction/1-overlapper/results/000009.counts\n", "FILE correction/1-overlapper/results/000010.counts\n", "FILE correction/1-overlapper/results/000011.counts\n", "FILE correction/1-overlapper/results/000012.counts\n", "FILE correction/1-overlapper/results/000013.counts\n", "FILE correction/1-overlapper/results/000014.counts\n", "FILE correction/1-overlapper/results/000015.counts\n", "FILE correction/1-overlapper/results/000016.counts\n", "FILE correction/1-overlapper/results/000017.counts\n", "FILE correction/1-overlapper/results/000018.counts\n", "FILE correction/1-overlapper/results/000019.counts\n", "FILE correction/1-overlapper/results/000020.counts\n", "FILE correction/1-overlapper/results/000021.counts\n", "FILE correction/1-overlapper/results/000022.counts\n", "FILE correction/1-overlapper/results/000023.counts\n", "FILE correction/1-overlapper/results/000024.counts\n", "FILE correction/1-overlapper/results/000025.counts\n", "FILE correction/1-overlapper/results/000026.counts\n", "FILE correction/1-overlapper/results/000027.counts\n", "FILE correction/1-overlapper/results/000028.counts\n", "FILE correction/1-overlapper/results/000029.counts\n", "FILE correction/1-overlapper/results/000030.counts\n", "FILE correction/1-overlapper/results/000031.counts\n", "FILE correction/1-overlapper/results/000032.counts\n", "FILE correction/1-overlapper/results/000033.counts\n", "FILE correction/1-overlapper/results/000034.counts\n", "FILE correction/1-overlapper/results/000035.counts\n", "FILE correction/1-overlapper/results/000036.counts\n", "FILE correction/1-overlapper/results/000037.counts\n", "FILE correction/1-overlapper/results/000038.counts\n", "FILE correction/1-overlapper/results/000039.counts\n", "FILE correction/1-overlapper/results/000040.counts\n", "FILE correction/1-overlapper/results/000041.counts\n", "FILE correction/1-overlapper/results/000042.counts\n", "FILE correction/1-overlapper/results/000043.counts\n", "FILE correction/1-overlapper/results/000044.counts\n", "FILE correction/1-overlapper/results/000045.counts\n", "FILE correction/1-overlapper/results/000046.counts\n", "FILE correction/1-overlapper/results/000047.counts\n", "FILE correction/1-overlapper/results/000048.counts\n", "FILE correction/1-overlapper/results/000049.counts\n", "FILE correction/1-overlapper/results/000050.counts\n", "FILE correction/1-overlapper/results/000051.counts\n", "FILE correction/1-overlapper/results/000052.counts\n", "FILE correction/1-overlapper/results/000053.counts\n", "FILE correction/1-overlapper/results/000054.counts\n", "FILE correction/1-overlapper/results/000055.counts\n", "FILE correction/1-overlapper/results/000056.counts\n", "FILE correction/1-overlapper/results/000057.counts\n", "FILE correction/1-overlapper/results/000058.counts\n", "FILE correction/1-overlapper/results/000059.counts\n", "FILE correction/1-overlapper/results/000060.counts\n", "FILE correction/1-overlapper/results/000061.counts\n", "FILE correction/1-overlapper/results/000062.counts\n", "FILE correction/1-overlapper/results/000063.counts\n", "FILE correction/1-overlapper/results/000064.counts\n", "FILE correction/1-overlapper/results/000065.counts\n", "FILE correction/1-overlapper/results/000066.counts\n", "FILE correction/1-overlapper/results/000067.counts\n", "FILE correction/1-overlapper/results/000068.counts\n", "FILE correction/1-overlapper/results/000069.counts\n", "FILE correction/1-overlapper/results/000070.counts\n", "FILE correction/1-overlapper/results/000071.counts\n", "FILE correction/1-overlapper/results/000072.counts\n", "FILE correction/1-overlapper/results/000073.counts\n", "FILE correction/1-overlapper/results/000074.counts\n", "FILE correction/1-overlapper/results/000075.counts\n", "FILE correction/1-overlapper/results/000076.counts\n", "FILE correction/1-overlapper/results/000077.counts\n", "FILE correction/1-overlapper/results/000078.counts\n", "FILE correction/1-overlapper/results/000079.counts\n", "FILE correction/1-overlapper/results/000080.counts\n", "FILE correction/1-overlapper/results/000081.counts\n", "FILE correction/1-overlapper/results/000082.counts\n", "FILE correction/1-overlapper/results/000083.counts\n", "FILE correction/1-overlapper/results/000084.counts\n", "FILE correction/1-overlapper/results/000085.counts\n", "FILE correction/1-overlapper/results/000086.counts\n", "FILE correction/1-overlapper/results/000087.counts\n", "FILE correction/1-overlapper/results/000088.counts\n", "FILE correction/1-overlapper/results/000089.counts\n", "FILE correction/1-overlapper/results/000090.counts\n", "FILE correction/1-overlapper/results/000091.counts\n", "DIRECTORY correction/1-overlapper/queries\n", "DIRECTORY correction/1-overlapper/queries/000004\n", "FILE correction/1-overlapper/queries/000004/000034.dat\n", "FILE correction/1-overlapper/queries/000004/000035.dat\n", "FILE correction/1-overlapper/queries/000004/000036.dat\n", "FILE correction/1-overlapper/queries/000004/000032.dat\n", "FILE correction/1-overlapper/queries/000004/000030.dat\n", "FILE correction/1-overlapper/queries/000004/000029.dat\n", "FILE correction/1-overlapper/queries/000004/000031.dat\n", "FILE correction/1-overlapper/queries/000004/000033.dat\n", "FILE correction/1-overlapper/queries/000004/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000059\n", "FILE correction/1-overlapper/queries/000059/000034.dat\n", "FILE correction/1-overlapper/queries/000059/000035.dat\n", "FILE correction/1-overlapper/queries/000059/000028.dat\n", "FILE correction/1-overlapper/queries/000059/000032.dat\n", "FILE correction/1-overlapper/queries/000059/000030.dat\n", "FILE correction/1-overlapper/queries/000059/000029.dat\n", "FILE correction/1-overlapper/queries/000059/000031.dat\n", "FILE correction/1-overlapper/queries/000059/000033.dat\n", "FILE correction/1-overlapper/queries/000059/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000022\n", "FILE correction/1-overlapper/queries/000022/000020.dat\n", "FILE correction/1-overlapper/queries/000022/000018.dat\n", "FILE correction/1-overlapper/queries/000022/000024.dat\n", "FILE correction/1-overlapper/queries/000022/000023.dat\n", "FILE correction/1-overlapper/queries/000022/000017.dat\n", "FILE correction/1-overlapper/queries/000022/000016.dat\n", "FILE correction/1-overlapper/queries/000022/000021.dat\n", "FILE correction/1-overlapper/queries/000022/000022.dat\n", "FILE correction/1-overlapper/queries/000022/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000015\n", "FILE correction/1-overlapper/queries/000015/000028.dat\n", "FILE correction/1-overlapper/queries/000015/000024.dat\n", "FILE correction/1-overlapper/queries/000015/000023.dat\n", "FILE correction/1-overlapper/queries/000015/000030.dat\n", "FILE correction/1-overlapper/queries/000015/000026.dat\n", "FILE correction/1-overlapper/queries/000015/000029.dat\n", "FILE correction/1-overlapper/queries/000015/000025.dat\n", "FILE correction/1-overlapper/queries/000015/000031.dat\n", "FILE correction/1-overlapper/queries/000015/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000090\n", "FILE correction/1-overlapper/queries/000090/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000013\n", "FILE correction/1-overlapper/queries/000013/000006.dat\n", "FILE correction/1-overlapper/queries/000013/000013.dat\n", "FILE correction/1-overlapper/queries/000013/000010.dat\n", "FILE correction/1-overlapper/queries/000013/000012.dat\n", "FILE correction/1-overlapper/queries/000013/000009.dat\n", "FILE correction/1-overlapper/queries/000013/000008.dat\n", "FILE correction/1-overlapper/queries/000013/000005.dat\n", "FILE correction/1-overlapper/queries/000013/000007.dat\n", "FILE correction/1-overlapper/queries/000013/000011.dat\n", "DIRECTORY correction/1-overlapper/queries/000080\n", "FILE correction/1-overlapper/queries/000080/000034.dat\n", "FILE correction/1-overlapper/queries/000080/000035.dat\n", "FILE correction/1-overlapper/queries/000080/000028.dat\n", "FILE correction/1-overlapper/queries/000080/000036.dat\n", "FILE correction/1-overlapper/queries/000080/000032.dat\n", "FILE correction/1-overlapper/queries/000080/000030.dat\n", "FILE correction/1-overlapper/queries/000080/000029.dat\n", "FILE correction/1-overlapper/queries/000080/000031.dat\n", "FILE correction/1-overlapper/queries/000080/000033.dat\n", "DIRECTORY correction/1-overlapper/queries/000058\n", "FILE correction/1-overlapper/queries/000058/000020.dat\n", "FILE correction/1-overlapper/queries/000058/000018.dat\n", "FILE correction/1-overlapper/queries/000058/000024.dat\n", "FILE correction/1-overlapper/queries/000058/000023.dat\n", "FILE correction/1-overlapper/queries/000058/000026.dat\n", "FILE correction/1-overlapper/queries/000058/000025.dat\n", "FILE correction/1-overlapper/queries/000058/000021.dat\n", "FILE correction/1-overlapper/queries/000058/000022.dat\n", "FILE correction/1-overlapper/queries/000058/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000057\n", "FILE correction/1-overlapper/queries/000057/000035.dat\n", "FILE correction/1-overlapper/queries/000057/000036.dat\n", "FILE correction/1-overlapper/queries/000057/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000027\n", "FILE correction/1-overlapper/queries/000027/000034.dat\n", "FILE correction/1-overlapper/queries/000027/000028.dat\n", "FILE correction/1-overlapper/queries/000027/000032.dat\n", "FILE correction/1-overlapper/queries/000027/000030.dat\n", "FILE correction/1-overlapper/queries/000027/000026.dat\n", "FILE correction/1-overlapper/queries/000027/000029.dat\n", "FILE correction/1-overlapper/queries/000027/000031.dat\n", "FILE correction/1-overlapper/queries/000027/000033.dat\n", "FILE correction/1-overlapper/queries/000027/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000084\n", "FILE correction/1-overlapper/queries/000084/000034.dat\n", "FILE correction/1-overlapper/queries/000084/000035.dat\n", "FILE correction/1-overlapper/queries/000084/000036.dat\n", "FILE correction/1-overlapper/queries/000084/000032.dat\n", "FILE correction/1-overlapper/queries/000084/000031.dat\n", "FILE correction/1-overlapper/queries/000084/000033.dat\n", "FILE correction/1-overlapper/queries/000084/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000070\n", "FILE correction/1-overlapper/queries/000070/000028.dat\n", "FILE correction/1-overlapper/queries/000070/000024.dat\n", "FILE correction/1-overlapper/queries/000070/000023.dat\n", "FILE correction/1-overlapper/queries/000070/000030.dat\n", "FILE correction/1-overlapper/queries/000070/000026.dat\n", "FILE correction/1-overlapper/queries/000070/000029.dat\n", "FILE correction/1-overlapper/queries/000070/000025.dat\n", "FILE correction/1-overlapper/queries/000070/000031.dat\n", "FILE correction/1-overlapper/queries/000070/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000068\n", "FILE correction/1-overlapper/queries/000068/000028.dat\n", "FILE correction/1-overlapper/queries/000068/000024.dat\n", "FILE correction/1-overlapper/queries/000068/000023.dat\n", "FILE correction/1-overlapper/queries/000068/000030.dat\n", "FILE correction/1-overlapper/queries/000068/000026.dat\n", "FILE correction/1-overlapper/queries/000068/000029.dat\n", "FILE correction/1-overlapper/queries/000068/000025.dat\n", "FILE correction/1-overlapper/queries/000068/000022.dat\n", "FILE correction/1-overlapper/queries/000068/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000071\n", "FILE correction/1-overlapper/queries/000071/000034.dat\n", "FILE correction/1-overlapper/queries/000071/000035.dat\n", "FILE correction/1-overlapper/queries/000071/000036.dat\n", "FILE correction/1-overlapper/queries/000071/000032.dat\n", "FILE correction/1-overlapper/queries/000071/000033.dat\n", "FILE correction/1-overlapper/queries/000071/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000024\n", "FILE correction/1-overlapper/queries/000024/000034.dat\n", "FILE correction/1-overlapper/queries/000024/000035.dat\n", "FILE correction/1-overlapper/queries/000024/000036.dat\n", "FILE correction/1-overlapper/queries/000024/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000033\n", "FILE correction/1-overlapper/queries/000033/000014.dat\n", "FILE correction/1-overlapper/queries/000033/000013.dat\n", "FILE correction/1-overlapper/queries/000033/000018.dat\n", "FILE correction/1-overlapper/queries/000033/000010.dat\n", "FILE correction/1-overlapper/queries/000033/000017.dat\n", "FILE correction/1-overlapper/queries/000033/000012.dat\n", "FILE correction/1-overlapper/queries/000033/000015.dat\n", "FILE correction/1-overlapper/queries/000033/000016.dat\n", "FILE correction/1-overlapper/queries/000033/000011.dat\n", "DIRECTORY correction/1-overlapper/queries/000019\n", "FILE correction/1-overlapper/queries/000019/000028.dat\n", "FILE correction/1-overlapper/queries/000019/000024.dat\n", "FILE correction/1-overlapper/queries/000019/000032.dat\n", "FILE correction/1-overlapper/queries/000019/000030.dat\n", "FILE correction/1-overlapper/queries/000019/000026.dat\n", "FILE correction/1-overlapper/queries/000019/000029.dat\n", "FILE correction/1-overlapper/queries/000019/000025.dat\n", "FILE correction/1-overlapper/queries/000019/000031.dat\n", "FILE correction/1-overlapper/queries/000019/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000040\n", "FILE correction/1-overlapper/queries/000040/000020.dat\n", "FILE correction/1-overlapper/queries/000040/000014.dat\n", "FILE correction/1-overlapper/queries/000040/000013.dat\n", "FILE correction/1-overlapper/queries/000040/000018.dat\n", "FILE correction/1-overlapper/queries/000040/000017.dat\n", "FILE correction/1-overlapper/queries/000040/000012.dat\n", "FILE correction/1-overlapper/queries/000040/000015.dat\n", "FILE correction/1-overlapper/queries/000040/000016.dat\n", "FILE correction/1-overlapper/queries/000040/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000028\n", "FILE correction/1-overlapper/queries/000028/000035.dat\n", "FILE correction/1-overlapper/queries/000028/000036.dat\n", "FILE correction/1-overlapper/queries/000028/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000075\n", "FILE correction/1-overlapper/queries/000075/000034.dat\n", "FILE correction/1-overlapper/queries/000075/000035.dat\n", "FILE correction/1-overlapper/queries/000075/000036.dat\n", "FILE correction/1-overlapper/queries/000075/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000060\n", "FILE correction/1-overlapper/queries/000060/000036.dat\n", "FILE correction/1-overlapper/queries/000060/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000047\n", "FILE correction/1-overlapper/queries/000047/000028.dat\n", "FILE correction/1-overlapper/queries/000047/000024.dat\n", "FILE correction/1-overlapper/queries/000047/000023.dat\n", "FILE correction/1-overlapper/queries/000047/000030.dat\n", "FILE correction/1-overlapper/queries/000047/000026.dat\n", "FILE correction/1-overlapper/queries/000047/000029.dat\n", "FILE correction/1-overlapper/queries/000047/000025.dat\n", "FILE correction/1-overlapper/queries/000047/000031.dat\n", "FILE correction/1-overlapper/queries/000047/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000056\n", "FILE correction/1-overlapper/queries/000056/000034.dat\n", "FILE correction/1-overlapper/queries/000056/000028.dat\n", "FILE correction/1-overlapper/queries/000056/000032.dat\n", "FILE correction/1-overlapper/queries/000056/000030.dat\n", "FILE correction/1-overlapper/queries/000056/000026.dat\n", "FILE correction/1-overlapper/queries/000056/000029.dat\n", "FILE correction/1-overlapper/queries/000056/000031.dat\n", "FILE correction/1-overlapper/queries/000056/000033.dat\n", "FILE correction/1-overlapper/queries/000056/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000064\n", "FILE correction/1-overlapper/queries/000064/000020.dat\n", "FILE correction/1-overlapper/queries/000064/000028.dat\n", "FILE correction/1-overlapper/queries/000064/000024.dat\n", "FILE correction/1-overlapper/queries/000064/000023.dat\n", "FILE correction/1-overlapper/queries/000064/000026.dat\n", "FILE correction/1-overlapper/queries/000064/000025.dat\n", "FILE correction/1-overlapper/queries/000064/000021.dat\n", "FILE correction/1-overlapper/queries/000064/000022.dat\n", "FILE correction/1-overlapper/queries/000064/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000009\n", "FILE correction/1-overlapper/queries/000009/000006.dat\n", "FILE correction/1-overlapper/queries/000009/000010.dat\n", "FILE correction/1-overlapper/queries/000009/000012.dat\n", "FILE correction/1-overlapper/queries/000009/000004.dat\n", "FILE correction/1-overlapper/queries/000009/000009.dat\n", "FILE correction/1-overlapper/queries/000009/000008.dat\n", "FILE correction/1-overlapper/queries/000009/000005.dat\n", "FILE correction/1-overlapper/queries/000009/000007.dat\n", "FILE correction/1-overlapper/queries/000009/000011.dat\n", "DIRECTORY correction/1-overlapper/queries/000003\n", "FILE correction/1-overlapper/queries/000003/000020.dat\n", "FILE correction/1-overlapper/queries/000003/000028.dat\n", "FILE correction/1-overlapper/queries/000003/000024.dat\n", "FILE correction/1-overlapper/queries/000003/000023.dat\n", "FILE correction/1-overlapper/queries/000003/000026.dat\n", "FILE correction/1-overlapper/queries/000003/000025.dat\n", "FILE correction/1-overlapper/queries/000003/000021.dat\n", "FILE correction/1-overlapper/queries/000003/000022.dat\n", "FILE correction/1-overlapper/queries/000003/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000087\n", "FILE correction/1-overlapper/queries/000087/000034.dat\n", "FILE correction/1-overlapper/queries/000087/000035.dat\n", "FILE correction/1-overlapper/queries/000087/000036.dat\n", "FILE correction/1-overlapper/queries/000087/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000016\n", "FILE correction/1-overlapper/queries/000016/000034.dat\n", "FILE correction/1-overlapper/queries/000016/000035.dat\n", "FILE correction/1-overlapper/queries/000016/000036.dat\n", "FILE correction/1-overlapper/queries/000016/000032.dat\n", "FILE correction/1-overlapper/queries/000016/000033.dat\n", "FILE correction/1-overlapper/queries/000016/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000036\n", "FILE correction/1-overlapper/queries/000036/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000010\n", "FILE correction/1-overlapper/queries/000010/000020.dat\n", "FILE correction/1-overlapper/queries/000010/000014.dat\n", "FILE correction/1-overlapper/queries/000010/000013.dat\n", "FILE correction/1-overlapper/queries/000010/000018.dat\n", "FILE correction/1-overlapper/queries/000010/000017.dat\n", "FILE correction/1-overlapper/queries/000010/000015.dat\n", "FILE correction/1-overlapper/queries/000010/000016.dat\n", "FILE correction/1-overlapper/queries/000010/000021.dat\n", "FILE correction/1-overlapper/queries/000010/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000020\n", "FILE correction/1-overlapper/queries/000020/000034.dat\n", "FILE correction/1-overlapper/queries/000020/000035.dat\n", "FILE correction/1-overlapper/queries/000020/000036.dat\n", "FILE correction/1-overlapper/queries/000020/000033.dat\n", "FILE correction/1-overlapper/queries/000020/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000086\n", "FILE correction/1-overlapper/queries/000086/000034.dat\n", "FILE correction/1-overlapper/queries/000086/000035.dat\n", "FILE correction/1-overlapper/queries/000086/000036.dat\n", "FILE correction/1-overlapper/queries/000086/000033.dat\n", "FILE correction/1-overlapper/queries/000086/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000025\n", "FILE correction/1-overlapper/queries/000025/000014.dat\n", "FILE correction/1-overlapper/queries/000025/000013.dat\n", "FILE correction/1-overlapper/queries/000025/000010.dat\n", "FILE correction/1-overlapper/queries/000025/000012.dat\n", "FILE correction/1-overlapper/queries/000025/000015.dat\n", "FILE correction/1-overlapper/queries/000025/000016.dat\n", "FILE correction/1-overlapper/queries/000025/000009.dat\n", "FILE correction/1-overlapper/queries/000025/000008.dat\n", "FILE correction/1-overlapper/queries/000025/000011.dat\n", "DIRECTORY correction/1-overlapper/queries/000049\n", "FILE correction/1-overlapper/queries/000049/000020.dat\n", "FILE correction/1-overlapper/queries/000049/000018.dat\n", "FILE correction/1-overlapper/queries/000049/000023.dat\n", "FILE correction/1-overlapper/queries/000049/000017.dat\n", "FILE correction/1-overlapper/queries/000049/000015.dat\n", "FILE correction/1-overlapper/queries/000049/000016.dat\n", "FILE correction/1-overlapper/queries/000049/000021.dat\n", "FILE correction/1-overlapper/queries/000049/000022.dat\n", "FILE correction/1-overlapper/queries/000049/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000046\n", "FILE correction/1-overlapper/queries/000046/000020.dat\n", "FILE correction/1-overlapper/queries/000046/000014.dat\n", "FILE correction/1-overlapper/queries/000046/000018.dat\n", "FILE correction/1-overlapper/queries/000046/000017.dat\n", "FILE correction/1-overlapper/queries/000046/000015.dat\n", "FILE correction/1-overlapper/queries/000046/000016.dat\n", "FILE correction/1-overlapper/queries/000046/000021.dat\n", "FILE correction/1-overlapper/queries/000046/000022.dat\n", "FILE correction/1-overlapper/queries/000046/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000076\n", "FILE correction/1-overlapper/queries/000076/000034.dat\n", "FILE correction/1-overlapper/queries/000076/000028.dat\n", "FILE correction/1-overlapper/queries/000076/000032.dat\n", "FILE correction/1-overlapper/queries/000076/000030.dat\n", "FILE correction/1-overlapper/queries/000076/000026.dat\n", "FILE correction/1-overlapper/queries/000076/000029.dat\n", "FILE correction/1-overlapper/queries/000076/000031.dat\n", "FILE correction/1-overlapper/queries/000076/000033.dat\n", "FILE correction/1-overlapper/queries/000076/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000038\n", "FILE correction/1-overlapper/queries/000038/000020.dat\n", "FILE correction/1-overlapper/queries/000038/000028.dat\n", "FILE correction/1-overlapper/queries/000038/000024.dat\n", "FILE correction/1-overlapper/queries/000038/000023.dat\n", "FILE correction/1-overlapper/queries/000038/000026.dat\n", "FILE correction/1-overlapper/queries/000038/000025.dat\n", "FILE correction/1-overlapper/queries/000038/000021.dat\n", "FILE correction/1-overlapper/queries/000038/000022.dat\n", "FILE correction/1-overlapper/queries/000038/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000031\n", "FILE correction/1-overlapper/queries/000031/000034.dat\n", "FILE correction/1-overlapper/queries/000031/000035.dat\n", "FILE correction/1-overlapper/queries/000031/000028.dat\n", "FILE correction/1-overlapper/queries/000031/000032.dat\n", "FILE correction/1-overlapper/queries/000031/000030.dat\n", "FILE correction/1-overlapper/queries/000031/000029.dat\n", "FILE correction/1-overlapper/queries/000031/000031.dat\n", "FILE correction/1-overlapper/queries/000031/000033.dat\n", "FILE correction/1-overlapper/queries/000031/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000066\n", "FILE correction/1-overlapper/queries/000066/000028.dat\n", "FILE correction/1-overlapper/queries/000066/000024.dat\n", "FILE correction/1-overlapper/queries/000066/000023.dat\n", "FILE correction/1-overlapper/queries/000066/000026.dat\n", "FILE correction/1-overlapper/queries/000066/000029.dat\n", "FILE correction/1-overlapper/queries/000066/000025.dat\n", "FILE correction/1-overlapper/queries/000066/000021.dat\n", "FILE correction/1-overlapper/queries/000066/000022.dat\n", "FILE correction/1-overlapper/queries/000066/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000008\n", "FILE correction/1-overlapper/queries/000008/000034.dat\n", "FILE correction/1-overlapper/queries/000008/000035.dat\n", "FILE correction/1-overlapper/queries/000008/000036.dat\n", "FILE correction/1-overlapper/queries/000008/000032.dat\n", "FILE correction/1-overlapper/queries/000008/000030.dat\n", "FILE correction/1-overlapper/queries/000008/000031.dat\n", "FILE correction/1-overlapper/queries/000008/000033.dat\n", "FILE correction/1-overlapper/queries/000008/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000083\n", "FILE correction/1-overlapper/queries/000083/000034.dat\n", "FILE correction/1-overlapper/queries/000083/000035.dat\n", "FILE correction/1-overlapper/queries/000083/000036.dat\n", "FILE correction/1-overlapper/queries/000083/000032.dat\n", "FILE correction/1-overlapper/queries/000083/000030.dat\n", "FILE correction/1-overlapper/queries/000083/000031.dat\n", "FILE correction/1-overlapper/queries/000083/000033.dat\n", "FILE correction/1-overlapper/queries/000083/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000053\n", "FILE correction/1-overlapper/queries/000053/000028.dat\n", "FILE correction/1-overlapper/queries/000053/000032.dat\n", "FILE correction/1-overlapper/queries/000053/000030.dat\n", "FILE correction/1-overlapper/queries/000053/000026.dat\n", "FILE correction/1-overlapper/queries/000053/000029.dat\n", "FILE correction/1-overlapper/queries/000053/000025.dat\n", "FILE correction/1-overlapper/queries/000053/000031.dat\n", "FILE correction/1-overlapper/queries/000053/000033.dat\n", "FILE correction/1-overlapper/queries/000053/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000030\n", "FILE correction/1-overlapper/queries/000030/000020.dat\n", "FILE correction/1-overlapper/queries/000030/000018.dat\n", "FILE correction/1-overlapper/queries/000030/000024.dat\n", "FILE correction/1-overlapper/queries/000030/000023.dat\n", "FILE correction/1-overlapper/queries/000030/000026.dat\n", "FILE correction/1-overlapper/queries/000030/000025.dat\n", "FILE correction/1-overlapper/queries/000030/000021.dat\n", "FILE correction/1-overlapper/queries/000030/000022.dat\n", "FILE correction/1-overlapper/queries/000030/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000085\n", "FILE correction/1-overlapper/queries/000085/000034.dat\n", "FILE correction/1-overlapper/queries/000085/000035.dat\n", "FILE correction/1-overlapper/queries/000085/000036.dat\n", "FILE correction/1-overlapper/queries/000085/000032.dat\n", "FILE correction/1-overlapper/queries/000085/000033.dat\n", "FILE correction/1-overlapper/queries/000085/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000055\n", "FILE correction/1-overlapper/queries/000055/000020.dat\n", "FILE correction/1-overlapper/queries/000055/000018.dat\n", "FILE correction/1-overlapper/queries/000055/000024.dat\n", "FILE correction/1-overlapper/queries/000055/000023.dat\n", "FILE correction/1-overlapper/queries/000055/000017.dat\n", "FILE correction/1-overlapper/queries/000055/000025.dat\n", "FILE correction/1-overlapper/queries/000055/000021.dat\n", "FILE correction/1-overlapper/queries/000055/000022.dat\n", "FILE correction/1-overlapper/queries/000055/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000001\n", "FILE correction/1-overlapper/queries/000001/000002.dat\n", "FILE correction/1-overlapper/queries/000001/000006.dat\n", "FILE correction/1-overlapper/queries/000001/000010.dat\n", "FILE correction/1-overlapper/queries/000001/000003.dat\n", "FILE correction/1-overlapper/queries/000001/000004.dat\n", "FILE correction/1-overlapper/queries/000001/000009.dat\n", "FILE correction/1-overlapper/queries/000001/000008.dat\n", "FILE correction/1-overlapper/queries/000001/000005.dat\n", "FILE correction/1-overlapper/queries/000001/000007.dat\n", "DIRECTORY correction/1-overlapper/queries/000078\n", "FILE correction/1-overlapper/queries/000078/000034.dat\n", "FILE correction/1-overlapper/queries/000078/000035.dat\n", "FILE correction/1-overlapper/queries/000078/000028.dat\n", "FILE correction/1-overlapper/queries/000078/000032.dat\n", "FILE correction/1-overlapper/queries/000078/000030.dat\n", "FILE correction/1-overlapper/queries/000078/000029.dat\n", "FILE correction/1-overlapper/queries/000078/000031.dat\n", "FILE correction/1-overlapper/queries/000078/000033.dat\n", "FILE correction/1-overlapper/queries/000078/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000091\n", "DIRECTORY correction/1-overlapper/queries/000005\n", "FILE correction/1-overlapper/queries/000005/000006.dat\n", "FILE correction/1-overlapper/queries/000005/000010.dat\n", "FILE correction/1-overlapper/queries/000005/000003.dat\n", "FILE correction/1-overlapper/queries/000005/000004.dat\n", "FILE correction/1-overlapper/queries/000005/000009.dat\n", "FILE correction/1-overlapper/queries/000005/000008.dat\n", "FILE correction/1-overlapper/queries/000005/000005.dat\n", "FILE correction/1-overlapper/queries/000005/000007.dat\n", "FILE correction/1-overlapper/queries/000005/000011.dat\n", "DIRECTORY correction/1-overlapper/queries/000035\n", "FILE correction/1-overlapper/queries/000035/000034.dat\n", "FILE correction/1-overlapper/queries/000035/000035.dat\n", "FILE correction/1-overlapper/queries/000035/000028.dat\n", "FILE correction/1-overlapper/queries/000035/000036.dat\n", "FILE correction/1-overlapper/queries/000035/000032.dat\n", "FILE correction/1-overlapper/queries/000035/000030.dat\n", "FILE correction/1-overlapper/queries/000035/000029.dat\n", "FILE correction/1-overlapper/queries/000035/000031.dat\n", "FILE correction/1-overlapper/queries/000035/000033.dat\n", "DIRECTORY correction/1-overlapper/queries/000034\n", "FILE correction/1-overlapper/queries/000034/000020.dat\n", "FILE correction/1-overlapper/queries/000034/000024.dat\n", "FILE correction/1-overlapper/queries/000034/000023.dat\n", "FILE correction/1-overlapper/queries/000034/000026.dat\n", "FILE correction/1-overlapper/queries/000034/000025.dat\n", "FILE correction/1-overlapper/queries/000034/000021.dat\n", "FILE correction/1-overlapper/queries/000034/000022.dat\n", "FILE correction/1-overlapper/queries/000034/000019.dat\n", "FILE correction/1-overlapper/queries/000034/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000029\n", "FILE correction/1-overlapper/queries/000029/000014.dat\n", "FILE correction/1-overlapper/queries/000029/000013.dat\n", "FILE correction/1-overlapper/queries/000029/000010.dat\n", "FILE correction/1-overlapper/queries/000029/000017.dat\n", "FILE correction/1-overlapper/queries/000029/000012.dat\n", "FILE correction/1-overlapper/queries/000029/000015.dat\n", "FILE correction/1-overlapper/queries/000029/000016.dat\n", "FILE correction/1-overlapper/queries/000029/000009.dat\n", "FILE correction/1-overlapper/queries/000029/000011.dat\n", "DIRECTORY correction/1-overlapper/queries/000007\n", "FILE correction/1-overlapper/queries/000007/000028.dat\n", "FILE correction/1-overlapper/queries/000007/000024.dat\n", "FILE correction/1-overlapper/queries/000007/000023.dat\n", "FILE correction/1-overlapper/queries/000007/000026.dat\n", "FILE correction/1-overlapper/queries/000007/000029.dat\n", "FILE correction/1-overlapper/queries/000007/000025.dat\n", "FILE correction/1-overlapper/queries/000007/000021.dat\n", "FILE correction/1-overlapper/queries/000007/000022.dat\n", "FILE correction/1-overlapper/queries/000007/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000050\n", "FILE correction/1-overlapper/queries/000050/000028.dat\n", "FILE correction/1-overlapper/queries/000050/000024.dat\n", "FILE correction/1-overlapper/queries/000050/000032.dat\n", "FILE correction/1-overlapper/queries/000050/000030.dat\n", "FILE correction/1-overlapper/queries/000050/000026.dat\n", "FILE correction/1-overlapper/queries/000050/000029.dat\n", "FILE correction/1-overlapper/queries/000050/000025.dat\n", "FILE correction/1-overlapper/queries/000050/000031.dat\n", "FILE correction/1-overlapper/queries/000050/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000062\n", "FILE correction/1-overlapper/queries/000062/000034.dat\n", "FILE correction/1-overlapper/queries/000062/000035.dat\n", "FILE correction/1-overlapper/queries/000062/000028.dat\n", "FILE correction/1-overlapper/queries/000062/000036.dat\n", "FILE correction/1-overlapper/queries/000062/000032.dat\n", "FILE correction/1-overlapper/queries/000062/000030.dat\n", "FILE correction/1-overlapper/queries/000062/000029.dat\n", "FILE correction/1-overlapper/queries/000062/000031.dat\n", "FILE correction/1-overlapper/queries/000062/000033.dat\n", "DIRECTORY correction/1-overlapper/queries/000018\n", "FILE correction/1-overlapper/queries/000018/000020.dat\n", "FILE correction/1-overlapper/queries/000018/000018.dat\n", "FILE correction/1-overlapper/queries/000018/000023.dat\n", "FILE correction/1-overlapper/queries/000018/000017.dat\n", "FILE correction/1-overlapper/queries/000018/000015.dat\n", "FILE correction/1-overlapper/queries/000018/000016.dat\n", "FILE correction/1-overlapper/queries/000018/000021.dat\n", "FILE correction/1-overlapper/queries/000018/000022.dat\n", "FILE correction/1-overlapper/queries/000018/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000045\n", "FILE correction/1-overlapper/queries/000045/000034.dat\n", "FILE correction/1-overlapper/queries/000045/000035.dat\n", "FILE correction/1-overlapper/queries/000045/000036.dat\n", "FILE correction/1-overlapper/queries/000045/000032.dat\n", "FILE correction/1-overlapper/queries/000045/000031.dat\n", "FILE correction/1-overlapper/queries/000045/000033.dat\n", "FILE correction/1-overlapper/queries/000045/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000065\n", "FILE correction/1-overlapper/queries/000065/000034.dat\n", "FILE correction/1-overlapper/queries/000065/000035.dat\n", "FILE correction/1-overlapper/queries/000065/000036.dat\n", "FILE correction/1-overlapper/queries/000065/000032.dat\n", "FILE correction/1-overlapper/queries/000065/000030.dat\n", "FILE correction/1-overlapper/queries/000065/000029.dat\n", "FILE correction/1-overlapper/queries/000065/000031.dat\n", "FILE correction/1-overlapper/queries/000065/000033.dat\n", "FILE correction/1-overlapper/queries/000065/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000061\n", "FILE correction/1-overlapper/queries/000061/000020.dat\n", "FILE correction/1-overlapper/queries/000061/000024.dat\n", "FILE correction/1-overlapper/queries/000061/000023.dat\n", "FILE correction/1-overlapper/queries/000061/000026.dat\n", "FILE correction/1-overlapper/queries/000061/000025.dat\n", "FILE correction/1-overlapper/queries/000061/000021.dat\n", "FILE correction/1-overlapper/queries/000061/000022.dat\n", "FILE correction/1-overlapper/queries/000061/000019.dat\n", "FILE correction/1-overlapper/queries/000061/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000011\n", "FILE correction/1-overlapper/queries/000011/000028.dat\n", "FILE correction/1-overlapper/queries/000011/000024.dat\n", "FILE correction/1-overlapper/queries/000011/000023.dat\n", "FILE correction/1-overlapper/queries/000011/000030.dat\n", "FILE correction/1-overlapper/queries/000011/000026.dat\n", "FILE correction/1-overlapper/queries/000011/000029.dat\n", "FILE correction/1-overlapper/queries/000011/000025.dat\n", "FILE correction/1-overlapper/queries/000011/000022.dat\n", "FILE correction/1-overlapper/queries/000011/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000044\n", "FILE correction/1-overlapper/queries/000044/000028.dat\n", "FILE correction/1-overlapper/queries/000044/000024.dat\n", "FILE correction/1-overlapper/queries/000044/000023.dat\n", "FILE correction/1-overlapper/queries/000044/000030.dat\n", "FILE correction/1-overlapper/queries/000044/000026.dat\n", "FILE correction/1-overlapper/queries/000044/000029.dat\n", "FILE correction/1-overlapper/queries/000044/000025.dat\n", "FILE correction/1-overlapper/queries/000044/000022.dat\n", "FILE correction/1-overlapper/queries/000044/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000037\n", "FILE correction/1-overlapper/queries/000037/000014.dat\n", "FILE correction/1-overlapper/queries/000037/000013.dat\n", "FILE correction/1-overlapper/queries/000037/000018.dat\n", "FILE correction/1-overlapper/queries/000037/000017.dat\n", "FILE correction/1-overlapper/queries/000037/000012.dat\n", "FILE correction/1-overlapper/queries/000037/000015.dat\n", "FILE correction/1-overlapper/queries/000037/000016.dat\n", "FILE correction/1-overlapper/queries/000037/000019.dat\n", "FILE correction/1-overlapper/queries/000037/000011.dat\n", "DIRECTORY correction/1-overlapper/queries/000041\n", "FILE correction/1-overlapper/queries/000041/000028.dat\n", "FILE correction/1-overlapper/queries/000041/000024.dat\n", "FILE correction/1-overlapper/queries/000041/000023.dat\n", "FILE correction/1-overlapper/queries/000041/000026.dat\n", "FILE correction/1-overlapper/queries/000041/000029.dat\n", "FILE correction/1-overlapper/queries/000041/000025.dat\n", "FILE correction/1-overlapper/queries/000041/000021.dat\n", "FILE correction/1-overlapper/queries/000041/000022.dat\n", "FILE correction/1-overlapper/queries/000041/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000026\n", "FILE correction/1-overlapper/queries/000026/000020.dat\n", "FILE correction/1-overlapper/queries/000026/000018.dat\n", "FILE correction/1-overlapper/queries/000026/000024.dat\n", "FILE correction/1-overlapper/queries/000026/000023.dat\n", "FILE correction/1-overlapper/queries/000026/000017.dat\n", "FILE correction/1-overlapper/queries/000026/000025.dat\n", "FILE correction/1-overlapper/queries/000026/000021.dat\n", "FILE correction/1-overlapper/queries/000026/000022.dat\n", "FILE correction/1-overlapper/queries/000026/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000063\n", "FILE correction/1-overlapper/queries/000063/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000042\n", "FILE correction/1-overlapper/queries/000042/000034.dat\n", "FILE correction/1-overlapper/queries/000042/000035.dat\n", "FILE correction/1-overlapper/queries/000042/000036.dat\n", "FILE correction/1-overlapper/queries/000042/000032.dat\n", "FILE correction/1-overlapper/queries/000042/000030.dat\n", "FILE correction/1-overlapper/queries/000042/000031.dat\n", "FILE correction/1-overlapper/queries/000042/000033.dat\n", "FILE correction/1-overlapper/queries/000042/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000069\n", "FILE correction/1-overlapper/queries/000069/000034.dat\n", "FILE correction/1-overlapper/queries/000069/000035.dat\n", "FILE correction/1-overlapper/queries/000069/000036.dat\n", "FILE correction/1-overlapper/queries/000069/000032.dat\n", "FILE correction/1-overlapper/queries/000069/000031.dat\n", "FILE correction/1-overlapper/queries/000069/000033.dat\n", "FILE correction/1-overlapper/queries/000069/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000048\n", "FILE correction/1-overlapper/queries/000048/000034.dat\n", "FILE correction/1-overlapper/queries/000048/000035.dat\n", "FILE correction/1-overlapper/queries/000048/000036.dat\n", "FILE correction/1-overlapper/queries/000048/000032.dat\n", "FILE correction/1-overlapper/queries/000048/000033.dat\n", "FILE correction/1-overlapper/queries/000048/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000002\n", "FILE correction/1-overlapper/queries/000002/000014.dat\n", "FILE correction/1-overlapper/queries/000002/000013.dat\n", "FILE correction/1-overlapper/queries/000002/000018.dat\n", "FILE correction/1-overlapper/queries/000002/000017.dat\n", "FILE correction/1-overlapper/queries/000002/000012.dat\n", "FILE correction/1-overlapper/queries/000002/000015.dat\n", "FILE correction/1-overlapper/queries/000002/000016.dat\n", "FILE correction/1-overlapper/queries/000002/000019.dat\n", "FILE correction/1-overlapper/queries/000002/000011.dat\n", "DIRECTORY correction/1-overlapper/queries/000072\n", "FILE correction/1-overlapper/queries/000072/000028.dat\n", "FILE correction/1-overlapper/queries/000072/000024.dat\n", "FILE correction/1-overlapper/queries/000072/000032.dat\n", "FILE correction/1-overlapper/queries/000072/000030.dat\n", "FILE correction/1-overlapper/queries/000072/000026.dat\n", "FILE correction/1-overlapper/queries/000072/000029.dat\n", "FILE correction/1-overlapper/queries/000072/000025.dat\n", "FILE correction/1-overlapper/queries/000072/000031.dat\n", "FILE correction/1-overlapper/queries/000072/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000021\n", "FILE correction/1-overlapper/queries/000021/000014.dat\n", "FILE correction/1-overlapper/queries/000021/000013.dat\n", "FILE correction/1-overlapper/queries/000021/000010.dat\n", "FILE correction/1-overlapper/queries/000021/000012.dat\n", "FILE correction/1-overlapper/queries/000021/000015.dat\n", "FILE correction/1-overlapper/queries/000021/000009.dat\n", "FILE correction/1-overlapper/queries/000021/000008.dat\n", "FILE correction/1-overlapper/queries/000021/000007.dat\n", "FILE correction/1-overlapper/queries/000021/000011.dat\n", "DIRECTORY correction/1-overlapper/queries/000088\n", "FILE correction/1-overlapper/queries/000088/000035.dat\n", "FILE correction/1-overlapper/queries/000088/000036.dat\n", "FILE correction/1-overlapper/queries/000088/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000077\n", "FILE correction/1-overlapper/queries/000077/000035.dat\n", "FILE correction/1-overlapper/queries/000077/000036.dat\n", "FILE correction/1-overlapper/queries/000077/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000043\n", "FILE correction/1-overlapper/queries/000043/000020.dat\n", "FILE correction/1-overlapper/queries/000043/000014.dat\n", "FILE correction/1-overlapper/queries/000043/000013.dat\n", "FILE correction/1-overlapper/queries/000043/000018.dat\n", "FILE correction/1-overlapper/queries/000043/000017.dat\n", "FILE correction/1-overlapper/queries/000043/000015.dat\n", "FILE correction/1-overlapper/queries/000043/000016.dat\n", "FILE correction/1-overlapper/queries/000043/000021.dat\n", "FILE correction/1-overlapper/queries/000043/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000051\n", "FILE correction/1-overlapper/queries/000051/000034.dat\n", "FILE correction/1-overlapper/queries/000051/000035.dat\n", "FILE correction/1-overlapper/queries/000051/000036.dat\n", "FILE correction/1-overlapper/queries/000051/000033.dat\n", "FILE correction/1-overlapper/queries/000051/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000006\n", "FILE correction/1-overlapper/queries/000006/000020.dat\n", "FILE correction/1-overlapper/queries/000006/000014.dat\n", "FILE correction/1-overlapper/queries/000006/000013.dat\n", "FILE correction/1-overlapper/queries/000006/000018.dat\n", "FILE correction/1-overlapper/queries/000006/000017.dat\n", "FILE correction/1-overlapper/queries/000006/000012.dat\n", "FILE correction/1-overlapper/queries/000006/000015.dat\n", "FILE correction/1-overlapper/queries/000006/000016.dat\n", "FILE correction/1-overlapper/queries/000006/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000089\n", "FILE correction/1-overlapper/queries/000089/000036.dat\n", "FILE correction/1-overlapper/queries/000089/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000032\n", "FILE correction/1-overlapper/queries/000032/000036.dat\n", "FILE correction/1-overlapper/queries/000032/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000073\n", "FILE correction/1-overlapper/queries/000073/000034.dat\n", "FILE correction/1-overlapper/queries/000073/000035.dat\n", "FILE correction/1-overlapper/queries/000073/000036.dat\n", "FILE correction/1-overlapper/queries/000073/000033.dat\n", "FILE correction/1-overlapper/queries/000073/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000082\n", "FILE correction/1-overlapper/queries/000082/000034.dat\n", "FILE correction/1-overlapper/queries/000082/000035.dat\n", "FILE correction/1-overlapper/queries/000082/000036.dat\n", "FILE correction/1-overlapper/queries/000082/000032.dat\n", "FILE correction/1-overlapper/queries/000082/000030.dat\n", "FILE correction/1-overlapper/queries/000082/000029.dat\n", "FILE correction/1-overlapper/queries/000082/000031.dat\n", "FILE correction/1-overlapper/queries/000082/000033.dat\n", "FILE correction/1-overlapper/queries/000082/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000023\n", "FILE correction/1-overlapper/queries/000023/000028.dat\n", "FILE correction/1-overlapper/queries/000023/000032.dat\n", "FILE correction/1-overlapper/queries/000023/000030.dat\n", "FILE correction/1-overlapper/queries/000023/000026.dat\n", "FILE correction/1-overlapper/queries/000023/000029.dat\n", "FILE correction/1-overlapper/queries/000023/000025.dat\n", "FILE correction/1-overlapper/queries/000023/000031.dat\n", "FILE correction/1-overlapper/queries/000023/000033.dat\n", "FILE correction/1-overlapper/queries/000023/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000079\n", "FILE correction/1-overlapper/queries/000079/000036.dat\n", "FILE correction/1-overlapper/queries/000079/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000017\n", "FILE correction/1-overlapper/queries/000017/000006.dat\n", "FILE correction/1-overlapper/queries/000017/000014.dat\n", "FILE correction/1-overlapper/queries/000017/000013.dat\n", "FILE correction/1-overlapper/queries/000017/000010.dat\n", "FILE correction/1-overlapper/queries/000017/000012.dat\n", "FILE correction/1-overlapper/queries/000017/000009.dat\n", "FILE correction/1-overlapper/queries/000017/000008.dat\n", "FILE correction/1-overlapper/queries/000017/000007.dat\n", "FILE correction/1-overlapper/queries/000017/000011.dat\n", "DIRECTORY correction/1-overlapper/queries/000012\n", "FILE correction/1-overlapper/queries/000012/000034.dat\n", "FILE correction/1-overlapper/queries/000012/000035.dat\n", "FILE correction/1-overlapper/queries/000012/000036.dat\n", "FILE correction/1-overlapper/queries/000012/000032.dat\n", "FILE correction/1-overlapper/queries/000012/000031.dat\n", "FILE correction/1-overlapper/queries/000012/000033.dat\n", "FILE correction/1-overlapper/queries/000012/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000067\n", "FILE correction/1-overlapper/queries/000067/000034.dat\n", "FILE correction/1-overlapper/queries/000067/000035.dat\n", "FILE correction/1-overlapper/queries/000067/000036.dat\n", "FILE correction/1-overlapper/queries/000067/000032.dat\n", "FILE correction/1-overlapper/queries/000067/000030.dat\n", "FILE correction/1-overlapper/queries/000067/000031.dat\n", "FILE correction/1-overlapper/queries/000067/000033.dat\n", "FILE correction/1-overlapper/queries/000067/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000054\n", "FILE correction/1-overlapper/queries/000054/000034.dat\n", "FILE correction/1-overlapper/queries/000054/000035.dat\n", "FILE correction/1-overlapper/queries/000054/000036.dat\n", "FILE correction/1-overlapper/queries/000054/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000014\n", "FILE correction/1-overlapper/queries/000014/000020.dat\n", "FILE correction/1-overlapper/queries/000014/000014.dat\n", "FILE correction/1-overlapper/queries/000014/000018.dat\n", "FILE correction/1-overlapper/queries/000014/000017.dat\n", "FILE correction/1-overlapper/queries/000014/000015.dat\n", "FILE correction/1-overlapper/queries/000014/000016.dat\n", "FILE correction/1-overlapper/queries/000014/000021.dat\n", "FILE correction/1-overlapper/queries/000014/000022.dat\n", "FILE correction/1-overlapper/queries/000014/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000052\n", "FILE correction/1-overlapper/queries/000052/000020.dat\n", "FILE correction/1-overlapper/queries/000052/000018.dat\n", "FILE correction/1-overlapper/queries/000052/000024.dat\n", "FILE correction/1-overlapper/queries/000052/000023.dat\n", "FILE correction/1-overlapper/queries/000052/000017.dat\n", "FILE correction/1-overlapper/queries/000052/000016.dat\n", "FILE correction/1-overlapper/queries/000052/000021.dat\n", "FILE correction/1-overlapper/queries/000052/000022.dat\n", "FILE correction/1-overlapper/queries/000052/000019.dat\n", "DIRECTORY correction/1-overlapper/queries/000074\n", "FILE correction/1-overlapper/queries/000074/000028.dat\n", "FILE correction/1-overlapper/queries/000074/000032.dat\n", "FILE correction/1-overlapper/queries/000074/000030.dat\n", "FILE correction/1-overlapper/queries/000074/000026.dat\n", "FILE correction/1-overlapper/queries/000074/000029.dat\n", "FILE correction/1-overlapper/queries/000074/000025.dat\n", "FILE correction/1-overlapper/queries/000074/000031.dat\n", "FILE correction/1-overlapper/queries/000074/000033.dat\n", "FILE correction/1-overlapper/queries/000074/000027.dat\n", "DIRECTORY correction/1-overlapper/queries/000039\n", "FILE correction/1-overlapper/queries/000039/000034.dat\n", "FILE correction/1-overlapper/queries/000039/000035.dat\n", "FILE correction/1-overlapper/queries/000039/000036.dat\n", "FILE correction/1-overlapper/queries/000039/000032.dat\n", "FILE correction/1-overlapper/queries/000039/000030.dat\n", "FILE correction/1-overlapper/queries/000039/000029.dat\n", "FILE correction/1-overlapper/queries/000039/000031.dat\n", "FILE correction/1-overlapper/queries/000039/000033.dat\n", "FILE correction/1-overlapper/queries/000039/000037.dat\n", "DIRECTORY correction/1-overlapper/queries/000081\n", "FILE correction/1-overlapper/queries/000081/000037.dat\n", "FILE correction/1-overlapper/blocks/000001.dat\n", "FILE correction/1-overlapper/blocks/000002.dat\n", "FILE correction/1-overlapper/blocks/000003.dat\n", "FILE correction/1-overlapper/blocks/000004.dat\n", "FILE correction/1-overlapper/blocks/000005.dat\n", "FILE correction/1-overlapper/blocks/000006.dat\n", "FILE correction/1-overlapper/blocks/000007.dat\n", "FILE correction/1-overlapper/blocks/000008.dat\n", "FILE correction/1-overlapper/blocks/000009.dat\n", "FILE correction/1-overlapper/blocks/000010.dat\n", "FILE correction/1-overlapper/blocks/000011.dat\n", "FILE correction/1-overlapper/blocks/000012.dat\n", "FILE correction/1-overlapper/blocks/000013.dat\n", "FILE correction/1-overlapper/blocks/000014.dat\n", "FILE correction/1-overlapper/blocks/000015.dat\n", "FILE correction/1-overlapper/blocks/000016.dat\n", "FILE correction/1-overlapper/blocks/000017.dat\n", "FILE correction/1-overlapper/blocks/000018.dat\n", "FILE correction/1-overlapper/blocks/000019.dat\n", "FILE correction/1-overlapper/blocks/000020.dat\n", "FILE correction/1-overlapper/blocks/000021.dat\n", "FILE correction/1-overlapper/blocks/000022.dat\n", "FILE correction/1-overlapper/blocks/000023.dat\n", "FILE correction/1-overlapper/blocks/000024.dat\n", "FILE correction/1-overlapper/blocks/000025.dat\n", "FILE correction/1-overlapper/blocks/000026.dat\n", "FILE correction/1-overlapper/blocks/000027.dat\n", "FILE correction/1-overlapper/blocks/000028.dat\n", "FILE correction/1-overlapper/blocks/000029.dat\n", "FILE correction/1-overlapper/blocks/000030.dat\n", "FILE correction/1-overlapper/blocks/000031.dat\n", "FILE correction/1-overlapper/blocks/000032.dat\n", "FILE correction/1-overlapper/blocks/000033.dat\n", "FILE correction/1-overlapper/blocks/000034.dat\n", "FILE correction/1-overlapper/blocks/000035.dat\n", "FILE correction/1-overlapper/blocks/000036.dat\n", "FILE correction/1-overlapper/blocks/000037.dat\n", "REMOVE TREE correction/1-overlapper/queries/000052\n", "REMOVE TREE correction/1-overlapper/queries/000030\n", "REMOVE TREE correction/1-overlapper/queries/000041\n", "REMOVE TREE correction/1-overlapper/queries/000069\n", "REMOVE TREE correction/1-overlapper/queries/000048\n", "REMOVE TREE correction/1-overlapper/queries/000079\n", "REMOVE TREE correction/1-overlapper/queries/000013\n", "REMOVE TREE correction/1-overlapper/queries/000033\n", "REMOVE TREE correction/1-overlapper/queries/000047\n", "REMOVE TREE correction/1-overlapper/queries/000020\n", "REMOVE TREE correction/1-overlapper/queries/000068\n", "REMOVE TREE correction/1-overlapper/queries/000059\n", "REMOVE TREE correction/1-overlapper/queries/000053\n", "REMOVE TREE correction/1-overlapper/queries/000034\n", "REMOVE TREE correction/1-overlapper/queries/000024\n", "REMOVE TREE correction/1-overlapper/queries/000012\n", "REMOVE TREE correction/1-overlapper/queries/000074\n", "REMOVE TREE correction/1-overlapper/queries/000032\n", "REMOVE TREE correction/1-overlapper/queries/000040\n", "REMOVE TREE correction/1-overlapper/queries/000028\n", "REMOVE TREE correction/1-overlapper/queries/000015\n", "REMOVE TREE correction/1-overlapper/queries/000014\n", "REMOVE TREE correction/1-overlapper/queries/000085\n", "REMOVE TREE correction/1-overlapper/queries/000004\n", "REMOVE TREE correction/1-overlapper/queries/000011\n", "REMOVE TREE correction/1-overlapper/queries/000060\n", "REMOVE TREE correction/1-overlapper/queries/000027\n", "REMOVE TREE correction/1-overlapper/queries/000086\n", "REMOVE TREE correction/1-overlapper/queries/000022\n", "REMOVE TREE correction/1-overlapper/queries/000090\n", "REMOVE TREE correction/1-overlapper/queries/000081\n", "REMOVE TREE correction/1-overlapper/queries/000018\n", "REMOVE TREE correction/1-overlapper/queries/000076\n", "REMOVE TREE correction/1-overlapper/queries/000083\n", "REMOVE TREE correction/1-overlapper/queries/000038\n", "REMOVE TREE correction/1-overlapper/queries/000078\n", "REMOVE TREE correction/1-overlapper/queries/000062\n", "REMOVE TREE correction/1-overlapper/queries/000089\n", "REMOVE TREE correction/1-overlapper/queries/000023\n", "REMOVE TREE correction/1-overlapper/queries/000016\n", "REMOVE TREE correction/1-overlapper/queries/000036\n", "REMOVE TREE correction/1-overlapper/queries/000026\n", "REMOVE TREE correction/1-overlapper/queries/000003\n", "REMOVE TREE correction/1-overlapper/queries/000046\n", "REMOVE TREE correction/1-overlapper/queries/000009\n", "REMOVE TREE correction/1-overlapper/queries/000055\n", "REMOVE TREE correction/1-overlapper/queries/000002\n", "REMOVE TREE correction/1-overlapper/queries/000056\n", "REMOVE TREE correction/1-overlapper/queries/000072\n", "REMOVE TREE correction/1-overlapper/queries/000067\n", "REMOVE TREE correction/1-overlapper/queries/000082\n", "REMOVE TREE correction/1-overlapper/queries/000005\n", "REMOVE TREE correction/1-overlapper/queries/000019\n", "REMOVE TREE correction/1-overlapper/queries/000029\n", "REMOVE TREE correction/1-overlapper/queries/000064\n", "REMOVE TREE correction/1-overlapper/queries/000077\n", "REMOVE TREE correction/1-overlapper/queries/000075\n", "REMOVE TREE correction/1-overlapper/queries/000063\n", "REMOVE TREE correction/1-overlapper/queries/000049\n", "REMOVE TREE correction/1-overlapper/queries/000044\n", "REMOVE TREE correction/1-overlapper/queries/000091\n", "REMOVE TREE correction/1-overlapper/queries/000031\n", "REMOVE TREE correction/1-overlapper/queries/000066\n", "REMOVE TREE correction/1-overlapper/queries/000070\n", "REMOVE TREE correction/1-overlapper/queries/000054\n", "REMOVE TREE correction/1-overlapper/queries/000035\n", "REMOVE TREE correction/1-overlapper/queries/000043\n", "REMOVE TREE correction/1-overlapper/queries/000006\n", "REMOVE TREE correction/1-overlapper/queries/000045\n", "REMOVE TREE correction/1-overlapper/queries/000071\n", "REMOVE TREE correction/1-overlapper/queries/000073\n", "REMOVE TREE correction/1-overlapper/queries/000050\n", "REMOVE TREE correction/1-overlapper/queries/000080\n", "REMOVE TREE correction/1-overlapper/queries/000017\n", "REMOVE TREE correction/1-overlapper/queries/000039\n", "REMOVE TREE correction/1-overlapper/queries/000021\n", "REMOVE TREE correction/1-overlapper/queries/000037\n", "REMOVE TREE correction/1-overlapper/queries/000061\n", "REMOVE TREE correction/1-overlapper/queries/000010\n", "REMOVE TREE correction/1-overlapper/queries/000051\n", "REMOVE TREE correction/1-overlapper/queries/000042\n", "REMOVE TREE correction/1-overlapper/queries/000065\n", "REMOVE TREE correction/1-overlapper/queries\n", "REMOVE TREE correction/1-overlapper/queries/000008\n", "REMOVE TREE correction/1-overlapper/queries/000058\n", "REMOVE TREE correction/1-overlapper/queries/000001\n", "REMOVE TREE correction/1-overlapper/queries/000057\n", "REMOVE TREE correction/1-overlapper/queries/000025\n", "REMOVE TREE correction/1-overlapper/queries/000007\n", "REMOVE TREE correction/1-overlapper/queries/000088\n", "REMOVE TREE correction/1-overlapper/queries/000084\n", "REMOVE TREE correction/1-overlapper/queries/000087\n", "--\n", "-- Purged 1008.114 GB in 885 overlap output files.\n", "-- Overlap store 'correction/20171018_oly_pacbio.ovlStore' statistics not available (skipped in correction and trimming stages).\n", "--\n", "-- Finished stage 'cor-createOverlapStore', reset canuIteration.\n", "-- Set corMinCoverage=0 based on read coverage of 6.\n", "-- Computing global filter scores 'correction/2-correction/20171018_oly_pacbio.globalScores'.\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 06:05:11 2017 with 674.787 GB free disk space\n", "\n", " cd correction/2-correction\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/filterCorrectionOverlaps \\\n", " -G ../20171018_oly_pacbio.gkpStore \\\n", " -O ../20171018_oly_pacbio.ovlStore \\\n", " -S ./20171018_oly_pacbio.globalScores.WORKING \\\n", " -c 40 \\\n", " -l 0 \\\n", " > ./20171018_oly_pacbio.globalScores.err 2>&1\n", "\n", "-- Finished on Fri Oct 20 06:37:26 2017 (1935 seconds) with 674.603 GB free disk space\n", "----------------------------------------\n", "-- PARAMETERS:\n", "-- ----------\n", "-- \n", "-- 40 (expected coverage)\n", "-- 0 (don't use overlaps shorter than this)\n", "-- 0.000 (don't use overlaps with erate less than this)\n", "-- 1.000 (don't use overlaps with erate more than this)\n", "-- \n", "-- OVERLAPS:\n", "-- --------\n", "-- \n", "-- IGNORED:\n", "-- \n", "-- 0 (< 0.0000 fraction error)\n", "-- 0 (> 0.4095 fraction error)\n", "-- 0 (< 0 bases long)\n", "-- 0 (> 2097151 bases long)\n", "-- \n", "-- FILTERED:\n", "-- \n", "-- 9033508064 (too many overlaps, discard these shortest ones)\n", "-- \n", "-- EVIDENCE:\n", "-- \n", "-- 68112774 (longest overlaps)\n", "-- \n", "-- TOTAL:\n", "-- \n", "-- 9101620838 (all overlaps)\n", "-- \n", "-- READS:\n", "-- -----\n", "-- \n", "-- 874 (no overlaps)\n", "-- 102785 (no overlaps filtered)\n", "-- 111724 (< 50% overlaps filtered)\n", "-- 303069 (< 80% overlaps filtered)\n", "-- 629330 (< 95% overlaps filtered)\n", "-- 1635193 (< 100% overlaps filtered)\n", "-- \n", "-- Computing expected corrected read lengths 'correction/2-correction/20171018_oly_pacbio.estimate.log'.\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 06:37:29 2017 with 674.603 GB free disk space\n", "\n", " cd correction/2-correction\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/generateCorrectionLayouts \\\n", " -G ../20171018_oly_pacbio.gkpStore \\\n", " -O ../20171018_oly_pacbio.ovlStore \\\n", " -S ./20171018_oly_pacbio.globalScores \\\n", " -c 0 \\\n", " -C 80 \\\n", " -p ./20171018_oly_pacbio.estimate.WORKING\n", "\n", "-- Finished on Fri Oct 20 07:08:45 2017 (1876 seconds) with 674.569 GB free disk space\n", "----------------------------------------\n", "-- Sorting reads by expected corrected length.\n", "-- Sorting reads by uncorrected length.\n", "-- Loading expected corrected read lengths.\n", "-- Picking longest corrected reads.\n", "-- Writing longest corrected reads to 'correction/2-correction/20171018_oly_pacbio.readsToCorrect'.\n", "-- Summarizing filter.\n", "--\n", "-- Reads to be corrected:\n", "-- 1737978 reads longer than 0 bp\n", "-- 12703460519 bp\n", "-- Expected corrected reads:\n", "-- 1737978 reads\n", "-- 10398007480 bp\n", "-- 0 bp minimum length\n", "-- 5983 bp mean length\n", "-- 14867 bp n50 length\n", "-- Using overlaps no worse than 0.3 fraction error for correcting reads (from corErrorRate parameter).\n", "-- Finished stage 'cor-buildCorrectionLayouts', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'cor' concurrent execution on Fri Oct 20 07:10:15 2017 with 673.78 GB free disk space (116 processes; 6 concurrently)\n", "\n", " cd correction/2-correction\n", " ./correctReads.sh 1 > ./correctReads.000001.out 2>&1\n", " ./correctReads.sh 2 > ./correctReads.000002.out 2>&1\n", " ./correctReads.sh 3 > ./correctReads.000003.out 2>&1\n", " ./correctReads.sh 4 > ./correctReads.000004.out 2>&1\n", " ./correctReads.sh 5 > ./correctReads.000005.out 2>&1\n", " ./correctReads.sh 6 > ./correctReads.000006.out 2>&1\n", " ./correctReads.sh 7 > ./correctReads.000007.out 2>&1\n", " ./correctReads.sh 8 > ./correctReads.000008.out 2>&1\n", " ./correctReads.sh 9 > ./correctReads.000009.out 2>&1\n", " ./correctReads.sh 10 > ./correctReads.000010.out 2>&1\n", " ./correctReads.sh 11 > ./correctReads.000011.out 2>&1\n", " ./correctReads.sh 12 > ./correctReads.000012.out 2>&1\n", " ./correctReads.sh 13 > ./correctReads.000013.out 2>&1\n", " ./correctReads.sh 14 > ./correctReads.000014.out 2>&1\n", " ./correctReads.sh 15 > ./correctReads.000015.out 2>&1\n", " ./correctReads.sh 16 > ./correctReads.000016.out 2>&1\n", " ./correctReads.sh 17 > ./correctReads.000017.out 2>&1\n", " ./correctReads.sh 18 > ./correctReads.000018.out 2>&1\n", " ./correctReads.sh 19 > ./correctReads.000019.out 2>&1\n", " ./correctReads.sh 20 > ./correctReads.000020.out 2>&1\n", " ./correctReads.sh 21 > ./correctReads.000021.out 2>&1\n", " ./correctReads.sh 22 > ./correctReads.000022.out 2>&1\n", " ./correctReads.sh 23 > ./correctReads.000023.out 2>&1\n", " ./correctReads.sh 24 > ./correctReads.000024.out 2>&1\n", " ./correctReads.sh 25 > ./correctReads.000025.out 2>&1\n", " ./correctReads.sh 26 > ./correctReads.000026.out 2>&1\n", " ./correctReads.sh 27 > ./correctReads.000027.out 2>&1\n", " ./correctReads.sh 28 > ./correctReads.000028.out 2>&1\n", " ./correctReads.sh 29 > ./correctReads.000029.out 2>&1\n", " ./correctReads.sh 30 > ./correctReads.000030.out 2>&1\n", " ./correctReads.sh 31 > ./correctReads.000031.out 2>&1\n", " ./correctReads.sh 32 > ./correctReads.000032.out 2>&1\n", " ./correctReads.sh 33 > ./correctReads.000033.out 2>&1\n", " ./correctReads.sh 34 > ./correctReads.000034.out 2>&1\n", " ./correctReads.sh 35 > ./correctReads.000035.out 2>&1\n", " ./correctReads.sh 36 > ./correctReads.000036.out 2>&1\n", " ./correctReads.sh 37 > ./correctReads.000037.out 2>&1\n", " ./correctReads.sh 38 > ./correctReads.000038.out 2>&1\n", " ./correctReads.sh 39 > ./correctReads.000039.out 2>&1\n", " ./correctReads.sh 40 > ./correctReads.000040.out 2>&1\n", " ./correctReads.sh 41 > ./correctReads.000041.out 2>&1\n", " ./correctReads.sh 42 > ./correctReads.000042.out 2>&1\n", " ./correctReads.sh 43 > ./correctReads.000043.out 2>&1\n", " ./correctReads.sh 44 > ./correctReads.000044.out 2>&1\n", " ./correctReads.sh 45 > ./correctReads.000045.out 2>&1\n", " ./correctReads.sh 46 > ./correctReads.000046.out 2>&1\n", " ./correctReads.sh 47 > ./correctReads.000047.out 2>&1\n", " ./correctReads.sh 48 > ./correctReads.000048.out 2>&1\n", " ./correctReads.sh 49 > ./correctReads.000049.out 2>&1\n", " ./correctReads.sh 50 > ./correctReads.000050.out 2>&1\n", " ./correctReads.sh 51 > ./correctReads.000051.out 2>&1\n", " ./correctReads.sh 52 > ./correctReads.000052.out 2>&1\n", " ./correctReads.sh 53 > ./correctReads.000053.out 2>&1\n", " ./correctReads.sh 54 > ./correctReads.000054.out 2>&1\n", " ./correctReads.sh 55 > ./correctReads.000055.out 2>&1\n", " ./correctReads.sh 56 > ./correctReads.000056.out 2>&1\n", " ./correctReads.sh 57 > ./correctReads.000057.out 2>&1\n", " ./correctReads.sh 58 > ./correctReads.000058.out 2>&1\n", " ./correctReads.sh 59 > ./correctReads.000059.out 2>&1\n", " ./correctReads.sh 60 > ./correctReads.000060.out 2>&1\n", " ./correctReads.sh 61 > ./correctReads.000061.out 2>&1\n", " ./correctReads.sh 62 > ./correctReads.000062.out 2>&1\n", " ./correctReads.sh 63 > ./correctReads.000063.out 2>&1\n", " ./correctReads.sh 64 > ./correctReads.000064.out 2>&1\n", " ./correctReads.sh 65 > ./correctReads.000065.out 2>&1\n", " ./correctReads.sh 66 > ./correctReads.000066.out 2>&1\n", " ./correctReads.sh 67 > ./correctReads.000067.out 2>&1\n", " ./correctReads.sh 68 > ./correctReads.000068.out 2>&1\n", " ./correctReads.sh 69 > ./correctReads.000069.out 2>&1\n", " ./correctReads.sh 70 > ./correctReads.000070.out 2>&1\n", " ./correctReads.sh 71 > ./correctReads.000071.out 2>&1\n", " ./correctReads.sh 72 > ./correctReads.000072.out 2>&1\n", " ./correctReads.sh 73 > ./correctReads.000073.out 2>&1\n", " ./correctReads.sh 74 > ./correctReads.000074.out 2>&1\n", " ./correctReads.sh 75 > ./correctReads.000075.out 2>&1\n", " ./correctReads.sh 76 > ./correctReads.000076.out 2>&1\n", " ./correctReads.sh 77 > ./correctReads.000077.out 2>&1\n", " ./correctReads.sh 78 > ./correctReads.000078.out 2>&1\n", " ./correctReads.sh 79 > ./correctReads.000079.out 2>&1\n", " ./correctReads.sh 80 > ./correctReads.000080.out 2>&1\n", " ./correctReads.sh 81 > ./correctReads.000081.out 2>&1\n", " ./correctReads.sh 82 > ./correctReads.000082.out 2>&1\n", " ./correctReads.sh 83 > ./correctReads.000083.out 2>&1\n", " ./correctReads.sh 84 > ./correctReads.000084.out 2>&1\n", " ./correctReads.sh 85 > ./correctReads.000085.out 2>&1\n", " ./correctReads.sh 86 > ./correctReads.000086.out 2>&1\n", " ./correctReads.sh 87 > ./correctReads.000087.out 2>&1\n", " ./correctReads.sh 88 > ./correctReads.000088.out 2>&1\n", " ./correctReads.sh 89 > ./correctReads.000089.out 2>&1\n", " ./correctReads.sh 90 > ./correctReads.000090.out 2>&1\n", " ./correctReads.sh 91 > ./correctReads.000091.out 2>&1\n", " ./correctReads.sh 92 > ./correctReads.000092.out 2>&1\n", " ./correctReads.sh 93 > ./correctReads.000093.out 2>&1\n", " ./correctReads.sh 94 > ./correctReads.000094.out 2>&1\n", " ./correctReads.sh 95 > ./correctReads.000095.out 2>&1\n", " ./correctReads.sh 96 > ./correctReads.000096.out 2>&1\n", " ./correctReads.sh 97 > ./correctReads.000097.out 2>&1\n", " ./correctReads.sh 98 > ./correctReads.000098.out 2>&1\n", " ./correctReads.sh 99 > ./correctReads.000099.out 2>&1\n", " ./correctReads.sh 100 > ./correctReads.000100.out 2>&1\n", " ./correctReads.sh 101 > ./correctReads.000101.out 2>&1\n", " ./correctReads.sh 102 > ./correctReads.000102.out 2>&1\n", " ./correctReads.sh 103 > ./correctReads.000103.out 2>&1\n", " ./correctReads.sh 104 > ./correctReads.000104.out 2>&1\n", " ./correctReads.sh 105 > ./correctReads.000105.out 2>&1\n", " ./correctReads.sh 106 > ./correctReads.000106.out 2>&1\n", " ./correctReads.sh 107 > ./correctReads.000107.out 2>&1\n", " ./correctReads.sh 108 > ./correctReads.000108.out 2>&1\n", " ./correctReads.sh 109 > ./correctReads.000109.out 2>&1\n", " ./correctReads.sh 110 > ./correctReads.000110.out 2>&1\n", " ./correctReads.sh 111 > ./correctReads.000111.out 2>&1\n", " ./correctReads.sh 112 > ./correctReads.000112.out 2>&1\n", " ./correctReads.sh 113 > ./correctReads.000113.out 2>&1\n", " ./correctReads.sh 114 > ./correctReads.000114.out 2>&1\n", " ./correctReads.sh 115 > ./correctReads.000115.out 2>&1\n", " ./correctReads.sh 116 > ./correctReads.000116.out 2>&1\n", "\n", "-- Finished on Fri Oct 20 11:44:54 2017 (16479 seconds) with 662.711 GB free disk space\n", "----------------------------------------\n", "-- Found 116 read correction output files.\n", "-- Finished stage 'cor-generateCorrectedReads', reset canuIteration.\n", "-- Found 116 read correction output files.\n", "-- Finished stage 'cor-generateCorrectedReads', reset canuIteration.\n", "-- Concatenating correctReads output.\n", "-- Analyzing correctReads output.\n", "--\n", "-- Reads to be corrected:\n", "-- 1737978 reads longer than 0 bp\n", "-- 12703460519 bp\n", "-- Expected corrected reads:\n", "-- 1737978 reads\n", "-- 10398007480 bp\n", "-- 0 bp minimum length\n", "-- 5983 bp mean length\n", "-- 14867 bp n50 length\n", "-- Actual corrected reads:\n", "-- 1665075 reads\n", "-- 11661226162 bp\n", "-- 72903 reads with 0 corrected blocks\n", "-- 1665075 reads with 1 corrected block\n", "--\n", "-- Purging correctReads output after merging to final output file.\n", "-- Purged 116 .dump.success sentinels.\n", "-- Purged 116 .fasta outputs.\n", "-- Purged 116 .err outputs.\n", "-- Purged 116 .out job log outputs.\n", "-- Finished stage 'cor-dumpCorrectedReads', reset canuIteration.\n", "--\n", "-- Corrected reads saved in '20171018_oly_pacbio.correctedReads.fasta.gz'.\n", "--\n", "--\n", "-- BEGIN TRIMMING\n", "--\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 11:52:06 2017 with 837.718 GB free disk space\n", "\n", " cd trimming\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/gatekeeperCreate \\\n", " -minlength 1000 \\\n", " -o ./20171018_oly_pacbio.gkpStore.BUILDING \\\n", " ./20171018_oly_pacbio.gkpStore.gkp \\\n", " > ./20171018_oly_pacbio.gkpStore.BUILDING.err 2>&1\n", "\n", "-- Finished on Fri Oct 20 11:55:10 2017 (184 seconds) with 834.594 GB free disk space\n", "----------------------------------------\n", "--\n", "-- In gatekeeper store 'trimming/20171018_oly_pacbio.gkpStore':\n", "-- Found 1665075 reads.\n", "-- Found 11661226162 bases (6.13 times coverage).\n", "--\n", "-- Read length histogram (one '*' equals 3544.54 reads):\n", "-- 0 999 0 \n", "-- 1000 1999 132249 *************************************\n", "-- 2000 2999 142073 ****************************************\n", "-- 3000 3999 138655 ***************************************\n", "-- 4000 4999 131179 *************************************\n", "-- 5000 5999 188994 *****************************************************\n", "-- 6000 6999 248118 **********************************************************************\n", "-- 7000 7999 175810 *************************************************\n", "-- 8000 8999 124541 ***********************************\n", "-- 9000 9999 89076 *************************\n", "-- 10000 10999 66103 ******************\n", "-- 11000 11999 49617 *************\n", "-- 12000 12999 38761 **********\n", "-- 13000 13999 30214 ********\n", "-- 14000 14999 23492 ******\n", "-- 15000 15999 18097 *****\n", "-- 16000 16999 14393 ****\n", "-- 17000 17999 11353 ***\n", "-- 18000 18999 8829 **\n", "-- 19000 19999 7023 *\n", "-- 20000 20999 5576 *\n", "-- 21000 21999 4398 *\n", "-- 22000 22999 3378 \n", "-- 23000 23999 2685 \n", "-- 24000 24999 2079 \n", "-- 25000 25999 1628 \n", "-- 26000 26999 1308 \n", "-- 27000 27999 1075 \n", "-- 28000 28999 838 \n", "-- 29000 29999 704 \n", "-- 30000 30999 543 \n", "-- 31000 31999 456 \n", "-- 32000 32999 365 \n", "-- 33000 33999 275 \n", "-- 34000 34999 201 \n", "-- 35000 35999 169 \n", "-- 36000 36999 153 \n", "-- 37000 37999 124 \n", "-- 38000 38999 98 \n", "-- 39000 39999 90 \n", "-- 40000 40999 75 \n", "-- 41000 41999 61 \n", "-- 42000 42999 44 \n", "-- 43000 43999 39 \n", "-- 44000 44999 31 \n", "-- 45000 45999 19 \n", "-- 46000 46999 16 \n", "-- 47000 47999 13 \n", "-- 48000 48999 18 \n", "-- 49000 49999 8 \n", "-- 50000 50999 5 \n", "-- 51000 51999 2 \n", "-- 52000 52999 6 \n", "-- 53000 53999 6 \n", "-- 54000 54999 2 \n", "-- 55000 55999 4 \n", "-- 56000 56999 2 \n", "-- 57000 57999 2 \n", "-- 58000 58999 1 \n", "-- 59000 59999 0 \n", "-- 60000 60999 0 \n", "-- 61000 61999 0 \n", "-- 62000 62999 0 \n", "-- 63000 63999 1 \n", "-- Finished stage 'obt-gatekeeper', reset canuIteration.\n", "-- Finished stage 'merylConfigure', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'meryl' concurrent execution on Fri Oct 20 11:55:42 2017 with 834.544 GB free disk space (1 processes; 1 concurrently)\n", "\n", " cd trimming/0-mercounts\n", " ./meryl.sh 1 > ./meryl.000001.out 2>&1\n", "\n", "-- Finished on Fri Oct 20 12:46:02 2017 (3020 seconds) with 790.643 GB free disk space\n", "----------------------------------------\n", "-- Meryl finished successfully.\n", "-- Finished stage 'merylCheck', reset canuIteration.\n", "--\n", "-- 22-mers Fraction\n", "-- Occurrences NumMers Unique Total\n", "-- 1- 1 7725326153 *******************************************************************--> 0.9280 0.6645\n", "-- 2- 2 252935243 ********************************************************************** 0.9584 0.7080\n", "-- 3- 4 154513749 ****************************************** 0.9701 0.7331\n", "-- 5- 7 92684893 ************************* 0.9817 0.7699\n", "-- 8- 11 51684289 ************** 0.9902 0.8115\n", "-- 12- 16 23204817 ****** 0.9951 0.8472\n", "-- 17- 22 9293416 ** 0.9974 0.8706\n", "-- 23- 29 4292264 * 0.9983 0.8840\n", "-- 30- 37 2636301 0.9988 0.8928\n", "-- 38- 46 1865506 0.9991 0.9001\n", "-- 47- 56 1362364 0.9993 0.9066\n", "-- 57- 67 985672 0.9994 0.9125\n", "-- 68- 79 724229 0.9995 0.9176\n", "-- 80- 92 554444 0.9996 0.9221\n", "-- 93- 106 426303 0.9997 0.9261\n", "-- 107- 121 335555 0.9997 0.9297\n", "-- 122- 137 271808 0.9998 0.9330\n", "-- 138- 154 225883 0.9998 0.9359\n", "-- 155- 172 188849 0.9998 0.9388\n", "-- 173- 191 152527 0.9999 0.9414\n", "-- 192- 211 122845 0.9999 0.9437\n", "-- 212- 232 101214 0.9999 0.9459\n", "-- 233- 254 84206 0.9999 0.9478\n", "-- 255- 277 71725 0.9999 0.9495\n", "-- 278- 301 61832 0.9999 0.9512\n", "-- 302- 326 53875 0.9999 0.9527\n", "-- 327- 352 46016 0.9999 0.9541\n", "-- 353- 379 41374 0.9999 0.9555\n", "-- 380- 407 36957 0.9999 0.9568\n", "-- 408- 436 32650 1.0000 0.9580\n", "-- 437- 466 29408 1.0000 0.9592\n", "-- 467- 497 27261 1.0000 0.9603\n", "-- 498- 529 25266 1.0000 0.9615\n", "-- 530- 562 23524 1.0000 0.9626\n", "-- 563- 596 21810 1.0000 0.9637\n", "-- 597- 631 19971 1.0000 0.9648\n", "-- 632- 667 17723 1.0000 0.9658\n", "-- 668- 704 16416 1.0000 0.9668\n", "-- 705- 742 14590 1.0000 0.9678\n", "-- 743- 781 12486 1.0000 0.9687\n", "-- 782- 821 10855 1.0000 0.9695\n", "--\n", "-- 2538138 (max occurrences)\n", "-- 3900933434 (total mers, non-unique)\n", "-- 599354004 (distinct mers, non-unique)\n", "-- 7725326153 (unique mers)\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 12:46:04 2017 with 790.643 GB free disk space\n", "\n", " cd trimming/0-mercounts\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/meryl \\\n", " -Dt \\\n", " -n 642 \\\n", " -s ./20171018_oly_pacbio.ms22 \\\n", " > ./20171018_oly_pacbio.ms22.frequentMers.fasta \\\n", " 2> ./20171018_oly_pacbio.ms22.frequentMers.fasta.err\n", "\n", "-- Finished on Fri Oct 20 12:50:41 2017 (277 seconds) with 790.638 GB free disk space\n", "----------------------------------------\n", "-- Reset obtOvlMerThreshold from auto to 642.\n", "--\n", "-- Found 11626259587 22-mers; 8324680157 distinct and 7725326153 unique. Largest count 2538138.\n", "-- Finished stage 'obt-meryl', reset canuIteration.\n", "--\n", "-- OVERLAPPER (normal) (trimming) erate=0.075\n", "--\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 12:50:46 2017 with 834.537 GB free disk space\n", "\n", " cd trimming/1-overlapper\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/overlapInCorePartition \\\n", " -g ../20171018_oly_pacbio.gkpStore \\\n", " -bl 100000000 \\\n", " -bs 0 \\\n", " -rs 2000000 \\\n", " -rl 0 \\\n", " -ol 500 \\\n", " -o ./20171018_oly_pacbio.partition \\\n", " > ./20171018_oly_pacbio.partition.err 2>&1\n", "\n", "-- Finished on Fri Oct 20 12:50:46 2017 (lickety-split) with 834.536 GB free disk space\n", "----------------------------------------\n", "--\n", "-- Configured 117 overlapInCore jobs.\n", "-- Finished stage 'obt-overlapConfigure', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'obtovl' concurrent execution on Fri Oct 20 12:50:46 2017 with 834.536 GB free disk space (117 processes; 3 concurrently)\n", "\n", " cd trimming/1-overlapper\n", " ./overlap.sh 1 > ./overlap.000001.out 2>&1\n", " ./overlap.sh 2 > ./overlap.000002.out 2>&1\n", " ./overlap.sh 3 > ./overlap.000003.out 2>&1\n", " ./overlap.sh 4 > ./overlap.000004.out 2>&1\n", " ./overlap.sh 5 > ./overlap.000005.out 2>&1\n", " ./overlap.sh 6 > ./overlap.000006.out 2>&1\n", " ./overlap.sh 7 > ./overlap.000007.out 2>&1\n", " ./overlap.sh 8 > ./overlap.000008.out 2>&1\n", " ./overlap.sh 9 > ./overlap.000009.out 2>&1\n", " ./overlap.sh 10 > ./overlap.000010.out 2>&1\n", " ./overlap.sh 11 > ./overlap.000011.out 2>&1\n", " ./overlap.sh 12 > ./overlap.000012.out 2>&1\n", " ./overlap.sh 13 > ./overlap.000013.out 2>&1\n", " ./overlap.sh 14 > ./overlap.000014.out 2>&1\n", " ./overlap.sh 15 > ./overlap.000015.out 2>&1\n", " ./overlap.sh 16 > ./overlap.000016.out 2>&1\n", " ./overlap.sh 17 > ./overlap.000017.out 2>&1\n", " ./overlap.sh 18 > ./overlap.000018.out 2>&1\n", " ./overlap.sh 19 > ./overlap.000019.out 2>&1\n", " ./overlap.sh 20 > ./overlap.000020.out 2>&1\n", " ./overlap.sh 21 > ./overlap.000021.out 2>&1\n", " ./overlap.sh 22 > ./overlap.000022.out 2>&1\n", " ./overlap.sh 23 > ./overlap.000023.out 2>&1\n", " ./overlap.sh 24 > ./overlap.000024.out 2>&1\n", " ./overlap.sh 25 > ./overlap.000025.out 2>&1\n", " ./overlap.sh 26 > ./overlap.000026.out 2>&1\n", " ./overlap.sh 27 > ./overlap.000027.out 2>&1\n", " ./overlap.sh 28 > ./overlap.000028.out 2>&1\n", " ./overlap.sh 29 > ./overlap.000029.out 2>&1\n", " ./overlap.sh 30 > ./overlap.000030.out 2>&1\n", " ./overlap.sh 31 > ./overlap.000031.out 2>&1\n", " ./overlap.sh 32 > ./overlap.000032.out 2>&1\n", " ./overlap.sh 33 > ./overlap.000033.out 2>&1\n", " ./overlap.sh 34 > ./overlap.000034.out 2>&1\n", " ./overlap.sh 35 > ./overlap.000035.out 2>&1\n", " ./overlap.sh 36 > ./overlap.000036.out 2>&1\n", " ./overlap.sh 37 > ./overlap.000037.out 2>&1\n", " ./overlap.sh 38 > ./overlap.000038.out 2>&1\n", " ./overlap.sh 39 > ./overlap.000039.out 2>&1\n", " ./overlap.sh 40 > ./overlap.000040.out 2>&1\n", " ./overlap.sh 41 > ./overlap.000041.out 2>&1\n", " ./overlap.sh 42 > ./overlap.000042.out 2>&1\n", " ./overlap.sh 43 > ./overlap.000043.out 2>&1\n", " ./overlap.sh 44 > ./overlap.000044.out 2>&1\n", " ./overlap.sh 45 > ./overlap.000045.out 2>&1\n", " ./overlap.sh 46 > ./overlap.000046.out 2>&1\n", " ./overlap.sh 47 > ./overlap.000047.out 2>&1\n", " ./overlap.sh 48 > ./overlap.000048.out 2>&1\n", " ./overlap.sh 49 > ./overlap.000049.out 2>&1\n", " ./overlap.sh 50 > ./overlap.000050.out 2>&1\n", " ./overlap.sh 51 > ./overlap.000051.out 2>&1\n", " ./overlap.sh 52 > ./overlap.000052.out 2>&1\n", " ./overlap.sh 53 > ./overlap.000053.out 2>&1\n", " ./overlap.sh 54 > ./overlap.000054.out 2>&1\n", " ./overlap.sh 55 > ./overlap.000055.out 2>&1\n", " ./overlap.sh 56 > ./overlap.000056.out 2>&1\n", " ./overlap.sh 57 > ./overlap.000057.out 2>&1\n", " ./overlap.sh 58 > ./overlap.000058.out 2>&1\n", " ./overlap.sh 59 > ./overlap.000059.out 2>&1\n", " ./overlap.sh 60 > ./overlap.000060.out 2>&1\n", " ./overlap.sh 61 > ./overlap.000061.out 2>&1\n", " ./overlap.sh 62 > ./overlap.000062.out 2>&1\n", " ./overlap.sh 63 > ./overlap.000063.out 2>&1\n", " ./overlap.sh 64 > ./overlap.000064.out 2>&1\n", " ./overlap.sh 65 > ./overlap.000065.out 2>&1\n", " ./overlap.sh 66 > ./overlap.000066.out 2>&1\n", " ./overlap.sh 67 > ./overlap.000067.out 2>&1\n", " ./overlap.sh 68 > ./overlap.000068.out 2>&1\n", " ./overlap.sh 69 > ./overlap.000069.out 2>&1\n", " ./overlap.sh 70 > ./overlap.000070.out 2>&1\n", " ./overlap.sh 71 > ./overlap.000071.out 2>&1\n", " ./overlap.sh 72 > ./overlap.000072.out 2>&1\n", " ./overlap.sh 73 > ./overlap.000073.out 2>&1\n", " ./overlap.sh 74 > ./overlap.000074.out 2>&1\n", " ./overlap.sh 75 > ./overlap.000075.out 2>&1\n", " ./overlap.sh 76 > ./overlap.000076.out 2>&1\n", " ./overlap.sh 77 > ./overlap.000077.out 2>&1\n", " ./overlap.sh 78 > ./overlap.000078.out 2>&1\n", " ./overlap.sh 79 > ./overlap.000079.out 2>&1\n", " ./overlap.sh 80 > ./overlap.000080.out 2>&1\n", " ./overlap.sh 81 > ./overlap.000081.out 2>&1\n", " ./overlap.sh 82 > ./overlap.000082.out 2>&1\n", " ./overlap.sh 83 > ./overlap.000083.out 2>&1\n", " ./overlap.sh 84 > ./overlap.000084.out 2>&1\n", " ./overlap.sh 85 > ./overlap.000085.out 2>&1\n", " ./overlap.sh 86 > ./overlap.000086.out 2>&1\n", " ./overlap.sh 87 > ./overlap.000087.out 2>&1\n", " ./overlap.sh 88 > ./overlap.000088.out 2>&1\n", " ./overlap.sh 89 > ./overlap.000089.out 2>&1\n", " ./overlap.sh 90 > ./overlap.000090.out 2>&1\n", " ./overlap.sh 91 > ./overlap.000091.out 2>&1\n", " ./overlap.sh 92 > ./overlap.000092.out 2>&1\n", " ./overlap.sh 93 > ./overlap.000093.out 2>&1\n", " ./overlap.sh 94 > ./overlap.000094.out 2>&1\n", " ./overlap.sh 95 > ./overlap.000095.out 2>&1\n", " ./overlap.sh 96 > ./overlap.000096.out 2>&1\n", " ./overlap.sh 97 > ./overlap.000097.out 2>&1\n", " ./overlap.sh 98 > ./overlap.000098.out 2>&1\n", " ./overlap.sh 99 > ./overlap.000099.out 2>&1\n", " ./overlap.sh 100 > ./overlap.000100.out 2>&1\n", " ./overlap.sh 101 > ./overlap.000101.out 2>&1\n", " ./overlap.sh 102 > ./overlap.000102.out 2>&1\n", " ./overlap.sh 103 > ./overlap.000103.out 2>&1\n", " ./overlap.sh 104 > ./overlap.000104.out 2>&1\n", " ./overlap.sh 105 > ./overlap.000105.out 2>&1\n", " ./overlap.sh 106 > ./overlap.000106.out 2>&1\n", " ./overlap.sh 107 > ./overlap.000107.out 2>&1\n", " ./overlap.sh 108 > ./overlap.000108.out 2>&1\n", " ./overlap.sh 109 > ./overlap.000109.out 2>&1\n", " ./overlap.sh 110 > ./overlap.000110.out 2>&1\n", " ./overlap.sh 111 > ./overlap.000111.out 2>&1\n", " ./overlap.sh 112 > ./overlap.000112.out 2>&1\n", " ./overlap.sh 113 > ./overlap.000113.out 2>&1\n", " ./overlap.sh 114 > ./overlap.000114.out 2>&1\n", " ./overlap.sh 115 > ./overlap.000115.out 2>&1\n", " ./overlap.sh 116 > ./overlap.000116.out 2>&1\n", " ./overlap.sh 117 > ./overlap.000117.out 2>&1\n", "\n", "-- Finished on Fri Oct 20 19:54:56 2017 (25450 seconds) with 833.147 GB free disk space\n", "----------------------------------------\n", "-- Found 117 overlapInCore output files.\n", "--\n", "-- overlapInCore compute 'trimming/1-overlapper':\n", "-- kmer hits\n", "-- with no overlap 8395434118 47.1623932 +- 54925643.046\n", "-- with an overlap 53892335 .247863248 +- 416346.085\n", "--\n", "-- overlaps 53890954 .444444444 +- 416335.571\n", "-- contained 0 0 +- 0\n", "-- dovetail 0 0 +- 0\n", "--\n", "-- overlaps rejected\n", "-- multiple per pair 0 0 +- 0\n", "-- bad short window 0 0 +- 0\n", "-- bad long window 0 0 +- 0\n", "-- Finished stage 'obt-overlapCheck', reset canuIteration.\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 19:54:56 2017 with 833.147 GB free disk space\n", "\n", " cd trimming\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/ovStoreBuild \\\n", " -O ./20171018_oly_pacbio.ovlStore.BUILDING \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -M 4-32 \\\n", " -L ./1-overlapper/ovljob.files \\\n", " > ./20171018_oly_pacbio.ovlStore.err 2>&1\n", "\n", "-- Finished on Fri Oct 20 19:55:45 2017 (49 seconds) with 831.101 GB free disk space\n", "----------------------------------------\n", "-- Checking store.\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 19:55:46 2017 with 831.101 GB free disk space\n", "\n", " cd trimming\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/ovStoreDump \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -O ./20171018_oly_pacbio.ovlStore \\\n", " -d -counts \\\n", " > ./20171018_oly_pacbio.ovlStore/counts.dat 2> ./20171018_oly_pacbio.ovlStore/counts.err\n", "\n", "-- Finished on Fri Oct 20 19:55:46 2017 (1 second) with 831.086 GB free disk space\n", "----------------------------------------\n", "--\n", "-- Overlap store 'trimming/20171018_oly_pacbio.ovlStore' successfully constructed.\n", "-- Found 107784670 overlaps for 797225 reads; 867847 reads have no overlaps.\n", "--\n", "FILE trimming/1-overlapper/001/000001.ovb\n", "FILE trimming/1-overlapper/001/000002.ovb\n", "FILE trimming/1-overlapper/001/000003.ovb\n", "FILE trimming/1-overlapper/001/000004.ovb\n", "FILE trimming/1-overlapper/001/000005.ovb\n", "FILE trimming/1-overlapper/001/000006.ovb\n", "FILE trimming/1-overlapper/001/000007.ovb\n", "FILE trimming/1-overlapper/001/000008.ovb\n", "FILE trimming/1-overlapper/001/000009.ovb\n", "FILE trimming/1-overlapper/001/000010.ovb\n", "FILE trimming/1-overlapper/001/000011.ovb\n", "FILE trimming/1-overlapper/001/000012.ovb\n", "FILE trimming/1-overlapper/001/000013.ovb\n", "FILE trimming/1-overlapper/001/000014.ovb\n", "FILE trimming/1-overlapper/001/000015.ovb\n", "FILE trimming/1-overlapper/001/000016.ovb\n", "FILE trimming/1-overlapper/001/000017.ovb\n", "FILE trimming/1-overlapper/001/000018.ovb\n", "FILE trimming/1-overlapper/001/000019.ovb\n", "FILE trimming/1-overlapper/001/000020.ovb\n", "FILE trimming/1-overlapper/001/000021.ovb\n", "FILE trimming/1-overlapper/001/000022.ovb\n", "FILE trimming/1-overlapper/001/000023.ovb\n", "FILE trimming/1-overlapper/001/000024.ovb\n", "FILE trimming/1-overlapper/001/000025.ovb\n", "FILE trimming/1-overlapper/001/000026.ovb\n", "FILE trimming/1-overlapper/001/000027.ovb\n", "FILE trimming/1-overlapper/001/000028.ovb\n", "FILE trimming/1-overlapper/001/000029.ovb\n", "FILE trimming/1-overlapper/001/000030.ovb\n", "FILE trimming/1-overlapper/001/000031.ovb\n", "FILE trimming/1-overlapper/001/000032.ovb\n", "FILE trimming/1-overlapper/001/000033.ovb\n", "FILE trimming/1-overlapper/001/000034.ovb\n", "FILE trimming/1-overlapper/001/000035.ovb\n", "FILE trimming/1-overlapper/001/000036.ovb\n", "FILE trimming/1-overlapper/001/000037.ovb\n", "FILE trimming/1-overlapper/001/000038.ovb\n", "FILE trimming/1-overlapper/001/000039.ovb\n", "FILE trimming/1-overlapper/001/000040.ovb\n", "FILE trimming/1-overlapper/001/000041.ovb\n", "FILE trimming/1-overlapper/001/000042.ovb\n", "FILE trimming/1-overlapper/001/000043.ovb\n", "FILE trimming/1-overlapper/001/000044.ovb\n", "FILE trimming/1-overlapper/001/000045.ovb\n", "FILE trimming/1-overlapper/001/000046.ovb\n", "FILE trimming/1-overlapper/001/000047.ovb\n", "FILE trimming/1-overlapper/001/000048.ovb\n", "FILE trimming/1-overlapper/001/000049.ovb\n", "FILE trimming/1-overlapper/001/000050.ovb\n", "FILE trimming/1-overlapper/001/000051.ovb\n", "FILE trimming/1-overlapper/001/000052.ovb\n", "FILE trimming/1-overlapper/001/000053.ovb\n", "FILE trimming/1-overlapper/001/000054.ovb\n", "FILE trimming/1-overlapper/001/000055.ovb\n", "FILE trimming/1-overlapper/001/000056.ovb\n", "FILE trimming/1-overlapper/001/000057.ovb\n", "FILE trimming/1-overlapper/001/000058.ovb\n", "FILE trimming/1-overlapper/001/000059.ovb\n", "FILE trimming/1-overlapper/001/000060.ovb\n", "FILE trimming/1-overlapper/001/000061.ovb\n", "FILE trimming/1-overlapper/001/000062.ovb\n", "FILE trimming/1-overlapper/001/000063.ovb\n", "FILE trimming/1-overlapper/001/000064.ovb\n", "FILE trimming/1-overlapper/001/000065.ovb\n", "FILE trimming/1-overlapper/001/000066.ovb\n", "FILE trimming/1-overlapper/001/000067.ovb\n", "FILE trimming/1-overlapper/001/000068.ovb\n", "FILE trimming/1-overlapper/001/000069.ovb\n", "FILE trimming/1-overlapper/001/000070.ovb\n", "FILE trimming/1-overlapper/001/000071.ovb\n", "FILE trimming/1-overlapper/001/000072.ovb\n", "FILE trimming/1-overlapper/001/000073.ovb\n", "FILE trimming/1-overlapper/001/000074.ovb\n", "FILE trimming/1-overlapper/001/000075.ovb\n", "FILE trimming/1-overlapper/001/000076.ovb\n", "FILE trimming/1-overlapper/001/000077.ovb\n", "FILE trimming/1-overlapper/001/000078.ovb\n", "FILE trimming/1-overlapper/001/000079.ovb\n", "FILE trimming/1-overlapper/001/000080.ovb\n", "FILE trimming/1-overlapper/001/000081.ovb\n", "FILE trimming/1-overlapper/001/000082.ovb\n", "FILE trimming/1-overlapper/001/000083.ovb\n", "FILE trimming/1-overlapper/001/000084.ovb\n", "FILE trimming/1-overlapper/001/000085.ovb\n", "FILE trimming/1-overlapper/001/000086.ovb\n", "FILE trimming/1-overlapper/001/000087.ovb\n", "FILE trimming/1-overlapper/001/000088.ovb\n", "FILE trimming/1-overlapper/001/000089.ovb\n", "FILE trimming/1-overlapper/001/000090.ovb\n", "FILE trimming/1-overlapper/001/000091.ovb\n", "FILE trimming/1-overlapper/001/000092.ovb\n", "FILE trimming/1-overlapper/001/000093.ovb\n", "FILE trimming/1-overlapper/001/000094.ovb\n", "FILE trimming/1-overlapper/001/000095.ovb\n", "FILE trimming/1-overlapper/001/000096.ovb\n", "FILE trimming/1-overlapper/001/000097.ovb\n", "FILE trimming/1-overlapper/001/000098.ovb\n", "FILE trimming/1-overlapper/001/000099.ovb\n", "FILE trimming/1-overlapper/001/000100.ovb\n", "FILE trimming/1-overlapper/001/000101.ovb\n", "FILE trimming/1-overlapper/001/000102.ovb\n", "FILE trimming/1-overlapper/001/000103.ovb\n", "FILE trimming/1-overlapper/001/000104.ovb\n", "FILE trimming/1-overlapper/001/000105.ovb\n", "FILE trimming/1-overlapper/001/000106.ovb\n", "FILE trimming/1-overlapper/001/000107.ovb\n", "FILE trimming/1-overlapper/001/000108.ovb\n", "FILE trimming/1-overlapper/001/000109.ovb\n", "FILE trimming/1-overlapper/001/000110.ovb\n", "FILE trimming/1-overlapper/001/000111.ovb\n", "FILE trimming/1-overlapper/001/000112.ovb\n", "FILE trimming/1-overlapper/001/000113.ovb\n", "FILE trimming/1-overlapper/001/000114.ovb\n", "FILE trimming/1-overlapper/001/000115.ovb\n", "FILE trimming/1-overlapper/001/000116.ovb\n", "FILE trimming/1-overlapper/001/000117.ovb\n", "FILE trimming/1-overlapper/001/000001.stats\n", "FILE trimming/1-overlapper/001/000001.counts\n", "FILE trimming/1-overlapper/001/000002.stats\n", "FILE trimming/1-overlapper/001/000002.counts\n", "FILE trimming/1-overlapper/001/000003.stats\n", "FILE trimming/1-overlapper/001/000003.counts\n", "FILE trimming/1-overlapper/001/000004.stats\n", "FILE trimming/1-overlapper/001/000004.counts\n", "FILE trimming/1-overlapper/001/000005.stats\n", "FILE trimming/1-overlapper/001/000005.counts\n", "FILE trimming/1-overlapper/001/000006.stats\n", "FILE trimming/1-overlapper/001/000006.counts\n", "FILE trimming/1-overlapper/001/000007.stats\n", "FILE trimming/1-overlapper/001/000007.counts\n", "FILE trimming/1-overlapper/001/000008.stats\n", "FILE trimming/1-overlapper/001/000008.counts\n", "FILE trimming/1-overlapper/001/000009.stats\n", "FILE trimming/1-overlapper/001/000009.counts\n", "FILE trimming/1-overlapper/001/000010.stats\n", "FILE trimming/1-overlapper/001/000010.counts\n", "FILE trimming/1-overlapper/001/000011.stats\n", "FILE trimming/1-overlapper/001/000011.counts\n", "FILE trimming/1-overlapper/001/000012.stats\n", "FILE trimming/1-overlapper/001/000012.counts\n", "FILE trimming/1-overlapper/001/000013.stats\n", "FILE trimming/1-overlapper/001/000013.counts\n", "FILE trimming/1-overlapper/001/000014.stats\n", "FILE trimming/1-overlapper/001/000014.counts\n", "FILE trimming/1-overlapper/001/000015.stats\n", "FILE trimming/1-overlapper/001/000015.counts\n", "FILE trimming/1-overlapper/001/000016.stats\n", "FILE trimming/1-overlapper/001/000016.counts\n", "FILE trimming/1-overlapper/001/000017.stats\n", "FILE trimming/1-overlapper/001/000017.counts\n", "FILE trimming/1-overlapper/001/000018.stats\n", "FILE trimming/1-overlapper/001/000018.counts\n", "FILE trimming/1-overlapper/001/000019.stats\n", "FILE trimming/1-overlapper/001/000019.counts\n", "FILE trimming/1-overlapper/001/000020.stats\n", "FILE trimming/1-overlapper/001/000020.counts\n", "FILE trimming/1-overlapper/001/000021.stats\n", "FILE trimming/1-overlapper/001/000021.counts\n", "FILE trimming/1-overlapper/001/000022.stats\n", "FILE trimming/1-overlapper/001/000022.counts\n", "FILE trimming/1-overlapper/001/000023.stats\n", "FILE trimming/1-overlapper/001/000023.counts\n", "FILE trimming/1-overlapper/001/000024.stats\n", "FILE trimming/1-overlapper/001/000024.counts\n", "FILE trimming/1-overlapper/001/000025.stats\n", "FILE trimming/1-overlapper/001/000025.counts\n", "FILE trimming/1-overlapper/001/000026.stats\n", "FILE trimming/1-overlapper/001/000026.counts\n", "FILE trimming/1-overlapper/001/000027.stats\n", "FILE trimming/1-overlapper/001/000027.counts\n", "FILE trimming/1-overlapper/001/000028.stats\n", "FILE trimming/1-overlapper/001/000028.counts\n", "FILE trimming/1-overlapper/001/000029.stats\n", "FILE trimming/1-overlapper/001/000029.counts\n", "FILE trimming/1-overlapper/001/000030.stats\n", "FILE trimming/1-overlapper/001/000030.counts\n", "FILE trimming/1-overlapper/001/000031.stats\n", "FILE trimming/1-overlapper/001/000031.counts\n", "FILE trimming/1-overlapper/001/000032.stats\n", "FILE trimming/1-overlapper/001/000032.counts\n", "FILE trimming/1-overlapper/001/000033.stats\n", "FILE trimming/1-overlapper/001/000033.counts\n", "FILE trimming/1-overlapper/001/000034.stats\n", "FILE trimming/1-overlapper/001/000034.counts\n", "FILE trimming/1-overlapper/001/000035.stats\n", "FILE trimming/1-overlapper/001/000035.counts\n", "FILE trimming/1-overlapper/001/000036.stats\n", "FILE trimming/1-overlapper/001/000036.counts\n", "FILE trimming/1-overlapper/001/000037.stats\n", "FILE trimming/1-overlapper/001/000037.counts\n", "FILE trimming/1-overlapper/001/000038.stats\n", "FILE trimming/1-overlapper/001/000038.counts\n", "FILE trimming/1-overlapper/001/000039.stats\n", "FILE trimming/1-overlapper/001/000039.counts\n", "FILE trimming/1-overlapper/001/000040.stats\n", "FILE trimming/1-overlapper/001/000040.counts\n", "FILE trimming/1-overlapper/001/000041.stats\n", "FILE trimming/1-overlapper/001/000041.counts\n", "FILE trimming/1-overlapper/001/000042.stats\n", "FILE trimming/1-overlapper/001/000042.counts\n", "FILE trimming/1-overlapper/001/000043.stats\n", "FILE trimming/1-overlapper/001/000043.counts\n", "FILE trimming/1-overlapper/001/000044.stats\n", "FILE trimming/1-overlapper/001/000044.counts\n", "FILE trimming/1-overlapper/001/000045.stats\n", "FILE trimming/1-overlapper/001/000045.counts\n", "FILE trimming/1-overlapper/001/000046.stats\n", "FILE trimming/1-overlapper/001/000046.counts\n", "FILE trimming/1-overlapper/001/000047.stats\n", "FILE trimming/1-overlapper/001/000047.counts\n", "FILE trimming/1-overlapper/001/000048.stats\n", "FILE trimming/1-overlapper/001/000048.counts\n", "FILE trimming/1-overlapper/001/000049.stats\n", "FILE trimming/1-overlapper/001/000049.counts\n", "FILE trimming/1-overlapper/001/000050.stats\n", "FILE trimming/1-overlapper/001/000050.counts\n", "FILE trimming/1-overlapper/001/000051.stats\n", "FILE trimming/1-overlapper/001/000051.counts\n", "FILE trimming/1-overlapper/001/000052.stats\n", "FILE trimming/1-overlapper/001/000052.counts\n", "FILE trimming/1-overlapper/001/000053.stats\n", "FILE trimming/1-overlapper/001/000053.counts\n", "FILE trimming/1-overlapper/001/000054.stats\n", "FILE trimming/1-overlapper/001/000054.counts\n", "FILE trimming/1-overlapper/001/000055.stats\n", "FILE trimming/1-overlapper/001/000055.counts\n", "FILE trimming/1-overlapper/001/000056.stats\n", "FILE trimming/1-overlapper/001/000056.counts\n", "FILE trimming/1-overlapper/001/000057.stats\n", "FILE trimming/1-overlapper/001/000057.counts\n", "FILE trimming/1-overlapper/001/000058.stats\n", "FILE trimming/1-overlapper/001/000058.counts\n", "FILE trimming/1-overlapper/001/000059.stats\n", "FILE trimming/1-overlapper/001/000059.counts\n", "FILE trimming/1-overlapper/001/000060.stats\n", "FILE trimming/1-overlapper/001/000060.counts\n", "FILE trimming/1-overlapper/001/000061.stats\n", "FILE trimming/1-overlapper/001/000061.counts\n", "FILE trimming/1-overlapper/001/000062.stats\n", "FILE trimming/1-overlapper/001/000062.counts\n", "FILE trimming/1-overlapper/001/000063.stats\n", "FILE trimming/1-overlapper/001/000063.counts\n", "FILE trimming/1-overlapper/001/000064.stats\n", "FILE trimming/1-overlapper/001/000064.counts\n", "FILE trimming/1-overlapper/001/000065.stats\n", "FILE trimming/1-overlapper/001/000065.counts\n", "FILE trimming/1-overlapper/001/000066.stats\n", "FILE trimming/1-overlapper/001/000066.counts\n", "FILE trimming/1-overlapper/001/000067.stats\n", "FILE trimming/1-overlapper/001/000067.counts\n", "FILE trimming/1-overlapper/001/000068.stats\n", "FILE trimming/1-overlapper/001/000068.counts\n", "FILE trimming/1-overlapper/001/000069.stats\n", "FILE trimming/1-overlapper/001/000069.counts\n", "FILE trimming/1-overlapper/001/000070.stats\n", "FILE trimming/1-overlapper/001/000070.counts\n", "FILE trimming/1-overlapper/001/000071.stats\n", "FILE trimming/1-overlapper/001/000071.counts\n", "FILE trimming/1-overlapper/001/000072.stats\n", "FILE trimming/1-overlapper/001/000072.counts\n", "FILE trimming/1-overlapper/001/000073.stats\n", "FILE trimming/1-overlapper/001/000073.counts\n", "FILE trimming/1-overlapper/001/000074.stats\n", "FILE trimming/1-overlapper/001/000074.counts\n", "FILE trimming/1-overlapper/001/000075.stats\n", "FILE trimming/1-overlapper/001/000075.counts\n", "FILE trimming/1-overlapper/001/000076.stats\n", "FILE trimming/1-overlapper/001/000076.counts\n", "FILE trimming/1-overlapper/001/000077.stats\n", "FILE trimming/1-overlapper/001/000077.counts\n", "FILE trimming/1-overlapper/001/000078.stats\n", "FILE trimming/1-overlapper/001/000078.counts\n", "FILE trimming/1-overlapper/001/000079.stats\n", "FILE trimming/1-overlapper/001/000079.counts\n", "FILE trimming/1-overlapper/001/000080.stats\n", "FILE trimming/1-overlapper/001/000080.counts\n", "FILE trimming/1-overlapper/001/000081.stats\n", "FILE trimming/1-overlapper/001/000081.counts\n", "FILE trimming/1-overlapper/001/000082.stats\n", "FILE trimming/1-overlapper/001/000082.counts\n", "FILE trimming/1-overlapper/001/000083.stats\n", "FILE trimming/1-overlapper/001/000083.counts\n", "FILE trimming/1-overlapper/001/000084.stats\n", "FILE trimming/1-overlapper/001/000084.counts\n", "FILE trimming/1-overlapper/001/000085.stats\n", "FILE trimming/1-overlapper/001/000085.counts\n", "FILE trimming/1-overlapper/001/000086.stats\n", "FILE trimming/1-overlapper/001/000086.counts\n", "FILE trimming/1-overlapper/001/000087.stats\n", "FILE trimming/1-overlapper/001/000087.counts\n", "FILE trimming/1-overlapper/001/000088.stats\n", "FILE trimming/1-overlapper/001/000088.counts\n", "FILE trimming/1-overlapper/001/000089.stats\n", "FILE trimming/1-overlapper/001/000089.counts\n", "FILE trimming/1-overlapper/001/000090.stats\n", "FILE trimming/1-overlapper/001/000090.counts\n", "FILE trimming/1-overlapper/001/000091.stats\n", "FILE trimming/1-overlapper/001/000091.counts\n", "FILE trimming/1-overlapper/001/000092.stats\n", "FILE trimming/1-overlapper/001/000092.counts\n", "FILE trimming/1-overlapper/001/000093.stats\n", "FILE trimming/1-overlapper/001/000093.counts\n", "FILE trimming/1-overlapper/001/000094.stats\n", "FILE trimming/1-overlapper/001/000094.counts\n", "FILE trimming/1-overlapper/001/000095.stats\n", "FILE trimming/1-overlapper/001/000095.counts\n", "FILE trimming/1-overlapper/001/000096.stats\n", "FILE trimming/1-overlapper/001/000096.counts\n", "FILE trimming/1-overlapper/001/000097.stats\n", "FILE trimming/1-overlapper/001/000097.counts\n", "FILE trimming/1-overlapper/001/000098.stats\n", "FILE trimming/1-overlapper/001/000098.counts\n", "FILE trimming/1-overlapper/001/000099.stats\n", "FILE trimming/1-overlapper/001/000099.counts\n", "FILE trimming/1-overlapper/001/000100.stats\n", "FILE trimming/1-overlapper/001/000100.counts\n", "FILE trimming/1-overlapper/001/000101.stats\n", "FILE trimming/1-overlapper/001/000101.counts\n", "FILE trimming/1-overlapper/001/000102.stats\n", "FILE trimming/1-overlapper/001/000102.counts\n", "FILE trimming/1-overlapper/001/000103.stats\n", "FILE trimming/1-overlapper/001/000103.counts\n", "FILE trimming/1-overlapper/001/000104.stats\n", "FILE trimming/1-overlapper/001/000104.counts\n", "FILE trimming/1-overlapper/001/000105.stats\n", "FILE trimming/1-overlapper/001/000105.counts\n", "FILE trimming/1-overlapper/001/000106.stats\n", "FILE trimming/1-overlapper/001/000106.counts\n", "FILE trimming/1-overlapper/001/000107.stats\n", "FILE trimming/1-overlapper/001/000107.counts\n", "FILE trimming/1-overlapper/001/000108.stats\n", "FILE trimming/1-overlapper/001/000108.counts\n", "FILE trimming/1-overlapper/001/000109.stats\n", "FILE trimming/1-overlapper/001/000109.counts\n", "FILE trimming/1-overlapper/001/000110.stats\n", "FILE trimming/1-overlapper/001/000110.counts\n", "FILE trimming/1-overlapper/001/000111.stats\n", "FILE trimming/1-overlapper/001/000111.counts\n", "FILE trimming/1-overlapper/001/000112.stats\n", "FILE trimming/1-overlapper/001/000112.counts\n", "FILE trimming/1-overlapper/001/000113.stats\n", "FILE trimming/1-overlapper/001/000113.counts\n", "FILE trimming/1-overlapper/001/000114.stats\n", "FILE trimming/1-overlapper/001/000114.counts\n", "FILE trimming/1-overlapper/001/000115.stats\n", "FILE trimming/1-overlapper/001/000115.counts\n", "FILE trimming/1-overlapper/001/000116.stats\n", "FILE trimming/1-overlapper/001/000116.counts\n", "FILE trimming/1-overlapper/001/000117.stats\n", "FILE trimming/1-overlapper/001/000117.counts\n", "--\n", "-- Purged 1.387 GB in 351 overlap output files.\n", "-- Overlap store 'trimming/20171018_oly_pacbio.ovlStore' statistics not available (skipped in correction and trimming stages).\n", "--\n", "-- Finished stage 'obt-createOverlapStore', reset canuIteration.\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 19:55:49 2017 with 832.49 GB free disk space\n", "\n", " cd trimming/3-overlapbasedtrimming\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/trimReads \\\n", " -G ../20171018_oly_pacbio.gkpStore \\\n", " -O ../20171018_oly_pacbio.ovlStore \\\n", " -Co ./20171018_oly_pacbio.1.trimReads.clear \\\n", " -e 0.075 \\\n", " -minlength 1000 \\\n", " -ol 1 \\\n", " -oc 1 \\\n", " -o ./20171018_oly_pacbio.1.trimReads \\\n", " > ./20171018_oly_pacbio.1.trimReads.err 2>&1\n", "\n", "-- Finished on Fri Oct 20 19:56:34 2017 (45 seconds) with 832.388 GB free disk space\n", "----------------------------------------\n", "-- PARAMETERS:\n", "-- ----------\n", "-- 1000 (reads trimmed below this many bases are deleted)\n", "-- 0.0750 (use overlaps at or below this fraction error)\n", "-- 1 (break region if overlap is less than this long, for 'largest covered' algorithm)\n", "-- 1 (break region if overlap coverage is less than this many read, for 'largest covered' algorithm)\n", "-- \n", "-- INPUT READS:\n", "-- -----------\n", "-- 1665075 reads 11661226162 bases (reads processed)\n", "-- 0 reads 0 bases (reads not processed, previously deleted)\n", "-- 0 reads 0 bases (reads not processed, in a library where trimming isn't allowed)\n", "-- \n", "-- OUTPUT READS:\n", "-- ------------\n", "-- 712481 reads 3458657537 bases (trimmed reads output)\n", "-- 10785 reads 59293896 bases (reads with no change, kept as is)\n", "-- 867850 reads 5755379456 bases (reads with no overlaps, deleted)\n", "-- 73959 reads 499189010 bases (reads with short trimmed length, deleted)\n", "-- \n", "-- TRIMMING DETAILS:\n", "-- ----------------\n", "-- 639125 reads 1149862364 bases (bases trimmed from the 5' end of a read)\n", "-- 686805 reads 738843899 bases (bases trimmed from the 3' end of a read)\n", "-- Finished stage 'obt-trimReads', reset canuIteration.\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 19:56:34 2017 with 832.388 GB free disk space\n", "\n", " cd trimming/3-overlapbasedtrimming\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/splitReads \\\n", " -G ../20171018_oly_pacbio.gkpStore \\\n", " -O ../20171018_oly_pacbio.ovlStore \\\n", " -Ci ./20171018_oly_pacbio.1.trimReads.clear \\\n", " -Co ./20171018_oly_pacbio.2.splitReads.clear \\\n", " -e 0.075 \\\n", " -minlength 1000 \\\n", " -o ./20171018_oly_pacbio.2.splitReads \\\n", " > ./20171018_oly_pacbio.2.splitReads.err 2>&1\n", "\n", "-- Finished on Fri Oct 20 19:57:06 2017 (32 seconds) with 832.375 GB free disk space\n", "----------------------------------------\n", "-- PARAMETERS:\n", "-- ----------\n", "-- 1000 (reads trimmed below this many bases are deleted)\n", "-- 0.0750 (use overlaps at or below this fraction error)\n", "-- INPUT READS:\n", "-- -----------\n", "-- 723266 reads 5406657696 bases (reads processed)\n", "-- 941809 reads 6254568466 bases (reads not processed, previously deleted)\n", "-- 0 reads 0 bases (reads not processed, in a library where trimming isn't allowed)\n", "-- \n", "-- PROCESSED:\n", "-- --------\n", "-- 0 reads 0 bases (no overlaps)\n", "-- 3211 reads 24048944 bases (no coverage after adjusting for trimming done already)\n", "-- 0 reads 0 bases (processed for chimera)\n", "-- 0 reads 0 bases (processed for spur)\n", "-- 720055 reads 5382608752 bases (processed for subreads)\n", "-- \n", "-- READS WITH SIGNALS:\n", "-- ------------------\n", "-- 0 reads 0 signals (number of 5' spur signal)\n", "-- 0 reads 0 signals (number of 3' spur signal)\n", "-- 0 reads 0 signals (number of chimera signal)\n", "-- 1289 reads 1310 signals (number of subread signal)\n", "-- \n", "-- SIGNALS:\n", "-- -------\n", "-- 0 reads 0 bases (size of 5' spur signal)\n", "-- 0 reads 0 bases (size of 3' spur signal)\n", "-- 0 reads 0 bases (size of chimera signal)\n", "-- 1310 reads 418184 bases (size of subread signal)\n", "-- \n", "-- TRIMMING:\n", "-- --------\n", "-- 655 reads 2190728 bases (trimmed from the 5' end of the read)\n", "-- 637 reads 2255145 bases (trimmed from the 3' end of the read)\n", "-- Finished stage 'obt-splitReads', reset canuIteration.\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 19:57:07 2017 with 832.375 GB free disk space\n", "\n", " cd trimming\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/gatekeeperDumpFASTQ -fasta -nolibname \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -c ./3-overlapbasedtrimming/20171018_oly_pacbio.2.splitReads.clear \\\n", " -o ../20171018_oly_pacbio.trimmedReads.gz \\\n", " > ../20171018_oly_pacbio.trimmedReads.err 2>&1\n", "\n", "-- Finished on Fri Oct 20 19:58:19 2017 (72 seconds) with 831.247 GB free disk space\n", "----------------------------------------\n", "-- Finished stage 'obt-dumpReads', reset canuIteration.\n", "--\n", "-- Trimmed reads saved in 'trimming/20171018_oly_pacbio.trimmedReads.fasta.gz'\n", "--\n", "--\n", "-- BEGIN ASSEMBLY\n", "--\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 19:58:20 2017 with 833.292 GB free disk space\n", "\n", " cd unitigging\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/gatekeeperCreate \\\n", " -minlength 1000 \\\n", " -o ./20171018_oly_pacbio.gkpStore.BUILDING \\\n", " ./20171018_oly_pacbio.gkpStore.gkp \\\n", " > ./20171018_oly_pacbio.gkpStore.BUILDING.err 2>&1\n", "\n", "-- Finished on Fri Oct 20 19:59:18 2017 (58 seconds) with 832.265 GB free disk space\n", "----------------------------------------\n", "--\n", "-- In gatekeeper store 'unitigging/20171018_oly_pacbio.gkpStore':\n", "-- Found 723260 reads.\n", "-- Found 3513500524 bases (1.84 times coverage).\n", "--\n", "-- Read length histogram (one '*' equals 1701.81 reads):\n", "-- 0 999 0 \n", "-- 1000 1999 112782 ******************************************************************\n", "-- 2000 2999 91499 *****************************************************\n", "-- 3000 3999 83298 ************************************************\n", "-- 4000 4999 78185 *********************************************\n", "-- 5000 5999 119127 **********************************************************************\n", "-- 6000 6999 114487 *******************************************************************\n", "-- 7000 7999 57597 *********************************\n", "-- 8000 8999 29853 *****************\n", "-- 9000 9999 16050 *********\n", "-- 10000 10999 8856 *****\n", "-- 11000 11999 4946 **\n", "-- 12000 12999 2980 *\n", "-- 13000 13999 1555 \n", "-- 14000 14999 900 \n", "-- 15000 15999 476 \n", "-- 16000 16999 284 \n", "-- 17000 17999 178 \n", "-- 18000 18999 79 \n", "-- 19000 19999 60 \n", "-- 20000 20999 29 \n", "-- 21000 21999 13 \n", "-- 22000 22999 9 \n", "-- 23000 23999 2 \n", "-- 24000 24999 9 \n", "-- 25000 25999 3 \n", "-- 26000 26999 2 \n", "-- 27000 27999 0 \n", "-- 28000 28999 0 \n", "-- 29000 29999 0 \n", "-- 30000 30999 0 \n", "-- 31000 31999 0 \n", "-- 32000 32999 1 \n", "-- Finished stage 'utg-gatekeeper', reset canuIteration.\n", "-- Finished stage 'merylConfigure', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'meryl' concurrent execution on Fri Oct 20 19:59:28 2017 with 832.244 GB free disk space (1 processes; 1 concurrently)\n", "\n", " cd unitigging/0-mercounts\n", " ./meryl.sh 1 > ./meryl.000001.out 2>&1\n", "\n", "-- Finished on Fri Oct 20 20:05:41 2017 (373 seconds) with 826.267 GB free disk space\n", "----------------------------------------\n", "-- Meryl finished successfully.\n", "-- Finished stage 'merylCheck', reset canuIteration.\n", "--\n", "-- 22-mers Fraction\n", "-- Occurrences NumMers Unique Total\n", "-- 1- 1 725696616 *******************************************************************--> 0.6568 0.2074\n", "-- 2- 2 123437132 ********************************************************************** 0.7685 0.2780\n", "-- 3- 4 104020258 ********************************************************** 0.8253 0.3319\n", "-- 5- 7 73227892 ***************************************** 0.8905 0.4230\n", "-- 8- 11 42101119 *********************** 0.9422 0.5347\n", "-- 12- 16 18520505 ********** 0.9720 0.6308\n", "-- 17- 22 6981818 *** 0.9854 0.6923\n", "-- 23- 29 3099691 * 0.9906 0.7255\n", "-- 30- 37 1925672 * 0.9932 0.7467\n", "-- 38- 46 1384781 0.9948 0.7644\n", "-- 47- 56 1004329 0.9960 0.7805\n", "-- 57- 67 724229 0.9969 0.7949\n", "-- 68- 79 531154 0.9975 0.8073\n", "-- 80- 92 405947 0.9980 0.8183\n", "-- 93- 106 312986 0.9983 0.8281\n", "-- 107- 121 247423 0.9986 0.8368\n", "-- 122- 137 200424 0.9988 0.8448\n", "-- 138- 154 168840 0.9990 0.8521\n", "-- 155- 172 138460 0.9991 0.8591\n", "-- 173- 191 106811 0.9993 0.8655\n", "-- 192- 211 85471 0.9994 0.8710\n", "-- 212- 232 67771 0.9994 0.8758\n", "-- 233- 254 58104 0.9995 0.8801\n", "-- 255- 277 49886 0.9995 0.8841\n", "-- 278- 301 43767 0.9996 0.8879\n", "-- 302- 326 37472 0.9996 0.8915\n", "-- 327- 352 33145 0.9997 0.8948\n", "-- 353- 379 29659 0.9997 0.8980\n", "-- 380- 407 26130 0.9997 0.9011\n", "-- 408- 436 23742 0.9997 0.9041\n", "-- 437- 466 22165 0.9998 0.9069\n", "-- 467- 497 20683 0.9998 0.9098\n", "-- 498- 529 19528 0.9998 0.9126\n", "-- 530- 562 18025 0.9998 0.9155\n", "-- 563- 596 16088 0.9998 0.9183\n", "-- 597- 631 14130 0.9999 0.9209\n", "-- 632- 667 12734 0.9999 0.9234\n", "-- 668- 704 10497 0.9999 0.9258\n", "-- 705- 742 8933 0.9999 0.9278\n", "-- 743- 781 7716 0.9999 0.9297\n", "-- 782- 821 6982 0.9999 0.9313\n", "--\n", "-- 1180657 (max occurrences)\n", "-- 2772615448 (total mers, non-unique)\n", "-- 379253455 (distinct mers, non-unique)\n", "-- 725696616 (unique mers)\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 20:05:41 2017 with 826.267 GB free disk space\n", "\n", " cd unitigging/0-mercounts\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/meryl \\\n", " -Dt \\\n", " -n 574 \\\n", " -s ./20171018_oly_pacbio.ms22 \\\n", " > ./20171018_oly_pacbio.ms22.frequentMers.fasta \\\n", " 2> ./20171018_oly_pacbio.ms22.frequentMers.fasta.err\n", "\n", "-- Finished on Fri Oct 20 20:06:11 2017 (30 seconds) with 826.263 GB free disk space\n", "----------------------------------------\n", "-- Reset utgOvlMerThreshold from auto to 574.\n", "--\n", "-- Found 3498312064 22-mers; 1104950071 distinct and 725696616 unique. Largest count 1180657.\n", "-- Finished stage 'utg-meryl', reset canuIteration.\n", "--\n", "-- OVERLAPPER (normal) (assembly) erate=0.075\n", "--\n", "----------------------------------------\n", "-- Starting command on Fri Oct 20 20:06:11 2017 with 832.239 GB free disk space\n", "\n", " cd unitigging/1-overlapper\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/overlapInCorePartition \\\n", " -g ../20171018_oly_pacbio.gkpStore \\\n", " -bl 100000000 \\\n", " -bs 0 \\\n", " -rs 2000000 \\\n", " -rl 0 \\\n", " -ol 500 \\\n", " -o ./20171018_oly_pacbio.partition \\\n", " > ./20171018_oly_pacbio.partition.err 2>&1\n", "\n", "-- Finished on Fri Oct 20 20:06:11 2017 (lickety-split) with 832.239 GB free disk space\n", "----------------------------------------\n", "--\n", "-- Configured 36 overlapInCore jobs.\n", "-- Finished stage 'utg-overlapConfigure', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'utgovl' concurrent execution on Fri Oct 20 20:06:11 2017 with 832.239 GB free disk space (36 processes; 3 concurrently)\n", "\n", " cd unitigging/1-overlapper\n", " ./overlap.sh 1 > ./overlap.000001.out 2>&1\n", " ./overlap.sh 2 > ./overlap.000002.out 2>&1\n", " ./overlap.sh 3 > ./overlap.000003.out 2>&1\n", " ./overlap.sh 4 > ./overlap.000004.out 2>&1\n", " ./overlap.sh 5 > ./overlap.000005.out 2>&1\n", " ./overlap.sh 6 > ./overlap.000006.out 2>&1\n", " ./overlap.sh 7 > ./overlap.000007.out 2>&1\n", " ./overlap.sh 8 > ./overlap.000008.out 2>&1\n", " ./overlap.sh 9 > ./overlap.000009.out 2>&1\n", " ./overlap.sh 10 > ./overlap.000010.out 2>&1\n", " ./overlap.sh 11 > ./overlap.000011.out 2>&1\n", " ./overlap.sh 12 > ./overlap.000012.out 2>&1\n", " ./overlap.sh 13 > ./overlap.000013.out 2>&1\n", " ./overlap.sh 14 > ./overlap.000014.out 2>&1\n", " ./overlap.sh 15 > ./overlap.000015.out 2>&1\n", " ./overlap.sh 16 > ./overlap.000016.out 2>&1\n", " ./overlap.sh 17 > ./overlap.000017.out 2>&1\n", " ./overlap.sh 18 > ./overlap.000018.out 2>&1\n", " ./overlap.sh 19 > ./overlap.000019.out 2>&1\n", " ./overlap.sh 20 > ./overlap.000020.out 2>&1\n", " ./overlap.sh 21 > ./overlap.000021.out 2>&1\n", " ./overlap.sh 22 > ./overlap.000022.out 2>&1\n", " ./overlap.sh 23 > ./overlap.000023.out 2>&1\n", " ./overlap.sh 24 > ./overlap.000024.out 2>&1\n", " ./overlap.sh 25 > ./overlap.000025.out 2>&1\n", " ./overlap.sh 26 > ./overlap.000026.out 2>&1\n", " ./overlap.sh 27 > ./overlap.000027.out 2>&1\n", " ./overlap.sh 28 > ./overlap.000028.out 2>&1\n", " ./overlap.sh 29 > ./overlap.000029.out 2>&1\n", " ./overlap.sh 30 > ./overlap.000030.out 2>&1\n", " ./overlap.sh 31 > ./overlap.000031.out 2>&1\n", " ./overlap.sh 32 > ./overlap.000032.out 2>&1\n", " ./overlap.sh 33 > ./overlap.000033.out 2>&1\n", " ./overlap.sh 34 > ./overlap.000034.out 2>&1\n", " ./overlap.sh 35 > ./overlap.000035.out 2>&1\n", " ./overlap.sh 36 > ./overlap.000036.out 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:09:56 2017 (18225 seconds) with 831.975 GB free disk space\n", "----------------------------------------\n", "-- Found 36 overlapInCore output files.\n", "--\n", "-- overlapInCore compute 'unitigging/1-overlapper':\n", "-- kmer hits\n", "-- with no overlap 3213673599 11.0833333 +- 54804988.866\n", "-- with an overlap 12904018 .944444444 +- 232589.324\n", "--\n", "-- overlaps 12904018 .944444444 +- 232589.324\n", "-- contained 5611059 155862.75 +- 109113.414\n", "-- dovetail 7292959 .194444444 +- 125630.562\n", "--\n", "-- overlaps rejected\n", "-- multiple per pair 0 0 +- 0\n", "-- bad short window 0 0 +- 0\n", "-- bad long window 0 0 +- 0\n", "-- Finished stage 'utg-overlapCheck', reset canuIteration.\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:09:56 2017 with 831.975 GB free disk space\n", "\n", " cd unitigging\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/ovStoreBuild \\\n", " -O ./20171018_oly_pacbio.ovlStore.BUILDING \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -M 4-32 \\\n", " -L ./1-overlapper/ovljob.files \\\n", " > ./20171018_oly_pacbio.ovlStore.err 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:10:08 2017 (12 seconds) with 831.478 GB free disk space\n", "----------------------------------------\n", "-- Checking store.\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:10:08 2017 with 831.478 GB free disk space\n", "\n", " cd unitigging\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/ovStoreDump \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -O ./20171018_oly_pacbio.ovlStore \\\n", " -d -counts \\\n", " > ./20171018_oly_pacbio.ovlStore/counts.dat 2> ./20171018_oly_pacbio.ovlStore/counts.err\n", "\n", "-- Finished on Sat Oct 21 01:10:08 2017 (lickety-split) with 831.471 GB free disk space\n", "----------------------------------------\n", "--\n", "-- Overlap store 'unitigging/20171018_oly_pacbio.ovlStore' successfully constructed.\n", "-- Found 25808036 overlaps for 718569 reads; 4691 reads have no overlaps.\n", "--\n", "FILE unitigging/1-overlapper/001/000001.ovb\n", "FILE unitigging/1-overlapper/001/000002.ovb\n", "FILE unitigging/1-overlapper/001/000003.ovb\n", "FILE unitigging/1-overlapper/001/000004.ovb\n", "FILE unitigging/1-overlapper/001/000005.ovb\n", "FILE unitigging/1-overlapper/001/000006.ovb\n", "FILE unitigging/1-overlapper/001/000007.ovb\n", "FILE unitigging/1-overlapper/001/000008.ovb\n", "FILE unitigging/1-overlapper/001/000009.ovb\n", "FILE unitigging/1-overlapper/001/000010.ovb\n", "FILE unitigging/1-overlapper/001/000011.ovb\n", "FILE unitigging/1-overlapper/001/000012.ovb\n", "FILE unitigging/1-overlapper/001/000013.ovb\n", "FILE unitigging/1-overlapper/001/000014.ovb\n", "FILE unitigging/1-overlapper/001/000015.ovb\n", "FILE unitigging/1-overlapper/001/000016.ovb\n", "FILE unitigging/1-overlapper/001/000017.ovb\n", "FILE unitigging/1-overlapper/001/000018.ovb\n", "FILE unitigging/1-overlapper/001/000019.ovb\n", "FILE unitigging/1-overlapper/001/000020.ovb\n", "FILE unitigging/1-overlapper/001/000021.ovb\n", "FILE unitigging/1-overlapper/001/000022.ovb\n", "FILE unitigging/1-overlapper/001/000023.ovb\n", "FILE unitigging/1-overlapper/001/000024.ovb\n", "FILE unitigging/1-overlapper/001/000025.ovb\n", "FILE unitigging/1-overlapper/001/000026.ovb\n", "FILE unitigging/1-overlapper/001/000027.ovb\n", "FILE unitigging/1-overlapper/001/000028.ovb\n", "FILE unitigging/1-overlapper/001/000029.ovb\n", "FILE unitigging/1-overlapper/001/000030.ovb\n", "FILE unitigging/1-overlapper/001/000031.ovb\n", "FILE unitigging/1-overlapper/001/000032.ovb\n", "FILE unitigging/1-overlapper/001/000033.ovb\n", "FILE unitigging/1-overlapper/001/000034.ovb\n", "FILE unitigging/1-overlapper/001/000035.ovb\n", "FILE unitigging/1-overlapper/001/000036.ovb\n", "FILE unitigging/1-overlapper/001/000001.stats\n", "FILE unitigging/1-overlapper/001/000001.counts\n", "FILE unitigging/1-overlapper/001/000002.stats\n", "FILE unitigging/1-overlapper/001/000002.counts\n", "FILE unitigging/1-overlapper/001/000003.stats\n", "FILE unitigging/1-overlapper/001/000003.counts\n", "FILE unitigging/1-overlapper/001/000004.stats\n", "FILE unitigging/1-overlapper/001/000004.counts\n", "FILE unitigging/1-overlapper/001/000005.stats\n", "FILE unitigging/1-overlapper/001/000005.counts\n", "FILE unitigging/1-overlapper/001/000006.stats\n", "FILE unitigging/1-overlapper/001/000006.counts\n", "FILE unitigging/1-overlapper/001/000007.stats\n", "FILE unitigging/1-overlapper/001/000007.counts\n", "FILE unitigging/1-overlapper/001/000008.stats\n", "FILE unitigging/1-overlapper/001/000008.counts\n", "FILE unitigging/1-overlapper/001/000009.stats\n", "FILE unitigging/1-overlapper/001/000009.counts\n", "FILE unitigging/1-overlapper/001/000010.stats\n", "FILE unitigging/1-overlapper/001/000010.counts\n", "FILE unitigging/1-overlapper/001/000011.stats\n", "FILE unitigging/1-overlapper/001/000011.counts\n", "FILE unitigging/1-overlapper/001/000012.stats\n", "FILE unitigging/1-overlapper/001/000012.counts\n", "FILE unitigging/1-overlapper/001/000013.stats\n", "FILE unitigging/1-overlapper/001/000013.counts\n", "FILE unitigging/1-overlapper/001/000014.stats\n", "FILE unitigging/1-overlapper/001/000014.counts\n", "FILE unitigging/1-overlapper/001/000015.stats\n", "FILE unitigging/1-overlapper/001/000015.counts\n", "FILE unitigging/1-overlapper/001/000016.stats\n", "FILE unitigging/1-overlapper/001/000016.counts\n", "FILE unitigging/1-overlapper/001/000017.stats\n", "FILE unitigging/1-overlapper/001/000017.counts\n", "FILE unitigging/1-overlapper/001/000018.stats\n", "FILE unitigging/1-overlapper/001/000018.counts\n", "FILE unitigging/1-overlapper/001/000019.stats\n", "FILE unitigging/1-overlapper/001/000019.counts\n", "FILE unitigging/1-overlapper/001/000020.stats\n", "FILE unitigging/1-overlapper/001/000020.counts\n", "FILE unitigging/1-overlapper/001/000021.stats\n", "FILE unitigging/1-overlapper/001/000021.counts\n", "FILE unitigging/1-overlapper/001/000022.stats\n", "FILE unitigging/1-overlapper/001/000022.counts\n", "FILE unitigging/1-overlapper/001/000023.stats\n", "FILE unitigging/1-overlapper/001/000023.counts\n", "FILE unitigging/1-overlapper/001/000024.stats\n", "FILE unitigging/1-overlapper/001/000024.counts\n", "FILE unitigging/1-overlapper/001/000025.stats\n", "FILE unitigging/1-overlapper/001/000025.counts\n", "FILE unitigging/1-overlapper/001/000026.stats\n", "FILE unitigging/1-overlapper/001/000026.counts\n", "FILE unitigging/1-overlapper/001/000027.stats\n", "FILE unitigging/1-overlapper/001/000027.counts\n", "FILE unitigging/1-overlapper/001/000028.stats\n", "FILE unitigging/1-overlapper/001/000028.counts\n", "FILE unitigging/1-overlapper/001/000029.stats\n", "FILE unitigging/1-overlapper/001/000029.counts\n", "FILE unitigging/1-overlapper/001/000030.stats\n", "FILE unitigging/1-overlapper/001/000030.counts\n", "FILE unitigging/1-overlapper/001/000031.stats\n", "FILE unitigging/1-overlapper/001/000031.counts\n", "FILE unitigging/1-overlapper/001/000032.stats\n", "FILE unitigging/1-overlapper/001/000032.counts\n", "FILE unitigging/1-overlapper/001/000033.stats\n", "FILE unitigging/1-overlapper/001/000033.counts\n", "FILE unitigging/1-overlapper/001/000034.stats\n", "FILE unitigging/1-overlapper/001/000034.counts\n", "FILE unitigging/1-overlapper/001/000035.stats\n", "FILE unitigging/1-overlapper/001/000035.counts\n", "FILE unitigging/1-overlapper/001/000036.stats\n", "FILE unitigging/1-overlapper/001/000036.counts\n", "--\n", "-- Purged 0.264 GB in 108 overlap output files.\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:10:09 2017 with 831.743 GB free disk space\n", "\n", " cd unitigging\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/ovStoreStats \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -O ./20171018_oly_pacbio.ovlStore \\\n", " -o ./20171018_oly_pacbio.ovlStore \\\n", " > ./20171018_oly_pacbio.ovlStore.summary.err 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:10:15 2017 (6 seconds) with 831.727 GB free disk space\n", "----------------------------------------\n", "--\n", "-- Overlap store 'unitigging/20171018_oly_pacbio.ovlStore' contains:\n", "--\n", "-- category reads % read length feature size or coverage analysis\n", "-- ---------------- ------- ------- ---------------------- ------------------------ --------------------\n", "-- middle-missing 1699 0.23 5836.53 +- 3147.72 626.11 +- 728.33 (bad trimming)\n", "-- middle-hump 18543 2.56 5119.56 +- 2621.57 111.13 +- 322.64 (bad trimming)\n", "-- no-5-prime 38530 5.33 5943.75 +- 2512.95 78.06 +- 283.14 (bad trimming)\n", "-- no-3-prime 33037 4.57 5855.59 +- 2636.73 88.36 +- 302.87 (bad trimming)\n", "-- \n", "-- low-coverage 266450 36.84 4000.00 +- 2281.65 4.18 +- 1.93 (easy to assemble, potential for lower quality consensus)\n", "-- unique 63758 8.82 3557.46 +- 1987.19 19.17 +- 8.73 (easy to assemble, perfect, yay)\n", "-- repeat-cont 21849 3.02 3844.08 +- 2434.09 384.74 +- 454.87 (potential for consensus errors, no impact on assembly)\n", "-- repeat-dove 102 0.01 10318.17 +- 3376.82 164.14 +- 117.96 (hard to assemble, likely won't assemble correctly or even at all)\n", "-- \n", "-- span-repeat 100087 13.84 6237.15 +- 2208.44 2815.30 +- 2079.79 (read spans a large repeat, usually easy to assemble)\n", "-- uniq-repeat-cont 142305 19.68 5250.49 +- 2081.27 (should be uniquely placed, low potential for consensus errors, no impact on assembly)\n", "-- uniq-repeat-dove 30539 4.22 7130.44 +- 2324.91 (will end contigs, potential to misassemble)\n", "-- uniq-anchor 1670 0.23 7121.67 +- 2410.15 2457.85 +- 1879.88 (repeat read, with unique section, probable bad read)\n", "-- Finished stage 'utg-createOverlapStore', reset canuIteration.\n", "\n", "Configure RED for 8gb memory with batches of at most 5000 reads and (unlimited) bases.\n", "\n", "RED job 1 from read 1 to read 5000 - 0.179 GB for 5000 reads - 0.154 GB for 12699528 olaps - 0.002 GB for evidence\n", "RED job 2 from read 5001 to read 10000 - 0.232 GB for 5000 reads - 0.200 GB for 16490428 olaps - 0.002 GB for evidence\n", "RED job 3 from read 10001 to read 15000 - 0.365 GB for 5000 reads - 0.314 GB for 25957103 olaps - 0.002 GB for evidence\n", "RED job 4 from read 15001 to read 20000 - 0.370 GB for 5000 reads - 0.319 GB for 26335141 olaps - 0.002 GB for evidence\n", "RED job 5 from read 20001 to read 25000 - 0.375 GB for 5000 reads - 0.323 GB for 26707638 olaps - 0.002 GB for evidence\n", "RED job 6 from read 25001 to read 30000 - 0.364 GB for 5000 reads - 0.313 GB for 25863790 olaps - 0.002 GB for evidence\n", "RED job 7 from read 30001 to read 35000 - 0.366 GB for 5000 reads - 0.315 GB for 26036510 olaps - 0.002 GB for evidence\n", "RED job 8 from read 35001 to read 40000 - 0.365 GB for 5000 reads - 0.315 GB for 26016912 olaps - 0.002 GB for evidence\n", "RED job 9 from read 40001 to read 45000 - 0.360 GB for 5000 reads - 0.310 GB for 25611209 olaps - 0.002 GB for evidence\n", "RED job 10 from read 45001 to read 50000 - 0.359 GB for 5000 reads - 0.310 GB for 25569349 olaps - 0.002 GB for evidence\n", "RED job 11 from read 50001 to read 55000 - 0.362 GB for 5000 reads - 0.312 GB for 25744876 olaps - 0.002 GB for evidence\n", "RED job 12 from read 55001 to read 60000 - 0.363 GB for 5000 reads - 0.313 GB for 25848749 olaps - 0.002 GB for evidence\n", "RED job 13 from read 60001 to read 65000 - 0.362 GB for 5000 reads - 0.312 GB for 25734564 olaps - 0.002 GB for evidence\n", "RED job 14 from read 65001 to read 70000 - 0.362 GB for 5000 reads - 0.312 GB for 25780279 olaps - 0.002 GB for evidence\n", "RED job 15 from read 70001 to read 75000 - 0.359 GB for 5000 reads - 0.310 GB for 25581342 olaps - 0.002 GB for evidence\n", "RED job 16 from read 75001 to read 80000 - 0.356 GB for 5000 reads - 0.306 GB for 25298494 olaps - 0.002 GB for evidence\n", "RED job 17 from read 80001 to read 85000 - 0.356 GB for 5000 reads - 0.306 GB for 25267326 olaps - 0.003 GB for evidence\n", "RED job 18 from read 85001 to read 90000 - 0.362 GB for 5000 reads - 0.312 GB for 25766329 olaps - 0.002 GB for evidence\n", "RED job 19 from read 90001 to read 95000 - 0.367 GB for 5000 reads - 0.317 GB for 26148506 olaps - 0.002 GB for evidence\n", "RED job 20 from read 95001 to read 100000 - 0.358 GB for 5000 reads - 0.308 GB for 25433634 olaps - 0.003 GB for evidence\n", "RED job 21 from read 100001 to read 105000 - 0.364 GB for 5000 reads - 0.314 GB for 25948473 olaps - 0.002 GB for evidence\n", "RED job 22 from read 105001 to read 110000 - 0.363 GB for 5000 reads - 0.312 GB for 25750752 olaps - 0.003 GB for evidence\n", "RED job 23 from read 110001 to read 115000 - 0.364 GB for 5000 reads - 0.313 GB for 25856651 olaps - 0.002 GB for evidence\n", "RED job 24 from read 115001 to read 120000 - 0.367 GB for 5000 reads - 0.316 GB for 26093606 olaps - 0.002 GB for evidence\n", "RED job 25 from read 120001 to read 125000 - 0.345 GB for 5000 reads - 0.297 GB for 24504092 olaps - 0.002 GB for evidence\n", "RED job 26 from read 125001 to read 130000 - 0.323 GB for 5000 reads - 0.278 GB for 22991050 olaps - 0.001 GB for evidence\n", "RED job 27 from read 130001 to read 135000 - 0.313 GB for 5000 reads - 0.269 GB for 22205184 olaps - 0.002 GB for evidence\n", "RED job 28 from read 135001 to read 140000 - 0.317 GB for 5000 reads - 0.273 GB for 22569315 olaps - 0.002 GB for evidence\n", "RED job 29 from read 140001 to read 145000 - 0.313 GB for 5000 reads - 0.269 GB for 22252079 olaps - 0.002 GB for evidence\n", "RED job 30 from read 145001 to read 150000 - 0.311 GB for 5000 reads - 0.268 GB for 22172846 olaps - 0.001 GB for evidence\n", "RED job 31 from read 150001 to read 155000 - 0.314 GB for 5000 reads - 0.271 GB for 22357589 olaps - 0.001 GB for evidence\n", "RED job 32 from read 155001 to read 160000 - 0.314 GB for 5000 reads - 0.271 GB for 22386372 olaps - 0.001 GB for evidence\n", "RED job 33 from read 160001 to read 165000 - 0.320 GB for 5000 reads - 0.276 GB for 22831650 olaps - 0.001 GB for evidence\n", "RED job 34 from read 165001 to read 170000 - 0.314 GB for 5000 reads - 0.271 GB for 22355267 olaps - 0.002 GB for evidence\n", "RED job 35 from read 170001 to read 175000 - 0.319 GB for 5000 reads - 0.275 GB for 22742124 olaps - 0.001 GB for evidence\n", "RED job 36 from read 175001 to read 180000 - 0.330 GB for 5000 reads - 0.284 GB for 23450790 olaps - 0.002 GB for evidence\n", "RED job 37 from read 180001 to read 185000 - 0.323 GB for 5000 reads - 0.279 GB for 23012499 olaps - 0.001 GB for evidence\n", "RED job 38 from read 185001 to read 190000 - 0.327 GB for 5000 reads - 0.282 GB for 23323168 olaps - 0.002 GB for evidence\n", "RED job 39 from read 190001 to read 195000 - 0.315 GB for 5000 reads - 0.272 GB for 22428042 olaps - 0.002 GB for evidence\n", "RED job 40 from read 195001 to read 200000 - 0.321 GB for 5000 reads - 0.277 GB for 22898421 olaps - 0.002 GB for evidence\n", "RED job 41 from read 200001 to read 205000 - 0.321 GB for 5000 reads - 0.277 GB for 22845916 olaps - 0.002 GB for evidence\n", "RED job 42 from read 205001 to read 210000 - 0.319 GB for 5000 reads - 0.275 GB for 22677202 olaps - 0.002 GB for evidence\n", "RED job 43 from read 210001 to read 215000 - 0.318 GB for 5000 reads - 0.274 GB for 22613114 olaps - 0.002 GB for evidence\n", "RED job 44 from read 215001 to read 220000 - 0.326 GB for 5000 reads - 0.281 GB for 23223569 olaps - 0.002 GB for evidence\n", "RED job 45 from read 220001 to read 225000 - 0.315 GB for 5000 reads - 0.271 GB for 22391128 olaps - 0.002 GB for evidence\n", "RED job 46 from read 225001 to read 230000 - 0.324 GB for 5000 reads - 0.279 GB for 23054719 olaps - 0.002 GB for evidence\n", "RED job 47 from read 230001 to read 235000 - 0.319 GB for 5000 reads - 0.275 GB for 22703059 olaps - 0.002 GB for evidence\n", "RED job 48 from read 235001 to read 240000 - 0.314 GB for 5000 reads - 0.271 GB for 22382874 olaps - 0.001 GB for evidence\n", "RED job 49 from read 240001 to read 245000 - 0.316 GB for 5000 reads - 0.272 GB for 22489149 olaps - 0.002 GB for evidence\n", "RED job 50 from read 245001 to read 250000 - 0.314 GB for 5000 reads - 0.270 GB for 22328431 olaps - 0.002 GB for evidence\n", "RED job 51 from read 250001 to read 255000 - 0.320 GB for 5000 reads - 0.276 GB for 22762815 olaps - 0.002 GB for evidence\n", "RED job 52 from read 255001 to read 260000 - 0.315 GB for 5000 reads - 0.271 GB for 22371562 olaps - 0.002 GB for evidence\n", "RED job 53 from read 260001 to read 265000 - 0.316 GB for 5000 reads - 0.272 GB for 22495407 olaps - 0.001 GB for evidence\n", "RED job 54 from read 265001 to read 270000 - 0.316 GB for 5000 reads - 0.273 GB for 22530392 olaps - 0.002 GB for evidence\n", "RED job 55 from read 270001 to read 275000 - 0.314 GB for 5000 reads - 0.271 GB for 22391897 olaps - 0.002 GB for evidence\n", "RED job 56 from read 275001 to read 280000 - 0.311 GB for 5000 reads - 0.268 GB for 22154065 olaps - 0.002 GB for evidence\n", "RED job 57 from read 280001 to read 285000 - 0.312 GB for 5000 reads - 0.269 GB for 22237041 olaps - 0.002 GB for evidence\n", "RED job 58 from read 285001 to read 290000 - 0.325 GB for 5000 reads - 0.280 GB for 23167594 olaps - 0.001 GB for evidence\n", "RED job 59 from read 290001 to read 295000 - 0.329 GB for 5000 reads - 0.284 GB for 23423581 olaps - 0.002 GB for evidence\n", "RED job 60 from read 295001 to read 300000 - 0.325 GB for 5000 reads - 0.280 GB for 23111858 olaps - 0.002 GB for evidence\n", "RED job 61 from read 300001 to read 305000 - 0.322 GB for 5000 reads - 0.277 GB for 22918482 olaps - 0.002 GB for evidence\n", "RED job 62 from read 305001 to read 310000 - 0.316 GB for 5000 reads - 0.273 GB for 22526904 olaps - 0.002 GB for evidence\n", "RED job 63 from read 310001 to read 315000 - 0.325 GB for 5000 reads - 0.280 GB for 23148371 olaps - 0.002 GB for evidence\n", "RED job 64 from read 315001 to read 320000 - 0.329 GB for 5000 reads - 0.284 GB for 23435958 olaps - 0.002 GB for evidence\n", "RED job 65 from read 320001 to read 325000 - 0.317 GB for 5000 reads - 0.274 GB for 22595084 olaps - 0.002 GB for evidence\n", "RED job 66 from read 325001 to read 330000 - 0.316 GB for 5000 reads - 0.272 GB for 22489182 olaps - 0.001 GB for evidence\n", "RED job 67 from read 330001 to read 335000 - 0.318 GB for 5000 reads - 0.274 GB for 22655119 olaps - 0.002 GB for evidence\n", "RED job 68 from read 335001 to read 340000 - 0.313 GB for 5000 reads - 0.270 GB for 22307862 olaps - 0.001 GB for evidence\n", "RED job 69 from read 340001 to read 345000 - 0.317 GB for 5000 reads - 0.273 GB for 22572975 olaps - 0.002 GB for evidence\n", "RED job 70 from read 345001 to read 350000 - 0.321 GB for 5000 reads - 0.277 GB for 22869877 olaps - 0.002 GB for evidence\n", "RED job 71 from read 350001 to read 355000 - 0.319 GB for 5000 reads - 0.275 GB for 22747650 olaps - 0.002 GB for evidence\n", "RED job 72 from read 355001 to read 360000 - 0.323 GB for 5000 reads - 0.279 GB for 23021710 olaps - 0.002 GB for evidence\n", "RED job 73 from read 360001 to read 365000 - 0.321 GB for 5000 reads - 0.276 GB for 22814404 olaps - 0.002 GB for evidence\n", "RED job 74 from read 365001 to read 370000 - 0.336 GB for 5000 reads - 0.289 GB for 23887432 olaps - 0.002 GB for evidence\n", "RED job 75 from read 370001 to read 375000 - 0.324 GB for 5000 reads - 0.280 GB for 23096541 olaps - 0.001 GB for evidence\n", "RED job 76 from read 375001 to read 380000 - 0.322 GB for 5000 reads - 0.278 GB for 22926314 olaps - 0.002 GB for evidence\n", "RED job 77 from read 380001 to read 385000 - 0.318 GB for 5000 reads - 0.274 GB for 22635464 olaps - 0.002 GB for evidence\n", "RED job 78 from read 385001 to read 390000 - 0.318 GB for 5000 reads - 0.274 GB for 22604104 olaps - 0.002 GB for evidence\n", "RED job 79 from read 390001 to read 395000 - 0.319 GB for 5000 reads - 0.275 GB for 22743884 olaps - 0.001 GB for evidence\n", "RED job 80 from read 395001 to read 400000 - 0.319 GB for 5000 reads - 0.275 GB for 22718821 olaps - 0.001 GB for evidence\n", "RED job 81 from read 400001 to read 405000 - 0.320 GB for 5000 reads - 0.275 GB for 22739842 olaps - 0.002 GB for evidence\n", "RED job 82 from read 405001 to read 410000 - 0.319 GB for 5000 reads - 0.276 GB for 22765841 olaps - 0.001 GB for evidence\n", "RED job 83 from read 410001 to read 415000 - 0.318 GB for 5000 reads - 0.274 GB for 22617799 olaps - 0.002 GB for evidence\n", "RED job 84 from read 415001 to read 420000 - 0.323 GB for 5000 reads - 0.278 GB for 22960144 olaps - 0.002 GB for evidence\n", "RED job 85 from read 420001 to read 425000 - 0.320 GB for 5000 reads - 0.275 GB for 22751340 olaps - 0.002 GB for evidence\n", "RED job 86 from read 425001 to read 430000 - 0.319 GB for 5000 reads - 0.275 GB for 22708614 olaps - 0.002 GB for evidence\n", "RED job 87 from read 430001 to read 435000 - 0.324 GB for 5000 reads - 0.280 GB for 23091800 olaps - 0.001 GB for evidence\n", "RED job 88 from read 435001 to read 440000 - 0.334 GB for 5000 reads - 0.287 GB for 23740279 olaps - 0.002 GB for evidence\n", "RED job 89 from read 440001 to read 445000 - 0.364 GB for 5000 reads - 0.314 GB for 25913215 olaps - 0.002 GB for evidence\n", "RED job 90 from read 445001 to read 450000 - 0.351 GB for 5000 reads - 0.302 GB for 24962345 olaps - 0.002 GB for evidence\n", "RED job 91 from read 450001 to read 455000 - 0.359 GB for 5000 reads - 0.310 GB for 25574367 olaps - 0.002 GB for evidence\n", "RED job 92 from read 455001 to read 460000 - 0.354 GB for 5000 reads - 0.305 GB for 25211327 olaps - 0.002 GB for evidence\n", "RED job 93 from read 460001 to read 465000 - 0.356 GB for 5000 reads - 0.306 GB for 25309280 olaps - 0.003 GB for evidence\n", "RED job 94 from read 465001 to read 470000 - 0.363 GB for 5000 reads - 0.313 GB for 25864570 olaps - 0.002 GB for evidence\n", "RED job 95 from read 470001 to read 475000 - 0.363 GB for 5000 reads - 0.313 GB for 25842910 olaps - 0.002 GB for evidence\n", "RED job 96 from read 475001 to read 480000 - 0.361 GB for 5000 reads - 0.311 GB for 25680078 olaps - 0.002 GB for evidence\n", "RED job 97 from read 480001 to read 485000 - 0.356 GB for 5000 reads - 0.307 GB for 25385509 olaps - 0.002 GB for evidence\n", "RED job 98 from read 485001 to read 490000 - 0.357 GB for 5000 reads - 0.308 GB for 25421336 olaps - 0.002 GB for evidence\n", "RED job 99 from read 490001 to read 495000 - 0.367 GB for 5000 reads - 0.317 GB for 26151253 olaps - 0.001 GB for evidence\n", "RED job 100 from read 495001 to read 500000 - 0.358 GB for 5000 reads - 0.309 GB for 25531031 olaps - 0.002 GB for evidence\n", "RED job 101 from read 500001 to read 505000 - 0.361 GB for 5000 reads - 0.311 GB for 25721368 olaps - 0.002 GB for evidence\n", "RED job 102 from read 505001 to read 510000 - 0.360 GB for 5000 reads - 0.310 GB for 25624760 olaps - 0.002 GB for evidence\n", "RED job 103 from read 510001 to read 515000 - 0.362 GB for 5000 reads - 0.311 GB for 25716013 olaps - 0.002 GB for evidence\n", "RED job 104 from read 515001 to read 520000 - 0.371 GB for 5000 reads - 0.320 GB for 26412419 olaps - 0.002 GB for evidence\n", "RED job 105 from read 520001 to read 525000 - 0.367 GB for 5000 reads - 0.316 GB for 26085074 olaps - 0.002 GB for evidence\n", "RED job 106 from read 525001 to read 530000 - 0.368 GB for 5000 reads - 0.317 GB for 26218930 olaps - 0.002 GB for evidence\n", "RED job 107 from read 530001 to read 535000 - 0.367 GB for 5000 reads - 0.316 GB for 26138395 olaps - 0.002 GB for evidence\n", "RED job 108 from read 535001 to read 540000 - 0.368 GB for 5000 reads - 0.318 GB for 26230674 olaps - 0.002 GB for evidence\n", "RED job 109 from read 540001 to read 545000 - 0.367 GB for 5000 reads - 0.315 GB for 26019450 olaps - 0.004 GB for evidence\n", "RED job 110 from read 545001 to read 550000 - 0.357 GB for 5000 reads - 0.307 GB for 25380106 olaps - 0.002 GB for evidence\n", "RED job 111 from read 550001 to read 555000 - 0.363 GB for 5000 reads - 0.312 GB for 25766550 olaps - 0.003 GB for evidence\n", "RED job 112 from read 555001 to read 560000 - 0.364 GB for 5000 reads - 0.313 GB for 25870029 olaps - 0.002 GB for evidence\n", "RED job 113 from read 560001 to read 565000 - 0.369 GB for 5000 reads - 0.318 GB for 26230125 olaps - 0.003 GB for evidence\n", "RED job 114 from read 565001 to read 570000 - 0.364 GB for 5000 reads - 0.314 GB for 25906075 olaps - 0.002 GB for evidence\n", "RED job 115 from read 570001 to read 575000 - 0.365 GB for 5000 reads - 0.315 GB for 25992499 olaps - 0.002 GB for evidence\n", "RED job 116 from read 575001 to read 580000 - 0.361 GB for 5000 reads - 0.311 GB for 25698446 olaps - 0.002 GB for evidence\n", "RED job 117 from read 580001 to read 585000 - 0.369 GB for 5000 reads - 0.317 GB for 26202365 olaps - 0.003 GB for evidence\n", "RED job 118 from read 585001 to read 590000 - 0.363 GB for 5000 reads - 0.312 GB for 25780416 olaps - 0.003 GB for evidence\n", "RED job 119 from read 590001 to read 595000 - 0.364 GB for 5000 reads - 0.313 GB for 25841536 olaps - 0.003 GB for evidence\n", "RED job 120 from read 595001 to read 600000 - 0.363 GB for 5000 reads - 0.313 GB for 25860290 olaps - 0.002 GB for evidence\n", "RED job 121 from read 600001 to read 605000 - 0.368 GB for 5000 reads - 0.317 GB for 26209600 olaps - 0.002 GB for evidence\n", "RED job 122 from read 605001 to read 610000 - 0.365 GB for 5000 reads - 0.315 GB for 25989460 olaps - 0.002 GB for evidence\n", "RED job 123 from read 610001 to read 615000 - 0.367 GB for 5000 reads - 0.316 GB for 26137820 olaps - 0.002 GB for evidence\n", "RED job 124 from read 615001 to read 620000 - 0.363 GB for 5000 reads - 0.313 GB for 25838450 olaps - 0.002 GB for evidence\n", "RED job 125 from read 620001 to read 625000 - 0.354 GB for 5000 reads - 0.304 GB for 25143547 olaps - 0.003 GB for evidence\n", "RED job 126 from read 625001 to read 630000 - 0.370 GB for 5000 reads - 0.318 GB for 26289543 olaps - 0.003 GB for evidence\n", "RED job 127 from read 630001 to read 635000 - 0.364 GB for 5000 reads - 0.313 GB for 25824204 olaps - 0.003 GB for evidence\n", "RED job 128 from read 635001 to read 640000 - 0.360 GB for 5000 reads - 0.310 GB for 25567252 olaps - 0.003 GB for evidence\n", "RED job 129 from read 640001 to read 645000 - 0.362 GB for 5000 reads - 0.311 GB for 25720497 olaps - 0.003 GB for evidence\n", "RED job 130 from read 645001 to read 650000 - 0.365 GB for 5000 reads - 0.314 GB for 25967823 olaps - 0.002 GB for evidence\n", "RED job 131 from read 650001 to read 655000 - 0.364 GB for 5000 reads - 0.313 GB for 25813801 olaps - 0.003 GB for evidence\n", "RED job 132 from read 655001 to read 660000 - 0.361 GB for 5000 reads - 0.311 GB for 25684159 olaps - 0.002 GB for evidence\n", "RED job 133 from read 660001 to read 665000 - 0.363 GB for 5000 reads - 0.314 GB for 25896972 olaps - 0.002 GB for evidence\n", "RED job 134 from read 665001 to read 670000 - 0.359 GB for 5000 reads - 0.310 GB for 25566000 olaps - 0.002 GB for evidence\n", "RED job 135 from read 670001 to read 675000 - 0.357 GB for 5000 reads - 0.308 GB for 25471331 olaps - 0.002 GB for evidence\n", "RED job 136 from read 675001 to read 680000 - 0.354 GB for 5000 reads - 0.304 GB for 25126490 olaps - 0.003 GB for evidence\n", "RED job 137 from read 680001 to read 685000 - 0.358 GB for 5000 reads - 0.308 GB for 25475469 olaps - 0.002 GB for evidence\n", "RED job 138 from read 685001 to read 690000 - 0.353 GB for 5000 reads - 0.303 GB for 25012500 olaps - 0.003 GB for evidence\n", "RED job 139 from read 690001 to read 695000 - 0.355 GB for 5000 reads - 0.305 GB for 25215268 olaps - 0.003 GB for evidence\n", "RED job 140 from read 695001 to read 700000 - 0.365 GB for 5000 reads - 0.314 GB for 25963312 olaps - 0.002 GB for evidence\n", "RED job 141 from read 700001 to read 705000 - 0.363 GB for 5000 reads - 0.312 GB for 25805994 olaps - 0.002 GB for evidence\n", "RED job 142 from read 705001 to read 710000 - 0.352 GB for 5000 reads - 0.302 GB for 24982725 olaps - 0.003 GB for evidence\n", "RED job 143 from read 710001 to read 715000 - 0.359 GB for 5000 reads - 0.309 GB for 25552488 olaps - 0.002 GB for evidence\n", "RED job 144 from read 715001 to read 720000 - 0.358 GB for 5000 reads - 0.309 GB for 25495995 olaps - 0.002 GB for evidence\n", "RED job 145 from read 720001 to read 723260 - 0.235 GB for 3260 reads - 0.203 GB for 16738236 olaps - 0.001 GB for evidence\n", "-- Finished stage 'readErrorDetectionConfigure', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'red' concurrent execution on Sat Oct 21 01:10:20 2017 with 831.727 GB free disk space (145 processes; 3 concurrently)\n", "\n", " cd unitigging/3-overlapErrorAdjustment\n", " ./red.sh 1 > ./red.000001.out 2>&1\n", " ./red.sh 2 > ./red.000002.out 2>&1\n", " ./red.sh 3 > ./red.000003.out 2>&1\n", " ./red.sh 4 > ./red.000004.out 2>&1\n", " ./red.sh 5 > ./red.000005.out 2>&1\n", " ./red.sh 6 > ./red.000006.out 2>&1\n", " ./red.sh 7 > ./red.000007.out 2>&1\n", " ./red.sh 8 > ./red.000008.out 2>&1\n", " ./red.sh 9 > ./red.000009.out 2>&1\n", " ./red.sh 10 > ./red.000010.out 2>&1\n", " ./red.sh 11 > ./red.000011.out 2>&1\n", " ./red.sh 12 > ./red.000012.out 2>&1\n", " ./red.sh 13 > ./red.000013.out 2>&1\n", " ./red.sh 14 > ./red.000014.out 2>&1\n", " ./red.sh 15 > ./red.000015.out 2>&1\n", " ./red.sh 16 > ./red.000016.out 2>&1\n", " ./red.sh 17 > ./red.000017.out 2>&1\n", " ./red.sh 18 > ./red.000018.out 2>&1\n", " ./red.sh 19 > ./red.000019.out 2>&1\n", " ./red.sh 20 > ./red.000020.out 2>&1\n", " ./red.sh 21 > ./red.000021.out 2>&1\n", " ./red.sh 22 > ./red.000022.out 2>&1\n", " ./red.sh 23 > ./red.000023.out 2>&1\n", " ./red.sh 24 > ./red.000024.out 2>&1\n", " ./red.sh 25 > ./red.000025.out 2>&1\n", " ./red.sh 26 > ./red.000026.out 2>&1\n", " ./red.sh 27 > ./red.000027.out 2>&1\n", " ./red.sh 28 > ./red.000028.out 2>&1\n", " ./red.sh 29 > ./red.000029.out 2>&1\n", " ./red.sh 30 > ./red.000030.out 2>&1\n", " ./red.sh 31 > ./red.000031.out 2>&1\n", " ./red.sh 32 > ./red.000032.out 2>&1\n", " ./red.sh 33 > ./red.000033.out 2>&1\n", " ./red.sh 34 > ./red.000034.out 2>&1\n", " ./red.sh 35 > ./red.000035.out 2>&1\n", " ./red.sh 36 > ./red.000036.out 2>&1\n", " ./red.sh 37 > ./red.000037.out 2>&1\n", " ./red.sh 38 > ./red.000038.out 2>&1\n", " ./red.sh 39 > ./red.000039.out 2>&1\n", " ./red.sh 40 > ./red.000040.out 2>&1\n", " ./red.sh 41 > ./red.000041.out 2>&1\n", " ./red.sh 42 > ./red.000042.out 2>&1\n", " ./red.sh 43 > ./red.000043.out 2>&1\n", " ./red.sh 44 > ./red.000044.out 2>&1\n", " ./red.sh 45 > ./red.000045.out 2>&1\n", " ./red.sh 46 > ./red.000046.out 2>&1\n", " ./red.sh 47 > ./red.000047.out 2>&1\n", " ./red.sh 48 > ./red.000048.out 2>&1\n", " ./red.sh 49 > ./red.000049.out 2>&1\n", " ./red.sh 50 > ./red.000050.out 2>&1\n", " ./red.sh 51 > ./red.000051.out 2>&1\n", " ./red.sh 52 > ./red.000052.out 2>&1\n", " ./red.sh 53 > ./red.000053.out 2>&1\n", " ./red.sh 54 > ./red.000054.out 2>&1\n", " ./red.sh 55 > ./red.000055.out 2>&1\n", " ./red.sh 56 > ./red.000056.out 2>&1\n", " ./red.sh 57 > ./red.000057.out 2>&1\n", " ./red.sh 58 > ./red.000058.out 2>&1\n", " ./red.sh 59 > ./red.000059.out 2>&1\n", " ./red.sh 60 > ./red.000060.out 2>&1\n", " ./red.sh 61 > ./red.000061.out 2>&1\n", " ./red.sh 62 > ./red.000062.out 2>&1\n", " ./red.sh 63 > ./red.000063.out 2>&1\n", " ./red.sh 64 > ./red.000064.out 2>&1\n", " ./red.sh 65 > ./red.000065.out 2>&1\n", " ./red.sh 66 > ./red.000066.out 2>&1\n", " ./red.sh 67 > ./red.000067.out 2>&1\n", " ./red.sh 68 > ./red.000068.out 2>&1\n", " ./red.sh 69 > ./red.000069.out 2>&1\n", " ./red.sh 70 > ./red.000070.out 2>&1\n", " ./red.sh 71 > ./red.000071.out 2>&1\n", " ./red.sh 72 > ./red.000072.out 2>&1\n", " ./red.sh 73 > ./red.000073.out 2>&1\n", " ./red.sh 74 > ./red.000074.out 2>&1\n", " ./red.sh 75 > ./red.000075.out 2>&1\n", " ./red.sh 76 > ./red.000076.out 2>&1\n", " ./red.sh 77 > ./red.000077.out 2>&1\n", " ./red.sh 78 > ./red.000078.out 2>&1\n", " ./red.sh 79 > ./red.000079.out 2>&1\n", " ./red.sh 80 > ./red.000080.out 2>&1\n", " ./red.sh 81 > ./red.000081.out 2>&1\n", " ./red.sh 82 > ./red.000082.out 2>&1\n", " ./red.sh 83 > ./red.000083.out 2>&1\n", " ./red.sh 84 > ./red.000084.out 2>&1\n", " ./red.sh 85 > ./red.000085.out 2>&1\n", " ./red.sh 86 > ./red.000086.out 2>&1\n", " ./red.sh 87 > ./red.000087.out 2>&1\n", " ./red.sh 88 > ./red.000088.out 2>&1\n", " ./red.sh 89 > ./red.000089.out 2>&1\n", " ./red.sh 90 > ./red.000090.out 2>&1\n", " ./red.sh 91 > ./red.000091.out 2>&1\n", " ./red.sh 92 > ./red.000092.out 2>&1\n", " ./red.sh 93 > ./red.000093.out 2>&1\n", " ./red.sh 94 > ./red.000094.out 2>&1\n", " ./red.sh 95 > ./red.000095.out 2>&1\n", " ./red.sh 96 > ./red.000096.out 2>&1\n", " ./red.sh 97 > ./red.000097.out 2>&1\n", " ./red.sh 98 > ./red.000098.out 2>&1\n", " ./red.sh 99 > ./red.000099.out 2>&1\n", " ./red.sh 100 > ./red.000100.out 2>&1\n", " ./red.sh 101 > ./red.000101.out 2>&1\n", " ./red.sh 102 > ./red.000102.out 2>&1\n", " ./red.sh 103 > ./red.000103.out 2>&1\n", " ./red.sh 104 > ./red.000104.out 2>&1\n", " ./red.sh 105 > ./red.000105.out 2>&1\n", " ./red.sh 106 > ./red.000106.out 2>&1\n", " ./red.sh 107 > ./red.000107.out 2>&1\n", " ./red.sh 108 > ./red.000108.out 2>&1\n", " ./red.sh 109 > ./red.000109.out 2>&1\n", " ./red.sh 110 > ./red.000110.out 2>&1\n", " ./red.sh 111 > ./red.000111.out 2>&1\n", " ./red.sh 112 > ./red.000112.out 2>&1\n", " ./red.sh 113 > ./red.000113.out 2>&1\n", " ./red.sh 114 > ./red.000114.out 2>&1\n", " ./red.sh 115 > ./red.000115.out 2>&1\n", " ./red.sh 116 > ./red.000116.out 2>&1\n", " ./red.sh 117 > ./red.000117.out 2>&1\n", " ./red.sh 118 > ./red.000118.out 2>&1\n", " ./red.sh 119 > ./red.000119.out 2>&1\n", " ./red.sh 120 > ./red.000120.out 2>&1\n", " ./red.sh 121 > ./red.000121.out 2>&1\n", " ./red.sh 122 > ./red.000122.out 2>&1\n", " ./red.sh 123 > ./red.000123.out 2>&1\n", " ./red.sh 124 > ./red.000124.out 2>&1\n", " ./red.sh 125 > ./red.000125.out 2>&1\n", " ./red.sh 126 > ./red.000126.out 2>&1\n", " ./red.sh 127 > ./red.000127.out 2>&1\n", " ./red.sh 128 > ./red.000128.out 2>&1\n", " ./red.sh 129 > ./red.000129.out 2>&1\n", " ./red.sh 130 > ./red.000130.out 2>&1\n", " ./red.sh 131 > ./red.000131.out 2>&1\n", " ./red.sh 132 > ./red.000132.out 2>&1\n", " ./red.sh 133 > ./red.000133.out 2>&1\n", " ./red.sh 134 > ./red.000134.out 2>&1\n", " ./red.sh 135 > ./red.000135.out 2>&1\n", " ./red.sh 136 > ./red.000136.out 2>&1\n", " ./red.sh 137 > ./red.000137.out 2>&1\n", " ./red.sh 138 > ./red.000138.out 2>&1\n", " ./red.sh 139 > ./red.000139.out 2>&1\n", " ./red.sh 140 > ./red.000140.out 2>&1\n", " ./red.sh 141 > ./red.000141.out 2>&1\n", " ./red.sh 142 > ./red.000142.out 2>&1\n", " ./red.sh 143 > ./red.000143.out 2>&1\n", " ./red.sh 144 > ./red.000144.out 2>&1\n", " ./red.sh 145 > ./red.000145.out 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:15:26 2017 (306 seconds) with 831.56 GB free disk space\n", "----------------------------------------\n", "-- Found 145 read error detection output files.\n", "-- Finished stage 'readErrorDetectionCheck', reset canuIteration.\n", "\n", "Configure OEA for 2gb memory with batches of at most 25000 reads and (unlimited) bases.\n", "Configured 29 jobs.\n", "\n", "OEA job 1 from read 1 to read 25000 - 103.2 bases + 448.8 adjusts + 0.8 reads + 26.9 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 907.6 MB\n", "OEA job 2 from read 25001 to read 50000 - 123.1 bases + 448.8 adjusts + 0.8 reads + 26.6 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 927.3 MB\n", "OEA job 3 from read 50001 to read 75000 - 122.7 bases + 448.8 adjusts + 0.8 reads + 27.3 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 927.6 MB\n", "OEA job 4 from read 75001 to read 100000 - 122.0 bases + 448.8 adjusts + 0.8 reads + 31.9 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 931.4 MB\n", "OEA job 5 from read 100001 to read 125000 - 122.2 bases + 448.8 adjusts + 0.8 reads + 31.4 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 931.2 MB\n", "OEA job 6 from read 125001 to read 150000 - 107.0 bases + 448.8 adjusts + 0.8 reads + 23.8 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 908.3 MB\n", "OEA job 7 from read 150001 to read 175000 - 107.5 bases + 448.8 adjusts + 0.8 reads + 20.0 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 905.1 MB\n", "OEA job 8 from read 175001 to read 200000 - 109.8 bases + 448.8 adjusts + 0.8 reads + 24.5 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 911.8 MB\n", "OEA job 9 from read 200001 to read 225000 - 108.5 bases + 448.8 adjusts + 0.8 reads + 24.6 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 910.6 MB\n", "OEA job 10 from read 225001 to read 250000 - 107.7 bases + 448.8 adjusts + 0.8 reads + 23.5 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 908.8 MB\n", "OEA job 11 from read 250001 to read 275000 - 107.3 bases + 448.8 adjusts + 0.8 reads + 23.3 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 908.2 MB\n", "OEA job 12 from read 275001 to read 300000 - 108.8 bases + 448.8 adjusts + 0.8 reads + 23.7 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 910.0 MB\n", "OEA job 13 from read 300001 to read 325000 - 109.3 bases + 448.8 adjusts + 0.8 reads + 22.9 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 909.7 MB\n", "OEA job 14 from read 325001 to read 350000 - 107.7 bases + 448.8 adjusts + 0.8 reads + 22.2 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 907.5 MB\n", "OEA job 15 from read 350001 to read 375000 - 110.2 bases + 448.8 adjusts + 0.8 reads + 26.1 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 913.8 MB\n", "OEA job 16 from read 375001 to read 400000 - 108.4 bases + 448.8 adjusts + 0.8 reads + 21.9 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 907.8 MB\n", "OEA job 17 from read 400001 to read 425000 - 108.6 bases + 448.8 adjusts + 0.8 reads + 23.4 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 909.5 MB\n", "OEA job 18 from read 425001 to read 450000 - 114.8 bases + 448.8 adjusts + 0.8 reads + 25.6 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 918.0 MB\n", "OEA job 19 from read 450001 to read 475000 - 121.9 bases + 448.8 adjusts + 0.8 reads + 28.9 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 928.4 MB\n", "OEA job 20 from read 475001 to read 500000 - 122.2 bases + 448.8 adjusts + 0.8 reads + 25.9 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 925.7 MB\n", "OEA job 21 from read 500001 to read 525000 - 123.6 bases + 448.8 adjusts + 0.8 reads + 27.3 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 928.5 MB\n", "OEA job 22 from read 525001 to read 550000 - 124.0 bases + 448.8 adjusts + 0.8 reads + 31.3 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 932.8 MB\n", "OEA job 23 from read 550001 to read 575000 - 123.8 bases + 448.8 adjusts + 0.8 reads + 31.8 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 933.1 MB\n", "OEA job 24 from read 575001 to read 600000 - 123.4 bases + 448.8 adjusts + 0.8 reads + 31.9 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 932.9 MB\n", "OEA job 25 from read 600001 to read 625000 - 123.3 bases + 448.8 adjusts + 0.8 reads + 30.2 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 931.1 MB\n", "OEA job 26 from read 625001 to read 650000 - 123.4 bases + 448.8 adjusts + 0.8 reads + 37.5 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 938.5 MB\n", "OEA job 27 from read 650001 to read 675000 - 122.5 bases + 448.8 adjusts + 0.8 reads + 28.2 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 928.2 MB\n", "OEA job 28 from read 675001 to read 700000 - 120.9 bases + 448.8 adjusts + 0.8 reads + 38.7 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 937.2 MB\n", "OEA job 29 from read 700001 to read 723260 - 113.1 bases + 448.8 adjusts + 0.7 reads + 26.4 olaps + 8.0 fseq/rseq + 32.0 fadj/radj + 32.0 work + 256.0 misc = 917.0 MB\n", "\n", "-- Finished stage 'overlapErrorAdjustmentConfigure', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'oea' concurrent execution on Sat Oct 21 01:15:32 2017 with 831.56 GB free disk space (29 processes; 24 concurrently)\n", "\n", " cd unitigging/3-overlapErrorAdjustment\n", " ./oea.sh 1 > ./oea.000001.out 2>&1\n", " ./oea.sh 2 > ./oea.000002.out 2>&1\n", " ./oea.sh 3 > ./oea.000003.out 2>&1\n", " ./oea.sh 4 > ./oea.000004.out 2>&1\n", " ./oea.sh 5 > ./oea.000005.out 2>&1\n", " ./oea.sh 6 > ./oea.000006.out 2>&1\n", " ./oea.sh 7 > ./oea.000007.out 2>&1\n", " ./oea.sh 8 > ./oea.000008.out 2>&1\n", " ./oea.sh 9 > ./oea.000009.out 2>&1\n", " ./oea.sh 10 > ./oea.000010.out 2>&1\n", " ./oea.sh 11 > ./oea.000011.out 2>&1\n", " ./oea.sh 12 > ./oea.000012.out 2>&1\n", " ./oea.sh 13 > ./oea.000013.out 2>&1\n", " ./oea.sh 14 > ./oea.000014.out 2>&1\n", " ./oea.sh 15 > ./oea.000015.out 2>&1\n", " ./oea.sh 16 > ./oea.000016.out 2>&1\n", " ./oea.sh 17 > ./oea.000017.out 2>&1\n", " ./oea.sh 18 > ./oea.000018.out 2>&1\n", " ./oea.sh 19 > ./oea.000019.out 2>&1\n", " ./oea.sh 20 > ./oea.000020.out 2>&1\n", " ./oea.sh 21 > ./oea.000021.out 2>&1\n", " ./oea.sh 22 > ./oea.000022.out 2>&1\n", " ./oea.sh 23 > ./oea.000023.out 2>&1\n", " ./oea.sh 24 > ./oea.000024.out 2>&1\n", " ./oea.sh 25 > ./oea.000025.out 2>&1\n", " ./oea.sh 26 > ./oea.000026.out 2>&1\n", " ./oea.sh 27 > ./oea.000027.out 2>&1\n", " ./oea.sh 28 > ./oea.000028.out 2>&1\n", " ./oea.sh 29 > ./oea.000029.out 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:19:43 2017 (251 seconds) with 831.51 GB free disk space\n", "----------------------------------------\n", "-- Found 29 overlap error adjustment output files.\n", "-- Finished stage 'overlapErrorAdjustmentCheck', reset canuIteration.\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:19:43 2017 with 831.51 GB free disk space\n", "\n", " cd unitigging/3-overlapErrorAdjustment\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/ovStoreBuild \\\n", " -G ../20171018_oly_pacbio.gkpStore \\\n", " -O ../20171018_oly_pacbio.ovlStore \\\n", " -evalues \\\n", " -L ./oea.files \\\n", " > ./oea.apply.err 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:19:43 2017 (lickety-split) with 831.462 GB free disk space\n", "----------------------------------------\n", "-- No report available.\n", "-- Finished stage 'updateOverlapStore', reset canuIteration.\n", "-- Finished stage 'unitig', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'bat' concurrent execution on Sat Oct 21 01:19:43 2017 with 831.462 GB free disk space (1 processes; 2 concurrently)\n", "\n", " cd unitigging/4-unitigger\n", " ./unitigger.sh 1 > ./unitigger.000001.out 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:19:57 2017 (14 seconds) with 831.201 GB free disk space\n", "----------------------------------------\n", "-- Unitigger finished successfully.\n", "-- Found, in version 1, after unitig construction:\n", "-- contigs: 11246 sequences, total length 132675816 bp (including 326 repeats of total length 2418909 bp).\n", "-- bubbles: 0 sequences, total length 0 bp.\n", "-- unassembled: 479693 sequences, total length 2277551160 bp.\n", "--\n", "-- Contig sizes based on genome size --\n", "-- NG (bp) LG (contigs) sum (bp)\n", "-- ---------- ------------ ----------\n", "--\n", "-- Finished stage 'unitigCheck', reset canuIteration.\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:19:58 2017 with 831.201 GB free disk space\n", "\n", " cd unitigging\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/gatekeeperPartition \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -T ./20171018_oly_pacbio.ctgStore 1 \\\n", " -b 25000 \\\n", " -p 256 \\\n", " > ./20171018_oly_pacbio.ctgStore/partitionedReads.log 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:19:59 2017 (1 second) with 830.25 GB free disk space\n", "----------------------------------------\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:20:00 2017 with 830.25 GB free disk space\n", "\n", " cd unitigging\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/gatekeeperPartition \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -T ./20171018_oly_pacbio.utgStore 1 \\\n", " -b 25000 \\\n", " -p 256 \\\n", " > ./20171018_oly_pacbio.utgStore/partitionedReads.log 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:20:00 2017 (1 second) with 830.005 GB free disk space\n", "----------------------------------------\n", "-- Using slow alignment for consensus (iteration '0').\n", "-- Configured 30 contig and 7 unitig consensus jobs.\n", "-- Finished stage 'consensusConfigure', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'cns' concurrent execution on Sat Oct 21 01:20:01 2017 with 830.005 GB free disk space (37 processes; 3 concurrently)\n", "\n", " cd unitigging/5-consensus\n", " ./consensus.sh 1 > ./consensus.000001.out 2>&1\n", " ./consensus.sh 2 > ./consensus.000002.out 2>&1\n", " ./consensus.sh 3 > ./consensus.000003.out 2>&1\n", " ./consensus.sh 4 > ./consensus.000004.out 2>&1\n", " ./consensus.sh 5 > ./consensus.000005.out 2>&1\n", " ./consensus.sh 6 > ./consensus.000006.out 2>&1\n", " ./consensus.sh 7 > ./consensus.000007.out 2>&1\n", " ./consensus.sh 8 > ./consensus.000008.out 2>&1\n", " ./consensus.sh 9 > ./consensus.000009.out 2>&1\n", " ./consensus.sh 10 > ./consensus.000010.out 2>&1\n", " ./consensus.sh 11 > ./consensus.000011.out 2>&1\n", " ./consensus.sh 12 > ./consensus.000012.out 2>&1\n", " ./consensus.sh 13 > ./consensus.000013.out 2>&1\n", " ./consensus.sh 14 > ./consensus.000014.out 2>&1\n", " ./consensus.sh 15 > ./consensus.000015.out 2>&1\n", " ./consensus.sh 16 > ./consensus.000016.out 2>&1\n", " ./consensus.sh 17 > ./consensus.000017.out 2>&1\n", " ./consensus.sh 18 > ./consensus.000018.out 2>&1\n", " ./consensus.sh 19 > ./consensus.000019.out 2>&1\n", " ./consensus.sh 20 > ./consensus.000020.out 2>&1\n", " ./consensus.sh 21 > ./consensus.000021.out 2>&1\n", " ./consensus.sh 22 > ./consensus.000022.out 2>&1\n", " ./consensus.sh 23 > ./consensus.000023.out 2>&1\n", " ./consensus.sh 24 > ./consensus.000024.out 2>&1\n", " ./consensus.sh 25 > ./consensus.000025.out 2>&1\n", " ./consensus.sh 26 > ./consensus.000026.out 2>&1\n", " ./consensus.sh 27 > ./consensus.000027.out 2>&1\n", " ./consensus.sh 28 > ./consensus.000028.out 2>&1\n", " ./consensus.sh 29 > ./consensus.000029.out 2>&1\n", " ./consensus.sh 30 > ./consensus.000030.out 2>&1\n", " ./consensus.sh 31 > ./consensus.000031.out 2>&1\n", " ./consensus.sh 32 > ./consensus.000032.out 2>&1\n", " ./consensus.sh 33 > ./consensus.000033.out 2>&1\n", " ./consensus.sh 34 > ./consensus.000034.out 2>&1\n", " ./consensus.sh 35 > ./consensus.000035.out 2>&1\n", " ./consensus.sh 36 > ./consensus.000036.out 2>&1\n", " ./consensus.sh 37 > ./consensus.000037.out 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:46:57 2017 (1616 seconds) with 825.166 GB free disk space\n", "----------------------------------------\n", "-- Using slow alignment for consensus (iteration '1').\n", "-- Configured 30 contig and 7 unitig consensus jobs.\n", "-- All 37 consensus jobs finished successfully.\n", "-- Finished stage 'consensusCheck', reset canuIteration.\n", "-- Using slow alignment for consensus (iteration '0').\n", "-- Configured 30 contig and 7 unitig consensus jobs.\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:46:58 2017 with 825.166 GB free disk space\n", "\n", " cd unitigging\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/tgStoreLoad \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -T ./20171018_oly_pacbio.ctgStore 2 \\\n", " -L ./5-consensus/ctgcns.files \\\n", " > ./5-consensus/ctgcns.files.ctgStoreLoad.err 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:47:04 2017 (6 seconds) with 820.591 GB free disk space\n", "----------------------------------------\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:47:05 2017 with 820.595 GB free disk space\n", "\n", " cd unitigging\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/tgStoreLoad \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -T ./20171018_oly_pacbio.utgStore 2 \\\n", " -L ./5-consensus/utgcns.files \\\n", " > ./5-consensus/utgcns.files.utgStoreLoad.err 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:47:05 2017 (1 second) with 820.306 GB free disk space\n", "----------------------------------------\n", "-- Purging consensus output after loading to ctgStore and/or utgStore.\n", "-- Purged 37 .cns outputs.\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:47:06 2017 with 826.331 GB free disk space\n", "\n", " cd unitigging\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/tgStoreDump \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -T ./20171018_oly_pacbio.ctgStore 2 \\\n", " -sizes -s 1900000000 \\\n", " > ./20171018_oly_pacbio.ctgStore/seqDB.v002.sizes.txt\n", "\n", "-- Finished on Sat Oct 21 01:47:18 2017 (12 seconds) with 826.331 GB free disk space\n", "----------------------------------------\n", "-- Found, in version 2, after consensus generation:\n", "-- contigs: 11246 sequences, total length 132146852 bp (including 326 repeats of total length 2387102 bp).\n", "-- bubbles: 0 sequences, total length 0 bp.\n", "-- unassembled: 479693 sequences, total length 2277137864 bp.\n", "--\n", "-- Contig sizes based on genome size --\n", "-- NG (bp) LG (contigs) sum (bp)\n", "-- ---------- ------------ ----------\n", "--\n", "-- Finished stage 'consensusLoad', reset canuIteration.\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:47:18 2017 with 826.331 GB free disk space\n", "\n", " cd unitigging\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/tgStoreCoverageStat \\\n", " -G ./20171018_oly_pacbio.gkpStore \\\n", " -T ./20171018_oly_pacbio.ctgStore 2 \\\n", " -s 1900000000 \\\n", " -o ./20171018_oly_pacbio.ctgStore.coverageStat \\\n", " > ./20171018_oly_pacbio.ctgStore.coverageStat.err 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:47:23 2017 (5 seconds) with 826.311 GB free disk space\n", "----------------------------------------\n", "-- Finished stage 'consensusAnalyze', reset canuIteration.\n", "--\n", "-- Running jobs. First attempt out of 2.\n", "----------------------------------------\n", "-- Starting 'gfa' concurrent execution on Sat Oct 21 01:47:33 2017 with 826.311 GB free disk space (1 processes; 2 concurrently)\n", "\n", " cd unitigging/4-unitigger\n", " ./alignGFA.sh 1 > ./alignGFA.000001.out 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:48:22 2017 (49 seconds) with 826.3 GB free disk space\n", "----------------------------------------\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:48:22 2017 with 826.3 GB free disk space\n", "\n", " cd .\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/tgStoreDump \\\n", " -G ./unitigging/20171018_oly_pacbio.gkpStore \\\n", " -T ./unitigging/20171018_oly_pacbio.ctgStore 2 \\\n", " -o ./20171018_oly_pacbio.contigs \\\n", " -layout \\\n", " > ./20171018_oly_pacbio.contigs.layout.err 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:48:52 2017 (30 seconds) with 821.639 GB free disk space\n", "----------------------------------------\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:48:52 2017 with 821.639 GB free disk space\n", "\n", " cd .\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/tgStoreDump \\\n", " -G ./unitigging/20171018_oly_pacbio.gkpStore \\\n", " -T ./unitigging/20171018_oly_pacbio.utgStore 2 \\\n", " -o ./20171018_oly_pacbio.unitigs \\\n", " -layout \\\n", " > ./20171018_oly_pacbio.unitigs.layout.err 2>&1\n", "\n", "-- Finished on Sat Oct 21 01:48:54 2017 (2 seconds) with 821.34 GB free disk space\n", "----------------------------------------\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:48:54 2017 with 821.34 GB free disk space\n", "\n", " cd .\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/tgStoreDump \\\n", " -G ./unitigging/20171018_oly_pacbio.gkpStore \\\n", " -T ./unitigging/20171018_oly_pacbio.ctgStore 2 \\\n", " -consensus -fasta \\\n", " -unassembled \\\n", " > ./20171018_oly_pacbio.unassembled.fasta\n", " 2> ./20171018_oly_pacbio.unassembled.err\n", "\n", "-- Finished on Sat Oct 21 01:49:16 2017 (22 seconds) with 819.15 GB free disk space\n", "----------------------------------------\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:49:16 2017 with 819.15 GB free disk space\n", "\n", " cd .\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/tgStoreDump \\\n", " -G ./unitigging/20171018_oly_pacbio.gkpStore \\\n", " -T ./unitigging/20171018_oly_pacbio.ctgStore 2 \\\n", " -consensus -fasta \\\n", " -contigs \\\n", " > ./20171018_oly_pacbio.contigs.fasta\n", " 2> ./20171018_oly_pacbio.contigs.err\n", "\n", "-- Finished on Sat Oct 21 01:49:28 2017 (12 seconds) with 819.025 GB free disk space\n", "----------------------------------------\n", "----------------------------------------\n", "-- Starting command on Sat Oct 21 01:49:28 2017 with 819.025 GB free disk space\n", "\n", " cd .\n", " /usr/local/bioinformatics/canu-1.6/Linux-amd64/bin/tgStoreDump \\\n", " -G ./unitigging/20171018_oly_pacbio.gkpStore \\\n", " -T ./unitigging/20171018_oly_pacbio.utgStore 2 \\\n", " -consensus -fasta \\\n", " -contigs \\\n", " > ./20171018_oly_pacbio.unitigs.fasta\n", " 2> ./20171018_oly_pacbio.unitigs.err\n", "\n", "-- Finished on Sat Oct 21 01:49:29 2017 (1 second) with 818.883 GB free disk space\n", "----------------------------------------\n", "-- Finished stage 'generateOutputs', reset canuIteration.\n", "--\n", "-- Assembly '20171018_oly_pacbio' finished in '/home/data/20171018_oly_pacbio_canu'.\n", "--\n", "-- Summary saved in 'unitigging.html'.\n", "--\n", "-- Sequences saved:\n", "-- Contigs -> '20171018_oly_pacbio.contigs.fasta'\n", "-- Unassembled -> '20171018_oly_pacbio.unassembled.fasta'\n", "-- Unitigs -> '20171018_oly_pacbio.unitigs.fasta'\n", "--\n", "-- Read layouts saved:\n", "-- Contigs -> '20171018_oly_pacbio.contigs.layout'.\n", "-- Unitigs -> '20171018_oly_pacbio.unitigs.layout'.\n", "--\n", "-- Graphs saved:\n", "-- Contigs -> '20171018_oly_pacbio.contigs.gfa'.\n", "-- Unitigs -> '20171018_oly_pacbio.unitigs.gfa'.\n", "--\n", "-- Bye.\n", "-- Finished stage 'outputSequence', reset canuIteration.\n", "--\n", "-- Bye.\n", "\n", "real\t3071m38.266s\n", "user\t53627m42.644s\n", "sys\t478m24.228s\n" ] } ], "source": [ "%%bash\n", "time canu \\\n", "useGrid=false \\\n", "ovsMethod=sequential \\\n", "-p 20171018_oly_pacbio \\\n", "-d /home/data/20171018_oly_pacbio_canu/ \\\n", "genomeSize=1.9g \\\n", "correctedErrorRate=0.075 \\\n", "-pacbio-raw m*" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 13G\n", "-rw-r--r-- 1 root root 129M Oct 21 01:49 20171018_oly_pacbio.contigs.fasta\n", "-rw-r--r-- 1 root root 2.2M Oct 21 01:49 20171018_oly_pacbio.contigs.gfa\n", "-rw-r--r-- 1 root root 4.7G Oct 21 01:48 20171018_oly_pacbio.contigs.layout\n", "-rw-r--r-- 1 root root 21M Oct 21 01:48 20171018_oly_pacbio.contigs.layout.readToTig\n", "-rw-r--r-- 1 root root 22M Oct 21 01:48 20171018_oly_pacbio.contigs.layout.tigInfo\n", "-rw-r--r-- 1 root root 3.6G Oct 20 11:50 20171018_oly_pacbio.correctedReads.fasta.gz\n", "-rw-r--r-- 1 root root 24M Oct 20 11:50 20171018_oly_pacbio.correctedReads.length\n", "-rw-r--r-- 1 root root 27K Oct 21 01:49 20171018_oly_pacbio.report\n", "-rw-r--r-- 1 root root 1.2G Oct 20 19:58 20171018_oly_pacbio.trimmedReads.fasta.gz\n", "-rw-r--r-- 1 root root 2.2G Oct 21 01:49 20171018_oly_pacbio.unassembled.fasta\n", "-rw-r--r-- 1 root root 504K Oct 21 01:49 20171018_oly_pacbio.unitigs.bed\n", "-rw-r--r-- 1 root root 146M Oct 21 01:49 20171018_oly_pacbio.unitigs.fasta\n", "-rw-r--r-- 1 root root 8.5M Oct 21 01:49 20171018_oly_pacbio.unitigs.gfa\n", "-rw-r--r-- 1 root root 301M Oct 21 01:48 20171018_oly_pacbio.unitigs.layout\n", "-rw-r--r-- 1 root root 5.0M Oct 21 01:48 20171018_oly_pacbio.unitigs.layout.readToTig\n", "-rw-r--r-- 1 root root 640K Oct 21 01:48 20171018_oly_pacbio.unitigs.layout.tigInfo\n", "drwxr-xr-x 2 root root 60K Oct 21 01:49 canu-logs\n", "drwxr-xr-x 2 root root 4.0K Oct 18 22:37 canu-scripts\n", "drwxr-xr-x 6 root root 4.0K Oct 20 11:52 correction\n", "-rw-r--r-- 1 root root 19K Oct 20 11:52 correction.html\n", "drwxr-xr-x 2 root root 4.0K Oct 20 11:52 correction.html.files\n", "drwxr-xr-x 6 root root 4.0K Oct 20 19:58 trimming\n", "-rw-r--r-- 1 root root 7.3K Oct 20 19:58 trimming.html\n", "drwxr-xr-x 2 root root 4.0K Oct 20 12:50 trimming.html.files\n", "drwxr-xr-x 11 root root 4.0K Oct 21 01:47 unitigging\n", "-rw-r--r-- 1 root root 7.4K Oct 21 01:49 unitigging.html\n", "drwxr-xr-x 2 root root 4.0K Oct 20 20:06 unitigging.html.files\n" ] } ], "source": [ "%%bash\n", "ls -lh /home/data/20171018_oly_pacbio_canu/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Things look good! Will re-launch notebook in order to mount Owl for coping Canu output folder." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "UsageError: Cell magic `%%date` not found.\n" ] } ], "source": [ "%%date" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Mon Oct 23 13:39:45 UTC 2017\n" ] } ], "source": [ "%%bash\n", "date" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t11m17.919s\n", "user\t0m0.180s\n", "sys\t0m43.088s\n" ] } ], "source": [ "%%bash\n", "time cp -R 20171018_oly_pacbio_canu/ /home/owl/Athaliana/" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 13G\n", "-rw-r--r-- 1 1027 users 129M Oct 23 13:53 20171018_oly_pacbio.contigs.fasta\n", "-rw-r--r-- 1 1027 users 2.2M Oct 23 13:53 20171018_oly_pacbio.contigs.gfa\n", "-rw-r--r-- 1 1027 users 4.7G Oct 23 13:53 20171018_oly_pacbio.contigs.layout\n", "-rw-r--r-- 1 1027 users 21M Oct 23 13:51 20171018_oly_pacbio.contigs.layout.readToTig\n", "-rw-r--r-- 1 1027 users 22M Oct 23 13:51 20171018_oly_pacbio.contigs.layout.tigInfo\n", "-rw-r--r-- 1 1027 users 3.6G Oct 23 13:46 20171018_oly_pacbio.correctedReads.fasta.gz\n", "-rw-r--r-- 1 1027 users 24M Oct 23 13:45 20171018_oly_pacbio.correctedReads.length\n", "-rw-r--r-- 1 1027 users 27K Oct 23 13:44 20171018_oly_pacbio.report\n", "-rw-r--r-- 1 1027 users 1.2G Oct 23 13:50 20171018_oly_pacbio.trimmedReads.fasta.gz\n", "-rw-r--r-- 1 1027 users 2.2G Oct 23 13:51 20171018_oly_pacbio.unassembled.fasta\n", "-rw-r--r-- 1 1027 users 504K Oct 23 13:53 20171018_oly_pacbio.unitigs.bed\n", "-rw-r--r-- 1 1027 users 146M Oct 23 13:53 20171018_oly_pacbio.unitigs.fasta\n", "-rw-r--r-- 1 1027 users 8.5M Oct 23 13:53 20171018_oly_pacbio.unitigs.gfa\n", "-rw-r--r-- 1 1027 users 301M Oct 23 13:53 20171018_oly_pacbio.unitigs.layout\n", "-rw-r--r-- 1 1027 users 5.0M Oct 23 13:53 20171018_oly_pacbio.unitigs.layout.readToTig\n", "-rw-r--r-- 1 1027 users 640K Oct 23 13:53 20171018_oly_pacbio.unitigs.layout.tigInfo\n", "drwxr-xr-x 2 root users 0 Oct 23 13:42 canu-logs\n", "drwxr-xr-x 2 root users 0 Oct 23 13:42 canu-scripts\n", "drwxr-xr-x 6 root users 0 Oct 23 13:43 correction\n", "-rw-r--r-- 1 1027 users 19K Oct 23 13:45 correction.html\n", "drwxr-xr-x 2 root users 0 Oct 23 13:45 correction.html.files\n", "drwxr-xr-x 6 root users 0 Oct 23 13:47 trimming\n", "-rw-r--r-- 1 1027 users 7.3K Oct 23 13:47 trimming.html\n", "drwxr-xr-x 2 root users 0 Oct 23 13:47 trimming.html.files\n", "drwxr-xr-x 11 root users 0 Oct 23 13:50 unitigging\n", "-rw-r--r-- 1 1027 users 7.4K Oct 23 13:50 unitigging.html\n", "drwxr-xr-x 2 root users 0 Oct 23 13:50 unitigging.html.files\n" ] } ], "source": [ "%%bash\n", "ls -lh /home/owl/Athaliana/20171018_oly_pacbio_canu/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This is the main file that is useful from this whole Canu assembly: [20171018_oly_pacbio.contigs.fasta](http://owl.fish.washington.edu/Athaliana/20171018_oly_pacbio_canu/20171018_oly_pacbio.contigs.fasta)" ] }, { "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": "3.5.2" } }, "nbformat": 4, "nbformat_minor": 2 }