Diff of the two buildlogs: -- --- b1/build.log 2024-04-26 00:37:22.798662535 +0000 +++ b2/build.log 2024-04-26 00:44:35.612183908 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Apr 25 12:30:19 -12 2024 -I: pbuilder-time-stamp: 1714091419 +I: Current time: Fri Apr 26 14:37:26 +14 2024 +I: pbuilder-time-stamp: 1714091846 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: unpacking pigx-rnaseq_0.1.0-1.1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2985120/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3085359/tmp/hooks/D01_modify_environment starting +debug: Running on codethink02-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 26 00:37 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3085359/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3085359/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='ed17c5a8e86e404d8db1398919909c9c' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2985120' - PS1='# ' - PS2='> ' + INVOCATION_ID=ef0a6536a83f416ba29219ad6e2c6ba2 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3085359 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.h7BgrbsU/pbuilderrc_sapy --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.h7BgrbsU/b1 --logfile b1/build.log pigx-rnaseq_0.1.0-1.1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.h7BgrbsU/pbuilderrc_fKsH --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.h7BgrbsU/b2 --logfile b2/build.log pigx-rnaseq_0.1.0-1.1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 23 11:23 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2985120/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 21 07:15 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3085359/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -1522,7 +1554,7 @@ Get: 679 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.19.2-1 [617 kB] Get: 680 http://deb.debian.org/debian trixie/main arm64 snakemake all 7.32.4-3 [318 kB] Get: 681 http://deb.debian.org/debian trixie/main arm64 trim-galore all 0.6.10-1 [17.8 MB] -Fetched 582 MB in 6s (99.5 MB/s) +Fetched 582 MB in 2s (242 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libnettle8:arm64: dependency problems, but removing anyway as you requested: libhogweed6:arm64 depends on libnettle8. @@ -3681,8 +3713,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Apr 26 00:31:56 UTC 2024. -Universal Time is now: Fri Apr 26 00:31:56 UTC 2024. +Local time is now: Fri Apr 26 00:38:59 UTC 2024. +Universal Time is now: Fri Apr 26 00:38:59 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17029-2) ... @@ -8087,7 +8119,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/pigx-rnaseq-0.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pigx-rnaseq_0.1.0-1.1_source.changes +I: user script /srv/workspace/pbuilder/3085359/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3085359/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/pigx-rnaseq-0.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pigx-rnaseq_0.1.0-1.1_source.changes dpkg-buildpackage: info: source package pigx-rnaseq dpkg-buildpackage: info: source version 0.1.0-1.1 dpkg-buildpackage: info: source distribution unstable @@ -8256,7 +8292,7 @@ Select jobs to execute... -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] rule check_annotation_files: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv @@ -8267,31 +8303,31 @@ /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//validate_input_annotation.R /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/check_annotation_files.log 2>&1 -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.json log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep2.log jobid: 13 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep2.log 2>&1 -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.json log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep1.log jobid: 11 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep1.log 2>&1 -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] rule translate_sample_sheet_for_report: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_sheet.csv output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv @@ -8301,7 +8337,7 @@ /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//translate_sample_sheet_for_report.R /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_sheet.csv -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.json @@ -8313,7 +8349,7 @@ /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep2.log 2>&1 -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] rule trim_qc_reads_se: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep1.se.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep1.se.fastp.json @@ -8324,12 +8360,12 @@ resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep1.se.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep1.se.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep1.log 2>&1 -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] Finished job 5. 1 of 48 steps (2%) done Select jobs to execute... -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] rule trim_qc_reads_se: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep3.se.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep3.se.fastp.json @@ -8340,12 +8376,12 @@ resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep3.se.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep3.se.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep3.log 2>&1 -[Thu Apr 25 12:36:18 2024] -Finished job 11. +[Fri Apr 26 14:43:30 2024] +Finished job 7. 2 of 48 steps (4%) done Select jobs to execute... -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.json @@ -8356,27 +8392,27 @@ resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep3.log 2>&1 -[Thu Apr 25 12:36:18 2024] -Finished job 7. +[Fri Apr 26 14:43:30 2024] +Finished job 11. 3 of 48 steps (6%) done -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] Finished job 13. 4 of 48 steps (8%) done -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] Finished job 15. 5 of 48 steps (10%) done -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] Finished job 9. 6 of 48 steps (12%) done -[Thu Apr 25 12:36:18 2024] +[Fri Apr 26 14:43:30 2024] Finished job 24. 7 of 48 steps (15%) done -[Thu Apr 25 12:36:27 2024] +[Fri Apr 26 14:43:39 2024] Finished job 1. 8 of 48 steps (17%) done Select jobs to execute... -[Thu Apr 25 12:36:27 2024] +[Fri Apr 26 14:43:39 2024] rule salmon_index: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin @@ -8387,28 +8423,28 @@ /usr/bin/salmon index -t /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -p 8 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_index.log 2>&1 -[Thu Apr 25 12:36:27 2024] +[Fri Apr 26 14:43:39 2024] rule hisat2_index: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2_index.log jobid: 17 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv resources: tmpdir=/tmp, mem_mb=32000, mem_mib=30518 /usr/bin/hisat2-build -f -p 2 --large-index /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2_index.log 2>&1 -[Thu Apr 25 12:36:28 2024] +[Fri Apr 26 14:43:41 2024] Finished job 17. 9 of 48 steps (19%) done Select jobs to execute... -[Thu Apr 25 12:36:28 2024] +[Fri Apr 26 14:43:41 2024] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep1.log, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep1.log jobid: 20 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -8418,13 +8454,13 @@ rm /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam -[Thu Apr 25 12:36:28 2024] +[Fri Apr 26 14:43:41 2024] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep2.log jobid: 21 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -8434,13 +8470,13 @@ rm /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam -[Thu Apr 25 12:36:28 2024] +[Fri Apr 26 14:43:41 2024] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep2.log, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep2.log jobid: 18 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -8450,13 +8486,13 @@ rm /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam -[Thu Apr 25 12:36:28 2024] +[Fri Apr 26 14:43:41 2024] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep3.log, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep3.log jobid: 19 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -8466,13 +8502,13 @@ rm /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam -[Thu Apr 25 12:36:28 2024] +[Fri Apr 26 14:43:41 2024] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep3.log, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep3.log jobid: 22 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -8481,18 +8517,18 @@ /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep3.log 2>&1 rm /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam -[Thu Apr 25 12:36:29 2024] -Finished job 19. +[Fri Apr 26 14:43:41 2024] +Finished job 4. 10 of 48 steps (21%) done Select jobs to execute... -[Thu Apr 25 12:36:29 2024] +[Fri Apr 26 14:43:41 2024] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep1.log, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep1.log jobid: 16 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -8501,28 +8537,72 @@ /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep1.log 2>&1 rm /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.out.sam -[Thu Apr 25 12:36:29 2024] -Finished job 18. +[Fri Apr 26 14:43:41 2024] +Finished job 22. 11 of 48 steps (23%) done Select jobs to execute... -[Thu Apr 25 12:36:29 2024] +[Fri Apr 26 14:43:41 2024] +rule salmon_quant: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log + jobid: 8 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz + wildcards: sample=HBR_Rep3 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + +[Fri Apr 26 14:43:41 2024] +Finished job 21. +12 of 48 steps (25%) done +Select jobs to execute... + +[Fri Apr 26 14:43:41 2024] rule index_bam: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep2.log - jobid: 29 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam - wildcards: sample=HBR_Rep2 + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep2.log + jobid: 35 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam + wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 -/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep2.log 2>&1 -[Thu Apr 25 12:36:29 2024] -Finished job 22. -12 of 48 steps (25%) done +/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep2.log 2>&1 +[Fri Apr 26 14:43:41 2024] +Finished job 16. +13 of 48 steps (27%) done +[Fri Apr 26 14:43:41 2024] +Finished job 20. +14 of 48 steps (29%) done +[Fri Apr 26 14:43:41 2024] +Finished job 18. +15 of 48 steps (31%) done +[Fri Apr 26 14:43:41 2024] +Finished job 19. +16 of 48 steps (33%) done Select jobs to execute... -[Thu Apr 25 12:36:29 2024] +[Fri Apr 26 14:43:41 2024] +rule salmon_quant: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log + jobid: 10 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz + wildcards: sample=UHR_Rep1 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + +[Fri Apr 26 14:43:41 2024] +rule salmon_quant: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log + jobid: 3 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz + wildcards: sample=HBR_Rep1 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + +[Fri Apr 26 14:43:41 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai @@ -8533,60 +8613,91 @@ resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep3.log 2>&1 -[Thu Apr 25 12:36:29 2024] -Finished job 20. -13 of 48 steps (27%) done -Select jobs to execute... -[Thu Apr 25 12:36:29 2024] +[Fri Apr 26 14:43:41 2024] rule index_bam: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep1.log - jobid: 33 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep1 + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep1.log + jobid: 27 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam + wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 -/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep1.log 2>&1 -[Thu Apr 25 12:36:29 2024] +/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep1.log 2>&1 +[Fri Apr 26 14:43:41 2024] +Finished job 35. +17 of 48 steps (35%) done +Select jobs to execute... + +[Fri Apr 26 14:43:41 2024] +rule coverage_megadepth: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log + jobid: 43 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=UHR_Rep2 + resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 + + + /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log 2>&1 + +[Fri Apr 26 14:43:41 2024] Finished job 37. -14 of 48 steps (29%) done -[Thu Apr 25 12:36:29 2024] -Finished job 29. -15 of 48 steps (31%) done -[Thu Apr 25 12:36:29 2024] -Finished job 21. -16 of 48 steps (33%) done +18 of 48 steps (38%) done +[Fri Apr 26 14:43:41 2024] +Finished job 27. +19 of 48 steps (40%) done Select jobs to execute... -[Thu Apr 25 12:36:29 2024] +[Fri Apr 26 14:43:41 2024] rule count_reads: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep3.count_reads.log - jobid: 36 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep3 + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log + jobid: 34 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep3 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep3.count_reads.log 2>&1 +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log 2>&1 -[Thu Apr 25 12:36:29 2024] +[Fri Apr 26 14:43:41 2024] rule coverage_megadepth: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log - jobid: 44 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep3 + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log + jobid: 39 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log 2>&1 + /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log 2>&1 +Select jobs to execute... +[Fri Apr 26 14:43:41 2024] +Finished job 43. +20 of 48 steps (42%) done + +[Fri Apr 26 14:43:41 2024] +rule index_bam: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep1.log + jobid: 33 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam + wildcards: sample=UHR_Rep1 + resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 + +/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep1.log 2>&1 +[Fri Apr 26 14:43:41 2024] +Finished job 39. +21 of 48 steps (44%) done +Select jobs to execute... -[Thu Apr 25 12:36:29 2024] +[Fri Apr 26 14:43:41 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai @@ -8597,245 +8708,154 @@ resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep3.log 2>&1 -[Thu Apr 25 12:36:29 2024] +[Fri Apr 26 14:43:41 2024] Finished job 33. -17 of 48 steps (35%) done +22 of 48 steps (46%) done Select jobs to execute... -[Thu Apr 25 12:36:29 2024] -rule index_bam: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep2.log - jobid: 35 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam +[Fri Apr 26 14:43:41 2024] +rule salmon_quant: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log + jobid: 12 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz wildcards: sample=UHR_Rep2 - resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 - -/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep2.log 2>&1 -[Thu Apr 25 12:36:29 2024] -Finished job 31. -18 of 48 steps (38%) done -Select jobs to execute... - -[Thu Apr 25 12:36:29 2024] -rule count_reads: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep2.count_reads.log - jobid: 28 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=HBR_Rep2 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep2.count_reads.log 2>&1 -[Thu Apr 25 12:36:29 2024] -Finished job 16. -19 of 48 steps (40%) done -[Thu Apr 25 12:36:29 2024] -Finished job 35. -20 of 48 steps (42%) done -Select jobs to execute... - -[Thu Apr 25 12:36:29 2024] -rule count_reads: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep3.count_reads.log - jobid: 30 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam - wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep3 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep3.count_reads.log 2>&1 - -[Thu Apr 25 12:36:29 2024] -rule count_reads: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep1.count_reads.log - jobid: 32 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep1 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep1.count_reads.log 2>&1 -[Thu Apr 25 12:36:29 2024] -Finished job 44. -21 of 48 steps (44%) done -Select jobs to execute... - -[Thu Apr 25 12:36:29 2024] -rule coverage_megadepth: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log - jobid: 43 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=UHR_Rep2 - resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - - - /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log 2>&1 - +[Fri Apr 26 14:43:41 2024] +Finished job 31. +23 of 48 steps (48%) done Select jobs to execute... -[Thu Apr 25 12:36:29 2024] -Finished job 43. -22 of 48 steps (46%) done -[Thu Apr 25 12:36:29 2024] +[Fri Apr 26 14:43:41 2024] rule coverage_megadepth: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log jobid: 41 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log 2>&1 -[Thu Apr 25 12:36:29 2024] +[Fri Apr 26 14:43:41 2024] Finished job 41. -23 of 48 steps (48%) done -Select jobs to execute... - -[Thu Apr 25 12:36:29 2024] -rule index_bam: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep1.log - jobid: 27 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=HBR_Rep1 - resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 - -/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep1.log 2>&1 -[Thu Apr 25 12:36:29 2024] -Finished job 27. 24 of 48 steps (50%) done Select jobs to execute... -[Thu Apr 25 12:36:29 2024] -rule coverage_megadepth: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log - jobid: 40 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai +[Fri Apr 26 14:43:41 2024] +rule index_bam: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep2.log + jobid: 29 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam wildcards: sample=HBR_Rep2 - resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - + resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 - /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log 2>&1 - -[Thu Apr 25 12:36:29 2024] -Finished job 40. +/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep2.log 2>&1 +[Fri Apr 26 14:43:41 2024] +Finished job 29. 25 of 48 steps (52%) done Select jobs to execute... -[Thu Apr 25 12:36:29 2024] -rule coverage_megadepth: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log - jobid: 39 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=HBR_Rep1 - resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - - - /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log 2>&1 - -[Thu Apr 25 12:36:29 2024] -Finished job 39. -26 of 48 steps (54%) done -Select jobs to execute... - -[Thu Apr 25 12:36:29 2024] +[Fri Apr 26 14:43:41 2024] rule count_reads: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep1.count_reads.log - jobid: 26 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=HBR_Rep1 + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep2.count_reads.log + jobid: 28 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep1.count_reads.log 2>&1 -[Thu Apr 25 12:36:30 2024] -Finished job 4. -27 of 48 steps (56%) done +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep2.count_reads.log 2>&1 +Building DAG of jobs... +Using shell: /usr/bin/bash +Provided cores: 6 +Rules claiming more threads will be scaled down. +Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... - -[Thu Apr 25 12:36:30 2024] -rule salmon_quant: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log - jobid: 8 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz - wildcards: sample=HBR_Rep3 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... -/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log 2>&1 -[Thu Apr 25 12:36:32 2024] -Finished job 8. -28 of 48 steps (58%) done +Building DAG of jobs... +Using shell: /usr/bin/bash +Provided cores: 6 +Rules claiming more threads will be scaled down. +Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... - -[Thu Apr 25 12:36:32 2024] -rule salmon_quant: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log - jobid: 12 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz - wildcards: sample=UHR_Rep2 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - +/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log 2>&1 +/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log 2>&1 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... +/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log 2>&1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log 2>&1 -[Thu Apr 25 12:36:34 2024] -Finished job 12. -29 of 48 steps (60%) done +[Fri Apr 26 14:43:43 2024] +Finished job 8. +26 of 48 steps (54%) done +Select jobs to execute... + +[Fri Apr 26 14:43:43 2024] +rule coverage_megadepth: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log + jobid: 40 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=HBR_Rep2 + resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 + + + /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log 2>&1 + +[Fri Apr 26 14:43:43 2024] +Finished job 3. +27 of 48 steps (56%) done Select jobs to execute... -[Thu Apr 25 12:36:34 2024] +[Fri Apr 26 14:43:43 2024] +rule count_reads: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep3.count_reads.log + jobid: 36 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=UHR_Rep3 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep3 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep3.count_reads.log 2>&1 +[Fri Apr 26 14:43:43 2024] +Finished job 40. +28 of 48 steps (58%) done +Select jobs to execute... + +[Fri Apr 26 14:43:43 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log jobid: 14 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 6 -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=6000, mem_mib=5723 -Select jobs to execute... -/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log 2>&1 -[Thu Apr 25 12:36:36 2024] -Finished job 14. -30 of 48 steps (62%) done +[Fri Apr 26 14:43:43 2024] +Finished job 10. +29 of 48 steps (60%) done Select jobs to execute... -[Thu Apr 25 12:36:36 2024] +[Fri Apr 26 14:43:43 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf @@ -8845,56 +8865,30 @@ wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 6 -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=6000, mem_mib=5723 -Select jobs to execute... -/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log 2>&1 -[Thu Apr 25 12:36:38 2024] -Finished job 6. -31 of 48 steps (65%) done +[Fri Apr 26 14:43:43 2024] +Finished job 12. +30 of 48 steps (62%) done Select jobs to execute... -[Thu Apr 25 12:36:38 2024] -rule salmon_quant: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log - jobid: 10 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz - wildcards: sample=UHR_Rep1 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 6 -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=6000, mem_mib=5723 -Select jobs to execute... -/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log 2>&1 -[Thu Apr 25 12:36:40 2024] -Finished job 36. -32 of 48 steps (67%) done -Select jobs to execute... +[Fri Apr 26 14:43:43 2024] +rule coverage_megadepth: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log + jobid: 44 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=UHR_Rep3 + resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 -[Thu Apr 25 12:36:40 2024] -rule salmon_quant: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log - jobid: 3 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin - wildcards: sample=HBR_Rep1 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -[Thu Apr 25 12:36:40 2024] -Finished job 10. -33 of 48 steps (69%) done + /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log 2>&1 + +[Fri Apr 26 14:43:43 2024] +Finished job 44. +31 of 48 steps (65%) done Select jobs to execute... -[Thu Apr 25 12:36:40 2024] +[Fri Apr 26 14:43:43 2024] rule coverage_megadepth: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw @@ -8907,76 +8901,116 @@ /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log 2>&1 -[Thu Apr 25 12:36:40 2024] -Finished job 30. -34 of 48 steps (71%) done +[Fri Apr 26 14:43:43 2024] +Finished job 42. +32 of 48 steps (67%) done Select jobs to execute... -[Thu Apr 25 12:36:40 2024] +[Fri Apr 26 14:43:43 2024] rule count_reads: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log - jobid: 34 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=UHR_Rep2 + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep1.count_reads.log + jobid: 32 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam + wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log 2>&1 -[Thu Apr 25 12:36:40 2024] -Finished job 26. -35 of 48 steps (73%) done -[Thu Apr 25 12:36:40 2024] -Finished job 42. -36 of 48 steps (75%) done -[Thu Apr 25 12:36:40 2024] -Finished job 32. -37 of 48 steps (77%) done +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep1.count_reads.log 2>&1 Building DAG of jobs... -[Thu Apr 25 12:36:40 2024] -Finished job 28. -38 of 48 steps (79%) done Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... -/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log 2>&1 -[Thu Apr 25 12:36:42 2024] -Finished job 3. -39 of 48 steps (81%) done +Building DAG of jobs... +Using shell: /usr/bin/bash +Provided cores: 6 +Rules claiming more threads will be scaled down. +Provided resources: mem_mb=6000, mem_mib=5723 +Select jobs to execute... +/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log 2>&1 +/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log 2>&1 +[Fri Apr 26 14:43:45 2024] +Finished job 14. +33 of 48 steps (69%) done Select jobs to execute... -[Thu Apr 25 12:36:42 2024] -rule counts_from_SALMON: - input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv - output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv - log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log - jobid: 23 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf - resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 +[Fri Apr 26 14:43:45 2024] +rule count_reads: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep3.count_reads.log + jobid: 30 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=HBR_Rep3 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//counts_matrix_from_SALMON.R /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log 2>&1 +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep3 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep3.count_reads.log 2>&1 +[Fri Apr 26 14:43:45 2024] +Finished job 6. +34 of 48 steps (71%) done +Select jobs to execute... -[Thu Apr 25 12:36:42 2024] +[Fri Apr 26 14:43:45 2024] rule multiqc: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/multiqc.hisat2.log jobid: 2 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/multiqc -f -o /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/multiqc /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/multiqc.hisat2.log 2>&1 -[Thu Apr 25 12:36:46 2024] +[Fri Apr 26 14:43:50 2024] Finished job 2. +35 of 48 steps (73%) done +Select jobs to execute... + +[Fri Apr 26 14:43:50 2024] +rule counts_from_SALMON: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log + jobid: 23 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf + resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 + +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//counts_matrix_from_SALMON.R /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/salmon_output /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log 2>&1 +[Fri Apr 26 14:43:52 2024] +Finished job 34. +36 of 48 steps (75%) done +Select jobs to execute... + +[Fri Apr 26 14:43:52 2024] +rule count_reads: + input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv + log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep1.count_reads.log + jobid: 26 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=HBR_Rep1 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep1 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep1.count_reads.log 2>&1 +[Fri Apr 26 14:43:53 2024] +Finished job 28. +37 of 48 steps (77%) done +[Fri Apr 26 14:43:54 2024] +Finished job 36. +38 of 48 steps (79%) done +[Fri Apr 26 14:43:55 2024] +Finished job 32. +39 of 48 steps (81%) done +[Fri Apr 26 14:43:56 2024] +Finished job 30. 40 of 48 steps (83%) done -[Thu Apr 25 12:36:51 2024] +[Fri Apr 26 14:43:59 2024] Finished job 23. 41 of 48 steps (85%) done Select jobs to execute... -[Thu Apr 25 12:36:51 2024] +[Fri Apr 26 14:43:59 2024] rule report2: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html @@ -8988,38 +9022,38 @@ /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.1.0/images/Logo_PiGx.png --prefix='analysis1.salmon.transcripts' --reportFile=/build/reproducible-path/pigx-rnaseq-0.1.0/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log 2>&1 -[Thu Apr 25 12:36:51 2024] +[Fri Apr 26 14:43:59 2024] rule report3: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.genes.log jobid: 47 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv wildcards: analysis=analysis1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.1.0/images/Logo_PiGx.png --prefix='analysis1.salmon.genes' --reportFile=/build/reproducible-path/pigx-rnaseq-0.1.0/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.genes.log 2>&1 -[Thu Apr 25 12:36:52 2024] -Finished job 34. +[Fri Apr 26 14:44:03 2024] +Finished job 26. 42 of 48 steps (88%) done Select jobs to execute... -[Thu Apr 25 12:36:52 2024] +[Fri Apr 26 14:44:03 2024] rule collate_read_counts: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv log: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/collate_read_counts.log jobid: 25 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts/collate_read_counts.R /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2 /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/collate_read_counts.log 2>&1 -[Thu Apr 25 12:36:52 2024] +[Fri Apr 26 14:44:04 2024] Finished job 25. 43 of 48 steps (90%) done Select jobs to execute... -[Thu Apr 25 12:36:52 2024] +[Fri Apr 26 14:44:04 2024] rule norm_counts_deseq: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv @@ -9030,7 +9064,7 @@ /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts/norm_counts_deseq.R /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2 >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/norm_counts_deseq.log 2>&1 -[Thu Apr 25 12:36:52 2024] +[Fri Apr 26 14:44:04 2024] rule report1: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html @@ -9041,31 +9075,31 @@ resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.0/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.1.0/images/Logo_PiGx.png --prefix='analysis1' --reportFile=/build/reproducible-path/pigx-rnaseq-0.1.0/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/hisat2 --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/analysis1.report.log 2>&1 -[Thu Apr 25 12:36:59 2024] +[Fri Apr 26 14:44:11 2024] Finished job 38. 44 of 48 steps (92%) done -[Thu Apr 25 12:37:13 2024] +[Fri Apr 26 14:44:21 2024] Finished job 47. 45 of 48 steps (94%) done -[Thu Apr 25 12:37:13 2024] +[Fri Apr 26 14:44:21 2024] Finished job 46. 46 of 48 steps (96%) done -[Thu Apr 25 12:37:14 2024] +[Fri Apr 26 14:44:26 2024] Finished job 45. 47 of 48 steps (98%) done Select jobs to execute... -[Thu Apr 25 12:37:14 2024] +[Fri Apr 26 14:44:26 2024] localrule all: input: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html jobid: 0 - reason: Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html + reason: Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv resources: tmpdir=/tmp -[Thu Apr 25 12:37:14 2024] +[Fri Apr 26 14:44:26 2024] Finished job 0. 48 of 48 steps (100%) done -Complete log: .snakemake/log/2024-04-25T123617.564790.snakemake.log +Complete log: .snakemake/log/2024-04-26T144329.626061.snakemake.log The following files have been generated: - /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv - /build/reproducible-path/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html @@ -9097,14 +9131,14 @@ make[2]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.0' /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' - /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/bin' + /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/pigx_rnaseq' /usr/bin/install -c snakefile.py qsub-template.sh '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' + /usr/bin/install -c pigx-rnaseq '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/bin' /usr/bin/install -c -m 644 README.md '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' - /usr/bin/install -c scripts/runDeseqReport.R scripts/translate_sample_sheet_for_report.R scripts/deseqReport.Rmd scripts/counts_matrix_from_SALMON.R scripts/validate_input.py scripts/norm_counts_deseq.R scripts/count_reads.R scripts/collate_read_counts.R scripts/validate_input_annotation.R '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' /usr/bin/install -c -m 644 etc/sample_sheet.csv.example etc/settings.yaml etc/pretty.txt images/Logo_PiGx.png '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/pigx_rnaseq' - /usr/bin/install -c pigx-rnaseq '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/bin' + /usr/bin/install -c scripts/runDeseqReport.R scripts/translate_sample_sheet_for_report.R scripts/deseqReport.Rmd scripts/counts_matrix_from_SALMON.R scripts/validate_input.py scripts/norm_counts_deseq.R scripts/count_reads.R scripts/collate_read_counts.R scripts/validate_input_annotation.R '/build/reproducible-path/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' make[2]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.0' make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.0' dh_installdocs @@ -9169,12 +9203,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3085359/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3085359/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2985120 and its subdirectories -I: Current time: Thu Apr 25 12:37:21 -12 2024 -I: pbuilder-time-stamp: 1714091841 +I: removing directory /srv/workspace/pbuilder/3085359 and its subdirectories +I: Current time: Fri Apr 26 14:44:34 +14 2024 +I: pbuilder-time-stamp: 1714092274