Diff of the two buildlogs: -- --- b1/build.log 2024-12-18 02:08:15.521538305 +0000 +++ b2/build.log 2024-12-18 02:21:59.636345007 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 19 20:25:34 -12 2026 -I: pbuilder-time-stamp: 1768897534 +I: Current time: Wed Dec 18 16:08:18 +14 2024 +I: pbuilder-time-stamp: 1734487698 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: unpacking pigx-rnaseq_0.1.1-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1812173/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1591680/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +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 Dec 18 02:08 /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/1591680/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1591680/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='0eabbf2b2dd54a259d504defc4db43d8' - 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='1812173' - PS1='# ' - PS2='> ' + INVOCATION_ID=edb2ae61f08a4438bd0ba868c8fa99d1 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=1591680 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.tTRzH070/pbuilderrc_rBzO --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tTRzH070/b1 --logfile b1/build.log pigx-rnaseq_0.1.1-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.tTRzH070/pbuilderrc_wAzR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tTRzH070/b2 --logfile b2/build.log pigx-rnaseq_0.1.1-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1812173/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1591680/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -833,7 +865,7 @@ Get: 655 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get: 656 http://deb.debian.org/debian unstable/main amd64 snakemake all 7.32.4-6 [318 kB] Get: 657 http://deb.debian.org/debian unstable/main amd64 trim-galore all 0.6.10-1 [17.8 MB] -Fetched 582 MB in 9s (63.2 MB/s) +Fetched 582 MB in 19s (31.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) @@ -2914,8 +2946,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jan 20 08:27:36 UTC 2026. -Universal Time is now: Tue Jan 20 08:27:36 UTC 2026. +Local time is now: Wed Dec 18 02:15:02 UTC 2024. +Universal Time is now: Wed Dec 18 02:15:02 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -3738,7 +3770,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/pigx-rnaseq-0.1.1/ && 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_0.1.1-1_source.changes +I: user script /srv/workspace/pbuilder/1591680/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1591680/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/pigx-rnaseq-0.1.1/ && 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_0.1.1-1_source.changes dpkg-buildpackage: info: source package pigx-rnaseq dpkg-buildpackage: info: source version 0.1.1-1 dpkg-buildpackage: info: source distribution unstable @@ -3866,7 +3902,7 @@ config.status: creating pigx-rnaseq make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' dh_auto_build - make -j42 + make -j20 make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.1' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' @@ -3908,7 +3944,7 @@ Select jobs to execute... -[Mon Jan 19 20:29:59 2026] +[Wed Dec 18 16:19:49 2024] rule trim_qc_reads_se: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep1.se.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep1.se.fastp.json @@ -3920,19 +3956,19 @@ /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep1.se.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep1.se.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.HBR_Rep1.log 2>&1 -[Mon Jan 19 20:29:59 2026] +[Wed Dec 18 16:19:49 2024] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep2.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep2.pe.fastp.json log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.UHR_Rep2.log jobid: 13 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.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-0.1.1/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep2.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep2.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.UHR_Rep2.log 2>&1 -[Mon Jan 19 20:29:59 2026] +[Wed Dec 18 16:19:49 2024] rule translate_sample_sheet_for_report: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_sheet.csv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv @@ -3942,7 +3978,7 @@ /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//translate_sample_sheet_for_report.R /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_sheet.csv -[Mon Jan 19 20:29:59 2026] +[Wed Dec 18 16:19:49 2024] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep1.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep1.pe.fastp.json @@ -3954,7 +3990,7 @@ /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep1.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep1.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.UHR_Rep1.log 2>&1 -[Mon Jan 19 20:29:59 2026] +[Wed Dec 18 16:19:49 2024] rule trim_qc_reads_se: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep3.se.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep3.se.fastp.json @@ -3966,23 +4002,23 @@ /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep3.se.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/UHR_Rep3.se.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.UHR_Rep3.log 2>&1 -[Mon Jan 19 20:29:59 2026] +[Wed Dec 18 16:19:49 2024] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep3.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep3.pe.fastp.json log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.HBR_Rep3.log jobid: 9 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz wildcards: sample=HBR_Rep3 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-0.1.1/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep3.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep3.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.HBR_Rep3.log 2>&1 -[Mon Jan 19 20:29:59 2026] +[Wed Dec 18 16:19:50 2024] Finished job 24. 1 of 49 steps (2%) done Select jobs to execute... -[Mon Jan 19 20:29:59 2026] +[Wed Dec 18 16:19:50 2024] rule check_annotation_files: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv @@ -3992,12 +4028,12 @@ resources: tmpdir=/tmp /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//validate_input_annotation.R /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.fasta /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/check_annotation_files.log 2>&1 -[Mon Jan 19 20:29:59 2026] -Finished job 5. +[Wed Dec 18 16:19:50 2024] +Finished job 11. 2 of 49 steps (4%) done Select jobs to execute... -[Mon Jan 19 20:29:59 2026] +[Wed Dec 18 16:19:50 2024] rule trim_qc_reads_pe: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep2.pe.fastp.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep2.pe.fastp.json @@ -4008,12 +4044,12 @@ 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-0.1.1/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz --in2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz --out1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz --out2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -h /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep2.pe.fastp.html -j /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/QC/HBR_Rep2.pe.fastp.json >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.HBR_Rep2.log 2>&1 -[Mon Jan 19 20:29:59 2026] -Finished job 15. +[Wed Dec 18 16:19:50 2024] +Finished job 5. 3 of 49 steps (6%) done Select jobs to execute... -[Mon Jan 19 20:29:59 2026] +[Wed Dec 18 16:19:50 2024] rule record_annotation_files: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations.tgz @@ -4026,27 +4062,27 @@ mkdir /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations; cp /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.fasta /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations tar -czvf annotations.tgz /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations --remove-files >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/record_annotation_files.log 2>&1 -[Mon Jan 19 20:29:59 2026] -Finished job 9. +[Wed Dec 18 16:19:50 2024] +Finished job 13. 4 of 49 steps (8%) done -[Mon Jan 19 20:29:59 2026] -Finished job 11. +[Wed Dec 18 16:19:51 2024] +Finished job 9. 5 of 49 steps (10%) done -[Mon Jan 19 20:29:59 2026] -Finished job 13. +[Wed Dec 18 16:19:51 2024] +Finished job 15. 6 of 49 steps (12%) done -[Mon Jan 19 20:30:00 2026] +[Wed Dec 18 16:19:51 2024] Finished job 7. 7 of 49 steps (14%) done -[Mon Jan 19 20:30:00 2026] +[Wed Dec 18 16:19:52 2024] Finished job 48. 8 of 49 steps (16%) done -[Mon Jan 19 20:30:09 2026] +[Wed Dec 18 16:20:05 2024] Finished job 1. 9 of 49 steps (18%) done Select jobs to execute... -[Mon Jan 19 20:30:09 2026] +[Wed Dec 18 16:20:05 2024] rule salmon_index: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin @@ -4057,103 +4093,92 @@ /usr/bin/salmon index -t /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.cdna.fasta -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -p 8 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_index.log 2>&1 -[Mon Jan 19 20:30:09 2026] +[Wed Dec 18 16:20:05 2024] rule hisat2_index: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.fasta, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2_index.log jobid: 17 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/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-0.1.1/tests/sample_data/sample.fasta /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2_index.log 2>&1 -[Mon Jan 19 20:30:11 2026] -Finished job 4. +[Wed Dec 18 16:20:08 2024] +Finished job 17. 10 of 49 steps (20%) done Select jobs to execute... -[Mon Jan 19 20:30:11 2026] -rule salmon_quant: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.genes.sf - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log - jobid: 10 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz +[Wed Dec 18 16:20:08 2024] +rule hisat2_map: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep1.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep1.log + jobid: 20 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l wildcards: sample=UHR_Rep1 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 -[Mon Jan 19 20:30:11 2026] -rule salmon_quant: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.genes.sf - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log - jobid: 8 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz - wildcards: sample=HBR_Rep3 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -[Mon Jan 19 20:30:11 2026] -rule salmon_quant: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.genes.sf - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log - jobid: 3 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.genes.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz - wildcards: sample=HBR_Rep1 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep1.log 2>&1 + /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep1.log 2>&1 + rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam + -[Mon Jan 19 20:30:11 2026] -rule salmon_quant: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log - jobid: 6 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz +[Wed Dec 18 16:20:08 2024] +rule hisat2_map: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep2.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep2.log + jobid: 18 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l wildcards: sample=HBR_Rep2 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 -[Mon Jan 19 20:30:11 2026] -rule salmon_quant: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.genes.sf - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log - jobid: 14 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.genes.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz - wildcards: sample=UHR_Rep3 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -[Mon Jan 19 20:30:11 2026] -Finished job 17. -11 of 49 steps (22%) done -Select jobs to execute... + /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep2.log 2>&1 + /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep2.log 2>&1 + rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam + -[Mon Jan 19 20:30:11 2026] +[Wed Dec 18 16:20:08 2024] rule hisat2_map: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep2.log - jobid: 21 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l - wildcards: sample=UHR_Rep2 + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep3.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep3.log + jobid: 19 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l + wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 - /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log 2>&1 - /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep2.log 2>&1 - rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam + /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep3.log 2>&1 + /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep3.log 2>&1 + rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam -[Mon Jan 19 20:30:11 2026] -Finished job 21. -12 of 49 steps (24%) done -Select jobs to execute... -[Mon Jan 19 20:30:11 2026] +[Wed Dec 18 16:20:08 2024] +rule hisat2_map: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep3.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep3.log + jobid: 22 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l + wildcards: sample=UHR_Rep3 + resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 + + + /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam -U /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep3.log 2>&1 + /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep3.log 2>&1 + rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam + + +[Wed Dec 18 16:20:08 2024] rule hisat2_map: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep1.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep1.log jobid: 16 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4162,164 +4187,153 @@ /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep1.log 2>&1 rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.out.sam -[Mon Jan 19 20:30:11 2026] +[Wed Dec 18 16:20:08 2024] +Finished job 4. +11 of 49 steps (22%) done +Select jobs to execute... + +[Wed Dec 18 16:20:08 2024] +rule hisat2_map: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep2.log + jobid: 21 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l + wildcards: sample=UHR_Rep2 + resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 + + + /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log 2>&1 + /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep2.log 2>&1 + rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam + +[Wed Dec 18 16:20:08 2024] Finished job 16. -13 of 49 steps (27%) done +12 of 49 steps (24%) done Select jobs to execute... -[Mon Jan 19 20:30:11 2026] +[Wed Dec 18 16:20:08 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log jobid: 12 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -Building DAG of jobs... -Building DAG of jobs... -Building DAG of jobs... -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... -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... -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... -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... -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-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log 2>&1 -/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log 2>&1 -/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log 2>&1 -/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log 2>&1 -/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/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-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 3. +[Wed Dec 18 16:20:08 2024] +Finished job 18. +13 of 49 steps (27%) done +[Wed Dec 18 16:20:08 2024] +Finished job 22. 14 of 49 steps (29%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] -rule hisat2_map: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep3.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep3.log - jobid: 22 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz - wildcards: sample=UHR_Rep3 - resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 +[Wed Dec 18 16:20:08 2024] +rule salmon_quant: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.genes.sf + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log + jobid: 10 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin + wildcards: sample=UHR_Rep1 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 +[Wed Dec 18 16:20:08 2024] +rule salmon_quant: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.genes.sf + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log + jobid: 8 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin + wildcards: sample=HBR_Rep3 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam -U /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep3.log 2>&1 - /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep3.log 2>&1 - rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam - -[Mon Jan 19 20:30:12 2026] -Finished job 14. +[Wed Dec 18 16:20:08 2024] +Finished job 19. 15 of 49 steps (31%) done +[Wed Dec 18 16:20:08 2024] +Finished job 20. +16 of 49 steps (33%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] -rule hisat2_map: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep3.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep3.log - jobid: 19 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz - wildcards: sample=HBR_Rep3 - resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 +[Wed Dec 18 16:20:08 2024] +rule index_bam: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep1.log + jobid: 27 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/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-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep1.log 2>&1 +[Wed Dec 18 16:20:08 2024] +rule index_bam: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep2.log + jobid: 29 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam + wildcards: sample=HBR_Rep2 + resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 - /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep3.log 2>&1 - /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep3.log 2>&1 - rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam - -[Mon Jan 19 20:30:12 2026] -Finished job 6. -16 of 49 steps (33%) done +/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep2.log 2>&1 Select jobs to execute... +[Wed Dec 18 16:20:08 2024] +Finished job 27. +17 of 49 steps (35%) done -[Mon Jan 19 20:30:12 2026] -rule hisat2_map: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep1.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep1.log - jobid: 20 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz - wildcards: sample=UHR_Rep1 - resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 +[Wed Dec 18 16:20:08 2024] +rule coverage_megadepth: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log + jobid: 39 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam + wildcards: sample=HBR_Rep1 + resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_UHR_Rep1.log 2>&1 - /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep1.log 2>&1 - rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam + /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 8. -17 of 49 steps (35%) done -[Mon Jan 19 20:30:12 2026] -Finished job 10. +[Wed Dec 18 16:20:08 2024] +Finished job 29. 18 of 49 steps (37%) done +[Wed Dec 18 16:20:08 2024] +Finished job 21. +19 of 49 steps (39%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] -rule hisat2_map: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep2.log, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep2.log - jobid: 18 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l - wildcards: sample=HBR_Rep2 - resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 - - - /usr/bin/hisat2 --fast -x /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/hisat2_map_HBR_Rep2.log 2>&1 - /usr/bin/samtools view -bh /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam | /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep2.log 2>&1 - rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam - +[Wed Dec 18 16:20:08 2024] +rule salmon_quant: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.genes.sf + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log + jobid: 3 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin + wildcards: sample=HBR_Rep1 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -[Mon Jan 19 20:30:12 2026] +[Wed Dec 18 16:20:08 2024] rule index_bam: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep1.log - jobid: 27 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=HBR_Rep1 + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep3.log + jobid: 31 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam + wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 -/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep1.log 2>&1 +/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep3.log 2>&1 Select jobs to execute... -[Mon Jan 19 20:30:12 2026] -Finished job 27. -19 of 49 steps (39%) done +[Wed Dec 18 16:20:08 2024] +Finished job 39. +20 of 49 steps (41%) done -[Mon Jan 19 20:30:12 2026] +[Wed Dec 18 16:20:08 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai @@ -4330,44 +4344,28 @@ resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep2.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 22. -20 of 49 steps (41%) done -Select jobs to execute... - -[Mon Jan 19 20:30:12 2026] -rule index_bam: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep3.log - jobid: 37 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep3 - resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 - -/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep3.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 35. +[Wed Dec 18 16:20:08 2024] +Finished job 31. 21 of 49 steps (43%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] +[Wed Dec 18 16:20:09 2024] rule count_reads: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep2.count_reads.log - jobid: 34 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=UHR_Rep2 + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep3.count_reads.log + jobid: 30 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/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-0.1.1/scripts//count_reads.R UHR_Rep2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep2.count_reads.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 37. +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R HBR_Rep3 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep3.count_reads.log 2>&1 +[Wed Dec 18 16:20:09 2024] +Finished job 35. 22 of 49 steps (45%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] +[Wed Dec 18 16:20:09 2024] rule coverage_megadepth: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw @@ -4380,111 +4378,162 @@ /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 19. +[Wed Dec 18 16:20:09 2024] +Finished job 43. 23 of 49 steps (47%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] -rule coverage_megadepth: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log - jobid: 44 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep3 - resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - +[Wed Dec 18 16:20:09 2024] +rule count_reads: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep2.count_reads.log + jobid: 34 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/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/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log 2>&1 - -[Mon Jan 19 20:30:12 2026] -Finished job 43. +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R UHR_Rep2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_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... +Building DAG of jobs... +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... +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-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log 2>&1 +/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log 2>&1 +/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep3.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-0.1.1/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log 2>&1 +[Wed Dec 18 16:20:10 2024] +Finished job 10. 24 of 49 steps (49%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] +[Wed Dec 18 16:20:10 2024] +rule salmon_quant: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.genes.sf + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log + jobid: 14 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin + wildcards: sample=UHR_Rep3 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + +[Wed Dec 18 16:20:10 2024] +Finished job 3. +25 of 49 steps (51%) done +Select jobs to execute... + +[Wed Dec 18 16:20:10 2024] rule coverage_megadepth: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log - jobid: 39 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=HBR_Rep1 + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log + jobid: 40 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/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-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log 2>&1 + /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 18. -25 of 49 steps (51%) done +[Wed Dec 18 16:20:11 2024] +Finished job 40. +26 of 49 steps (53%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] -rule index_bam: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep2.log - jobid: 29 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam +[Wed Dec 18 16:20:11 2024] +rule count_reads: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep2.count_reads.log + jobid: 28 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai wildcards: sample=HBR_Rep2 - resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep2.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 20. -26 of 49 steps (53%) done -[Mon Jan 19 20:30:12 2026] -Finished job 44. +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R HBR_Rep2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep2.count_reads.log 2>&1 +[Wed Dec 18 16:20:11 2024] +Finished job 8. 27 of 49 steps (55%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] +[Wed Dec 18 16:20:11 2024] rule index_bam: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep3.log - jobid: 31 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam - wildcards: sample=HBR_Rep3 + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep3.log + jobid: 37 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam + wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 -/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_HBR_Rep3.log 2>&1 +/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep3.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-0.1.1/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log 2>&1 +[Wed Dec 18 16:20:11 2024] +Finished job 37. +28 of 49 steps (57%) done +Select jobs to execute... -[Mon Jan 19 20:30:12 2026] -rule index_bam: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep1.log - jobid: 33 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep1 - resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 +[Wed Dec 18 16:20:11 2024] +rule coverage_megadepth: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log + jobid: 44 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/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 -/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep1.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 39. -28 of 49 steps (57%) done + + /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log 2>&1 + +[Wed Dec 18 16:20:11 2024] +Finished job 44. +29 of 49 steps (59%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] +[Wed Dec 18 16:20:11 2024] rule count_reads: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep1.count_reads.log - jobid: 26 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=HBR_Rep1 + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep3.count_reads.log + jobid: 36 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/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-0.1.1/scripts//count_reads.R HBR_Rep1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep1.count_reads.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 31. -29 of 49 steps (59%) done +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R UHR_Rep3 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep3.count_reads.log 2>&1 +[Wed Dec 18 16:20:11 2024] +Finished job 12. +30 of 49 steps (61%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] +[Wed Dec 18 16:20:11 2024] rule coverage_megadepth: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw @@ -4497,124 +4546,96 @@ /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log 2>&1 +[Wed Dec 18 16:20:11 2024] +Finished job 41. +31 of 49 steps (63%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] -Finished job 29. -30 of 49 steps (61%) done -[Mon Jan 19 20:30:12 2026] -rule count_reads: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep3.count_reads.log - jobid: 30 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam - wildcards: sample=HBR_Rep3 +[Wed Dec 18 16:20:11 2024] +rule salmon_quant: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log + jobid: 6 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin + wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R HBR_Rep3 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep3.count_reads.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 33. -31 of 49 steps (63%) done +[Wed Dec 18 16:20:12 2024] +Finished job 14. +32 of 49 steps (65%) done Select jobs to execute... +Building DAG of jobs... -[Mon Jan 19 20:30:12 2026] +[Wed Dec 18 16:20:12 2024] rule count_reads: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep3.count_reads.log - jobid: 36 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep3 + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep1.count_reads.log + jobid: 26 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam + wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R UHR_Rep3 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep3.count_reads.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 41. -32 of 49 steps (65%) done +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R HBR_Rep1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep1.count_reads.log 2>&1 +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... - -[Mon Jan 19 20:30:12 2026] -rule coverage_megadepth: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log - jobid: 40 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/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-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log 2>&1 - -[Mon Jan 19 20:30:12 2026] -Finished job 12. +/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz -2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log 2>&1 +[Wed Dec 18 16:20:13 2024] +Finished job 6. 33 of 49 steps (67%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] +[Wed Dec 18 16:20:13 2024] rule counts_from_SALMON: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_import_counts.log jobid: 23 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//counts_matrix_from_SALMON.R /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/salmon_import_counts.log 2>&1 -[Mon Jan 19 20:30:12 2026] -Finished job 40. +[Wed Dec 18 16:20:31 2024] +Finished job 30. 34 of 49 steps (69%) done Select jobs to execute... -[Mon Jan 19 20:30:12 2026] -rule count_reads: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep2.count_reads.log - jobid: 28 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/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 +[Wed Dec 18 16:20:31 2024] +rule index_bam: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep1.log + jobid: 33 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/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/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R HBR_Rep2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/HBR_Rep2.count_reads.log 2>&1 -[Mon Jan 19 20:30:23 2026] -Finished job 23. +/usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/samtools_index_UHR_Rep1.log 2>&1 +[Wed Dec 18 16:20:31 2024] +Finished job 33. 35 of 49 steps (71%) done Select jobs to execute... -[Mon Jan 19 20:30:23 2026] +[Wed Dec 18 16:20:31 2024] rule multiqc: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/multiqc.hisat2.log jobid: 2 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/UHR_Rep3/quant.sf resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/multiqc -f -o /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/multiqc.hisat2.log 2>&1 -[Mon Jan 19 20:30:26 2026] -Finished job 36. +[Wed Dec 18 16:20:32 2024] +Finished job 23. 36 of 49 steps (73%) done Select jobs to execute... -[Mon Jan 19 20:30:26 2026] -rule report2: - input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv - output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log - jobid: 46 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv - wildcards: analysis=analysis1 - resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 - -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.1.1/images/Logo_PiGx.png --prefix='analysis1.salmon.transcripts' --reportFile=/build/reproducible-path/pigx-rnaseq-0.1.1/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log 2>&1 -[Mon Jan 19 20:30:26 2026] -Finished job 28. -37 of 49 steps (76%) done -Select jobs to execute... - -[Mon Jan 19 20:30:26 2026] +[Wed Dec 18 16:20:32 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv @@ -4625,12 +4646,12 @@ resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts//count_reads.R UHR_Rep1 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep1.count_reads.log 2>&1 -[Mon Jan 19 20:30:27 2026] -Finished job 2. -38 of 49 steps (78%) done +[Wed Dec 18 16:20:33 2024] +Finished job 34. +37 of 49 steps (76%) done Select jobs to execute... -[Mon Jan 19 20:30:27 2026] +[Wed Dec 18 16:20:33 2024] rule coverage_megadepth: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw @@ -4643,12 +4664,28 @@ /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log 2>&1 -[Mon Jan 19 20:30:27 2026] -Finished job 30. +[Wed Dec 18 16:20:33 2024] +Finished job 42. +38 of 49 steps (78%) done +Select jobs to execute... + +[Wed Dec 18 16:20:33 2024] +rule report2: + input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv + output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log + jobid: 46 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv + wildcards: analysis=analysis1 + resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 + +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.1.1/images/Logo_PiGx.png --prefix='analysis1.salmon.transcripts' --reportFile=/build/reproducible-path/pigx-rnaseq-0.1.1/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log 2>&1 +[Wed Dec 18 16:20:33 2024] +Finished job 36. 39 of 49 steps (80%) done Select jobs to execute... -[Mon Jan 19 20:30:27 2026] +[Wed Dec 18 16:20:33 2024] rule report3: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html @@ -4659,36 +4696,36 @@ resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.1.1/images/Logo_PiGx.png --prefix='analysis1.salmon.genes' --reportFile=/build/reproducible-path/pigx-rnaseq-0.1.1/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/analysis1.report.salmon.genes.log 2>&1 -[Mon Jan 19 20:30:27 2026] -Finished job 42. +[Wed Dec 18 16:20:34 2024] +Finished job 28. 40 of 49 steps (82%) done -[Mon Jan 19 20:30:27 2026] +[Wed Dec 18 16:20:35 2024] Finished job 26. 41 of 49 steps (84%) done -[Mon Jan 19 20:30:27 2026] -Finished job 34. +[Wed Dec 18 16:20:36 2024] +Finished job 2. 42 of 49 steps (86%) done -[Mon Jan 19 20:30:41 2026] +[Wed Dec 18 16:20:53 2024] Finished job 32. 43 of 49 steps (88%) done Select jobs to execute... -[Mon Jan 19 20:30:41 2026] +[Wed Dec 18 16:20:53 2024] rule collate_read_counts: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/collate_read_counts.log jobid: 25 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv; Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts/collate_read_counts.R /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2 /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/collate_read_counts.log 2>&1 -[Mon Jan 19 20:30:41 2026] +[Wed Dec 18 16:20:54 2024] Finished job 25. 44 of 49 steps (90%) done Select jobs to execute... -[Mon Jan 19 20:30:41 2026] +[Wed Dec 18 16:20:54 2024] rule norm_counts_deseq: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv @@ -4699,7 +4736,7 @@ /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts/norm_counts_deseq.R /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2 >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/norm_counts_deseq.log 2>&1 -[Mon Jan 19 20:30:41 2026] +[Wed Dec 18 16:20:54 2024] rule report1: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2/analysis1.deseq.report.html @@ -4710,31 +4747,31 @@ resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.1.1/images/Logo_PiGx.png --prefix='analysis1' --reportFile=/build/reproducible-path/pigx-rnaseq-0.1.1/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2 --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/analysis1.report.log 2>&1 -[Mon Jan 19 20:30:50 2026] +[Wed Dec 18 16:21:09 2024] Finished job 38. 45 of 49 steps (92%) done -[Mon Jan 19 20:30:50 2026] +[Wed Dec 18 16:21:11 2024] Finished job 46. 46 of 49 steps (94%) done -[Mon Jan 19 20:30:50 2026] +[Wed Dec 18 16:21:14 2024] Finished job 47. 47 of 49 steps (96%) done -[Mon Jan 19 20:31:04 2026] +[Wed Dec 18 16:21:36 2024] Finished job 45. 48 of 49 steps (98%) done Select jobs to execute... -[Mon Jan 19 20:31:04 2026] +[Wed Dec 18 16:21:36 2024] localrule all: input: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2/analysis1.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations.tgz jobid: 0 - reason: Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations.tgz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2/analysis1.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv + reason: Input files updated by another job: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2/analysis1.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations.tgz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html resources: tmpdir=/tmp -[Mon Jan 19 20:31:04 2026] +[Wed Dec 18 16:21:36 2024] Finished job 0. 49 of 49 steps (100%) done -Complete log: .snakemake/log/2026-01-19T202958.762870.snakemake.log +Complete log: .snakemake/log/2024-12-18T161949.284152.snakemake.log The following files have been generated: - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/input_annotation_stats.tsv - /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html @@ -4762,7 +4799,7 @@ rm -fr -- debian/.debhelper/generated/pigx-rnaseq/ debian/pigx-rnaseq/ debian/tmp/ dh_auto_install --destdir=debian/pigx-rnaseq/ install -m0755 -d /build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq - make -j42 install DESTDIR=/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq AM_UPDATE_INFO_DIR=no + make -j20 install DESTDIR=/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.1' make[2]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.1.1' /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' @@ -4773,8 +4810,8 @@ /usr/bin/install -c snakefile.py qsub-template.sh '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /usr/bin/install -c pigx-rnaseq '/build/reproducible-path/pigx-rnaseq-0.1.1/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-0.1.1/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' - /usr/bin/install -c -m 644 README.md '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /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-0.1.1/debian/pigx-rnaseq/usr/share/pigx_rnaseq' + /usr/bin/install -c -m 644 README.md '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' make[2]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' dh_installdocs @@ -4839,12 +4876,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1591680/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1591680/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/1812173 and its subdirectories -I: Current time: Mon Jan 19 20:31:13 -12 2026 -I: pbuilder-time-stamp: 1768897873 +I: removing directory /srv/workspace/pbuilder/1591680 and its subdirectories +I: Current time: Wed Dec 18 16:21:59 +14 2024 +I: pbuilder-time-stamp: 1734488519