Diff of the two buildlogs: -- --- b1/build.log 2024-10-08 19:57:34.470581524 +0000 +++ b2/build.log 2024-10-08 20:01:28.368607687 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Oct 8 07:53:46 -12 2024 -I: pbuilder-time-stamp: 1728417226 +I: Current time: Tue Nov 11 16:20:37 +14 2025 +I: pbuilder-time-stamp: 1762827637 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/2067088/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2430203/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 11 02:20 /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/2430203/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2430203/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='a700e471bbb243418925896cdc3a5c37' - 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='2067088' - PS1='# ' - PS2='> ' + INVOCATION_ID=5cd5e000f978422b8707326398861338 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2430203 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.4UAE0gNw/pbuilderrc_3C44 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4UAE0gNw/b1 --logfile b1/build.log pigx-rnaseq_0.1.1-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4UAE0gNw/pbuilderrc_MhzV --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4UAE0gNw/b2 --logfile b2/build.log pigx-rnaseq_0.1.1-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2067088/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2430203/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -825,7 +857,7 @@ Get: 647 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.20-3 [624 kB] Get: 648 http://deb.debian.org/debian trixie/main arm64 snakemake all 7.32.4-5 [318 kB] Get: 649 http://deb.debian.org/debian trixie/main arm64 trim-galore all 0.6.10-1 [17.8 MB] -Fetched 548 MB in 11s (48.5 MB/s) +Fetched 548 MB in 2s (234 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:arm64. (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 ... 19899 files and directories currently installed.) @@ -2882,8 +2914,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Oct 8 19:55:17 UTC 2024. -Universal Time is now: Tue Oct 8 19:55:17 UTC 2024. +Local time is now: Tue Nov 11 02:21:59 UTC 2025. +Universal Time is now: Tue Nov 11 02:21:59 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2) ... @@ -3680,7 +3712,11 @@ 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/2430203/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2430203/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 @@ -3850,19 +3886,19 @@ Select jobs to execute... -[Tue Oct 8 07:56:32 2024] +[Tue Nov 11 16:23:24 2025] 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.R2.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz + 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 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 -[Tue Oct 8 07:56:32 2024] +[Tue Nov 11 16:23:24 2025] 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 @@ -3874,7 +3910,7 @@ /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 -[Tue Oct 8 07:56:32 2024] +[Tue Nov 11 16:23:24 2025] 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 @@ -3888,7 +3924,7 @@ 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 -[Tue Oct 8 07:56:32 2024] +[Tue Nov 11 16:23:24 2025] 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 @@ -3899,7 +3935,7 @@ /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 -[Tue Oct 8 07:56:32 2024] +[Tue Nov 11 16:23:24 2025] 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 @@ -3911,7 +3947,7 @@ /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 -[Tue Oct 8 07:56:32 2024] +[Tue Nov 11 16:23:24 2025] 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 @@ -3922,12 +3958,12 @@ 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/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 -[Tue Oct 8 07:56:32 2024] +[Tue Nov 11 16:23:24 2025] Finished job 5. 1 of 49 steps (2%) done Select jobs to execute... -[Tue Oct 8 07:56:32 2024] +[Tue Nov 11 16:23:24 2025] 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 @@ -3938,27 +3974,28 @@ 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_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 -[Tue Oct 8 07:56:32 2024] +[Tue Nov 11 16:23:24 2025] Finished job 9. 2 of 49 steps (4%) done -[Tue Oct 8 07:56:32 2024] -Finished job 13. -3 of 49 steps (6%) done Select jobs to execute... -[Tue Oct 8 07:56:33 2024] +[Tue Nov 11 16:23:24 2025] 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 log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/trim_reads.UHR_Rep1.log jobid: 11 - reason: Missing output files: /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 + reason: Missing output files: /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 wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/reproducible-path/pigx-rnaseq-0.1.1/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 +[Tue Nov 11 16:23:24 2025] +Finished job 7. +3 of 49 steps (6%) done +Select jobs to execute... -[Tue Oct 8 07:56:33 2024] +[Tue Nov 11 16:23:24 2025] 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 @@ -3967,27 +4004,27 @@ resources: tmpdir=/tmp /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 -[Tue Oct 8 07:56:33 2024] -Finished job 7. +[Tue Nov 11 16:23:24 2025] +Finished job 13. 4 of 49 steps (8%) done -[Tue Oct 8 07:56:33 2024] +[Tue Nov 11 16:23:24 2025] Finished job 15. 5 of 49 steps (10%) done -[Tue Oct 8 07:56:33 2024] +[Tue Nov 11 16:23:25 2025] Finished job 11. 6 of 49 steps (12%) done -[Tue Oct 8 07:56:33 2024] +[Tue Nov 11 16:23:25 2025] Finished job 24. 7 of 49 steps (14%) done -[Tue Oct 8 07:56:33 2024] +[Tue Nov 11 16:23:25 2025] Finished job 48. 8 of 49 steps (16%) done -[Tue Oct 8 07:56:41 2024] +[Tue Nov 11 16:23:33 2025] Finished job 1. 9 of 49 steps (18%) done Select jobs to execute... -[Tue Oct 8 07:56:41 2024] +[Tue Nov 11 16:23:33 2025] 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 @@ -3998,28 +4035,28 @@ /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 -[Tue Oct 8 07:56:41 2024] +[Tue Nov 11 16:23:33 2025] 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.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/hisat2_index/GRCm38_index.3.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.6.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; 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.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.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.6.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.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.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 -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] Finished job 17. 10 of 49 steps (20%) done Select jobs to execute... -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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.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/hisat2_index/GRCm38_index.3.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/trimmed_reads/HBR_Rep1.trimmed.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.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l + 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.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.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.6.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.1.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.7.ht2l wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4029,13 +4066,13 @@ rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.out.sam -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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.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/hisat2_index/GRCm38_index.3.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_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/trimmed_reads/UHR_Rep2.trimmed.R1.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.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l + 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.5.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.4.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.6.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.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/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4045,13 +4082,13 @@ rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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.7.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.8.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.2.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.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.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l + 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.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.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.6.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.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/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4061,13 +4098,13 @@ rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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.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/hisat2_index/GRCm38_index.3.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/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/hisat2_index/GRCm38_index.6.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 + 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.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/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/trimmed_reads/HBR_Rep2.trimmed.R1.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.6.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.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4077,13 +4114,13 @@ rm /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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/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/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/hisat2_index/GRCm38_index.3.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.6.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 + 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.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/trimmed_reads/HBR_Rep3.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/trimmed_reads/HBR_Rep3.trimmed.R1.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.6.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.1.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.7.ht2l wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4092,12 +4129,12 @@ /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 -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] Finished job 16. 11 of 49 steps (22%) done Select jobs to execute... -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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 @@ -4108,18 +4145,18 @@ 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 -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] Finished job 27. 12 of 49 steps (24%) done Select jobs to execute... -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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.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/hisat2_index/GRCm38_index.3.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/trimmed_reads/UHR_Rep3.trimmed.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.4.ht2l, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/hisat2_index/GRCm38_index.1.ht2l + 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.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.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.3.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.8.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 wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4128,12 +4165,28 @@ /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 -[Tue Oct 8 07:56:42 2024] -Finished job 18. +[Tue Nov 11 16:23:34 2025] +Finished job 19. 13 of 49 steps (27%) done Select jobs to execute... -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] +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 + 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 +[Tue Nov 11 16:23:34 2025] +Finished job 18. +14 of 49 steps (29%) done +Select jobs to execute... + +[Tue Nov 11 16:23:34 2025] 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 @@ -4144,46 +4197,15 @@ 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_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 -[Tue Oct 8 07:56:42 2024] -Finished job 29. -14 of 49 steps (29%) done -Select jobs to execute... - -[Tue Oct 8 07:56:42 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.bai, /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=6000, mem_mib=5723 - -/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 -[Tue Oct 8 07:56:42 2024] -Finished job 19. -15 of 49 steps (31%) done -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] Finished job 21. +15 of 49 steps (31%) done +[Tue Nov 11 16:23:34 2025] +Finished job 31. 16 of 49 steps (33%) done -[Tue Oct 8 07:56:42 2024] -Finished job 20. -17 of 49 steps (35%) done Select jobs to execute... -[Tue Oct 8 07:56:42 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/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 - -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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 @@ -4197,39 +4219,56 @@ /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 -[Tue Oct 8 07:56:42 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 +[Tue Nov 11 16:23:34 2025] +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 + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log + jobid: 41 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw; 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=500, mem_mib=477 + 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/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... -[Tue Oct 8 07:56:42 2024] -Finished job 33. + + /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 + +[Tue Nov 11 16:23:34 2025] +Finished job 20. +17 of 49 steps (35%) done +[Tue Nov 11 16:23:34 2025] +Finished job 29. 18 of 49 steps (37%) done +Select jobs to execute... -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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 - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep1.count_reads.log - jobid: 32 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv; 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.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep1 + 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, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/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 -[Tue Oct 8 07:56:42 2024] -Finished job 31. -19 of 49 steps (39%) 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 + +[Tue Nov 11 16:23:34 2025] +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 + +/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 Select jobs to execute... +[Tue Nov 11 16:23:34 2025] +Finished job 39. +19 of 49 steps (39%) done -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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 @@ -4240,47 +4279,30 @@ 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 -[Tue Oct 8 07:56:42 2024] -Finished job 22. +[Tue Nov 11 16:23:34 2025] +Finished job 41. 20 of 49 steps (41%) done -[Tue Oct 8 07:56:42 2024] -Finished job 39. -21 of 49 steps (43%) done Select jobs to execute... -[Tue Oct 8 07:56:42 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 - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log - jobid: 41 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw; 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=4000, mem_mib=3815, threads=2 - - - /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 - - -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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 - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log - jobid: 42 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw; 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.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_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/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 + /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 +[Tue Nov 11 16:23:34 2025] +Finished job 22. +21 of 49 steps (43%) done Select jobs to execute... -[Tue Oct 8 07:56:42 2024] -Finished job 41. -22 of 49 steps (45%) done -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] 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 @@ -4291,30 +4313,12 @@ 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 -[Tue Oct 8 07:56:42 2024] -Finished job 42. -23 of 49 steps (47%) done -Select jobs to execute... - -[Tue Oct 8 07:56:42 2024] -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.bai, /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=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 - -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:34 2025] Finished job 37. -24 of 49 steps (49%) done +22 of 49 steps (45%) done Select jobs to execute... -[Tue Oct 8 07:56:42 2024] +[Tue Nov 11 16:23:35 2025] 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 @@ -4325,12 +4329,12 @@ 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_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 -[Tue Oct 8 07:56:43 2024] +[Tue Nov 11 16:23:35 2025] Finished job 40. -25 of 49 steps (51%) done +23 of 49 steps (47%) done Select jobs to execute... -[Tue Oct 8 07:56:43 2024] +[Tue Nov 11 16:23:35 2025] 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 @@ -4343,34 +4347,50 @@ /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 -[Tue Oct 8 07:56:43 2024] +[Tue Nov 11 16:23:35 2025] Finished job 44. -26 of 49 steps (53%) done +24 of 49 steps (49%) done +Select jobs to execute... + +[Tue Nov 11 16:23:35 2025] +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/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 +[Tue Nov 11 16:23:35 2025] +Finished job 33. +25 of 49 steps (51%) done Select jobs to execute... -[Tue Oct 8 07:56:43 2024] +[Tue Nov 11 16:23:35 2025] 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, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=HBR_Rep1 + 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 + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/UHR_Rep1.count_reads.log + jobid: 32 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv; 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.bai, /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=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 -[Tue Oct 8 07:56:43 2024] +/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 +[Tue Nov 11 16:23:35 2025] Finished job 4. -27 of 49 steps (55%) done +26 of 49 steps (53%) done Select jobs to execute... -[Tue Oct 8 07:56:43 2024] +[Tue Nov 11 16:23:35 2025] 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/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_index/pos.bin + 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 @@ -4381,12 +4401,12 @@ 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 -[Tue Oct 8 07:56:44 2024] +[Tue Nov 11 16:23:36 2025] Finished job 3. -28 of 49 steps (57%) done +27 of 49 steps (55%) done Select jobs to execute... -[Tue Oct 8 07:56:44 2024] +[Tue Nov 11 16:23:36 2025] 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 @@ -4397,18 +4417,18 @@ 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 -[Tue Oct 8 07:56:44 2024] +[Tue Nov 11 16:23:36 2025] Finished job 35. -29 of 49 steps (59%) done +28 of 49 steps (57%) done Select jobs to execute... -[Tue Oct 8 07:56:44 2024] +[Tue Nov 11 16:23:36 2025] 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.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/salmon_index/pos.bin + 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 wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 @@ -4419,18 +4439,18 @@ 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/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 -[Tue Oct 8 07:56:46 2024] +[Tue Nov 11 16:23:38 2025] Finished job 6. -30 of 49 steps (61%) done +29 of 49 steps (59%) done Select jobs to execute... -[Tue Oct 8 07:56:46 2024] +[Tue Nov 11 16:23:38 2025] 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 + 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 @@ -4441,18 +4461,36 @@ 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/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 -[Tue Oct 8 07:56:48 2024] +[Tue Nov 11 16:23:40 2025] Finished job 8. +30 of 49 steps (61%) done +Select jobs to execute... + +[Tue Nov 11 16:23:40 2025] +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 + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log + jobid: 42 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw; 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.bai, /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=4000, mem_mib=3815, threads=2 + + + /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 + +[Tue Nov 11 16:23:40 2025] +Finished job 42. 31 of 49 steps (63%) done Select jobs to execute... -[Tue Oct 8 07:56:48 2024] +[Tue Nov 11 16:23:40 2025] 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 + 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/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 wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 @@ -4463,52 +4501,43 @@ 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 -[Tue Oct 8 07:56:50 2024] +[Tue Nov 11 16:23:42 2025] Finished job 10. 32 of 49 steps (65%) done Select jobs to execute... -[Tue Oct 8 07:56:50 2024] -rule coverage_megadepth: +[Tue Nov 11 16:23:42 2025] +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/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log - jobid: 43 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw; 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.bai, /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.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.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep2 - resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - + 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_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 - -[Tue Oct 8 07:56:50 2024] -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 +[Tue Nov 11 16:23:46 2025] +Finished job 36. 33 of 49 steps (67%) done Select jobs to execute... -[Tue Oct 8 07:56:50 2024] +[Tue Nov 11 16:23:46 2025] 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/trimmed_reads/UHR_Rep2.trimmed.R1.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_Rep2.trimmed.R2.fq.gz + reason: Missing output files: /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; 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/salmon_index/pos.bin, /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=6000, mem_mib=5723 -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 6 -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=6000, mem_mib=5723 -Select jobs to execute... -/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/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 -[Tue Oct 8 07:56:52 2024] -Finished job 12. +[Tue Nov 11 16:23:46 2025] +Finished job 26. 34 of 49 steps (69%) done Select jobs to execute... -[Tue Oct 8 07:56:52 2024] +[Tue Nov 11 16:23:46 2025] 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 @@ -4518,166 +4547,174 @@ wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 +[Tue Nov 11 16:23:46 2025] +Finished job 32. +35 of 49 steps (71%) done +Select jobs to execute... + +[Tue Nov 11 16:23:46 2025] +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 + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log + jobid: 43 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw; 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.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam + wildcards: sample=UHR_Rep2 + resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 + + + /usr/bin/megadepth /build/reproducible-path/pigx-rnaseq-0.1.1/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 + +Building DAG of jobs... +[Tue Nov 11 16:23:46 2025] +Finished job 43. +36 of 49 steps (73%) done +Using shell: /usr/bin/bash +Provided cores: 6 +Rules claiming more threads will be scaled down. +Provided resources: mem_mb=6000, mem_mib=5723 +Select jobs to execute... +/usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.1.1/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 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... +[Tue Nov 11 16:23:47 2025] +Finished job 28. +37 of 49 steps (76%) done /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 -[Tue Oct 8 07:56:54 2024] +[Tue Nov 11 16:23:47 2025] +Finished job 30. +38 of 49 steps (78%) done +[Tue Nov 11 16:23:48 2025] +Finished job 12. +39 of 49 steps (80%) done +[Tue Nov 11 16:23:48 2025] Finished job 14. -35 of 49 steps (71%) done -Select jobs to execute... - -[Tue Oct 8 07:56:54 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/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/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/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.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_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/salmon_output/UHR_Rep2/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.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_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/quant.genes.sf - resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 - -/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/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 -[Tue Oct 8 07:56:54 2024] -Finished job 32. -36 of 49 steps (73%) done +40 of 49 steps (82%) done Select jobs to execute... -[Tue Oct 8 07:56:54 2024] +[Tue Nov 11 16:23:48 2025] 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/HBR_Rep1_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_Rep2/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/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/HBR_Rep1/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/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /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_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_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/HBR_Rep1_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/HBR_Rep1/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/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /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_Rep2_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/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/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/salmon_output/HBR_Rep2/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 -[Tue Oct 8 07:56:54 2024] -Finished job 28. -37 of 49 steps (76%) done -Select jobs to execute... -[Tue Oct 8 07:56:54 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.bai, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep2 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 +[Tue Nov 11 16:23:48 2025] +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.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, /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/colData.tsv, /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.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/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/UHR_Rep2/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/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/HBR_Rep3/quant.genes.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_Rep2/quant.sf + resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 -/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 -[Tue Oct 8 07:56:54 2024] -Finished job 36. -38 of 49 steps (78%) done -[Tue Oct 8 07:56:54 2024] -Finished job 30. -39 of 49 steps (80%) done -[Tue Oct 8 07:56:54 2024] -Finished job 26. -40 of 49 steps (82%) done -[Tue Oct 8 07:56:56 2024] +/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 +[Tue Nov 11 16:23:50 2025] Finished job 2. 41 of 49 steps (84%) done -[Tue Oct 8 07:57:02 2024] -Finished job 23. -42 of 49 steps (86%) done -Select jobs to execute... - -[Tue Oct 8 07:57:02 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/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/colData.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 - -[Tue Oct 8 07:57:02 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 - log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/analysis1.report.salmon.genes.log - jobid: 47 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html; Input files updated by another job: /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 - 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.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 -[Tue Oct 8 07:57:05 2024] +[Tue Nov 11 16:23:53 2025] Finished job 34. -43 of 49 steps (88%) done +42 of 49 steps (86%) done Select jobs to execute... -[Tue Oct 8 07:57:05 2024] +[Tue Nov 11 16:23:53 2025] 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/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_Rep3.read_counts.csv, /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/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/colData.tsv + 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_Rep2.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_Rep3.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/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/mapped_reads/hisat2/HBR_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 -[Tue Oct 8 07:57:06 2024] +[Tue Nov 11 16:23:54 2025] Finished job 25. -44 of 49 steps (90%) done +43 of 49 steps (88%) done Select jobs to execute... -[Tue Oct 8 07:57:06 2024] +[Tue Nov 11 16:23:54 2025] 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 log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/norm_counts_deseq.log jobid: 38 - reason: Missing output files: /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; Input files updated by another job: /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 + reason: Missing output files: /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; 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/hisat2/counts.tsv resources: tmpdir=/tmp, mem_mb=1000, mem_mib=954 /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 -[Tue Oct 8 07:57:06 2024] +[Tue Nov 11 16:23:54 2025] 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 log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/hisat2/analysis1.report.log jobid: 45 - reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2/analysis1.deseq.report.html; Input files updated by another job: /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 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/hisat2/analysis1.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/hisat2/counts.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' --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 -[Tue Oct 8 07:57:13 2024] +[Tue Nov 11 16:23:57 2025] +Finished job 23. +44 of 49 steps (90%) done +Select jobs to execute... + +[Tue Nov 11 16:23:57 2025] +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 + +[Tue Nov 11 16:23:57 2025] +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 + log: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/logs/salmon/analysis1.report.salmon.genes.log + jobid: 47 + reason: Missing output files: /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/report/salmon/analysis1.salmon.genes.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.genes.tsv + wildcards: analysis=analysis1 + resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 + +/usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.1.1/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 +[Tue Nov 11 16:24:01 2025] Finished job 38. 45 of 49 steps (92%) done -[Tue Oct 8 07:57:24 2024] -Finished job 46. +[Tue Nov 11 16:24:17 2025] +Finished job 45. 46 of 49 steps (94%) done -[Tue Oct 8 07:57:24 2024] -Finished job 47. +[Tue Nov 11 16:24:20 2025] +Finished job 46. 47 of 49 steps (96%) done -[Tue Oct 8 07:57:27 2024] -Finished job 45. +[Tue Nov 11 16:24:20 2025] +Finished job 47. 48 of 49 steps (98%) done Select jobs to execute... -[Tue Oct 8 07:57:27 2024] +[Tue Nov 11 16:24:20 2025] 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/raw_counts/salmon/counts_from_SALMON.genes.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_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/feature_counts/raw_counts/hisat2/counts.tsv, /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/report/hisat2/analysis1.deseq.report.html, /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_Rep3.all.bw, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/annotations.tgz, /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/normalized/salmon/TPM_counts_from_SALMON.transcripts.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/report/salmon/analysis1.salmon.genes.deseq.report.html, /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/bigwig_files/hisat2/megadepth/HBR_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/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv + 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/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/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/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.1.1/tests/output/multiqc/multiqc_report.html, /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/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/bigwig_files/hisat2/megadepth/HBR_Rep3.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/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.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/salmon/TPM_counts_from_SALMON.transcripts.tsv, /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/raw_counts/hisat2/counts.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/hisat2/analysis1.deseq.report.html resources: tmpdir=/tmp -[Tue Oct 8 07:57:27 2024] +[Tue Nov 11 16:24:20 2025] Finished job 0. 49 of 49 steps (100%) done -Complete log: .snakemake/log/2024-10-08T075632.526451.snakemake.log +Complete log: .snakemake/log/2025-11-11T162324.418948.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 @@ -4714,9 +4751,9 @@ /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /usr/bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/share/pigx_rnaseq' /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 pigx-rnaseq '/build/reproducible-path/pigx-rnaseq-0.1.1/debian/pigx-rnaseq/usr/bin' /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' make[2]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.1.1' @@ -4782,12 +4819,14 @@ 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/2430203/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2430203/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/2067088 and its subdirectories -I: Current time: Tue Oct 8 07:57:33 -12 2024 -I: pbuilder-time-stamp: 1728417453 +I: removing directory /srv/workspace/pbuilder/2430203 and its subdirectories +I: Current time: Tue Nov 11 16:24:27 +14 2025 +I: pbuilder-time-stamp: 1762827867