Diff of the two buildlogs: -- --- b1/build.log 2023-04-21 18:53:05.616594526 +0000 +++ b2/build.log 2023-04-21 19:06:32.448795357 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 21 06:35:47 -12 2023 -I: pbuilder-time-stamp: 1682102147 +I: Current time: Fri May 24 15:16:09 +14 2024 +I: pbuilder-time-stamp: 1716513369 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./pigx-rnaseq_0.1.0.orig.tar.xz] I: copying [./pigx-rnaseq_0.1.0-1.1.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Dec 13 06:32:19 2022 -12 +gpgv: Signature made Wed Dec 14 08:32:19 2022 +14 gpgv: using RSA key 406220C8B8552802378CCE411F5C7A8B45564314 gpgv: issuer "bage@debian.org" gpgv: Can't check signature: No public key @@ -26,52 +26,84 @@ dpkg-source: info: unpacking pigx-rnaseq_0.1.0-1.1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/30554/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/5808/tmp/hooks/D01_modify_environment starting +debug: Running on codethink13-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 May 24 15:16 /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/5808/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/5808/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='30554' - PS1='# ' - PS2='> ' + 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=5808 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.WHlbkvWw/pbuilderrc_mGbD --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WHlbkvWw/b1 --logfile b1/build.log pigx-rnaseq_0.1.0-1.1.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.WHlbkvWw/pbuilderrc_ciTN --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WHlbkvWw/b2 --logfile b2/build.log --extrapackages usrmerge pigx-rnaseq_0.1.0-1.1.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink12-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 20 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/30554/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 23 06:50 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/5808/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -842,7 +874,7 @@ Get: 663 http://deb.debian.org/debian bookworm/main arm64 samtools arm64 1.16.1-1 [580 kB] Get: 664 http://deb.debian.org/debian bookworm/main arm64 snakemake all 7.21.0-1 [301 kB] Get: 665 http://deb.debian.org/debian bookworm/main arm64 trim-galore all 0.6.10-1 [17.8 MB] -Fetched 566 MB in 49s (11.5 MB/s) +Fetched 566 MB in 12s (46.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (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 ... 19616 files and directories currently installed.) @@ -3697,8 +3729,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/pigx-rnaseq-0.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pigx-rnaseq_0.1.0-1.1_source.changes +I: user script /srv/workspace/pbuilder/5808/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/5808/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/pigx-rnaseq-0.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pigx-rnaseq_0.1.0-1.1_source.changes dpkg-buildpackage: info: source package pigx-rnaseq dpkg-buildpackage: info: source version 0.1.0-1.1 dpkg-buildpackage: info: source distribution unstable @@ -3867,19 +3908,19 @@ Select jobs to execute... -[Fri Apr 21 06:46:39 2023] +[Fri May 24 15:25:09 2024] rule trim_qc_reads_pe: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz, /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.json log: /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep2.log jobid: 7 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz --in2 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz --out1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz --out2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -h /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.html -j /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.json >> /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep2.log 2>&1 -[Fri Apr 21 06:46:40 2023] +[Fri May 24 15:25:09 2024] rule trim_qc_reads_se: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep1.se.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep1.se.fastp.json @@ -3891,7 +3932,7 @@ /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz --out1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -h /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep1.se.fastp.html -j /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep1.se.fastp.json >> /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep1.log 2>&1 -[Fri Apr 21 06:46:40 2023] +[Fri May 24 15:25:09 2024] rule translate_sample_sheet_for_report: input: /build/pigx-rnaseq-0.1.0/tests/sample_sheet.csv output: /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv @@ -3901,7 +3942,7 @@ /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//translate_sample_sheet_for_report.R /build/pigx-rnaseq-0.1.0/tests/sample_sheet.csv -[Fri Apr 21 06:46:40 2023] +[Fri May 24 15:25:09 2024] rule trim_qc_reads_se: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep3.se.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep3.se.fastp.json @@ -3913,7 +3954,7 @@ /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz --out1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -h /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep3.se.fastp.html -j /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep3.se.fastp.json >> /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep3.log 2>&1 -[Fri Apr 21 06:46:40 2023] +[Fri May 24 15:25:09 2024] rule trim_qc_reads_pe: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz, /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.json @@ -3925,22 +3966,7 @@ /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz --in2 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz --out1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz --out2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -h /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.html -j /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.json >> /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep3.log 2>&1 -[Fri Apr 21 06:46:40 2023] -rule check_annotation_files: - input: /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta, /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta, /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf - output: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/check_annotation_files.log - jobid: 1 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv - resources: tmpdir=/tmp - -/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//validate_input_annotation.R /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta /build/pigx-rnaseq-0.1.0/tests/output >> /build/pigx-rnaseq-0.1.0/tests/output/logs/check_annotation_files.log 2>&1 -[Fri Apr 21 06:46:41 2023] -Finished job 7. -1 of 48 steps (2%) done -Select jobs to execute... - -[Fri Apr 21 06:46:42 2023] +[Fri May 24 15:25:09 2024] rule trim_qc_reads_pe: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz, /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.json @@ -3951,15 +3977,27 @@ resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz --in2 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz --out1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz --out2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -h /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.html -j /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.json >> /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep2.log 2>&1 -[Fri Apr 21 06:46:42 2023] -Finished job 15. -2 of 48 steps (4%) done -[Fri Apr 21 06:46:42 2023] +[Fri May 24 15:25:10 2024] Finished job 5. -3 of 48 steps (6%) done +1 of 48 steps (2%) done +Select jobs to execute... + +[Fri May 24 15:25:10 2024] +rule check_annotation_files: + input: /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta, /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta, /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf + output: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/check_annotation_files.log + jobid: 1 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv + resources: tmpdir=/tmp + +/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//validate_input_annotation.R /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta /build/pigx-rnaseq-0.1.0/tests/output >> /build/pigx-rnaseq-0.1.0/tests/output/logs/check_annotation_files.log 2>&1 +[Fri May 24 15:25:10 2024] +Finished job 7. +2 of 48 steps (4%) done Select jobs to execute... -[Fri Apr 21 06:46:42 2023] +[Fri May 24 15:25:10 2024] rule trim_qc_reads_pe: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz, /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.json @@ -3970,24 +4008,27 @@ resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz --in2 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz --out1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz --out2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -h /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.html -j /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.json >> /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep1.log 2>&1 -[Fri Apr 21 06:46:42 2023] -Finished job 24. -4 of 48 steps (8%) done -[Fri Apr 21 06:46:42 2023] +[Fri May 24 15:25:10 2024] +Finished job 15. +3 of 48 steps (6%) done +[Fri May 24 15:25:11 2024] Finished job 9. +4 of 48 steps (8%) done +[Fri May 24 15:25:11 2024] +Finished job 13. 5 of 48 steps (10%) done -[Fri Apr 21 06:46:43 2023] -Finished job 11. +[Fri May 24 15:25:11 2024] +Finished job 24. 6 of 48 steps (12%) done -[Fri Apr 21 06:46:43 2023] -Finished job 13. +[Fri May 24 15:25:11 2024] +Finished job 11. 7 of 48 steps (15%) done -[Fri Apr 21 06:47:14 2023] +[Fri May 24 15:25:37 2024] Finished job 1. 8 of 48 steps (17%) done Select jobs to execute... -[Fri Apr 21 06:47:14 2023] +[Fri May 24 15:25:37 2024] rule salmon_index: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta, /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin @@ -3998,28 +4039,28 @@ /usr/bin/salmon index -t /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -p 8 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_index.log 2>&1 -[Fri Apr 21 06:47:14 2023] +[Fri May 24 15:25:37 2024] rule hisat2_index: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta, /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2_index.log jobid: 17 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv resources: tmpdir=/tmp, mem_mb=32000, mem_mib=30518 /usr/bin/hisat2-build -f -p 2 --large-index /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2_index.log 2>&1 -[Fri Apr 21 06:47:36 2023] +[Fri May 24 15:25:45 2024] Finished job 17. 9 of 48 steps (19%) done Select jobs to execute... -[Fri Apr 21 06:47:36 2023] +[Fri May 24 15:25:45 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep3.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep3.log jobid: 22 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4029,13 +4070,13 @@ rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam -[Fri Apr 21 06:47:36 2023] +[Fri May 24 15:25:45 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep3.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep3.log jobid: 19 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4045,13 +4086,13 @@ rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam -[Fri Apr 21 06:47:36 2023] +[Fri May 24 15:25:45 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep1.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep1.log jobid: 20 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4061,13 +4102,13 @@ rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam -[Fri Apr 21 06:47:36 2023] +[Fri May 24 15:25:45 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep2.log jobid: 21 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4077,13 +4118,13 @@ rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam -[Fri Apr 21 06:47:36 2023] +[Fri May 24 15:25:45 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep1.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep1.log jobid: 16 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4092,12 +4133,12 @@ /usr/bin/samtools view -bh /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.out.sam | /usr/bin/samtools sort -o /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep1.log 2>&1 rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.out.sam -[Fri Apr 21 06:47:38 2023] +[Fri May 24 15:25:46 2024] Finished job 22. 10 of 48 steps (21%) done Select jobs to execute... -[Fri Apr 21 06:47:39 2023] +[Fri May 24 15:25:46 2024] rule index_bam: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai @@ -4108,18 +4149,18 @@ resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep3.log 2>&1 -[Fri Apr 21 06:47:39 2023] -Finished job 16. +[Fri May 24 15:25:46 2024] +Finished job 37. 11 of 48 steps (23%) done Select jobs to execute... -[Fri Apr 21 06:47:39 2023] +[Fri May 24 15:25:46 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep2.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep2.log jobid: 18 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4128,18 +4169,12 @@ /usr/bin/samtools view -bh /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam | /usr/bin/samtools sort -o /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep2.log 2>&1 rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.out.sam -[Fri Apr 21 06:47:39 2023] -Finished job 37. +[Fri May 24 15:25:46 2024] +Finished job 16. 12 of 48 steps (25%) done -[Fri Apr 21 06:47:39 2023] -Finished job 19. -13 of 48 steps (27%) done -[Fri Apr 21 06:47:39 2023] -Finished job 21. -14 of 48 steps (29%) done Select jobs to execute... -[Fri Apr 21 06:47:39 2023] +[Fri May 24 15:25:46 2024] rule index_bam: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai @@ -4150,38 +4185,12 @@ resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep1.log 2>&1 - -[Fri Apr 21 06:47:39 2023] -rule coverage_megadepth: - input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai - output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log - jobid: 44 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=UHR_Rep3 - resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - - - /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log 2>&1 - - -[Fri Apr 21 06:47:39 2023] -rule index_bam: - input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam - output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep2.log - jobid: 35 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep2 - resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 - -/usr/bin/samtools index /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep2.log 2>&1 -[Fri Apr 21 06:47:39 2023] -Finished job 20. -15 of 48 steps (31%) done +[Fri May 24 15:25:46 2024] +Finished job 19. +13 of 48 steps (27%) done Select jobs to execute... -[Fri Apr 21 06:47:40 2023] +[Fri May 24 15:25:47 2024] rule index_bam: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai @@ -4192,30 +4201,18 @@ resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep3.log 2>&1 -[Fri Apr 21 06:47:40 2023] +[Fri May 24 15:25:47 2024] +Finished job 21. +14 of 48 steps (29%) done +[Fri May 24 15:25:47 2024] Finished job 27. +15 of 48 steps (31%) done +[Fri May 24 15:25:47 2024] +Finished job 20. 16 of 48 steps (33%) done -[Fri Apr 21 06:47:40 2023] -Finished job 35. -17 of 48 steps (35%) done -[Fri Apr 21 06:47:40 2023] -Finished job 44. -18 of 48 steps (38%) done Select jobs to execute... -[Fri Apr 21 06:47:40 2023] -rule count_reads: - input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai - output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log - jobid: 34 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=UHR_Rep2 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - -/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep2 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log 2>&1 - -[Fri Apr 21 06:47:40 2023] +[Fri May 24 15:25:47 2024] rule index_bam: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai @@ -4227,25 +4224,37 @@ /usr/bin/samtools index /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep1.log 2>&1 -[Fri Apr 21 06:47:40 2023] +[Fri May 24 15:25:47 2024] rule coverage_megadepth: - input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log - jobid: 39 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=HBR_Rep1 + input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai + output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log + jobid: 44 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log 2>&1 + /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log 2>&1 -[Fri Apr 21 06:47:40 2023] + +[Fri May 24 15:25:47 2024] +rule index_bam: + input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam + output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep2.log + jobid: 35 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam + wildcards: sample=UHR_Rep2 + resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 + +/usr/bin/samtools index /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep2.log 2>&1 +[Fri May 24 15:25:47 2024] Finished job 31. -19 of 48 steps (40%) done +17 of 48 steps (35%) done Select jobs to execute... -[Fri Apr 21 06:47:40 2023] +[Fri May 24 15:25:47 2024] rule count_reads: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv @@ -4256,46 +4265,65 @@ resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep3 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep3.count_reads.log 2>&1 -[Fri Apr 21 06:47:40 2023] +[Fri May 24 15:25:47 2024] Finished job 33. +18 of 48 steps (38%) done +[Fri May 24 15:25:47 2024] +Finished job 35. +19 of 48 steps (40%) done +Select jobs to execute... + +[Fri May 24 15:25:47 2024] +rule coverage_megadepth: + input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai + output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log + jobid: 41 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam + wildcards: sample=HBR_Rep3 + resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 + + + /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log 2>&1 + + +[Fri May 24 15:25:47 2024] +rule coverage_megadepth: + input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai + output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log + jobid: 42 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam + wildcards: sample=UHR_Rep1 + resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 + + + /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log 2>&1 + +[Fri May 24 15:25:47 2024] +Finished job 44. 20 of 48 steps (42%) done Select jobs to execute... -[Fri Apr 21 06:47:41 2023] +[Fri May 24 15:25:47 2024] rule coverage_megadepth: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log jobid: 43 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log 2>&1 -[Fri Apr 21 06:47:41 2023] -Finished job 39. +[Fri May 24 15:25:47 2024] +Finished job 18. 21 of 48 steps (44%) done Select jobs to execute... -[Fri Apr 21 06:47:41 2023] -rule count_reads: - input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep1.count_reads.log - jobid: 26 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=HBR_Rep1 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - -/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep1 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep1.count_reads.log 2>&1 -Select jobs to execute... -[Fri Apr 21 06:47:41 2023] -Finished job 18. -22 of 48 steps (46%) done - -[Fri Apr 21 06:47:41 2023] +[Fri May 24 15:25:48 2024] rule index_bam: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai @@ -4306,225 +4334,209 @@ resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep2.log 2>&1 -[Fri Apr 21 06:47:41 2023] -Finished job 43. +[Fri May 24 15:25:48 2024] +Finished job 41. +22 of 48 steps (46%) done +[Fri May 24 15:25:48 2024] +Finished job 42. 23 of 48 steps (48%) done Select jobs to execute... -[Fri Apr 21 06:47:42 2023] +[Fri May 24 15:25:48 2024] +rule count_reads: + input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai + output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep3.count_reads.log + jobid: 30 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam + wildcards: sample=HBR_Rep3 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + +/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep3 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep3.count_reads.log 2>&1 + +[Fri May 24 15:25:48 2024] rule coverage_megadepth: - input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai - output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log - jobid: 42 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep1 + input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log + jobid: 39 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log 2>&1 + /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log 2>&1 -[Fri Apr 21 06:47:42 2023] +[Fri May 24 15:25:48 2024] Finished job 29. 24 of 48 steps (50%) done +[Fri May 24 15:25:48 2024] +Finished job 43. +25 of 48 steps (52%) done Select jobs to execute... -[Fri Apr 21 06:47:42 2023] +[Fri May 24 15:25:48 2024] +rule count_reads: + input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai + output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep1.count_reads.log + jobid: 32 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam + wildcards: sample=UHR_Rep1 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + +/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep1 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep1.count_reads.log 2>&1 + +[Fri May 24 15:25:48 2024] +rule count_reads: + input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai + output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep2.count_reads.log + jobid: 28 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam + wildcards: sample=HBR_Rep2 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + +/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep2 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep2.count_reads.log 2>&1 +Select jobs to execute... +[Fri May 24 15:25:48 2024] +Finished job 39. +26 of 48 steps (54%) done + +[Fri May 24 15:25:48 2024] rule coverage_megadepth: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log jobid: 40 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log 2>&1 -[Fri Apr 21 06:47:42 2023] -Finished job 42. -25 of 48 steps (52%) done +[Fri May 24 15:25:49 2024] +Finished job 40. +27 of 48 steps (56%) done Select jobs to execute... -[Fri Apr 21 06:47:42 2023] +[Fri May 24 15:25:49 2024] rule count_reads: - input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai - output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep2.count_reads.log - jobid: 28 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=HBR_Rep2 + input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai + output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log + jobid: 34 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam + wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep2 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep2.count_reads.log 2>&1 -[Fri Apr 21 06:47:42 2023] -Finished job 40. -26 of 48 steps (54%) done +/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep2 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log 2>&1 +[Fri May 24 15:26:06 2024] +Finished job 4. +28 of 48 steps (58%) done Select jobs to execute... -[Fri Apr 21 06:47:42 2023] +[Fri May 24 15:26:06 2024] rule count_reads: - input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai - output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep1.count_reads.log - jobid: 32 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep1 + input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep1.count_reads.log + jobid: 26 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai + wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep1 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep1.count_reads.log 2>&1 -[Fri Apr 21 06:48:19 2023] -Finished job 4. -27 of 48 steps (56%) done +/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep1 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep1.count_reads.log 2>&1 +[Fri May 24 15:26:43 2024] +Finished job 34. +29 of 48 steps (60%) done Select jobs to execute... -[Fri Apr 21 06:48:19 2023] +[Fri May 24 15:26:43 2024] rule salmon_quant: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log jobid: 8 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 6 -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=6000, mem_mib=5723 -Select jobs to execute... -/usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log 2>&1 -[Fri Apr 21 06:48:36 2023] -Finished job 8. -28 of 48 steps (58%) done +[Fri May 24 15:26:43 2024] +Finished job 30. +30 of 48 steps (62%) done Select jobs to execute... -[Fri Apr 21 06:48:36 2023] +[Fri May 24 15:26:43 2024] rule salmon_quant: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log jobid: 12 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.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/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log 2>&1 -[Fri Apr 21 06:48:50 2023] -Finished job 12. -29 of 48 steps (60%) done -Select jobs to execute... - -[Fri Apr 21 06:48:50 2023] -rule salmon_quant: - input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz - output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log - jobid: 14 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin - wildcards: sample=UHR_Rep3 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - -Building DAG of jobs... -Using shell: /usr/bin/bash -Provided cores: 6 -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=6000, mem_mib=5723 -Select jobs to execute... -/usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -r /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log 2>&1 -[Fri Apr 21 06:49:05 2023] -Finished job 14. -30 of 48 steps (62%) done -Select jobs to execute... - -[Fri Apr 21 06:49:05 2023] -rule count_reads: - input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai - output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep3.count_reads.log - jobid: 30 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=HBR_Rep3 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - -/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep3 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep3.count_reads.log 2>&1 -[Fri Apr 21 06:49:41 2023] -Finished job 28. +[Fri May 24 15:26:44 2024] +Finished job 36. 31 of 48 steps (65%) done Select jobs to execute... -[Fri Apr 21 06:49:41 2023] +[Fri May 24 15:26:44 2024] rule salmon_quant: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log jobid: 6 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -[Fri Apr 21 06:49:43 2023] -Finished job 36. +[Fri May 24 15:26:45 2024] +Finished job 28. 32 of 48 steps (67%) done Select jobs to execute... -[Fri Apr 21 06:49:43 2023] +[Fri May 24 15:26:45 2024] rule salmon_quant: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log jobid: 10 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -[Fri Apr 21 06:49:45 2023] -Finished job 34. +[Fri May 24 15:26:46 2024] +Finished job 32. 33 of 48 steps (69%) done Select jobs to execute... -[Fri Apr 21 06:49:45 2023] -rule coverage_megadepth: - input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai - output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log - jobid: 41 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=HBR_Rep3 - resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - - - /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log 2>&1 - -[Fri Apr 21 06:49:45 2023] -Finished job 41. -34 of 48 steps (71%) done -Select jobs to execute... - -[Fri Apr 21 06:49:45 2023] +[Fri May 24 15:26:46 2024] rule salmon_quant: - input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz - output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log - jobid: 3 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin - wildcards: sample=HBR_Rep1 + input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz + output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log + jobid: 14 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin + wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -[Fri Apr 21 06:49:48 2023] -Finished job 26. -35 of 48 steps (73%) done -[Fri Apr 21 06:49:50 2023] -Finished job 32. -36 of 48 steps (75%) done +Building DAG of jobs... +Using shell: /usr/bin/bash +Provided cores: 6 +Rules claiming more threads will be scaled down. +Provided resources: mem_mb=6000, mem_mib=5723 +Select jobs to execute... +/usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log 2>&1 +Building DAG of jobs... +Using shell: /usr/bin/bash +Provided cores: 6 +Rules claiming more threads will be scaled down. +Provided resources: mem_mb=6000, mem_mib=5723 +Select jobs to execute... +/usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log 2>&1 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 @@ -4545,63 +4557,62 @@ 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/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -r /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log 2>&1 -[Fri Apr 21 06:49:58 2023] -Finished job 6. -37 of 48 steps (77%) done -[Fri Apr 21 06:49:58 2023] -Finished job 10. -38 of 48 steps (79%) done -[Fri Apr 21 06:49:59 2023] -Finished job 3. -39 of 48 steps (81%) done +/usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -r /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log 2>&1 +[Fri May 24 15:26:52 2024] +Finished job 8. +34 of 48 steps (71%) done Select jobs to execute... -[Fri Apr 21 06:50:00 2023] -rule counts_from_SALMON: - input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv - output: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log - jobid: 23 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf - resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 - -/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//counts_matrix_from_SALMON.R /build/pigx-rnaseq-0.1.0/tests/output/salmon_output /build/pigx-rnaseq-0.1.0/tests/output/feature_counts /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log 2>&1 - -[Fri Apr 21 06:50:00 2023] -rule multiqc: - input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam - output: /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/multiqc.hisat2.log - jobid: 2 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam - resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 +[Fri May 24 15:26:52 2024] +rule salmon_quant: + input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz + output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log + jobid: 3 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin + wildcards: sample=HBR_Rep1 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/usr/bin/multiqc -f -o /build/pigx-rnaseq-0.1.0/tests/output/multiqc /build/pigx-rnaseq-0.1.0/tests/output >> /build/pigx-rnaseq-0.1.0/tests/output/logs/multiqc.hisat2.log 2>&1 -[Fri Apr 21 06:50:23 2023] -Finished job 30. -40 of 48 steps (83%) done +[Fri May 24 15:26:53 2024] +Finished job 12. +35 of 48 steps (73%) done +[Fri May 24 15:26:54 2024] +Finished job 6. +36 of 48 steps (75%) done +[Fri May 24 15:26:54 2024] +Finished job 26. +37 of 48 steps (77%) done Select jobs to execute... -[Fri Apr 21 06:50:23 2023] +[Fri May 24 15:26:54 2024] rule collate_read_counts: input: /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv output: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/collate_read_counts.log jobid: 25 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts/collate_read_counts.R /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2 /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/collate_read_counts.log 2>&1 -[Fri Apr 21 06:50:23 2023] -Finished job 2. -41 of 48 steps (85%) done -[Fri Apr 21 06:50:24 2023] +[Fri May 24 15:26:55 2024] +Finished job 10. +38 of 48 steps (79%) done +[Fri May 24 15:26:55 2024] +Finished job 14. +39 of 48 steps (81%) done +Building DAG of jobs... +Using shell: /usr/bin/bash +Provided cores: 6 +Rules claiming more threads will be scaled down. +Provided resources: mem_mb=6000, mem_mib=5723 +Select jobs to execute... +/usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -r /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log 2>&1 +[Fri May 24 15:26:56 2024] Finished job 25. -42 of 48 steps (88%) done +40 of 48 steps (83%) done Select jobs to execute... -[Fri Apr 21 06:50:24 2023] +[Fri May 24 15:26:56 2024] rule norm_counts_deseq: input: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv @@ -4612,7 +4623,7 @@ /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts/norm_counts_deseq.R /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/norm_counts_deseq.log 2>&1 -[Fri Apr 21 06:50:24 2023] +[Fri May 24 15:26:56 2024] rule report1: input: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html @@ -4623,24 +4634,56 @@ resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts/runDeseqReport.R --logo=/build/pigx-rnaseq-0.1.0/images/Logo_PiGx.png --prefix='analysis1' --reportFile=/build/pigx-rnaseq-0.1.0/scripts/deseqReport.Rmd --countDataFile=/build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv --colDataFile=/build/pigx-rnaseq-0.1.0/tests/output/colData.tsv --gtfFile=/build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/pigx-rnaseq-0.1.0/tests/output/report/hisat2 --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/analysis1.report.log 2>&1 -[Fri Apr 21 06:50:47 2023] -Finished job 23. +[Fri May 24 15:26:58 2024] +Finished job 3. +41 of 48 steps (85%) done +Select jobs to execute... + +[Fri May 24 15:26:58 2024] +rule counts_from_SALMON: + input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv + output: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log + jobid: 23 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf + resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 + +/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//counts_matrix_from_SALMON.R /build/pigx-rnaseq-0.1.0/tests/output/salmon_output /build/pigx-rnaseq-0.1.0/tests/output/feature_counts /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log 2>&1 + +[Fri May 24 15:26:58 2024] +rule multiqc: + input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam + output: /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/multiqc.hisat2.log + jobid: 2 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf + resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 + +/usr/bin/multiqc -f -o /build/pigx-rnaseq-0.1.0/tests/output/multiqc /build/pigx-rnaseq-0.1.0/tests/output >> /build/pigx-rnaseq-0.1.0/tests/output/logs/multiqc.hisat2.log 2>&1 +[Fri May 24 15:27:18 2024] +Finished job 2. +42 of 48 steps (88%) done +[Fri May 24 15:27:26 2024] +Finished job 38. 43 of 48 steps (90%) done +[Fri May 24 15:27:34 2024] +Finished job 23. +44 of 48 steps (92%) done Select jobs to execute... -[Fri Apr 21 06:50:47 2023] +[Fri May 24 15:27:34 2024] rule report2: input: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log jobid: 46 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv wildcards: analysis=analysis1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts/runDeseqReport.R --logo=/build/pigx-rnaseq-0.1.0/images/Logo_PiGx.png --prefix='analysis1.salmon.transcripts' --reportFile=/build/pigx-rnaseq-0.1.0/scripts/deseqReport.Rmd --countDataFile=/build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv --colDataFile=/build/pigx-rnaseq-0.1.0/tests/output/colData.tsv --gtfFile=/build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/pigx-rnaseq-0.1.0/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log 2>&1 -[Fri Apr 21 06:50:47 2023] +[Fri May 24 15:27:34 2024] rule report3: input: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html @@ -4651,31 +4694,28 @@ resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts/runDeseqReport.R --logo=/build/pigx-rnaseq-0.1.0/images/Logo_PiGx.png --prefix='analysis1.salmon.genes' --reportFile=/build/pigx-rnaseq-0.1.0/scripts/deseqReport.Rmd --countDataFile=/build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv --colDataFile=/build/pigx-rnaseq-0.1.0/tests/output/colData.tsv --gtfFile=/build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/pigx-rnaseq-0.1.0/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.genes.log 2>&1 -[Fri Apr 21 06:51:08 2023] -Finished job 38. -44 of 48 steps (92%) done -[Fri Apr 21 06:52:29 2023] +[Fri May 24 15:28:39 2024] Finished job 45. 45 of 48 steps (94%) done -[Fri Apr 21 06:52:44 2023] -Finished job 47. -46 of 48 steps (96%) done -[Fri Apr 21 06:52:48 2023] +[Fri May 24 15:29:14 2024] Finished job 46. +46 of 48 steps (96%) done +[Fri May 24 15:29:14 2024] +Finished job 47. 47 of 48 steps (98%) done Select jobs to execute... -[Fri Apr 21 06:52:48 2023] +[Fri May 24 15:29:14 2024] localrule all: input: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv, /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html jobid: 0 - reason: Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv + reason: Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv, /build/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw resources: tmpdir=/tmp -[Fri Apr 21 06:52:48 2023] +[Fri May 24 15:29:14 2024] Finished job 0. 48 of 48 steps (100%) done -Complete log: .snakemake/log/2023-04-21T064638.224135.snakemake.log +Complete log: .snakemake/log/2024-05-24T152508.582747.snakemake.log The following files have been generated: - /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv - /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html @@ -4707,14 +4747,14 @@ make[2]: Entering directory '/build/pigx-rnaseq-0.1.0' /usr/bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /usr/bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' + /usr/bin/install -c snakefile.py qsub-template.sh '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /usr/bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/bin' /usr/bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' + /usr/bin/install -c pigx-rnaseq '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/bin' + /usr/bin/install -c scripts/runDeseqReport.R scripts/translate_sample_sheet_for_report.R scripts/deseqReport.Rmd scripts/counts_matrix_from_SALMON.R scripts/validate_input.py scripts/norm_counts_deseq.R scripts/count_reads.R scripts/collate_read_counts.R scripts/validate_input_annotation.R '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' /usr/bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/pigx_rnaseq' - /usr/bin/install -c snakefile.py qsub-template.sh '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /usr/bin/install -c -m 644 README.md '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' - /usr/bin/install -c pigx-rnaseq '/build/pigx-rnaseq-0.1.0/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/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/pigx_rnaseq' - /usr/bin/install -c scripts/runDeseqReport.R scripts/translate_sample_sheet_for_report.R scripts/deseqReport.Rmd scripts/counts_matrix_from_SALMON.R scripts/validate_input.py scripts/norm_counts_deseq.R scripts/count_reads.R scripts/collate_read_counts.R scripts/validate_input_annotation.R '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' make[2]: Leaving directory '/build/pigx-rnaseq-0.1.0' make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0' dh_installdocs @@ -4779,12 +4819,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/5808/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/5808/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/30554 and its subdirectories -I: Current time: Fri Apr 21 06:53:04 -12 2023 -I: pbuilder-time-stamp: 1682103184 +I: removing directory /srv/workspace/pbuilder/5808 and its subdirectories +I: Current time: Fri May 24 15:29:31 +14 2024 +I: pbuilder-time-stamp: 1716514171