Diff of the two buildlogs: -- --- b1/build.log 2024-01-07 08:09:48.256324786 +0000 +++ b2/build.log 2024-01-07 08:16:59.021478167 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 6 20:01:50 -12 2024 -I: pbuilder-time-stamp: 1704614510 +I: Current time: Sun Jan 7 22:09:51 +14 2024 +I: pbuilder-time-stamp: 1704614991 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./pigx-rnaseq_0.0.10+ds-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.dSzvDw30/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.vH_IXmLG/trustedkeys.kbx': General error gpgv: Signature made Fri Oct 23 14:13:09 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" @@ -31,49 +31,80 @@ dpkg-source: info: applying notSelfContained.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/476780/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3217408/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Jan 7 08:09 /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/3217408/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3217408/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=12 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='595823d678184422a2222c786ebf230c' - 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='476780' - PS1='# ' - PS2='> ' + INVOCATION_ID=6732fbaf0a7e40a183d6eb8bc9ed8745 + 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=3217408 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.UR3y8s4j/pbuilderrc_ipSd --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UR3y8s4j/b1 --logfile b1/build.log pigx-rnaseq_0.0.10+ds-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.104:3128' + 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.UR3y8s4j/pbuilderrc_5RG2 --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UR3y8s4j/b2 --logfile b2/build.log pigx-rnaseq_0.0.10+ds-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.104:3128 I: uname -a - Linux codethink02-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Mar 27 2022 bash @@ -133,7 +164,7 @@ -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Dec 7 09:24 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 7 08:09 sh -> /bin/bash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jan 20 2022 su @@ -159,7 +190,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/476780/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/3217408/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -944,7 +975,7 @@ Get: 683 http://deb.debian.org/debian bullseye/main arm64 samtools arm64 1.11-1 [526 kB] Get: 684 http://deb.debian.org/debian bullseye/main arm64 snakemake all 5.24.1-2 [6107 kB] Get: 685 http://deb.debian.org/debian bullseye/main arm64 trim-galore all 0.6.6-1 [17.8 MB] -Fetched 463 MB in 15s (31.6 MB/s) +Fetched 463 MB in 2s (192 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17734 files and directories currently installed.) @@ -3082,8 +3113,8 @@ Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jan 7 08:03:43 UTC 2024. -Universal Time is now: Sun Jan 7 08:03:43 UTC 2024. +Local time is now: Sun Jan 7 08:11:06 UTC 2024. +Universal Time is now: Sun Jan 7 08:11:06 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up liberror-perl (0.17029-1) ... @@ -3893,7 +3924,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/pigx-rnaseq-0.0.10+ds/ && 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_0.0.10+ds-2_source.changes +I: user script /srv/workspace/pbuilder/3217408/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/3217408/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/pigx-rnaseq-0.0.10+ds/ && 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_0.0.10+ds-2_source.changes dpkg-buildpackage: info: source package pigx-rnaseq dpkg-buildpackage: info: source version 0.0.10+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -4049,7 +4084,7 @@ 2 trim_galore_se 59 -[Sat Jan 6 20:04:38 2024] +[Sun Jan 7 22:12:05 2024] rule trim_galore_se: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz @@ -4058,11 +4093,11 @@ wildcards: sample=HBR_Rep1 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep1.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1.read1_trimmed.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz -[Sat Jan 6 20:04:49 2024] +[Sun Jan 7 22:12:16 2024] Finished job 47. 1 of 59 steps (2%) done -[Sat Jan 6 20:04:49 2024] +[Sun Jan 7 22:12:16 2024] rule trim_galore_se: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz @@ -4071,11 +4106,11 @@ wildcards: sample=UHR_Rep3 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep3.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3.read1_trimmed.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz -[Sat Jan 6 20:04:59 2024] +[Sun Jan 7 22:12:26 2024] Finished job 52. 2 of 59 steps (3%) done -[Sat Jan 6 20:04:59 2024] +[Sun Jan 7 22:12:26 2024] rule trim_galore_pe: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz @@ -4084,11 +4119,11 @@ wildcards: sample=UHR_Rep2 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep2.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2.read1_val_1.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2.read2_val_2.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz -[Sat Jan 6 20:05:10 2024] +[Sun Jan 7 22:12:37 2024] Finished job 51. 3 of 59 steps (5%) done -[Sat Jan 6 20:05:10 2024] +[Sun Jan 7 22:12:37 2024] rule trim_galore_pe: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz @@ -4097,11 +4132,11 @@ wildcards: sample=HBR_Rep3 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep3.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3.read1_val_1.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3.read2_val_2.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz -[Sat Jan 6 20:05:21 2024] +[Sun Jan 7 22:12:48 2024] Finished job 49. 4 of 59 steps (7%) done -[Sat Jan 6 20:05:21 2024] +[Sun Jan 7 22:12:48 2024] rule trim_galore_pe: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz @@ -4110,11 +4145,11 @@ wildcards: sample=UHR_Rep1 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep1.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1.read1_val_1.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1.read2_val_2.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz -[Sat Jan 6 20:05:32 2024] +[Sun Jan 7 22:12:59 2024] Finished job 50. 5 of 59 steps (8%) done -[Sat Jan 6 20:05:32 2024] +[Sun Jan 7 22:12:59 2024] rule trim_galore_pe: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz @@ -4123,22 +4158,22 @@ wildcards: sample=HBR_Rep2 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep2.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2.read1_val_1.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2.read2_val_2.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz -[Sat Jan 6 20:05:42 2024] +[Sun Jan 7 22:13:09 2024] Finished job 48. 6 of 59 steps (10%) done -[Sat Jan 6 20:05:42 2024] +[Sun Jan 7 22:13:09 2024] rule translate_sample_sheet_for_report: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_sheet.csv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv jobid: 34 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//translate_sample_sheet_for_report.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_sheet.csv -[Sat Jan 6 20:05:43 2024] +[Sun Jan 7 22:13:10 2024] Finished job 34. 7 of 59 steps (12%) done -[Sat Jan 6 20:05:43 2024] +[Sun Jan 7 22:13:10 2024] rule salmon_index: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.cdna.fasta output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin @@ -4146,11 +4181,11 @@ jobid: 2 /usr/bin/salmon index -t /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.cdna.fasta -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -p 8 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_index.log 2>&1 -[Sat Jan 6 20:05:48 2024] +[Sun Jan 7 22:13:11 2024] Finished job 2. 8 of 59 steps (14%) done -[Sat Jan 6 20:05:48 2024] +[Sun Jan 7 22:13:12 2024] rule star_index: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.fasta output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex @@ -4158,11 +4193,11 @@ jobid: 1 /usr/bin/STAR --runMode genomeGenerate --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --genomeFastaFiles /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.fasta --sjdbGTFfile /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_index.log 2>&1 -[Sat Jan 6 20:06:00 2024] +[Sun Jan 7 22:13:23 2024] Finished job 1. 9 of 59 steps (15%) done -[Sat Jan 6 20:06:00 2024] +[Sun Jan 7 22:13:23 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.out.bam @@ -4171,11 +4206,11 @@ wildcards: sample=UHR_Rep1 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep1.log 2>&1 -[Sat Jan 6 20:06:00 2024] +[Sun Jan 7 22:13:24 2024] Finished job 56. 10 of 59 steps (17%) done -[Sat Jan 6 20:06:00 2024] +[Sun Jan 7 22:13:24 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.out.bam @@ -4184,11 +4219,11 @@ wildcards: sample=UHR_Rep3 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep3.log 2>&1 -[Sat Jan 6 20:06:01 2024] +[Sun Jan 7 22:13:24 2024] Finished job 58. 11 of 59 steps (19%) done -[Sat Jan 6 20:06:01 2024] +[Sun Jan 7 22:13:25 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.out.bam @@ -4197,11 +4232,11 @@ wildcards: sample=HBR_Rep3 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep3.log 2>&1 -[Sat Jan 6 20:06:02 2024] +[Sun Jan 7 22:13:25 2024] Finished job 55. 12 of 59 steps (20%) done -[Sat Jan 6 20:06:02 2024] +[Sun Jan 7 22:13:25 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.out.bam @@ -4210,11 +4245,11 @@ wildcards: sample=UHR_Rep2 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep2.log 2>&1 -[Sat Jan 6 20:06:02 2024] +[Sun Jan 7 22:13:26 2024] Finished job 57. 13 of 59 steps (22%) done -[Sat Jan 6 20:06:03 2024] +[Sun Jan 7 22:13:26 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.out.bam @@ -4223,11 +4258,11 @@ wildcards: sample=HBR_Rep1 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep1.log 2>&1 -[Sat Jan 6 20:06:03 2024] +[Sun Jan 7 22:13:27 2024] Finished job 53. 14 of 59 steps (24%) done -[Sat Jan 6 20:06:03 2024] +[Sun Jan 7 22:13:27 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.out.bam @@ -4236,11 +4271,11 @@ wildcards: sample=HBR_Rep2 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep2.log 2>&1 -[Sat Jan 6 20:06:04 2024] +[Sun Jan 7 22:13:28 2024] Finished job 54. 15 of 59 steps (25%) done -[Sat Jan 6 20:06:04 2024] +[Sun Jan 7 22:13:28 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam @@ -4249,11 +4284,11 @@ wildcards: sample=HBR_Rep3 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep3.log 2>&1 -[Sat Jan 6 20:06:04 2024] +[Sun Jan 7 22:13:28 2024] Finished job 24. 16 of 59 steps (27%) done -[Sat Jan 6 20:06:04 2024] +[Sun Jan 7 22:13:28 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam @@ -4262,11 +4297,11 @@ wildcards: sample=HBR_Rep2 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep2.log 2>&1 -[Sat Jan 6 20:06:04 2024] +[Sun Jan 7 22:13:28 2024] Finished job 23. 17 of 59 steps (29%) done -[Sat Jan 6 20:06:04 2024] +[Sun Jan 7 22:13:28 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam @@ -4275,11 +4310,11 @@ wildcards: sample=UHR_Rep3 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep3.log 2>&1 -[Sat Jan 6 20:06:04 2024] +[Sun Jan 7 22:13:28 2024] Finished job 27. 18 of 59 steps (31%) done -[Sat Jan 6 20:06:04 2024] +[Sun Jan 7 22:13:28 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam @@ -4288,11 +4323,11 @@ wildcards: sample=HBR_Rep1 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep1.log 2>&1 -[Sat Jan 6 20:06:04 2024] +[Sun Jan 7 22:13:28 2024] Finished job 22. 19 of 59 steps (32%) done -[Sat Jan 6 20:06:04 2024] +[Sun Jan 7 22:13:28 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep2_Aligned.sortedByCoord.out_fastqc.zip @@ -4301,11 +4336,11 @@ wildcards: sample=HBR_Rep2 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep2.log 2>&1 -[Sat Jan 6 20:06:07 2024] +[Sun Jan 7 22:13:31 2024] Finished job 29. 20 of 59 steps (34%) done -[Sat Jan 6 20:06:07 2024] +[Sun Jan 7 22:13:31 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam @@ -4314,11 +4349,11 @@ wildcards: sample=UHR_Rep1 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep1.log 2>&1 -[Sat Jan 6 20:06:07 2024] +[Sun Jan 7 22:13:31 2024] Finished job 25. 21 of 59 steps (36%) done -[Sat Jan 6 20:06:07 2024] +[Sun Jan 7 22:13:31 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep1_Aligned.sortedByCoord.out_fastqc.zip @@ -4327,11 +4362,11 @@ wildcards: sample=UHR_Rep1 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep1.log 2>&1 -[Sat Jan 6 20:06:11 2024] +[Sun Jan 7 22:13:33 2024] Finished job 31. 22 of 59 steps (37%) done -[Sat Jan 6 20:06:11 2024] +[Sun Jan 7 22:13:33 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam @@ -4340,11 +4375,11 @@ wildcards: sample=UHR_Rep2 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep2.log 2>&1 -[Sat Jan 6 20:06:11 2024] +[Sun Jan 7 22:13:33 2024] Finished job 26. 23 of 59 steps (39%) done -[Sat Jan 6 20:06:11 2024] +[Sun Jan 7 22:13:33 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep1_Aligned.sortedByCoord.out_fastqc.zip @@ -4353,11 +4388,11 @@ wildcards: sample=HBR_Rep1 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep1.log 2>&1 -[Sat Jan 6 20:06:16 2024] +[Sun Jan 7 22:13:37 2024] Finished job 28. 24 of 59 steps (41%) done -[Sat Jan 6 20:06:16 2024] +[Sun Jan 7 22:13:37 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.genes.sf @@ -4370,11 +4405,11 @@ 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz -2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep2.log 2>&1 -[Sat Jan 6 20:06:18 2024] +[Sun Jan 7 22:13:38 2024] Finished job 20. 25 of 59 steps (42%) done -[Sat Jan 6 20:06:18 2024] +[Sun Jan 7 22:13:38 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.genes.sf @@ -4387,11 +4422,11 @@ 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep1.log 2>&1 -[Sat Jan 6 20:06:19 2024] +[Sun Jan 7 22:13:39 2024] Finished job 16. 26 of 59 steps (44%) done -[Sat Jan 6 20:06:19 2024] +[Sun Jan 7 22:13:39 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.genes.sf @@ -4404,11 +4439,11 @@ 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz -2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep2.log 2>&1 -[Sat Jan 6 20:06:22 2024] +[Sun Jan 7 22:13:41 2024] Finished job 17. 27 of 59 steps (46%) done -[Sat Jan 6 20:06:22 2024] +[Sun Jan 7 22:13:41 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.genes.sf @@ -4421,11 +4456,11 @@ 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep3.log 2>&1 -[Sat Jan 6 20:06:23 2024] +[Sun Jan 7 22:13:43 2024] Finished job 21. 28 of 59 steps (47%) done -[Sat Jan 6 20:06:23 2024] +[Sun Jan 7 22:13:43 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.genes.sf @@ -4438,11 +4473,11 @@ 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz -2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep1.log 2>&1 -[Sat Jan 6 20:06:25 2024] +[Sun Jan 7 22:13:44 2024] Finished job 19. 29 of 59 steps (49%) done -[Sat Jan 6 20:06:25 2024] +[Sun Jan 7 22:13:44 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.genes.sf @@ -4455,11 +4490,11 @@ 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz -2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep3.log 2>&1 -[Sat Jan 6 20:06:27 2024] +[Sun Jan 7 22:13:46 2024] Finished job 18. 30 of 59 steps (51%) done -[Sat Jan 6 20:06:27 2024] +[Sun Jan 7 22:13:46 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai @@ -4468,11 +4503,11 @@ wildcards: sample=HBR_Rep3 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep3.log 2>&1 -[Sat Jan 6 20:06:27 2024] +[Sun Jan 7 22:13:46 2024] Finished job 43. 31 of 59 steps (53%) done -[Sat Jan 6 20:06:27 2024] +[Sun Jan 7 22:13:46 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai @@ -4481,11 +4516,11 @@ wildcards: sample=UHR_Rep3 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep3.log 2>&1 -[Sat Jan 6 20:06:27 2024] +[Sun Jan 7 22:13:46 2024] Finished job 46. 32 of 59 steps (54%) done -[Sat Jan 6 20:06:27 2024] +[Sun Jan 7 22:13:46 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai @@ -4494,11 +4529,11 @@ wildcards: sample=HBR_Rep2 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep2.log 2>&1 -[Sat Jan 6 20:06:27 2024] +[Sun Jan 7 22:13:46 2024] Finished job 42. 33 of 59 steps (56%) done -[Sat Jan 6 20:06:27 2024] +[Sun Jan 7 22:13:46 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai @@ -4507,11 +4542,11 @@ wildcards: sample=UHR_Rep2 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep2.log 2>&1 -[Sat Jan 6 20:06:27 2024] +[Sun Jan 7 22:13:46 2024] Finished job 45. 34 of 59 steps (58%) done -[Sat Jan 6 20:06:27 2024] +[Sun Jan 7 22:13:46 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai @@ -4520,11 +4555,11 @@ wildcards: sample=HBR_Rep1 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep1.log 2>&1 -[Sat Jan 6 20:06:28 2024] +[Sun Jan 7 22:13:46 2024] Finished job 41. 35 of 59 steps (59%) done -[Sat Jan 6 20:06:28 2024] +[Sun Jan 7 22:13:46 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai @@ -4533,11 +4568,11 @@ wildcards: sample=UHR_Rep1 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep1.log 2>&1 -[Sat Jan 6 20:06:28 2024] +[Sun Jan 7 22:13:46 2024] Finished job 44. 36 of 59 steps (61%) done -[Sat Jan 6 20:06:28 2024] +[Sun Jan 7 22:13:46 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep2_Aligned.sortedByCoord.out_fastqc.zip @@ -4546,11 +4581,11 @@ wildcards: sample=UHR_Rep2 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep2.log 2>&1 -[Sat Jan 6 20:06:30 2024] +[Sun Jan 7 22:13:49 2024] Finished job 32. 37 of 59 steps (63%) done -[Sat Jan 6 20:06:30 2024] +[Sun Jan 7 22:13:49 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep3_Aligned.sortedByCoord.out_fastqc.zip @@ -4559,11 +4594,11 @@ wildcards: sample=HBR_Rep3 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep3.log 2>&1 -[Sat Jan 6 20:06:33 2024] +[Sun Jan 7 22:13:52 2024] Finished job 30. 38 of 59 steps (64%) done -[Sat Jan 6 20:06:33 2024] +[Sun Jan 7 22:13:52 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep3_Aligned.sortedByCoord.out_fastqc.zip @@ -4572,11 +4607,11 @@ wildcards: sample=UHR_Rep3 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep3.log 2>&1 -[Sat Jan 6 20:06:38 2024] +[Sun Jan 7 22:13:57 2024] Finished job 33. 39 of 59 steps (66%) done -[Sat Jan 6 20:06:38 2024] +[Sun Jan 7 22:13:57 2024] rule multiqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep1_Aligned.sortedByCoord.out_fastqc.zip, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep2_Aligned.sortedByCoord.out_fastqc.zip, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep3_Aligned.sortedByCoord.out_fastqc.zip, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep1_Aligned.sortedByCoord.out_fastqc.zip, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep2_Aligned.sortedByCoord.out_fastqc.zip, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep3_Aligned.sortedByCoord.out_fastqc.zip output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/multiqc/multiqc_report.html @@ -4584,11 +4619,11 @@ jobid: 3 /usr/bin/multiqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/multiqc /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/multiqc.log 2>&1 -[Sat Jan 6 20:06:45 2024] +[Sun Jan 7 22:14:01 2024] Finished job 3. 40 of 59 steps (68%) done -[Sat Jan 6 20:06:45 2024] +[Sun Jan 7 22:14:01 2024] rule counts_from_SALMON: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.genes.tsv @@ -4596,11 +4631,11 @@ jobid: 4 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//counts_matrix_from_SALMON.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_import_counts.log 2>&1 -[Sat Jan 6 20:06:55 2024] +[Sun Jan 7 22:14:09 2024] Finished job 4. 41 of 59 steps (69%) done -[Sat Jan 6 20:06:55 2024] +[Sun Jan 7 22:14:09 2024] rule report3: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.genes.deseq.report.html @@ -4609,11 +4644,11 @@ wildcards: analysis=analysis1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/images/Logo_PiGx.png --prefix='analysis1.salmon.genes' --reportFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report --organism='' --selfContained=FALSE >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.salmon.genes.log 2>&1 -[Sat Jan 6 20:07:18 2024] +[Sun Jan 7 22:14:29 2024] Finished job 15. 42 of 59 steps (71%) done -[Sat Jan 6 20:07:18 2024] +[Sun Jan 7 22:14:29 2024] rule report2: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.transcripts.deseq.report.html @@ -4622,11 +4657,11 @@ wildcards: analysis=analysis1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/images/Logo_PiGx.png --prefix='analysis1.salmon.transcripts' --reportFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report --organism='' >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.salmon.transcripts.log 2>&1 -[Sat Jan 6 20:07:37 2024] +[Sun Jan 7 22:14:48 2024] Finished job 14. 43 of 59 steps (73%) done -[Sat Jan 6 20:07:37 2024] +[Sun Jan 7 22:14:48 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1.read_counts.csv @@ -4635,11 +4670,11 @@ wildcards: sample=HBR_Rep1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R HBR_Rep1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep1.count_reads.log 2>&1 -[Sat Jan 6 20:07:46 2024] +[Sun Jan 7 22:14:57 2024] Finished job 35. 44 of 59 steps (75%) done -[Sat Jan 6 20:07:46 2024] +[Sun Jan 7 22:14:57 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2.read_counts.csv @@ -4648,11 +4683,11 @@ wildcards: sample=UHR_Rep2 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R UHR_Rep2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep2.count_reads.log 2>&1 -[Sat Jan 6 20:07:55 2024] +[Sun Jan 7 22:15:07 2024] Finished job 39. 45 of 59 steps (76%) done -[Sat Jan 6 20:07:55 2024] +[Sun Jan 7 22:15:07 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1.read_counts.csv @@ -4661,11 +4696,11 @@ wildcards: sample=UHR_Rep1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R UHR_Rep1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep1.count_reads.log 2>&1 -[Sat Jan 6 20:08:03 2024] +[Sun Jan 7 22:15:16 2024] Finished job 38. 46 of 59 steps (78%) done -[Sat Jan 6 20:08:03 2024] +[Sun Jan 7 22:15:16 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3.read_counts.csv @@ -4674,11 +4709,11 @@ wildcards: sample=HBR_Rep3 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R HBR_Rep3 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep3.count_reads.log 2>&1 -[Sat Jan 6 20:08:12 2024] +[Sun Jan 7 22:15:25 2024] Finished job 37. 47 of 59 steps (80%) done -[Sat Jan 6 20:08:12 2024] +[Sun Jan 7 22:15:25 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3.read_counts.csv @@ -4687,11 +4722,11 @@ wildcards: sample=UHR_Rep3 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R UHR_Rep3 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep3.count_reads.log 2>&1 -[Sat Jan 6 20:08:21 2024] +[Sun Jan 7 22:15:34 2024] Finished job 40. 48 of 59 steps (81%) done -[Sat Jan 6 20:08:21 2024] +[Sun Jan 7 22:15:34 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2.read_counts.csv @@ -4700,11 +4735,11 @@ wildcards: sample=HBR_Rep2 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R HBR_Rep2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep2.count_reads.log 2>&1 -[Sat Jan 6 20:08:29 2024] +[Sun Jan 7 22:15:43 2024] Finished job 36. 49 of 59 steps (83%) done -[Sat Jan 6 20:08:29 2024] +[Sun Jan 7 22:15:43 2024] rule collate_read_counts: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3.read_counts.csv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv @@ -4712,11 +4747,11 @@ jobid: 5 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/collate_read_counts.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/collate_read_counts.log 2>&1 -[Sat Jan 6 20:08:29 2024] +[Sun Jan 7 22:15:43 2024] Finished job 5. 50 of 59 steps (85%) done -[Sat Jan 6 20:08:29 2024] +[Sun Jan 7 22:15:43 2024] rule norm_counts_deseq: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_normalized_counts.tsv @@ -4724,11 +4759,11 @@ jobid: 6 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/norm_counts_deseq.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/norm_counts_deseq.log 2>&1 -[Sat Jan 6 20:08:36 2024] +[Sun Jan 7 22:15:50 2024] Finished job 6. 51 of 59 steps (86%) done -[Sat Jan 6 20:08:36 2024] +[Sun Jan 7 22:15:50 2024] rule report1: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.star.deseq.report.html @@ -4737,11 +4772,11 @@ wildcards: analysis=analysis1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/images/Logo_PiGx.png --prefix='analysis1.star' --reportFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report --organism='' >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.star.log 2>&1 -[Sat Jan 6 20:08:55 2024] +[Sun Jan 7 22:16:08 2024] Finished job 13. 52 of 59 steps (88%) done -[Sat Jan 6 20:08:55 2024] +[Sun Jan 7 22:16:08 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.reverse.bigwig @@ -4750,11 +4785,11 @@ wildcards: sample=UHR_Rep1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam UHR_Rep1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep1.log 2>&1 -[Sat Jan 6 20:09:02 2024] +[Sun Jan 7 22:16:16 2024] Finished job 10. 53 of 59 steps (90%) done -[Sat Jan 6 20:09:02 2024] +[Sun Jan 7 22:16:16 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.reverse.bigwig @@ -4763,11 +4798,11 @@ wildcards: sample=HBR_Rep3 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam HBR_Rep3 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep3.log 2>&1 -[Sat Jan 6 20:09:09 2024] +[Sun Jan 7 22:16:22 2024] Finished job 9. 54 of 59 steps (92%) done -[Sat Jan 6 20:09:09 2024] +[Sun Jan 7 22:16:22 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.reverse.bigwig @@ -4776,11 +4811,11 @@ wildcards: sample=UHR_Rep3 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam UHR_Rep3 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep3.log 2>&1 -[Sat Jan 6 20:09:16 2024] +[Sun Jan 7 22:16:30 2024] Finished job 12. 55 of 59 steps (93%) done -[Sat Jan 6 20:09:16 2024] +[Sun Jan 7 22:16:30 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.reverse.bigwig @@ -4789,11 +4824,11 @@ wildcards: sample=HBR_Rep2 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam HBR_Rep2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep2.log 2>&1 -[Sat Jan 6 20:09:23 2024] +[Sun Jan 7 22:16:37 2024] Finished job 8. 56 of 59 steps (95%) done -[Sat Jan 6 20:09:23 2024] +[Sun Jan 7 22:16:37 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.reverse.bigwig @@ -4802,11 +4837,11 @@ wildcards: sample=HBR_Rep1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam HBR_Rep1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep1.log 2>&1 -[Sat Jan 6 20:09:33 2024] +[Sun Jan 7 22:16:44 2024] Finished job 7. 57 of 59 steps (97%) done -[Sat Jan 6 20:09:33 2024] +[Sun Jan 7 22:16:44 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.reverse.bigwig @@ -4815,19 +4850,19 @@ wildcards: sample=UHR_Rep2 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam UHR_Rep2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep2.log 2>&1 -[Sat Jan 6 20:09:43 2024] +[Sun Jan 7 22:16:51 2024] Finished job 11. 58 of 59 steps (98%) done -[Sat Jan 6 20:09:43 2024] +[Sun Jan 7 22:16:51 2024] localrule all: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/multiqc/multiqc_report.html, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.star.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.transcripts.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.genes.deseq.report.html jobid: 0 -[Sat Jan 6 20:09:43 2024] +[Sun Jan 7 22:16:51 2024] Finished job 0. 59 of 59 steps (100%) done -Complete log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/.snakemake/log/2024-01-06T200438.351172.snakemake.log +Complete log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/.snakemake/log/2024-01-07T221205.344544.snakemake.log The following files have been generated: - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin @@ -4867,14 +4902,14 @@ make[3]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' /bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' - /usr/bin/install -c pigx_rnaseq.py qsub-template.sh '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/bin' /bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/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/export_bigwig.R scripts/norm_counts_deseq.R scripts/count_reads.R scripts/collate_read_counts.R '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' - /usr/bin/install -c -m 644 README.md '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' + /usr/bin/install -c pigx_rnaseq.py qsub-template.sh '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /usr/bin/install -c pigx-rnaseq '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/bin' + /usr/bin/install -c -m 644 README.md '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /usr/bin/install -c -m 644 etc/sample_sheet.csv.example etc/settings.yaml etc/pretty.txt images/Logo_PiGx.png '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/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/export_bigwig.R scripts/norm_counts_deseq.R scripts/count_reads.R scripts/collate_read_counts.R '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' make[3]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' make[2]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' find debian/pigx-rnaseq/usr/libexec/pigx_rnaseq -name "*.R"|xargs -r chmod -x @@ -4934,12 +4969,14 @@ 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/3217408/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3217408/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/476780 and its subdirectories -I: Current time: Sat Jan 6 20:09:47 -12 2024 -I: pbuilder-time-stamp: 1704614987 +I: removing directory /srv/workspace/pbuilder/3217408 and its subdirectories +I: Current time: Sun Jan 7 22:16:57 +14 2024 +I: pbuilder-time-stamp: 1704615417