Diff of the two buildlogs: -- --- b1/build.log 2023-04-14 22:23:40.789574214 +0000 +++ b2/build.log 2023-04-14 22:32:23.734347100 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 14 09:54:00 -12 2023 -I: pbuilder-time-stamp: 1681509240 +I: Current time: Fri May 17 18:46:44 +14 2024 +I: pbuilder-time-stamp: 1715921204 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 @@ -26,135 +26,144 @@ 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/3203782/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2740028/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash +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/2740028/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2740028/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' + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME='pbuilder2' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' - INVOCATION_ID='d3537012cdb4449ab7db40de73f2f1fb' + INVOCATION_ID='ead8c3767a4246579c64c1040d309ab3' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='et_EE:et' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='3203782' + PPID='2740028' PS1='# ' PS2='> ' 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.dSllwiae/pbuilderrc_ScPV --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.dSllwiae/b1 --logfile b1/build.log pigx-rnaseq_0.1.0-1.1.dsc' - SUDO_GID='110' - SUDO_UID='105' + 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.dSllwiae/pbuilderrc_mH5i --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.dSllwiae/b2 --logfile b2/build.log --extrapackages usrmerge pigx-rnaseq_0.1.0-1.1.dsc' + SUDO_GID='111' + SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + http_proxy='http://85.184.249.68:3128' I: uname -a - Linux ionos1-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/3203782/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 4 Jan 6 2023 sh -> dash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -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/2740028/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -927,7 +936,7 @@ Get: 665 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get: 666 http://deb.debian.org/debian bookworm/main amd64 snakemake all 7.21.0-1 [301 kB] Get: 667 http://deb.debian.org/debian bookworm/main amd64 trim-galore all 0.6.10-1 [17.8 MB] -Fetched 576 MB in 24s (24.2 MB/s) +Fetched 576 MB in 8s (68.1 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 ... 19596 files and directories currently installed.) @@ -3790,8 +3799,19 @@ 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/2740028/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/2740028/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +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 @@ -3848,7 +3868,7 @@ ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking GUNZIP=/bin/gunzip SED=/bin/sed checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -3919,7 +3939,7 @@ config.status: creating pigx-rnaseq make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0' dh_auto_build - make -j15 + make -j16 make[1]: Entering directory '/build/pigx-rnaseq-0.1.0' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0' @@ -3931,7 +3951,7 @@ ./test.sh Commencing snakemake run submission locally Building DAG of jobs... -Using shell: /bin/bash +Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Job stats: @@ -3960,19 +3980,19 @@ Select jobs to execute... -[Fri Apr 14 10:19:52 2023] +[Fri May 17 18:53:40 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.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz + 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 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 14 10:19:52 2023] +[Fri May 17 18:53:40 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 @@ -3984,7 +4004,7 @@ /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 14 10:19:52 2023] +[Fri May 17 18:53:40 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 @@ -3994,7 +4014,7 @@ /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 14 10:19:52 2023] +[Fri May 17 18:53:40 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 @@ -4006,19 +4026,19 @@ /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 14 10:19:52 2023] +[Fri May 17 18:53:40 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 log: /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep3.log jobid: 9 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz + reason: Missing output files: /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 wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/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 14 10:19:52 2023] +[Fri May 17 18:53:40 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 @@ -4028,59 +4048,59 @@ 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 14 10:19:53 2023] +[Fri May 17 18:53:41 2024] Finished job 24. 1 of 48 steps (2%) done Select jobs to execute... -[Fri Apr 14 10:19:53 2023] +[Fri May 17 18:53:41 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 log: /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep2.log jobid: 13 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz + reason: Missing output files: /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 wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/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 14 10:19:54 2023] +[Fri May 17 18:53:41 2024] Finished job 5. 2 of 48 steps (4%) done Select jobs to execute... -[Fri Apr 14 10:19:54 2023] +[Fri May 17 18:53:41 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 log: /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep1.log jobid: 11 - reason: Missing output files: /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 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/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 14 10:19:55 2023] +[Fri May 17 18:53:41 2024] Finished job 7. 3 of 48 steps (6%) done -[Fri Apr 14 10:19:55 2023] +[Fri May 17 18:53:41 2024] Finished job 15. 4 of 48 steps (8%) done -[Fri Apr 14 10:19:55 2023] +[Fri May 17 18:53:41 2024] Finished job 9. 5 of 48 steps (10%) done -[Fri Apr 14 10:19:55 2023] +[Fri May 17 18:53:42 2024] Finished job 13. 6 of 48 steps (12%) done -[Fri Apr 14 10:19:56 2023] +[Fri May 17 18:53:42 2024] Finished job 11. 7 of 48 steps (15%) done -[Fri Apr 14 10:20:16 2023] +[Fri May 17 18:53:53 2024] Finished job 1. 8 of 48 steps (17%) done Select jobs to execute... -[Fri Apr 14 10:20:16 2023] +[Fri May 17 18:53:53 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 @@ -4091,28 +4111,28 @@ /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 14 10:20:16 2023] +[Fri May 17 18:53:53 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.8.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.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.6.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.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.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.1.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.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.5.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.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.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 14 10:20:21 2023] +[Fri May 17 18:53:56 2024] Finished job 17. 9 of 48 steps (19%) done Select jobs to execute... -[Fri Apr 14 10:20:21 2023] +[Fri May 17 18:53:56 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.8.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.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.6.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.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.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.1.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.8.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.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.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.7.ht2l wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4122,13 +4142,13 @@ rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam -[Fri Apr 14 10:20:21 2023] +[Fri May 17 18:53:56 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/hisat2_index/GRCm38_index.8.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.2.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/trimmed_reads/HBR_Rep3.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/hisat2_index/GRCm38_index.6.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.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.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.1.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.6.ht2l, /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.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.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.7.ht2l wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4138,13 +4158,13 @@ rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam -[Fri Apr 14 10:20:21 2023] +[Fri May 17 18:53:56 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.8.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.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.6.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.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.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.1.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.8.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.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/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.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4154,29 +4174,13 @@ rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam -[Fri Apr 14 10:20:21 2023] -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.8.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.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/trimmed_reads/UHR_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/hisat2_index/GRCm38_index.6.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.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l - wildcards: sample=UHR_Rep2 - resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 - - - /usr/bin/hisat2 --fast -x /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam -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 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log 2>&1 - /usr/bin/samtools view -bh /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam | /usr/bin/samtools sort -o /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/logs/hisat2/samtools.hisat2.UHR_Rep2.log 2>&1 - rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam - - -[Fri Apr 14 10:20:21 2023] +[Fri May 17 18:53:56 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.8.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.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.6.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.4.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/HBR_Rep1.trimmed.fq.gz + 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.1.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.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.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.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.7.ht2l wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4185,49 +4189,34 @@ /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 14 10:20:22 2023] -Finished job 22. -10 of 48 steps (21%) done -Select jobs to execute... -[Fri Apr 14 10:20:23 2023] -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 - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep3.log - jobid: 37 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep3 - resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 +[Fri May 17 18:53:56 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.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.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.8.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.5.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.7.ht2l, /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=8000, mem_mib=7630 -/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 14 10:20:23 2023] + + /usr/bin/hisat2 --fast -x /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam -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 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log 2>&1 + /usr/bin/samtools view -bh /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam | /usr/bin/samtools sort -o /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/logs/hisat2/samtools.hisat2.UHR_Rep2.log 2>&1 + rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam + +[Fri May 17 18:53:56 2024] Finished job 16. -11 of 48 steps (23%) done -[Fri Apr 14 10:20:23 2023] -Finished job 19. -12 of 48 steps (25%) done +10 of 48 steps (21%) done Select jobs to execute... -[Fri Apr 14 10:20:23 2023] -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 - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep1.log - jobid: 27 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=HBR_Rep1 - resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 - -/usr/bin/samtools index /build/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 14 10:20:23 2023] +[Fri May 17 18:53:56 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.8.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.2.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.3.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.5.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.7.ht2l, /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/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.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.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.8.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.5.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.7.ht2l wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 @@ -4236,60 +4225,53 @@ /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 14 10:20:23 2023] -Finished job 20. +[Fri May 17 18:53:56 2024] +Finished job 22. +11 of 48 steps (23%) done +[Fri May 17 18:53:56 2024] +Finished job 4. +12 of 48 steps (25%) done +[Fri May 17 18:53:56 2024] +Finished job 19. 13 of 48 steps (27%) done -[Fri Apr 14 10:20:23 2023] -Finished job 21. -14 of 48 steps (29%) done -[Fri Apr 14 10:20:23 2023] -Finished job 37. -15 of 48 steps (31%) done Select jobs to execute... -[Fri Apr 14 10:20:23 2023] -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 - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep1.log - jobid: 33 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /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=500, mem_mib=477 - -/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 14 10:20:23 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.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam - wildcards: sample=UHR_Rep3 - resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - +[Fri May 17 18:53:56 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/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz + wildcards: sample=HBR_Rep1 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - /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 May 17 18:53:56 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.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.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz + wildcards: sample=UHR_Rep1 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -[Fri Apr 14 10:20:23 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 +[Fri May 17 18:53:56 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/salmon_index/pos.bin, /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 + wildcards: sample=HBR_Rep2 + resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 -/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 14 10:20:23 2023] -Finished job 27. -16 of 48 steps (33%) done +[Fri May 17 18:53:56 2024] +Finished job 20. +14 of 48 steps (29%) done Select jobs to execute... -[Fri Apr 14 10:20:23 2023] +[Fri May 17 18:53:56 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 @@ -4300,112 +4282,63 @@ 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 14 10:20:23 2023] -Finished job 35. -17 of 48 steps (35%) done -[Fri Apr 14 10:20:23 2023] -Finished job 33. -18 of 48 steps (38%) done +[Fri May 17 18:53:56 2024] +Finished job 21. +15 of 48 steps (31%) done Select jobs to execute... -[Fri Apr 14 10:20:23 2023] -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, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai - wildcards: sample=UHR_Rep1 - resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - +[Fri May 17 18:53:56 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 + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep3.log + jobid: 37 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam + wildcards: sample=UHR_Rep3 + resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 - /usr/bin/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/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 May 17 18:53:56 2024] +Finished job 31. +16 of 48 steps (33%) done +Select jobs to execute... -[Fri Apr 14 10:20:23 2023] -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.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam +[Fri May 17 18:53:56 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 + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep1.log + jobid: 27 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam wildcards: sample=HBR_Rep1 - resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 - + resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 - /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 14 10:20:23 2023] -Finished job 31. -19 of 48 steps (40%) done +/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 May 17 18:53:56 2024] +Finished job 37. +17 of 48 steps (35%) done Select jobs to execute... -[Fri Apr 14 10:20:23 2023] +[Fri May 17 18:53:56 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 log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep3.count_reads.log jobid: 36 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv; Input files updated by another job: /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/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv; 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=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 14 10:20:23 2023] -Finished job 44. -20 of 48 steps (42%) done -Select jobs to execute... - -[Fri Apr 14 10:20:23 2023] -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 - 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 14 10:20:23 2023] -Finished job 42. -21 of 48 steps (44%) done -Select jobs to execute... - -[Fri Apr 14 10:20:23 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.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam - wildcards: sample=HBR_Rep1 - resources: tmpdir=/tmp, mem_mb=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 -[Fri Apr 14 10:20:23 2023] -Finished job 39. -22 of 48 steps (46%) done -[Fri Apr 14 10:20:23 2023] +[Fri May 17 18:53:56 2024] +Finished job 27. +18 of 48 steps (38%) done +[Fri May 17 18:53:56 2024] Finished job 18. -23 of 48 steps (48%) done +19 of 48 steps (40%) done Select jobs to execute... -[Fri Apr 14 10:20:23 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 14 10:20:23 2023] +[Fri May 17 18:53:56 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 @@ -4418,44 +4351,40 @@ /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 14 10:20:23 2023] -Finished job 43. -24 of 48 steps (50%) done -Select jobs to execute... -[Fri Apr 14 10:20:23 2023] -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, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai +[Fri May 17 18:53:56 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 + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep1.log + jobid: 33 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /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 + resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 -/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 +/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 Select jobs to execute... -[Fri Apr 14 10:20:23 2023] -Finished job 41. -25 of 48 steps (52%) done +[Fri May 17 18:53:56 2024] +Finished job 33. +20 of 48 steps (42%) done -[Fri Apr 14 10:20:24 2023] +[Fri May 17 18:53:56 2024] 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 + 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_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 14 10:20:26 2023] -Finished job 4. -26 of 48 steps (54%) 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 17 18:53:56 2024] +Finished job 41. +21 of 48 steps (44%) done Select jobs to execute... -[Fri Apr 14 10:20:26 2023] +[Fri May 17 18:53:56 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 @@ -4466,74 +4395,122 @@ 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 14 10:20:26 2023] +[Fri May 17 18:53:56 2024] Finished job 29. -27 of 48 steps (56%) done +22 of 48 steps (46%) done Select jobs to execute... -[Fri Apr 14 10:20:26 2023] +[Fri May 17 18:53:56 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.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam + 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 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 14 10:20:27 2023] +[Fri May 17 18:53:56 2024] Finished job 40. -28 of 48 steps (58%) done +23 of 48 steps (48%) done Select jobs to execute... -[Fri Apr 14 10:20:27 2023] +[Fri May 17 18:53:56 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.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.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: /bin/bash +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_Rep2.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_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_HBR_Rep2.log 2>&1 +Building DAG of jobs... +Using shell: /usr/bin/bash +Provided cores: 6 +Rules claiming more threads will be scaled down. +Provided resources: mem_mb=6000, mem_mib=5723 +Select jobs to execute... +/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_Rep1.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_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_UHR_Rep1.log 2>&1 +Building DAG of jobs... +Using shell: /usr/bin/bash +Provided cores: 6 +Rules claiming more threads will be scaled down. +Provided resources: mem_mb=6000, mem_mib=5723 +Select jobs to execute... +/usr/bin/salmon quant -i /build/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 +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 14 10:20:31 2023] -Finished job 8. -29 of 48 steps (60%) done +[Fri May 17 18:53:58 2024] +Finished job 6. +24 of 48 steps (50%) done Select jobs to execute... -[Fri Apr 14 10:20:31 2023] +[Fri May 17 18:53:58 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, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai + 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 17 18:53:58 2024] +Finished job 10. +25 of 48 steps (52%) done +Select jobs to execute... + +[Fri May 17 18:53:59 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.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /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 + reason: Missing output files: /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_Rep2/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_Rep2.trimmed.R1.fq.gz, /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: /bin/bash -Provided cores: 6 -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=6000, mem_mib=5723 +[Fri May 17 18:53:59 2024] +Finished job 3. +26 of 48 steps (54%) done 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 14 10:20:36 2023] -Finished job 12. -30 of 48 steps (62%) done + +[Fri May 17 18:53:59 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 + 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 + +[Fri May 17 18:53:59 2024] +Finished job 39. +27 of 48 steps (56%) done Select jobs to execute... -[Fri Apr 14 10:20:36 2023] +[Fri May 17 18:53:59 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_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 @@ -4543,231 +4520,275 @@ wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 +[Fri May 17 18:53:59 2024] +Finished job 8. +28 of 48 steps (58%) done +Select jobs to execute... + +[Fri May 17 18:53:59 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, /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 Building DAG of jobs... -Using shell: /bin/bash +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 14 10:20:41 2023] -Finished job 14. -31 of 48 steps (65%) done -Select jobs to execute... - -[Fri Apr 14 10:20:41 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/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.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.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 - wildcards: sample=HBR_Rep2 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 - Building DAG of jobs... -Using shell: /bin/bash +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_Rep2.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_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_HBR_Rep2.log 2>&1 -[Fri Apr 14 10:20:47 2023] -Finished job 6. -32 of 48 steps (67%) done +/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 May 17 18:54:01 2024] +Finished job 12. +29 of 48 steps (60%) done Select jobs to execute... -[Fri Apr 14 10:20:47 2023] -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 +[Fri May 17 18:54:01 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/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 14 10:20:52 2023] -Finished job 32. -33 of 48 steps (69%) done +/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 17 18:54:01 2024] +Finished job 35. +30 of 48 steps (62%) done Select jobs to execute... -[Fri Apr 14 10:20:52 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/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 +[Fri May 17 18:54:01 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.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 -[Fri Apr 14 10:20:56 2023] -Finished job 26. -34 of 48 steps (71%) done + + /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 May 17 18:54:01 2024] +Finished job 43. +31 of 48 steps (65%) done Select jobs to execute... -[Fri Apr 14 10:20:56 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_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 +[Fri May 17 18:54:01 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, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai wildcards: sample=UHR_Rep1 - resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 + resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 -Building DAG of jobs... -Using shell: /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 Apr 14 10:20:57 2023] -Finished job 34. -35 of 48 steps (73%) done -[Fri Apr 14 10:20:57 2023] -Finished job 36. -36 of 48 steps (75%) done -[Fri Apr 14 10:21:00 2023] -Finished job 3. -37 of 48 steps (77%) done -Building DAG of jobs... -Using shell: /bin/bash -Provided cores: 6 -Rules claiming more threads will be scaled down. -Provided resources: mem_mb=6000, mem_mib=5723 + + /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 17 18:54:01 2024] +Finished job 14. +32 of 48 steps (67%) done 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_Rep1.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_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_UHR_Rep1.log 2>&1 -[Fri Apr 14 10:21:02 2023] -Finished job 30. -38 of 48 steps (79%) done -[Fri Apr 14 10:21:03 2023] -Finished job 10. -39 of 48 steps (81%) done + +[Fri May 17 18:54:01 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/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/salmon_output/UHR_Rep2/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/UHR_Rep2_Aligned.sortedByCoord.out.bam, /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_Rep3/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/HBR_Rep1/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/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf + resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 + +/usr/bin/multiqc -f -o /build/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 17 18:54:01 2024] +Finished job 42. +33 of 48 steps (69%) done Select jobs to execute... -[Fri Apr 14 10:21:03 2023] +[Fri May 17 18:54:01 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/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, /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_Rep1/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/HBR_Rep1/quant.genes.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_Rep3/quant.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.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_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/HBR_Rep2/quant.sf + reason: Missing output files: /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, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.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/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/UHR_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_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/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_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.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 17 18:54:11 2024] +Finished job 2. +34 of 48 steps (71%) done +Select jobs to execute... -[Fri Apr 14 10:21:03 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/HBR_Rep1/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/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/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_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/salmon_output/UHR_Rep2/quant.sf, /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 - resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 +[Fri May 17 18:54:11 2024] +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/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 14 10:21:20 2023] -Finished job 28. + + /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 May 17 18:54:11 2024] +Finished job 44. +35 of 48 steps (73%) done +Select jobs to execute... + +[Fri May 17 18:54:11 2024] +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.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 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 17 18:54:16 2024] +Finished job 26. +36 of 48 steps (75%) done +Select jobs to execute... + +[Fri May 17 18:54:16 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 + 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 May 17 18:54:16 2024] +Finished job 36. +37 of 48 steps (77%) done +[Fri May 17 18:54:18 2024] +Finished job 32. +38 of 48 steps (79%) done +[Fri May 17 18:54:19 2024] +Finished job 30. +39 of 48 steps (81%) done +[Fri May 17 18:54:21 2024] +Finished job 23. 40 of 48 steps (83%) done Select jobs to execute... -[Fri Apr 14 10:21:20 2023] +[Fri May 17 18:54:21 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 + 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 May 17 18:54:21 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 + log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.genes.log + jobid: 47 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.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.genes.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.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 May 17 18:54:28 2024] +Finished job 34. +41 of 48 steps (85%) done +[Fri May 17 18:54:36 2024] +Finished job 28. +42 of 48 steps (88%) done +Select jobs to execute... + +[Fri May 17 18:54:36 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/mapped_reads/hisat2/UHR_Rep3.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_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_Rep1.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv + 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/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/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/mapped_reads/hisat2/HBR_Rep3.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 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 14 10:21:20 2023] -Finished job 2. -41 of 48 steps (85%) done -[Fri Apr 14 10:21:21 2023] +[Fri May 17 18:54:36 2024] Finished job 25. -42 of 48 steps (88%) done +43 of 48 steps (90%) done Select jobs to execute... -[Fri Apr 14 10:21:21 2023] +[Fri May 17 18:54:36 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 log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/norm_counts_deseq.log jobid: 38 - reason: Missing output files: /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; Input files updated by another job: /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 + reason: Missing output files: /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; 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/hisat2/counts.tsv resources: tmpdir=/tmp, mem_mb=1000, mem_mib=954 /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 14 10:21:21 2023] +[Fri May 17 18:54:36 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 log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/analysis1.report.log jobid: 45 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html; Input files updated by another job: /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 + reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.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/hisat2/counts.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' --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 14 10:21:29 2023] -Finished job 23. -43 of 48 steps (90%) done -Select jobs to execute... - -[Fri Apr 14 10:21:29 2023] -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/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 14 10:21:29 2023] -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 - log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.genes.log - jobid: 47 - reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.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.genes.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.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 14 10:21:43 2023] +[Fri May 17 18:54:50 2024] Finished job 38. 44 of 48 steps (92%) done -[Fri Apr 14 10:23:04 2023] +[Fri May 17 18:55:03 2024] Finished job 47. 45 of 48 steps (94%) done -[Fri Apr 14 10:23:04 2023] +[Fri May 17 18:55:04 2024] Finished job 46. 46 of 48 steps (96%) done -[Fri Apr 14 10:23:08 2023] +[Fri May 17 18:55:15 2024] Finished job 45. 47 of 48 steps (98%) done Select jobs to execute... -[Fri Apr 14 10:23:08 2023] +[Fri May 17 18:55:15 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/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.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/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /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/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/report/salmon/analysis1.salmon.genes.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/bigwig_files/hisat2/megadepth/UHR_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/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /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/hisat2/deseq_normalized_counts.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/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.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/HBR_Rep3.all.bw + reason: Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.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/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /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_Rep3.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/UHR_Rep2.all.bw, /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/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/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/salmon/TPM_counts_from_SALMON.transcripts.tsv, /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/salmon/analysis1.salmon.genes.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv resources: tmpdir=/tmp -[Fri Apr 14 10:23:08 2023] +[Fri May 17 18:55:15 2024] Finished job 0. 48 of 48 steps (100%) done -Complete log: .snakemake/log/2023-04-14T101948.877977.snakemake.log +Complete log: .snakemake/log/2024-05-17T185340.014054.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 @@ -4794,19 +4815,19 @@ rm -fr -- debian/.debhelper/generated/pigx-rnaseq/ debian/pigx-rnaseq/ debian/tmp/ dh_auto_install --destdir=debian/pigx-rnaseq/ install -m0755 -d /build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq - make -j15 install DESTDIR=/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq AM_UPDATE_INFO_DIR=no + make -j16 install DESTDIR=/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/pigx-rnaseq-0.1.0' make[2]: Entering directory '/build/pigx-rnaseq-0.1.0' - /bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' - /bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' - /bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/bin' - /bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' - /bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/pigx_rnaseq' + /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/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/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 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/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 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/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 -m 644 README.md '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' make[2]: Leaving directory '/build/pigx-rnaseq-0.1.0' make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0' dh_installdocs @@ -4871,12 +4892,14 @@ 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/2740028/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2740028/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/3203782 and its subdirectories -I: Current time: Fri Apr 14 10:23:38 -12 2023 -I: pbuilder-time-stamp: 1681511019 +I: removing directory /srv/workspace/pbuilder/2740028 and its subdirectories +I: Current time: Fri May 17 18:55:23 +14 2024 +I: pbuilder-time-stamp: 1715921723