Fri Apr 14 21:53:55 UTC 2023 I: starting to build pigx-rnaseq/bookworm/amd64 on jenkins on '2023-04-14 21:53'
Fri Apr 14 21:53:55 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_11/14542/console.log
Fri Apr 14 21:53:55 UTC 2023 I: Downloading source for bookworm/pigx-rnaseq=0.1.0-1.1
--2023-04-14 21:53:55-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/pigx-rnaseq/pigx-rnaseq_0.1.0-1.1.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2685 (2.6K) [text/prs.lines.tag]
Saving to: ‘pigx-rnaseq_0.1.0-1.1.dsc’
0K .. 100% 136M=0s
2023-04-14 21:53:55 (136 MB/s) - ‘pigx-rnaseq_0.1.0-1.1.dsc’ saved [2685/2685]
Fri Apr 14 21:53:55 UTC 2023 I: pigx-rnaseq_0.1.0-1.1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: pigx-rnaseq
Binary: pigx-rnaseq
Architecture: all
Version: 0.1.0-1.1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>,
Homepage: https://github.com/BIMSBbioinfo/pigx_rnaseq
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/pigx-rnaseq
Vcs-Git: https://salsa.debian.org/med-team/pigx-rnaseq.git
Build-Depends: debhelper-compat (= 13), autoconf-archive, fastp, fastqc <!nocheck>, hisat2 <!nocheck>, libjs-jquery-datatables <!nocheck>, libjs-jquery-tablesorter <!nocheck>, megadepth, multiqc, python3-all, python3-deeptools, python3-htseq, r-bioc-deseq2 <!nocheck>, r-bioc-rtracklayer <!nocheck>, r-bioc-summarizedexperiment <!nocheck>, r-bioc-tximport <!nocheck>, r-cran-corrplot <!nocheck>, r-cran-crosstalk <!nocheck>, r-cran-data.table <!nocheck>, r-cran-dt (>= 0.15+dfsg-2) <!nocheck>, r-cran-ggplot2 <!nocheck>, r-cran-ggrepel <!nocheck>, r-cran-gprofiler2 <!nocheck>, r-cran-ggpubr <!nocheck>, r-cran-locfit <!nocheck>, r-cran-pheatmap <!nocheck>, r-cran-plotly <!nocheck>, r-cran-reshape2 <!nocheck>, r-cran-rjson <!nocheck>, r-cran-rlang <!nocheck>, r-cran-rmarkdown <!nocheck>, r-cran-scales <!nocheck>, salmon <!nocheck>, samtools <!nocheck>, snakemake <!nocheck>, trim-galore <!nocheck>
Package-List:
pigx-rnaseq deb science optional arch=all
Checksums-Sha1:
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b93fa0713a94bf87e9cc6c18144386b86b4b484b 15148 pigx-rnaseq_0.1.0-1.1.debian.tar.xz
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09973d40dbfa5882e9194d06f868d7608f697ee563d5b6eae22f017fe8955afe 15148 pigx-rnaseq_0.1.0-1.1.debian.tar.xz
Files:
56333dbaed1000597d05ddf50818332b 4423380 pigx-rnaseq_0.1.0.orig.tar.xz
9e11de20a4efa2bd7920f067e5fbf20c 15148 pigx-rnaseq_0.1.0-1.1.debian.tar.xz
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Fri Apr 14 21:53:55 UTC 2023 I: Checking whether the package is not for us
Fri Apr 14 21:53:55 UTC 2023 I: Starting 1st build on remote node ionos1-amd64.debian.net.
Fri Apr 14 21:53:55 UTC 2023 I: Preparing to do remote build '1' on ionos1-amd64.debian.net.
Fri Apr 14 22:23:40 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net.
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: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [pigx-rnaseq_0.1.0-1.1.dsc]
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: using RSA key 406220C8B8552802378CCE411F5C7A8B45564314
gpgv: issuer "bage@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./pigx-rnaseq_0.1.0-1.1.dsc: no acceptable signature found
dpkg-source: info: extracting pigx-rnaseq in pigx-rnaseq-0.1.0
dpkg-source: info: unpacking pigx-rnaseq_0.1.0.orig.tar.xz
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: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='d3537012cdb4449ab7db40de73f2f1fb'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='3203782'
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_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://78.137.99.97:3128'
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
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
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), autoconf-archive, fastp, fastqc, hisat2, libjs-jquery-datatables, libjs-jquery-tablesorter, megadepth, multiqc, python3-all, python3-deeptools, python3-htseq, r-bioc-deseq2, r-bioc-rtracklayer, r-bioc-summarizedexperiment, r-bioc-tximport, r-cran-corrplot, r-cran-crosstalk, r-cran-data.table, r-cran-dt (>= 0.15+dfsg-2), r-cran-ggplot2, r-cran-ggrepel, r-cran-gprofiler2, r-cran-ggpubr, r-cran-locfit, r-cran-pheatmap, r-cran-plotly, r-cran-reshape2, r-cran-rjson, r-cran-rlang, r-cran-rmarkdown, r-cran-scales, salmon, samtools, snakemake, trim-galore
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19596 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on autoconf-archive; however:
Package autoconf-archive is not installed.
pbuilder-satisfydepends-dummy depends on fastp; however:
Package fastp is not installed.
pbuilder-satisfydepends-dummy depends on fastqc; however:
Package fastqc is not installed.
pbuilder-satisfydepends-dummy depends on hisat2; however:
Package hisat2 is not installed.
pbuilder-satisfydepends-dummy depends on libjs-jquery-datatables; however:
Package libjs-jquery-datatables is not installed.
pbuilder-satisfydepends-dummy depends on libjs-jquery-tablesorter; however:
Package libjs-jquery-tablesorter is not installed.
pbuilder-satisfydepends-dummy depends on megadepth; however:
Package megadepth is not installed.
pbuilder-satisfydepends-dummy depends on multiqc; however:
Package multiqc is not installed.
pbuilder-satisfydepends-dummy depends on python3-all; however:
Package python3-all is not installed.
pbuilder-satisfydepends-dummy depends on python3-deeptools; however:
Package python3-deeptools is not installed.
pbuilder-satisfydepends-dummy depends on python3-htseq; however:
Package python3-htseq is not installed.
pbuilder-satisfydepends-dummy depends on r-bioc-deseq2; however:
Package r-bioc-deseq2 is not installed.
pbuilder-satisfydepends-dummy depends on r-bioc-rtracklayer; however:
Package r-bioc-rtracklayer is not installed.
pbuilder-satisfydepends-dummy depends on r-bioc-summarizedexperiment; however:
Package r-bioc-summarizedexperiment is not installed.
pbuilder-satisfydepends-dummy depends on r-bioc-tximport; however:
Package r-bioc-tximport is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-corrplot; however:
Package r-cran-corrplot is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-crosstalk; however:
Package r-cran-crosstalk is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-data.table; however:
Package r-cran-data.table is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-dt (>= 0.15+dfsg-2); however:
Package r-cran-dt is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-ggplot2; however:
Package r-cran-ggplot2 is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-ggrepel; however:
Package r-cran-ggrepel is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-gprofiler2; however:
Package r-cran-gprofiler2 is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-ggpubr; however:
Package r-cran-ggpubr is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-locfit; however:
Package r-cran-locfit is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-pheatmap; however:
Package r-cran-pheatmap is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-plotly; however:
Package r-cran-plotly is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-reshape2; however:
Package r-cran-reshape2 is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-rjson; however:
Package r-cran-rjson is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-rlang; however:
Package r-cran-rlang is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-rmarkdown; however:
Package r-cran-rmarkdown is not installed.
pbuilder-satisfydepends-dummy depends on r-cran-scales; however:
Package r-cran-scales is not installed.
pbuilder-satisfydepends-dummy depends on salmon; however:
Package salmon is not installed.
pbuilder-satisfydepends-dummy depends on samtools; however:
Package samtools is not installed.
pbuilder-satisfydepends-dummy depends on snakemake; however:
Package snakemake is not installed.
pbuilder-satisfydepends-dummy depends on trim-galore; however:
Package trim-galore is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
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libboost-dev{a} libboost-filesystem1.74.0{a} libboost-program-options1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcups2{a} libcurl3-gnutls{a} libcurl4{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1{a} liberror-perl{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfindbin-libs-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran5{a} libgif7{a} libgirepository-1.0-1{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgtk2.0-0{a} libgtk2.0-common{a} libharfbuzz0b{a} libhdf5-103-1{a} 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The following packages are RECOMMENDED but will NOT be installed:
alsa-topology-conf alsa-ucm-conf bcftools curl cwltool dbus fonts-dejavu-extra graphicsmagick-imagemagick-compat imagemagick imagemagick-6.q16 isympy-common less libarchive-cpio-perl libatk-wrapper-java-jni libfile-mimeinfo-perl libgail-common libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libgtk2.0-bin libhwloc-plugins libjs-filesaver libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl librsvg2-common libsasl2-modules libx11-protocol-perl lynx node-clipboard node-highlight.js node-jquery openssh-client publicsuffix python3-biopython python3-bs4 python3-dropbox python3-flask python3-ftputil python3-gdal python3-hisat2 python3-html5lib python3-invoke python3-irodsclient python3-json-pointer python3-kubernetes python3-olefile python3-pydot python3-pygraphviz python3-rfc3987 python3-uritemplate python3-webcolors python3-yappi r-base-dev r-cran-bench r-cran-bookdown r-cran-cba r-cran-cliapp r-cran-coin r-cran-covr r-cran-dbitest r-cran-dbplyr r-cran-ddalpha r-cran-decor r-cran-devtools r-cran-dimred r-cran-domc r-cran-dygraphs r-cran-earth r-cran-ellipse r-cran-emmeans r-cran-fastica r-cran-fields r-cran-formattable r-cran-geepack r-cran-ggbeeswarm r-cran-ggthemes r-cran-gh r-cran-hexbin r-cran-hmisc r-cran-igraph r-cran-interp r-cran-kernlab r-cran-lavasearch2 r-cran-lobstr r-cran-logcondens r-cran-mapproj r-cran-maps r-cran-markdown r-cran-mda r-cran-mets r-cran-mlbench r-cran-mlmetrics r-cran-mockery r-cran-mockr r-cran-modeldata r-cran-multcomp r-cran-optimx r-cran-pkgbuild r-cran-pls r-cran-polycor r-cran-r.rsp r-cran-ragg r-cran-rann r-cran-rcpproll r-cran-rgl r-cran-rmysql r-cran-roxygen2 r-cran-rpostgresql r-cran-rsample r-cran-rsclient r-cran-rsconnect r-cran-rspectra r-cran-rsvg r-cran-runit r-cran-rversions r-cran-setrng r-cran-sf r-cran-sodium r-cran-spelling r-cran-svglite r-cran-testit r-cran-thematic r-cran-themis r-cran-tikzdevice r-cran-tufte r-cran-usethis r-cran-vdiffr r-cran-webutils r-cran-xml2 r-cran-zoo r-doc-html r-recommended texlive-xetex wget x11-utils x11-xserver-utils xdg-user-dirs
0 packages upgraded, 667 newly installed, 0 to remove and 0 not upgraded.
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Get: 27 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-1 [1397 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.37-2 [43.3 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 49 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 50 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB]
Get: 51 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB]
Get: 52 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-4 [399 kB]
Get: 53 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 54 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB]
Get: 55 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB]
Get: 56 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB]
Get: 57 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB]
Get: 58 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB]
Get: 59 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB]
Get: 60 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB]
Get: 61 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB]
Get: 62 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB]
Get: 63 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB]
Get: 64 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get: 65 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB]
Get: 66 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB]
Get: 67 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB]
Get: 68 http://deb.debian.org/debian bookworm/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB]
Get: 69 http://deb.debian.org/debian bookworm/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB]
Get: 70 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B]
Get: 71 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-9 [107 kB]
Get: 72 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-9 [41.3 kB]
Get: 73 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.6-1 [200 kB]
Get: 74 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-9 [45.1 kB]
Get: 75 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3 [244 kB]
Get: 76 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB]
Get: 77 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB]
Get: 78 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB]
Get: 79 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB]
Get: 80 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB]
Get: 81 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB]
Get: 82 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB]
Get: 83 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-1 [60.8 kB]
Get: 84 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.6+10-1 [43.6 MB]
Get: 85 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B]
Get: 86 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230103 [11.4 kB]
Get: 87 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB]
Get: 88 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB]
Get: 89 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB]
Get: 90 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB]
Get: 91 http://deb.debian.org/debian bookworm/main amd64 coinor-libcoinutils3v5 amd64 2.11.4+repack1-2 [440 kB]
Get: 92 http://deb.debian.org/debian bookworm/main amd64 coinor-libosi1v5 amd64 0.108.6+repack1-2 [276 kB]
Get: 93 http://deb.debian.org/debian bookworm/main amd64 coinor-libclp1 amd64 1.17.6-3 [843 kB]
Get: 94 http://deb.debian.org/debian bookworm/main amd64 coinor-libcgl1 amd64 0.60.3+repack1-4 [409 kB]
Get: 95 http://deb.debian.org/debian bookworm/main amd64 coinor-libcbc3 amd64 2.10.8+ds1-1 [715 kB]
Get: 96 http://deb.debian.org/debian bookworm/main amd64 coinor-cbc amd64 2.10.8+ds1-1 [14.8 kB]
Get: 97 http://deb.debian.org/debian bookworm/main amd64 python3-typing-extensions all 4.4.0-1 [45.2 kB]
Get: 98 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 99 http://deb.debian.org/debian bookworm/main amd64 python3-xopen all 1.7.0-2 [16.9 kB]
Get: 100 http://deb.debian.org/debian bookworm/main amd64 python3-dnaio amd64 0.10.0-1+b1 [58.4 kB]
Get: 101 http://deb.debian.org/debian bookworm/main amd64 python3-cutadapt amd64 4.2-1+b1 [222 kB]
Get: 102 http://deb.debian.org/debian bookworm/main amd64 cutadapt all 4.2-1 [23.5 kB]
Get: 103 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 104 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 105 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 106 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 107 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 108 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 109 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 110 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 111 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 112 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 113 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 114 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 115 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 116 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB]
Get: 117 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB]
Get: 118 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB]
Get: 119 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB]
Get: 120 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB]
Get: 121 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB]
Get: 122 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB]
Get: 123 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB]
Get: 124 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB]
Get: 125 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB]
Get: 126 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB]
Get: 127 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB]
Get: 128 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB]
Get: 129 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB]
Get: 130 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB]
Get: 131 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB]
Get: 132 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB]
Get: 133 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB]
Get: 134 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB]
Get: 135 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB]
Get: 136 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB]
Get: 137 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB]
Get: 138 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB]
Get: 139 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B]
Get: 140 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB]
Get: 141 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB]
Get: 142 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2 [192 kB]
Get: 143 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB]
Get: 144 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB]
Get: 145 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB]
Get: 146 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB]
Get: 147 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB]
Get: 148 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB]
Get: 149 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB]
Get: 150 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B]
Get: 151 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB]
Get: 152 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB]
Get: 153 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB]
Get: 154 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB]
Get: 155 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB]
Get: 156 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB]
Get: 157 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB]
Get: 158 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB]
Get: 159 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB]
Get: 160 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB]
Get: 161 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB]
Get: 162 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB]
Get: 163 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB]
Get: 164 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB]
Get: 165 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB]
Get: 166 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB]
Get: 167 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB]
Get: 168 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.6+10-1 [168 kB]
Get: 169 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B]
Get: 170 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB]
Get: 171 http://deb.debian.org/debian bookworm/main amd64 docutils-common all 0.19+dfsg-6 [127 kB]
Get: 172 http://deb.debian.org/debian bookworm/main amd64 libisal2 amd64 2.30.0-5 [107 kB]
Get: 173 http://deb.debian.org/debian bookworm/main amd64 fastp amd64 0.23.2+dfsg-2+b1 [203 kB]
Get: 174 http://deb.debian.org/debian bookworm/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB]
Get: 175 http://deb.debian.org/debian bookworm/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB]
Get: 176 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B]
Get: 177 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 178 http://deb.debian.org/debian bookworm/main amd64 libcommons-compress-java all 1.22-1 [615 kB]
Get: 179 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB]
Get: 180 http://deb.debian.org/debian bookworm/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB]
Get: 181 http://deb.debian.org/debian bookworm/main amd64 libmjson-java all 1.4.0-3 [60.4 kB]
Get: 182 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB]
Get: 183 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB]
Get: 184 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB]
Get: 185 http://deb.debian.org/debian bookworm/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB]
Get: 186 http://deb.debian.org/debian bookworm/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1050 kB]
Get: 187 http://deb.debian.org/debian bookworm/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-5 [153 kB]
Get: 188 http://deb.debian.org/debian bookworm/main amd64 libngs-jni amd64 3.0.3+dfsg-5 [23.4 kB]
Get: 189 http://deb.debian.org/debian bookworm/main amd64 libngs-java amd64 3.0.3+dfsg-5 [110 kB]
Get: 190 http://deb.debian.org/debian bookworm/main amd64 librhino-java all 1.7.7.2-3 [1200 kB]
Get: 191 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB]
Get: 192 http://deb.debian.org/debian bookworm/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B]
Get: 193 http://deb.debian.org/debian bookworm/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB]
Get: 194 http://deb.debian.org/debian bookworm/main amd64 libhtsjdk-java all 3.0.4+dfsg-2 [1813 kB]
Get: 195 http://deb.debian.org/debian bookworm/main amd64 libfindbin-libs-perl all 3.0.2-1 [29.7 kB]
Get: 196 http://deb.debian.org/debian bookworm/main amd64 libargs4j-java all 2.33-2 [138 kB]
Get: 197 http://deb.debian.org/debian bookworm/main amd64 libcommons-io-java all 2.11.0-2 [319 kB]
Get: 198 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang3-java all 3.12.0-2 [561 kB]
Get: 199 http://deb.debian.org/debian bookworm/main amd64 libsis-base-jni amd64 18.09~pre1+git20180928.45fbd31+dfsg-3 [12.5 kB]
Get: 200 http://deb.debian.org/debian bookworm/main amd64 libsis-base-java all 18.09~pre1+git20180928.45fbd31+dfsg-3 [97.8 kB]
Get: 201 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB]
Get: 202 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB]
Get: 203 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB]
Get: 204 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB]
Get: 205 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB]
Get: 206 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB]
Get: 207 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB]
Get: 208 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-8 [386 kB]
Get: 209 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB]
Get: 210 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B]
Get: 211 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB]
Get: 212 http://deb.debian.org/debian bookworm/main amd64 libsis-jhdf5-jni amd64 19.04.1+dfsg-3 [95.9 kB]
Get: 213 http://deb.debian.org/debian bookworm/main amd64 libsis-jhdf5-java all 19.04.1+dfsg-3 [1491 kB]
Get: 214 http://deb.debian.org/debian bookworm/main amd64 fastqc all 0.11.9+dfsg-6 [390 kB]
Get: 215 http://deb.debian.org/debian bookworm/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get: 216 http://deb.debian.org/debian bookworm/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB]
Get: 217 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB]
Get: 218 http://deb.debian.org/debian bookworm/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB]
Get: 219 http://deb.debian.org/debian bookworm/main amd64 libgirepository-1.0-1 amd64 1.74.0-3 [101 kB]
Get: 220 http://deb.debian.org/debian bookworm/main amd64 gir1.2-glib-2.0 amd64 1.74.0-3 [159 kB]
Get: 221 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-8 [380 kB]
Get: 222 http://deb.debian.org/debian bookworm/main amd64 liberror-perl all 0.17029-2 [29.0 kB]
Get: 223 http://deb.debian.org/debian bookworm/main amd64 git-man all 1:2.39.2-1.1 [2049 kB]
Get: 224 http://deb.debian.org/debian bookworm/main amd64 git amd64 1:2.39.2-1.1 [7171 kB]
Get: 225 http://deb.debian.org/debian bookworm/main amd64 hisat2 amd64 2.2.1-4+b2 [3658 kB]
Get: 226 http://deb.debian.org/debian bookworm/main amd64 javascript-common all 11+nmu1 [6260 B]
Get: 227 http://deb.debian.org/debian bookworm/main amd64 libbigwig0 amd64 0.4.7+dfsg-3 [27.9 kB]
Get: 228 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB]
Get: 229 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B]
Get: 230 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74.0 amd64 1.74.0+ds1-20 [258 kB]
Get: 231 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-20 [328 kB]
Get: 232 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB]
Get: 233 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB]
Get: 234 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB]
Get: 235 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB]
Get: 236 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB]
Get: 237 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB]
Get: 238 http://deb.debian.org/debian bookworm/main amd64 libjemalloc2 amd64 5.3.0-1 [275 kB]
Get: 239 http://deb.debian.org/debian bookworm/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB]
Get: 240 http://deb.debian.org/debian bookworm/main amd64 libjs-popper.js all 1.16.1+ds-6 [52.4 kB]
Get: 241 http://deb.debian.org/debian bookworm/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [517 kB]
Get: 242 http://deb.debian.org/debian bookworm/main amd64 libjs-d3 all 3.5.17-4 [132 kB]
Get: 243 http://deb.debian.org/debian bookworm/main amd64 libjs-es5-shim all 4.6.7-2 [47.4 kB]
Get: 244 http://deb.debian.org/debian bookworm/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB]
Get: 245 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 246 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB]
Get: 247 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-datatables-extensions all 0.0+git20150910.28fd64e+dfsg-5 [648 kB]
Get: 248 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-metadata all 12-4 [6532 B]
Get: 249 http://deb.debian.org/debian bookworm/main amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.2 kB]
Get: 250 http://deb.debian.org/debian bookworm/main amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B]
Get: 251 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB]
Get: 252 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [184 kB]
Get: 253 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 254 http://deb.debian.org/debian bookworm/main amd64 libjs-json all 0~20221030+~1.0.8-1 [20.0 kB]
Get: 255 http://deb.debian.org/debian bookworm/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB]
Get: 256 http://deb.debian.org/debian bookworm/main amd64 libjs-modernizr all 2.6.2+ds1-5 [47.1 kB]
Get: 257 http://deb.debian.org/debian bookworm/main amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB]
Get: 258 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 259 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get: 260 http://deb.debian.org/debian bookworm/main amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB]
Get: 261 http://deb.debian.org/debian bookworm/main amd64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 262 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB]
Get: 263 http://deb.debian.org/debian bookworm/main amd64 liblua5.3-0 amd64 5.3.6-2 [123 kB]
Get: 264 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-2 [103 kB]
Get: 265 http://deb.debian.org/debian bookworm/main amd64 libnlopt0 amd64 2.7.1-4+b4 [174 kB]
Get: 266 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB]
Get: 267 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB]
Get: 268 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB]
Get: 269 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-1+b1 [189 kB]
Get: 270 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB]
Get: 271 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B]
Get: 272 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB]
Get: 273 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Get: 274 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB]
Get: 275 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B]
Get: 276 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B]
Get: 277 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB]
Get: 278 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB]
Get: 279 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB]
Get: 280 http://deb.debian.org/debian bookworm/main amd64 libsodium23 amd64 1.0.18-1 [161 kB]
Get: 281 http://deb.debian.org/debian bookworm/main amd64 libstaden-read14 amd64 1.14.15-1 [265 kB]
Get: 282 http://deb.debian.org/debian bookworm/main amd64 libtbbmalloc2 amd64 2021.8.0-1 [46.1 kB]
Get: 283 http://deb.debian.org/debian bookworm/main amd64 libtbbbind-2-5 amd64 2021.8.0-1 [13.3 kB]
Get: 284 http://deb.debian.org/debian bookworm/main amd64 libtbb12 amd64 2021.8.0-1 [79.0 kB]
Get: 285 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB]
Get: 286 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.1 [99.2 kB]
Get: 287 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.1 [109 kB]
Get: 288 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB]
Get: 289 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB]
Get: 290 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB]
Get: 291 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB]
Get: 292 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB]
Get: 293 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB]
Get: 294 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB]
Get: 295 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB]
Get: 296 http://deb.debian.org/debian bookworm/main amd64 r-cran-littler amd64 0.3.17-1 [96.3 kB]
Get: 297 http://deb.debian.org/debian bookworm/main amd64 littler all 0.3.17-1 [14.4 kB]
Get: 298 http://deb.debian.org/debian bookworm/main amd64 megadepth amd64 1.2.0-4 [80.2 kB]
Get: 299 http://deb.debian.org/debian bookworm/main amd64 python3-colorama all 0.4.6-2 [36.8 kB]
Get: 300 http://deb.debian.org/debian bookworm/main amd64 python3-click all 8.1.3-2 [92.2 kB]
Get: 301 http://deb.debian.org/debian bookworm/main amd64 python3-humanfriendly all 10.0-3 [85.2 kB]
Get: 302 http://deb.debian.org/debian bookworm/main amd64 python3-coloredlogs all 15.0.1-1 [47.4 kB]
Get: 303 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB]
Get: 304 http://deb.debian.org/debian bookworm/main amd64 python3-future all 0.18.2-6 [348 kB]
Get: 305 http://deb.debian.org/debian bookworm/main amd64 python3-markupsafe amd64 2.1.2-1+b1 [13.2 kB]
Get: 306 http://deb.debian.org/debian bookworm/main amd64 python3-jinja2 all 3.1.2-1 [119 kB]
Get: 307 http://deb.debian.org/debian bookworm/main amd64 python3-lzstring all 1.0.4-2 [5604 B]
Get: 308 http://deb.debian.org/debian bookworm/main amd64 python3-markdown all 3.4.1-2 [64.7 kB]
Get: 309 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB]
Get: 310 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB]
Get: 311 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB]
Get: 312 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB]
Get: 313 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-2 [98.2 kB]
Get: 314 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+b1 [74.4 kB]
Get: 315 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB]
Get: 316 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB]
Get: 317 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB]
Get: 318 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B]
Get: 319 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB]
Get: 320 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB]
Get: 321 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB]
Get: 322 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B]
Get: 323 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB]
Get: 324 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB]
Get: 325 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B]
Get: 326 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B]
Get: 327 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B]
Get: 328 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB]
Get: 329 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB]
Get: 330 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB]
Get: 331 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB]
Get: 332 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB]
Get: 333 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB]
Get: 334 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB]
Get: 335 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-3 [30.1 kB]
Get: 336 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB]
Get: 337 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB]
Get: 338 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB]
Get: 339 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB]
Get: 340 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB]
Get: 341 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB]
Get: 342 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB]
Get: 343 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB]
Get: 344 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB]
Get: 345 http://deb.debian.org/debian bookworm/main amd64 python3-networkx all 2.8.8-1 [1425 kB]
Get: 346 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB]
Get: 347 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB]
Get: 348 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1 [39.4 kB]
Get: 349 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB]
Get: 350 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB]
Get: 351 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB]
Get: 352 http://deb.debian.org/debian bookworm/main amd64 python3-mdurl all 0.1.2-1 [9444 B]
Get: 353 http://deb.debian.org/debian bookworm/main amd64 python3-markdown-it all 2.1.0-5 [58.8 kB]
Get: 354 http://deb.debian.org/debian bookworm/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB]
Get: 355 http://deb.debian.org/debian bookworm/main amd64 python3-rich all 13.3.1-1 [202 kB]
Get: 356 http://deb.debian.org/debian bookworm/main amd64 python3-rich-click all 1.6.0-1 [20.8 kB]
Get: 357 http://deb.debian.org/debian bookworm/main amd64 python3-simplejson amd64 3.18.3-1 [59.8 kB]
Get: 358 http://deb.debian.org/debian bookworm/main amd64 python3-colormath all 3.0.0-4 [34.7 kB]
Get: 359 http://deb.debian.org/debian bookworm/main amd64 python3-spectra all 0.0.11-4 [16.5 kB]
Get: 360 http://deb.debian.org/debian bookworm/main amd64 python3-yaml amd64 6.0-3+b2 [119 kB]
Get: 361 http://deb.debian.org/debian bookworm/main amd64 multiqc all 1.14+dfsg-1 [657 kB]
Get: 362 http://deb.debian.org/debian bookworm/main amd64 node-bootstrap-sass all 3.4.3-2 [186 kB]
Get: 363 http://deb.debian.org/debian bookworm/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB]
Get: 364 http://deb.debian.org/debian bookworm/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB]
Get: 365 http://deb.debian.org/debian bookworm/main amd64 pandoc-data all 2.17.1.1-1.1 [417 kB]
Get: 366 http://deb.debian.org/debian bookworm/main amd64 pandoc amd64 2.17.1.1-1.1 [21.3 MB]
Get: 367 http://deb.debian.org/debian bookworm/main amd64 python-babel-localedata all 2.10.3-1 [5615 kB]
Get: 368 http://deb.debian.org/debian bookworm/main amd64 python3-cffi-backend amd64 1.15.1-5+b1 [84.6 kB]
Get: 369 http://deb.debian.org/debian bookworm/main amd64 python3-cryptography amd64 38.0.4-3 [666 kB]
Get: 370 http://deb.debian.org/debian bookworm/main amd64 python3-jwt all 2.6.0-1 [26.6 kB]
Get: 371 http://deb.debian.org/debian bookworm/main amd64 python3-adal all 1.2.7-2 [32.1 kB]
Get: 372 http://deb.debian.org/debian bookworm/main amd64 python3-multidict amd64 6.0.4-1+b1 [31.6 kB]
Get: 373 http://deb.debian.org/debian bookworm/main amd64 python3-yarl amd64 1.8.2-1+b1 [49.8 kB]
Get: 374 http://deb.debian.org/debian bookworm/main amd64 python3-async-timeout all 4.0.2-1 [7476 B]
Get: 375 http://deb.debian.org/debian bookworm/main amd64 python3-frozenlist amd64 1.3.3-1+b1 [30.0 kB]
Get: 376 http://deb.debian.org/debian bookworm/main amd64 python3-aiosignal all 1.3.1-1 [6016 B]
Get: 377 http://deb.debian.org/debian bookworm/main amd64 python3-aiohttp amd64 3.8.4-1 [251 kB]
Get: 378 http://deb.debian.org/debian bookworm/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB]
Get: 379 http://deb.debian.org/debian bookworm/main amd64 python3-avro all 1.11.1+dfsg-2 [70.5 kB]
Get: 380 http://deb.debian.org/debian bookworm/main amd64 python3-isodate all 0.6.1-1 [25.3 kB]
Get: 381 http://deb.debian.org/debian bookworm/main amd64 python3-blinker all 1.5-1 [14.7 kB]
Get: 382 http://deb.debian.org/debian bookworm/main amd64 python3-oauthlib all 3.2.2-1 [95.4 kB]
Get: 383 http://deb.debian.org/debian bookworm/main amd64 python3-requests-oauthlib all 1.3.0+ds-1 [20.7 kB]
Get: 384 http://deb.debian.org/debian bookworm/main amd64 python3-msrest all 0.6.21-2 [48.0 kB]
Get: 385 http://deb.debian.org/debian bookworm/main amd64 python3-msrestazure all 0.6.4-2 [26.4 kB]
Get: 386 http://deb.debian.org/debian bookworm/main amd64 python3-azure-storage all 20230112+git-1 [280 kB]
Get: 387 http://deb.debian.org/debian bookworm/main amd64 python3-pyrsistent amd64 0.18.1-1+b3 [60.0 kB]
Get: 388 http://deb.debian.org/debian bookworm/main amd64 python3-jsonschema all 4.10.3-1 [67.9 kB]
Get: 389 http://deb.debian.org/debian bookworm/main amd64 python3-marshmallow all 3.18.0-1 [66.3 kB]
Get: 390 http://deb.debian.org/debian bookworm/main amd64 python3-msal all 1.21.0-1 [85.9 kB]
Get: 391 http://deb.debian.org/debian bookworm/main amd64 python3-gi amd64 3.42.2-3+b1 [219 kB]
Get: 392 http://deb.debian.org/debian bookworm/main amd64 python3-portalocker all 2.2.1-1 [18.5 kB]
Get: 393 http://deb.debian.org/debian bookworm/main amd64 python3-msal-extensions all 1.0.0-2 [16.9 kB]
Get: 394 http://deb.debian.org/debian bookworm/main amd64 python3-ruamel.yaml.clib amd64 0.2.7-1+b2 [113 kB]
Get: 395 http://deb.debian.org/debian bookworm/main amd64 python3-ruamel.yaml all 0.17.21-1 [103 kB]
Get: 396 http://deb.debian.org/debian bookworm/main amd64 python3-strictyaml all 1.6.1-3 [92.9 kB]
Get: 397 http://deb.debian.org/debian bookworm/main amd64 python3-tqdm all 4.64.1-1 [97.7 kB]
Get: 398 http://deb.debian.org/debian bookworm/main amd64 python3-uamqp amd64 1.5.3-1+b4 [647 kB]
Get: 399 http://deb.debian.org/debian bookworm/main amd64 python3-azure all 20230112+git-1 [11.9 MB]
Get: 400 http://deb.debian.org/debian bookworm/main amd64 python3-babel all 2.10.3-1 [103 kB]
Get: 401 http://deb.debian.org/debian bookworm/main amd64 python3-bcrypt amd64 3.2.2-1 [32.2 kB]
Get: 402 http://deb.debian.org/debian bookworm/main amd64 python3-jmespath all 1.0.1-1 [21.1 kB]
Get: 403 http://deb.debian.org/debian bookworm/main amd64 python3-botocore all 1.29.27+repack-1 [5502 kB]
Get: 404 http://deb.debian.org/debian bookworm/main amd64 python3-s3transfer all 0.6.0-1 [53.0 kB]
Get: 405 http://deb.debian.org/debian bookworm/main amd64 python3-boto3 all 1.26.27+dfsg-1 [187 kB]
Get: 406 http://deb.debian.org/debian bookworm/main amd64 python3-configargparse all 1.5.3-1 [26.1 kB]
Get: 407 http://deb.debian.org/debian bookworm/main amd64 python3-connection-pool all 0.0.3-2 [5584 B]
Get: 408 http://deb.debian.org/debian bookworm/main amd64 python3-datrie amd64 0.8.2-4+b1 [97.7 kB]
Get: 409 http://deb.debian.org/debian bookworm/main amd64 python3-deeptoolsintervals amd64 0.1.9-3+b6 [51.1 kB]
Get: 410 http://deb.debian.org/debian bookworm/main amd64 sphinx-common all 5.3.0-4 [653 kB]
Get: 411 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B]
Get: 412 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB]
Get: 413 http://deb.debian.org/debian bookworm/main amd64 python3-imagesize all 1.4.1-1 [6688 B]
Get: 414 http://deb.debian.org/debian bookworm/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB]
Get: 415 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB]
Get: 416 http://deb.debian.org/debian bookworm/main amd64 python3-numpydoc all 1.5.0-1 [43.0 kB]
Get: 417 http://deb.debian.org/debian bookworm/main amd64 python3-fastjsonschema all 2.16.3-2 [21.6 kB]
Get: 418 http://deb.debian.org/debian bookworm/main amd64 python3-traitlets all 5.5.0-1 [92.4 kB]
Get: 419 http://deb.debian.org/debian bookworm/main amd64 python3-jupyter-core all 4.12.0-1 [27.3 kB]
Get: 420 http://deb.debian.org/debian bookworm/main amd64 python3-nbformat all 5.5.0-1 [43.2 kB]
Get: 421 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB]
Get: 422 http://deb.debian.org/debian bookworm/main amd64 python3-pbr all 5.10.0-2 [61.4 kB]
Get: 423 http://deb.debian.org/debian bookworm/main amd64 python3-tenacity all 8.2.1-1 [43.6 kB]
Get: 424 http://deb.debian.org/debian bookworm/main amd64 python3-plotly all 5.4.1+dfsg-1 [2613 kB]
Get: 425 http://deb.debian.org/debian bookworm/main amd64 python3-py2bit amd64 0.3.1-1+b2 [18.7 kB]
Get: 426 http://deb.debian.org/debian bookworm/main amd64 python3-pybigwig amd64 0.3.18+dfsg-1+b3 [34.8 kB]
Get: 427 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB]
Get: 428 http://deb.debian.org/debian bookworm/main amd64 python3-deeptools all 3.5.1-3 [159 kB]
Get: 429 http://deb.debian.org/debian bookworm/main amd64 python3-smmap all 5.0.0-1 [21.0 kB]
Get: 430 http://deb.debian.org/debian bookworm/main amd64 python3-gitdb all 4.0.9-2 [45.7 kB]
Get: 431 http://deb.debian.org/debian bookworm/main amd64 python3-git all 3.1.30-1 [135 kB]
Get: 432 http://deb.debian.org/debian bookworm/main amd64 python3-htseq amd64 1.99.2-1+b3 [268 kB]
Get: 433 http://deb.debian.org/debian bookworm/main amd64 python3-nacl amd64 1.5.0-2 [59.3 kB]
Get: 434 http://deb.debian.org/debian bookworm/main amd64 python3-paramiko all 2.12.0-2 [133 kB]
Get: 435 http://deb.debian.org/debian bookworm/main amd64 python3-psutil amd64 5.9.4-1+b1 [189 kB]
Get: 436 http://deb.debian.org/debian bookworm/main amd64 python3-pulp all 2.6.0+dfsg-1 [66.0 kB]
Get: 437 http://deb.debian.org/debian bookworm/main amd64 python3-py all 1.11.0-1 [89.2 kB]
Get: 438 http://deb.debian.org/debian bookworm/main amd64 python3-ratelimiter amd64 1.2.0.post0-4 [5740 B]
Get: 439 http://deb.debian.org/debian bookworm/main amd64 python3-retry all 0.9.2-2 [7020 B]
Get: 440 http://deb.debian.org/debian bookworm/main amd64 python3-smart-open all 5.2.1-5 [87.9 kB]
Get: 441 http://deb.debian.org/debian bookworm/main amd64 python3-stopit all 1.1.2-2 [12.6 kB]
Get: 442 http://deb.debian.org/debian bookworm/main amd64 python3-tabulate all 0.8.9-1 [35.2 kB]
Get: 443 http://deb.debian.org/debian bookworm/main amd64 python3-throttler all 1.2.2-2 [7072 B]
Get: 444 http://deb.debian.org/debian bookworm/main amd64 python3-toposort all 1.9-1 [7272 B]
Get: 445 http://deb.debian.org/debian bookworm/main amd64 python3-wrapt amd64 1.14.1-2+b2 [42.1 kB]
Get: 446 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocgenerics all 0.44.0-2 [600 kB]
Get: 447 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biobase amd64 2.58.0-2 [2112 kB]
Get: 448 http://deb.debian.org/debian bookworm/main amd64 r-bioc-s4vectors amd64 0.36.1-1 [2026 kB]
Get: 449 http://deb.debian.org/debian bookworm/main amd64 r-bioc-iranges amd64 2.32.0-1 [2222 kB]
Get: 450 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbi all 1.1.3-1 [687 kB]
Get: 451 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB]
Get: 452 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB]
Get: 453 http://deb.debian.org/debian bookworm/main amd64 r-cran-rlang amd64 1.0.6-1 [1618 kB]
Get: 454 http://deb.debian.org/debian bookworm/main amd64 r-cran-cli amd64 3.6.0-1 [1287 kB]
Get: 455 http://deb.debian.org/debian bookworm/main amd64 r-cran-glue amd64 1.6.2-1 [152 kB]
Get: 456 http://deb.debian.org/debian bookworm/main amd64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB]
Get: 457 http://deb.debian.org/debian bookworm/main amd64 r-cran-vctrs amd64 0.5.2-1 [1371 kB]
Get: 458 http://deb.debian.org/debian bookworm/main amd64 r-cran-blob all 1.2.3-1 [49.5 kB]
Get: 459 http://deb.debian.org/debian bookworm/main amd64 r-cran-fastmap amd64 1.1.1-1 [68.9 kB]
Get: 460 http://deb.debian.org/debian bookworm/main amd64 r-cran-cachem amd64 1.0.7-1 [71.6 kB]
Get: 461 http://deb.debian.org/debian bookworm/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB]
Get: 462 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB]
Get: 463 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgkitten all 0.2.2-2 [27.0 kB]
Get: 464 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpp amd64 1.0.10-1 [2059 kB]
Get: 465 http://deb.debian.org/debian bookworm/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB]
Get: 466 http://deb.debian.org/debian bookworm/main amd64 r-cran-rsqlite amd64 2.2.20-1 [1123 kB]
Get: 467 http://deb.debian.org/debian bookworm/main amd64 r-cran-curl amd64 5.0.0+dfsg-1 [172 kB]
Get: 468 http://deb.debian.org/debian bookworm/main amd64 r-cran-jsonlite amd64 1.8.4+dfsg-1 [442 kB]
Get: 469 http://deb.debian.org/debian bookworm/main amd64 r-cran-mime amd64 0.12-1+b1 [36.0 kB]
Get: 470 http://deb.debian.org/debian bookworm/main amd64 r-cran-sys amd64 3.4.1-1 [42.7 kB]
Get: 471 http://deb.debian.org/debian bookworm/main amd64 r-cran-askpass amd64 1.1-2 [22.2 kB]
Get: 472 http://deb.debian.org/debian bookworm/main amd64 r-cran-openssl amd64 2.0.5+dfsg-1 [391 kB]
Get: 473 http://deb.debian.org/debian bookworm/main amd64 r-cran-r6 all 2.5.1-1 [105 kB]
Get: 474 http://deb.debian.org/debian bookworm/main amd64 r-cran-httr all 1.4.5+dfsg-1 [465 kB]
Get: 475 http://deb.debian.org/debian bookworm/main amd64 r-cran-png amd64 0.1-8-1 [41.1 kB]
Get: 476 http://deb.debian.org/debian bookworm/main amd64 r-bioc-zlibbioc all 1.44.0+dfsg-1 [9200 B]
Get: 477 http://deb.debian.org/debian bookworm/main amd64 r-bioc-xvector amd64 0.38.0-1 [618 kB]
Get: 478 http://deb.debian.org/debian bookworm/main amd64 r-cran-bitops amd64 1.0-7-1 [30.2 kB]
Get: 479 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcurl amd64 1.98-1.10+dfsg-1 [783 kB]
Get: 480 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodbdata all 1.2.9-1 [11.7 MB]
Get: 481 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodb all 1.34.9-1 [3938 kB]
Get: 482 http://deb.debian.org/debian bookworm/main amd64 r-cran-crayon all 1.5.2-1 [165 kB]
Get: 483 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biostrings amd64 2.66.0-1 [13.8 MB]
Get: 484 http://deb.debian.org/debian bookworm/main amd64 r-bioc-keggrest all 1.38.0+dfsg-1 [179 kB]
Get: 485 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotationdbi all 1.60.0-1 [4696 kB]
Get: 486 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml amd64 3.99-0.13-1 [1717 kB]
Get: 487 http://deb.debian.org/debian bookworm/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB]
Get: 488 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotate all 1.76.0+dfsg-1 [1727 kB]
Get: 489 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocio all 1.8.0+dfsg-1 [201 kB]
Get: 490 http://deb.debian.org/debian bookworm/main amd64 r-cran-formatr all 1.14-1 [152 kB]
Get: 491 http://deb.debian.org/debian bookworm/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB]
Get: 492 http://deb.debian.org/debian bookworm/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB]
Get: 493 http://deb.debian.org/debian bookworm/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB]
Get: 494 http://deb.debian.org/debian bookworm/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB]
Get: 495 http://deb.debian.org/debian bookworm/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB]
Get: 496 http://deb.debian.org/debian bookworm/main amd64 r-cran-bh all 1.74.0-2 [5524 B]
Get: 497 http://deb.debian.org/debian bookworm/main amd64 r-cran-cpp11 all 0.4.3-1 [223 kB]
Get: 498 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocparallel amd64 1.32.5-1 [1337 kB]
Get: 499 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB]
Get: 500 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB]
Get: 501 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrixstats amd64 0.63.0-1 [470 kB]
Get: 502 http://deb.debian.org/debian bookworm/main amd64 r-bioc-matrixgenerics all 1.10.0-1 [302 kB]
Get: 503 http://deb.debian.org/debian bookworm/main amd64 r-bioc-delayedarray amd64 0.24.0+dfsg-1 [1937 kB]
Get: 504 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicranges amd64 1.50.2+dfsg-1 [1796 kB]
Get: 505 http://deb.debian.org/debian bookworm/main amd64 r-bioc-summarizedexperiment all 1.28.0+dfsg-1 [2018 kB]
Get: 506 http://deb.debian.org/debian bookworm/main amd64 r-cran-locfit amd64 1.5-9.7-1 [507 kB]
Get: 507 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB]
Get: 508 http://deb.debian.org/debian bookworm/main amd64 r-bioc-geneplotter all 1.76.0-1 [1488 kB]
Get: 509 http://deb.debian.org/debian bookworm/main amd64 r-cran-gtable all 0.3.1+dfsg-1 [165 kB]
Get: 510 http://deb.debian.org/debian bookworm/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB]
Get: 511 http://deb.debian.org/debian bookworm/main amd64 r-cran-mass amd64 7.3-58.2-1 [1121 kB]
Get: 512 http://deb.debian.org/debian bookworm/main amd64 r-cran-nlme amd64 3.1.162-1 [2260 kB]
Get: 513 http://deb.debian.org/debian bookworm/main amd64 r-cran-mgcv amd64 1.8-41-1 [3171 kB]
Get: 514 http://deb.debian.org/debian bookworm/main amd64 r-cran-farver amd64 2.1.1-1 [1404 kB]
Get: 515 http://deb.debian.org/debian bookworm/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB]
Get: 516 http://deb.debian.org/debian bookworm/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB]
Get: 517 http://deb.debian.org/debian bookworm/main amd64 r-cran-munsell all 0.5.0-2 [236 kB]
Get: 518 http://deb.debian.org/debian bookworm/main amd64 r-cran-viridislite all 0.4.1-1 [1299 kB]
Get: 519 http://deb.debian.org/debian bookworm/main amd64 r-cran-scales all 1.2.1-1 [614 kB]
Get: 520 http://deb.debian.org/debian bookworm/main amd64 r-cran-fansi amd64 1.0.4-1 [619 kB]
Get: 521 http://deb.debian.org/debian bookworm/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB]
Get: 522 http://deb.debian.org/debian bookworm/main amd64 r-cran-utf8 amd64 1.2.3-1 [133 kB]
Get: 523 http://deb.debian.org/debian bookworm/main amd64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB]
Get: 524 http://deb.debian.org/debian bookworm/main amd64 r-cran-tibble amd64 3.1.8+dfsg-1 [513 kB]
Get: 525 http://deb.debian.org/debian bookworm/main amd64 r-cran-withr all 2.5.0-1 [236 kB]
Get: 526 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggplot2 all 3.4.1+dfsg-1 [3333 kB]
Get: 527 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpparmadillo amd64 0.12.0.1.0-1 [841 kB]
Get: 528 http://deb.debian.org/debian bookworm/main amd64 r-bioc-deseq2 amd64 1.38.3+dfsg-1 [1288 kB]
Get: 529 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhtslib amd64 2.0.0+dfsg-1 [1287 kB]
Get: 530 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rsamtools amd64 2.14.0-1 [3755 kB]
Get: 531 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicalignments amd64 1.34.0-1 [2112 kB]
Get: 532 http://deb.debian.org/debian bookworm/main amd64 r-cran-rjson amd64 0.2.21-1 [139 kB]
Get: 533 http://deb.debian.org/debian bookworm/main amd64 r-cran-yaml amd64 2.3.7-1 [104 kB]
Get: 534 http://deb.debian.org/debian bookworm/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB]
Get: 535 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rtracklayer amd64 1.58.0-1 [5104 kB]
Get: 536 http://deb.debian.org/debian bookworm/main amd64 r-bioc-tximport all 1.26.1+dfsg-1 [87.9 kB]
Get: 537 http://deb.debian.org/debian bookworm/main amd64 r-cran-abind all 1.4-5-2 [64.6 kB]
Get: 538 http://deb.debian.org/debian bookworm/main amd64 r-cran-backports amd64 1.4.1-1 [101 kB]
Get: 539 http://deb.debian.org/debian bookworm/main amd64 r-cran-base64enc amd64 0.1-3-3 [27.9 kB]
Get: 540 http://deb.debian.org/debian bookworm/main amd64 r-cran-boot all 1.3-28.1-1 [620 kB]
Get: 541 http://deb.debian.org/debian bookworm/main amd64 r-cran-brio amd64 1.1.3-1+b1 [35.5 kB]
Get: 542 http://deb.debian.org/debian bookworm/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB]
Get: 543 http://deb.debian.org/debian bookworm/main amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [219 kB]
Get: 544 http://deb.debian.org/debian bookworm/main amd64 r-cran-dplyr amd64 1.0.10-1 [1227 kB]
Get: 545 http://deb.debian.org/debian bookworm/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB]
Get: 546 http://deb.debian.org/debian bookworm/main amd64 r-cran-purrr amd64 1.0.1-1 [507 kB]
Get: 547 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringi amd64 1.7.12-1 [858 kB]
Get: 548 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringr all 1.5.0-1 [295 kB]
Get: 549 http://deb.debian.org/debian bookworm/main amd64 r-cran-tidyr amd64 1.3.0-1 [1183 kB]
Get: 550 http://deb.debian.org/debian bookworm/main amd64 r-cran-broom all 1.0.3+dfsg-2 [1776 kB]
Get: 551 http://deb.debian.org/debian bookworm/main amd64 r-cran-digest amd64 0.6.31-1 [184 kB]
Get: 552 http://deb.debian.org/debian bookworm/main amd64 r-cran-htmltools amd64 0.5.4-1 [364 kB]
Get: 553 http://deb.debian.org/debian bookworm/main amd64 r-cran-fs amd64 1.6.1+dfsg-1 [226 kB]
Get: 554 http://deb.debian.org/debian bookworm/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB]
Get: 555 http://deb.debian.org/debian bookworm/main amd64 r-cran-sass amd64 0.4.5+dfsg-1 [942 kB]
Get: 556 http://deb.debian.org/debian bookworm/main amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.1 kB]
Get: 557 http://deb.debian.org/debian bookworm/main amd64 r-cran-bslib all 0.4.2+dfsg-1 [3773 kB]
Get: 558 http://deb.debian.org/debian bookworm/main amd64 r-cran-ps amd64 1.7.2-1 [308 kB]
Get: 559 http://deb.debian.org/debian bookworm/main amd64 r-cran-processx amd64 3.8.0-1 [339 kB]
Get: 560 http://deb.debian.org/debian bookworm/main amd64 r-cran-callr all 3.7.3-2 [426 kB]
Get: 561 http://deb.debian.org/debian bookworm/main amd64 r-cran-cardata all 3.0.5-1 [1797 kB]
Get: 562 http://deb.debian.org/debian bookworm/main amd64 r-cran-nnet amd64 7.3-18-1 [112 kB]
Get: 563 http://deb.debian.org/debian bookworm/main amd64 r-cran-minqa amd64 1.2.5-1 [113 kB]
Get: 564 http://deb.debian.org/debian bookworm/main amd64 r-cran-rprojroot all 2.0.3-1 [119 kB]
Get: 565 http://deb.debian.org/debian bookworm/main amd64 r-cran-desc all 1.4.2-1 [348 kB]
Get: 566 http://deb.debian.org/debian bookworm/main amd64 r-cran-evaluate all 0.20-1 [85.9 kB]
Get: 567 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgload all 1.3.2-1 [206 kB]
Get: 568 http://deb.debian.org/debian bookworm/main amd64 r-cran-praise all 1.0.0-4 [20.1 kB]
Get: 569 http://deb.debian.org/debian bookworm/main amd64 r-cran-diffobj amd64 0.3.5-1+b1 [1122 kB]
Get: 570 http://deb.debian.org/debian bookworm/main amd64 r-cran-rematch2 all 2.1.2-2 [46.3 kB]
Get: 571 http://deb.debian.org/debian bookworm/main amd64 r-cran-waldo all 0.4.0-1 [116 kB]
Get: 572 http://deb.debian.org/debian bookworm/main amd64 r-cran-testthat amd64 3.1.6-1 [1545 kB]
Get: 573 http://deb.debian.org/debian bookworm/main amd64 r-cran-nloptr amd64 2.0.3-1 [375 kB]
Get: 574 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcppeigen amd64 0.3.3.9.3-1 [1191 kB]
Get: 575 http://deb.debian.org/debian bookworm/main amd64 r-cran-statmod amd64 1.5.0-1 [295 kB]
Get: 576 http://deb.debian.org/debian bookworm/main amd64 r-cran-lme4 amd64 1.1-31-1 [4087 kB]
Get: 577 http://deb.debian.org/debian bookworm/main amd64 r-cran-numderiv all 2016.8-1.1-3 [115 kB]
Get: 578 http://deb.debian.org/debian bookworm/main amd64 r-cran-xfun amd64 0.37+dfsg-1 [394 kB]
Get: 579 http://deb.debian.org/debian bookworm/main amd64 r-cran-highr all 0.10+dfsg-1 [38.1 kB]
Get: 580 http://deb.debian.org/debian bookworm/main amd64 r-cran-knitr all 1.42+dfsg-1 [901 kB]
Get: 581 http://deb.debian.org/debian bookworm/main amd64 r-cran-pbkrtest all 0.5.2-2 [184 kB]
Get: 582 http://deb.debian.org/debian bookworm/main amd64 r-cran-sparsem amd64 1.81-1 [905 kB]
Get: 583 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrixmodels all 0.5-1-1 [375 kB]
Get: 584 http://deb.debian.org/debian bookworm/main amd64 r-cran-survival amd64 3.5-3-1 [5910 kB]
Get: 585 http://deb.debian.org/debian bookworm/main amd64 r-cran-class amd64 7.3-21-1 [86.7 kB]
Get: 586 http://deb.debian.org/debian bookworm/main amd64 r-cran-proxy amd64 0.4-27-1 [182 kB]
Get: 587 http://deb.debian.org/debian bookworm/main amd64 r-cran-e1071 amd64 1.7-13-1 [568 kB]
Get: 588 http://deb.debian.org/debian bookworm/main amd64 r-cran-iterators all 1.0.14-1 [337 kB]
Get: 589 http://deb.debian.org/debian bookworm/main amd64 r-cran-foreach all 1.5.2-1 [122 kB]
Get: 590 http://deb.debian.org/debian bookworm/main amd64 r-cran-data.table amd64 1.14.8+dfsg-1 [1683 kB]
Get: 591 http://deb.debian.org/debian bookworm/main amd64 r-cran-modelmetrics amd64 1.2.2.2-1+b1 [125 kB]
Get: 592 http://deb.debian.org/debian bookworm/main amd64 r-cran-plyr amd64 1.8.8-1 [832 kB]
Get: 593 http://deb.debian.org/debian bookworm/main amd64 r-cran-proc amd64 1.18.0-1+b1 [983 kB]
Get: 594 http://deb.debian.org/debian bookworm/main amd64 r-cran-tzdb amd64 0.3.0-1 [484 kB]
Get: 595 http://deb.debian.org/debian bookworm/main amd64 r-cran-clock amd64 0.6.1-2 [1768 kB]
Get: 596 http://deb.debian.org/debian bookworm/main amd64 r-cran-gower amd64 1.0.1-1 [207 kB]
Get: 597 http://deb.debian.org/debian bookworm/main amd64 r-cran-hardhat all 1.2.0+dfsg-1 [622 kB]
Get: 598 http://deb.debian.org/debian bookworm/main amd64 r-cran-rpart amd64 4.1.19-1 [917 kB]
Get: 599 http://deb.debian.org/debian bookworm/main amd64 r-cran-kernsmooth amd64 2.23-20-1 [91.5 kB]
Get: 600 http://deb.debian.org/debian bookworm/main amd64 r-cran-globals all 0.16.2-1 [118 kB]
Get: 601 http://deb.debian.org/debian bookworm/main amd64 r-cran-listenv all 0.9.0+dfsg-1 [112 kB]
Get: 602 http://deb.debian.org/debian bookworm/main amd64 r-cran-parallelly all 1.34.0-1 [337 kB]
Get: 603 http://deb.debian.org/debian bookworm/main amd64 r-cran-future all 1.31.0+dfsg-1 [612 kB]
Get: 604 http://deb.debian.org/debian bookworm/main amd64 r-cran-future.apply all 1.10.0+dfsg-1 [165 kB]
Get: 605 http://deb.debian.org/debian bookworm/main amd64 r-cran-progressr all 0.13.0-1 [336 kB]
Get: 606 http://deb.debian.org/debian bookworm/main amd64 r-cran-squarem all 2021.1-1 [179 kB]
Get: 607 http://deb.debian.org/debian bookworm/main amd64 r-cran-lava all 1.7.2.1+dfsg-1 [2203 kB]
Get: 608 http://deb.debian.org/debian bookworm/main amd64 r-cran-prodlim amd64 2019.11.13-1+b1 [395 kB]
Get: 609 http://deb.debian.org/debian bookworm/main amd64 r-cran-ipred amd64 0.9-13-1 [386 kB]
Get: 610 http://deb.debian.org/debian bookworm/main amd64 r-cran-timechange amd64 0.2.0-1 [178 kB]
Get: 611 http://deb.debian.org/debian bookworm/main amd64 r-cran-lubridate amd64 1.9.2+dfsg-1 [994 kB]
Get: 612 http://deb.debian.org/debian bookworm/main amd64 r-cran-timedate amd64 4022.108-1 [1185 kB]
Get: 613 http://deb.debian.org/debian bookworm/main amd64 r-cran-recipes all 1.0.4+dfsg-1 [1871 kB]
Get: 614 http://deb.debian.org/debian bookworm/main amd64 r-cran-reshape2 amd64 1.4.4-2 [114 kB]
Get: 615 http://deb.debian.org/debian bookworm/main amd64 r-cran-caret amd64 6.0-93+dfsg-1 [3447 kB]
Get: 616 http://deb.debian.org/debian bookworm/main amd64 r-cran-conquer amd64 1.3.2-1 [459 kB]
Get: 617 http://deb.debian.org/debian bookworm/main amd64 r-cran-quantreg amd64 5.94-1 [1535 kB]
Get: 618 http://deb.debian.org/debian bookworm/main amd64 r-cran-sp amd64 1:1.6-0+dfsg-1 [1532 kB]
Get: 619 http://deb.debian.org/debian bookworm/main amd64 r-cran-foreign amd64 0.8.84-1 [250 kB]
Get: 620 http://deb.debian.org/debian bookworm/main amd64 r-cran-maptools amd64 1:1.1-6+dfsg-1 [1558 kB]
Get: 621 http://deb.debian.org/debian bookworm/main amd64 r-cran-forcats all 1.0.0-1 [413 kB]
Get: 622 http://deb.debian.org/debian bookworm/main amd64 r-cran-hms all 1.1.2-1 [104 kB]
Get: 623 http://deb.debian.org/debian bookworm/main amd64 r-cran-clipr all 0.8.0-1 [53.0 kB]
Get: 624 http://deb.debian.org/debian bookworm/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB]
Get: 625 http://deb.debian.org/debian bookworm/main amd64 r-cran-progress all 1.2.2-2 [88.9 kB]
Get: 626 http://deb.debian.org/debian bookworm/main amd64 r-cran-vroom amd64 1.6.1-1 [842 kB]
Get: 627 http://deb.debian.org/debian bookworm/main amd64 r-cran-readr amd64 2.1.4-1 [776 kB]
Get: 628 http://deb.debian.org/debian bookworm/main amd64 r-cran-haven amd64 2.5.1-1 [343 kB]
Get: 629 http://deb.debian.org/debian bookworm/main amd64 r-cran-rematch all 1.0.1-3 [14.1 kB]
Get: 630 http://deb.debian.org/debian bookworm/main amd64 r-cran-cellranger all 1.1.0-3 [100 kB]
Get: 631 http://deb.debian.org/debian bookworm/main amd64 r-cran-readxl amd64 1.4.2-1 [723 kB]
Get: 632 http://deb.debian.org/debian bookworm/main amd64 r-cran-zip amd64 2.2.2-1+b1 [113 kB]
Get: 633 http://deb.debian.org/debian bookworm/main amd64 r-cran-openxlsx amd64 4.2.5.2-1 [1929 kB]
Get: 634 http://deb.debian.org/debian bookworm/main amd64 r-cran-rio all 0.5.29-1 [474 kB]
Get: 635 http://deb.debian.org/debian bookworm/main amd64 r-cran-car all 3.1-1-1 [1699 kB]
Get: 636 http://deb.debian.org/debian bookworm/main amd64 r-cran-tinytex all 0.44-1 [138 kB]
Get: 637 http://deb.debian.org/debian bookworm/main amd64 r-cran-later amd64 1.3.0+dfsg-1+b1 [117 kB]
Get: 638 http://deb.debian.org/debian bookworm/main amd64 r-cran-promises amd64 1.2.0.1+dfsg-1 [274 kB]
Get: 639 http://deb.debian.org/debian bookworm/main amd64 r-cran-httpuv amd64 1.6.9+dfsg-1 [478 kB]
Get: 640 http://deb.debian.org/debian bookworm/main amd64 r-cran-fontawesome all 0.5.0-1 [1304 kB]
Get: 641 http://deb.debian.org/debian bookworm/main amd64 r-cran-sourcetools amd64 0.1.7-1-1 [45.9 kB]
Get: 642 http://deb.debian.org/debian bookworm/main amd64 r-cran-commonmark amd64 1.8.1-1 [117 kB]
Get: 643 http://deb.debian.org/debian bookworm/main amd64 r-cran-shiny all 1.7.4+dfsg-2 [2732 kB]
Get: 644 http://deb.debian.org/debian bookworm/main amd64 r-cran-rmarkdown all 2.20+dfsg-1 [2265 kB]
Get: 645 http://deb.debian.org/debian bookworm/main amd64 r-cran-htmlwidgets all 1.6.1+dfsg-1 [120 kB]
Get: 646 http://deb.debian.org/debian bookworm/main amd64 r-cran-miniui all 0.1.1.1-3 [35.9 kB]
Get: 647 http://deb.debian.org/debian bookworm/main amd64 r-cran-shinyjs all 2.1.0-1 [1009 kB]
Get: 648 http://deb.debian.org/debian bookworm/main amd64 r-cran-colourpicker all 1.2.0+dfsg-1 [1165 kB]
Get: 649 http://deb.debian.org/debian bookworm/main amd64 r-cran-corrplot all 0.92-1 [131 kB]
Get: 650 http://deb.debian.org/debian bookworm/main amd64 r-cran-cowplot all 1.1.1+dfsg-1 [636 kB]
Get: 651 http://deb.debian.org/debian bookworm/main amd64 r-cran-lazyeval amd64 0.2.2-1+b1 [142 kB]
Get: 652 http://deb.debian.org/debian bookworm/main amd64 r-cran-crosstalk all 1.2.0+dfsg-1 [171 kB]
Get: 653 http://deb.debian.org/debian bookworm/main amd64 r-cran-dt all 0.27+dfsg-1 [236 kB]
Get: 654 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggrepel amd64 0.9.3-1 [247 kB]
Get: 655 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggsci all 2.9-3 [2905 kB]
Get: 656 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggsignif all 0.6.4-1 [589 kB]
Get: 657 http://deb.debian.org/debian bookworm/main amd64 r-cran-gridextra all 2.3-3 [1024 kB]
Get: 658 http://deb.debian.org/debian bookworm/main amd64 r-cran-polynom all 1.4-1+dfsg-1 [92.5 kB]
Get: 659 http://deb.debian.org/debian bookworm/main amd64 r-cran-rstatix all 0.7.2-1 [609 kB]
Get: 660 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggpubr all 0.6.0-1 [2080 kB]
Get: 661 http://deb.debian.org/debian bookworm/main amd64 r-cran-plotly all 4.10.1+dfsg-2 [3339 kB]
Get: 662 http://deb.debian.org/debian bookworm/main amd64 r-cran-gprofiler2 all 0.2.1+dfsg-1 [124 kB]
Get: 663 http://deb.debian.org/debian bookworm/main amd64 r-cran-pheatmap all 1.0.12-2 [77.9 kB]
Get: 664 http://deb.debian.org/debian bookworm/main amd64 salmon amd64 1.10.1+ds1-1+b1 [3297 kB]
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)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package autoconf-archive.
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(Reading database ... 19596 files and directories currently installed.)
Preparing to unpack .../autoconf-archive_20220903-3_all.deb ...
Unpacking autoconf-archive (20220903-3) ...
Selecting previously unselected package pigz.
Preparing to unpack .../archives/pigz_2.6-1_amd64.deb ...
Unpacking pigz (2.6-1) ...
Selecting previously unselected package libpython3.11-minimal:amd64.
Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.5.0-1) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking python3.11-minimal (3.11.2-6) ...
Setting up libpython3.11-minimal:amd64 (3.11.2-6) ...
Setting up libexpat1:amd64 (2.5.0-1) ...
Setting up python3.11-minimal (3.11.2-6) ...
Selecting previously unselected package python3-minimal.
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(Reading database ... 21103 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ...
Unpacking python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.0.0_all.deb ...
Unpacking media-types (10.0.0) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ...
Unpacking readline-common (8.2-1.3) ...
Selecting previously unselected package libreadline8:amd64.
Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ...
Unpacking libreadline8:amd64 (8.2-1.3) ...
Selecting previously unselected package libpython3.11-stdlib:amd64.
Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ...
Selecting previously unselected package python3.11.
Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ...
Unpacking python3.11 (3.11.2-6) ...
Selecting previously unselected package libpython3-stdlib:amd64.
Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ...
Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ...
Setting up python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package python3.
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Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ...
Unpacking python3 (3.11.2-1+b1) ...
Selecting previously unselected package sgml-base.
Preparing to unpack .../001-sgml-base_1.31_all.deb ...
Unpacking sgml-base (1.31) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../002-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package openssl.
Preparing to unpack .../003-openssl_3.0.8-1_amd64.deb ...
Unpacking openssl (3.0.8-1) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../004-ca-certificates_20230311_all.deb ...
Unpacking ca-certificates (20230311) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../005-libmagic-mgc_1%3a5.44-3_amd64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:amd64.
Preparing to unpack .../006-libmagic1_1%3a5.44-3_amd64.deb ...
Unpacking libmagic1:amd64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../007-file_1%3a5.44-3_amd64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../008-gettext-base_0.21-12_amd64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../009-libuchardet0_0.0.7-1_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../010-groff-base_1.22.4-10_amd64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../011-bsdextrautils_2.38.1-5+b1_amd64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../012-libpipeline1_1.5.7-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../013-man-db_2.11.2-2_amd64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package ucf.
Preparing to unpack .../014-ucf_3.0043+nmu1_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0043+nmu1) ...
Selecting previously unselected package hicolor-icon-theme.
Preparing to unpack .../015-hicolor-icon-theme_0.17-2_all.deb ...
Unpacking hicolor-icon-theme (0.17-2) ...
Selecting previously unselected package libgdk-pixbuf2.0-common.
Preparing to unpack .../016-libgdk-pixbuf2.0-common_2.42.10+dfsg-1_all.deb ...
Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-1) ...
Selecting previously unselected package libglib2.0-0:amd64.
Preparing to unpack .../017-libglib2.0-0_2.74.6-1_amd64.deb ...
Unpacking libglib2.0-0:amd64 (2.74.6-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../018-libicu72_72.1-3_amd64.deb ...
Unpacking libicu72:amd64 (72.1-3) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../019-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ...
Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ...
Selecting previously unselected package shared-mime-info.
Preparing to unpack .../020-shared-mime-info_2.2-1_amd64.deb ...
Unpacking shared-mime-info (2.2-1) ...
Selecting previously unselected package libjpeg62-turbo:amd64.
Preparing to unpack .../021-libjpeg62-turbo_1%3a2.1.5-2_amd64.deb ...
Unpacking libjpeg62-turbo:amd64 (1:2.1.5-2) ...
Selecting previously unselected package libpng16-16:amd64.
Preparing to unpack .../022-libpng16-16_1.6.39-2_amd64.deb ...
Unpacking libpng16-16:amd64 (1.6.39-2) ...
Selecting previously unselected package libdeflate0:amd64.
Preparing to unpack .../023-libdeflate0_1.14-1_amd64.deb ...
Unpacking libdeflate0:amd64 (1.14-1) ...
Selecting previously unselected package libjbig0:amd64.
Preparing to unpack .../024-libjbig0_2.1-6.1_amd64.deb ...
Unpacking libjbig0:amd64 (2.1-6.1) ...
Selecting previously unselected package liblerc4:amd64.
Preparing to unpack .../025-liblerc4_4.0.0+ds-2_amd64.deb ...
Unpacking liblerc4:amd64 (4.0.0+ds-2) ...
Selecting previously unselected package libwebp7:amd64.
Preparing to unpack .../026-libwebp7_1.2.4-0.1_amd64.deb ...
Unpacking libwebp7:amd64 (1.2.4-0.1) ...
Selecting previously unselected package libtiff6:amd64.
Preparing to unpack .../027-libtiff6_4.5.0-5_amd64.deb ...
Unpacking libtiff6:amd64 (4.5.0-5) ...
Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64.
Preparing to unpack .../028-libgdk-pixbuf-2.0-0_2.42.10+dfsg-1+b1_amd64.deb ...
Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ...
Selecting previously unselected package gtk-update-icon-cache.
Preparing to unpack .../029-gtk-update-icon-cache_3.24.37-2_amd64.deb ...
Unpacking gtk-update-icon-cache (3.24.37-2) ...
Selecting previously unselected package adwaita-icon-theme.
Preparing to unpack .../030-adwaita-icon-theme_43-1_all.deb ...
Unpacking adwaita-icon-theme (43-1) ...
Selecting previously unselected package at-spi2-common.
Preparing to unpack .../031-at-spi2-common_2.46.0-5_all.deb ...
Unpacking at-spi2-common (2.46.0-5) ...
Selecting previously unselected package m4.
Preparing to unpack .../032-m4_1.4.19-3_amd64.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../033-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../034-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../035-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
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Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libtcl8.6:amd64.
Preparing to unpack .../037-libtcl8.6_8.6.13+dfsg-2_amd64.deb ...
Unpacking libtcl8.6:amd64 (8.6.13+dfsg-2) ...
Selecting previously unselected package libbrotli1:amd64.
Preparing to unpack .../038-libbrotli1_1.0.9-2+b6_amd64.deb ...
Unpacking libbrotli1:amd64 (1.0.9-2+b6) ...
Selecting previously unselected package libfreetype6:amd64.
Preparing to unpack .../039-libfreetype6_2.12.1+dfsg-4_amd64.deb ...
Unpacking libfreetype6:amd64 (2.12.1+dfsg-4) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../040-fonts-dejavu-core_2.37-6_all.deb ...
Unpacking fonts-dejavu-core (2.37-6) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../041-fontconfig-config_2.14.1-4_amd64.deb ...
Unpacking fontconfig-config (2.14.1-4) ...
Selecting previously unselected package libfontconfig1:amd64.
Preparing to unpack .../042-libfontconfig1_2.14.1-4_amd64.deb ...
Unpacking libfontconfig1:amd64 (2.14.1-4) ...
Selecting previously unselected package libxau6:amd64.
Preparing to unpack .../043-libxau6_1%3a1.0.9-1_amd64.deb ...
Unpacking libxau6:amd64 (1:1.0.9-1) ...
Selecting previously unselected package libbsd0:amd64.
Preparing to unpack .../044-libbsd0_0.11.7-2_amd64.deb ...
Unpacking libbsd0:amd64 (0.11.7-2) ...
Selecting previously unselected package libxdmcp6:amd64.
Preparing to unpack .../045-libxdmcp6_1%3a1.1.2-3_amd64.deb ...
Unpacking libxdmcp6:amd64 (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:amd64.
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Setting up r-cran-bslib (0.4.2+dfsg-1) ...
Setting up r-cran-readr (2.1.4-1) ...
Setting up r-cran-waldo (0.4.0-1) ...
Setting up r-cran-ggrepel (0.9.3-1) ...
Setting up r-cran-tidyr (1.3.0-1) ...
Setting up python3-boto3 (1.26.27+dfsg-1) ...
Setting up r-bioc-rsamtools (2.14.0-1) ...
Setting up r-cran-recipes (1.0.4+dfsg-1) ...
Setting up python3-msrestazure (0.6.4-2) ...
Setting up r-cran-cowplot (1.1.1+dfsg-1) ...
Setting up r-bioc-summarizedexperiment (1.28.0+dfsg-1) ...
Setting up r-cran-readxl (1.4.2-1) ...
Setting up trim-galore (0.6.10-1) ...
Setting up r-bioc-keggrest (1.38.0+dfsg-1) ...
Setting up r-cran-haven (2.5.1-1) ...
Setting up r-bioc-annotationdbi (1.60.0-1) ...
Setting up r-cran-caret (6.0-93+dfsg-1) ...
Setting up r-cran-shiny (1.7.4+dfsg-2) ...
Setting up r-cran-shinyjs (2.1.0-1) ...
Setting up r-cran-testthat (3.1.6-1) ...
Setting up r-cran-miniui (0.1.1.1-3) ...
Setting up r-cran-broom (1.0.3+dfsg-2) ...
Setting up r-bioc-annotate (1.76.0+dfsg-1) ...
Setting up r-cran-rmarkdown (2.20+dfsg-1) ...
Setting up r-cran-conquer (1.3.2-1) ...
Setting up r-bioc-genomicalignments (1.34.0-1) ...
Setting up r-bioc-geneplotter (1.76.0-1) ...
Setting up r-cran-crosstalk (1.2.0+dfsg-1) ...
Setting up r-cran-rio (0.5.29-1) ...
Setting up r-bioc-rtracklayer (1.58.0-1) ...
Setting up r-cran-nloptr (2.0.3-1) ...
Setting up r-cran-quantreg (5.94-1) ...
Setting up r-bioc-deseq2 (1.38.3+dfsg-1) ...
Setting up r-cran-lme4 (1.1-31-1) ...
Setting up r-cran-htmlwidgets (1.6.1+dfsg-1) ...
Setting up r-cran-colourpicker (1.2.0+dfsg-1) ...
Setting up r-cran-pbkrtest (0.5.2-2) ...
Setting up r-cran-car (3.1-1-1) ...
Setting up r-cran-dt (0.27+dfsg-1) ...
Setting up r-cran-rstatix (0.7.2-1) ...
Setting up r-cran-plotly (4.10.1+dfsg-2) ...
Setting up r-cran-ggpubr (0.6.0-1) ...
Setting up r-cran-gprofiler2 (0.2.1+dfsg-1) ...
Setting up default-jre-headless (2:1.17-74) ...
Setting up python3-fonttools (4.38.0-1+b1) ...
Setting up python3-pil.imagetk:amd64 (9.4.0-1.1+b1) ...
Setting up python3-ufolib2 (0.14.0+dfsg1-1) ...
Setting up openjdk-17-jre-headless:amd64 (17.0.6+10-1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up python3-azure (20230112+git-1) ...
Setting up ca-certificates-java (20230103) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem
Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:ISRG_Root_X2.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_RootCA3.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Telia_Root_CA_v2.pem
Adding debian:TrustCor_ECA-1.pem
Adding debian:TrustCor_RootCert_CA-1.pem
Adding debian:TrustCor_RootCert_CA-2.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:TunTrust_Root_CA.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up openjdk-17-jre:amd64 (17.0.6+10-1) ...
Setting up default-jre (2:1.17-74) ...
Setting up python3-azure-storage (20230112+git-1) ...
Setting up python3-pil:amd64 (9.4.0-1.1+b1) ...
Setting up python3-matplotlib (3.6.3-1+b1) ...
Setting up python3-smart-open (5.2.1-5) ...
Setting up fastqc (0.11.9+dfsg-6) ...
Setting up multiqc (1.14+dfsg-1) ...
Processing triggers for libc-bin (2.36-8) ...
Processing triggers for sgml-base (1.31) ...
Setting up docutils-common (0.19+dfsg-6) ...
Processing triggers for sgml-base (1.31) ...
Setting up python3-docutils (0.19+dfsg-6) ...
Setting up snakemake (7.21.0-1) ...
Setting up python3-sphinx (5.3.0-4) ...
Setting up python3-numpydoc (1.5.0-1) ...
Setting up python3-deeptools (3.5.1-3) ...
Processing triggers for ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for ca-certificates-java (20230103) ...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
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
dpkg-buildpackage: info: source package pigx-rnaseq
dpkg-buildpackage: info: source version 0.1.0-1.1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Bastian Germann <bage@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/pigx-rnaseq-0.1.0'
dh_auto_clean
rm -rf pigx-common
rm -f config.log test.sh
rm -rf tests/output
rm -f Makefile.in aclocal.m4 build-aux/install-sh build-aux/missing build-aux/test-driver
rm -f scripts/jquery.min.js
rm -f conftest.tar confdefs.h
make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/pigx-rnaseq.substvars debian/files
rm -fr -- debian/pigx-rnaseq/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
debian/rules execute_before_dh_autoreconf
make[1]: Entering directory '/build/pigx-rnaseq-0.1.0'
mkdir -p /build/pigx-rnaseq-0.1.0/pigx-common
cp -a debian/common /build/pigx-rnaseq-0.1.0/pigx-common
make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0'
dh_autoreconf
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p
" > debian/autoreconf.before
grep -q ^XDT_ configure.ac
autoreconf -f -i
aclocal: warning: couldn't open directory 'm4': No such file or directory
configure.ac:6: installing 'build-aux/install-sh'
configure.ac:6: installing 'build-aux/missing'
parallel-tests: installing 'build-aux/test-driver'
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p
" > debian/autoreconf.after
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/pigx-rnaseq-0.1.0'
dh_auto_configure -- GUNZIP=/bin/gunzip SED=/bin/sed
./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 gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking how to create a pax tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for a Python interpreter with version >= 3.5... python3
checking for python3... /usr/bin/python3
checking for python3 version... 3.11
checking for python3 platform... linux
checking for GNU default python3 prefix... ${prefix}
checking for GNU default python3 exec_prefix... ${exec_prefix}
checking for python3 script directory (pythondir)... ${PYTHON_PREFIX}/lib/python3.11/site-packages
checking for python3 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.11/site-packages
checking python3 module: yaml... yes
configure: Using /bin/gunzip as gunzip executable.
configure: Using /bin/sed as sed executable.
configure: Using /bin/bash as bash executable.
checking for snakemake... /usr/bin/snakemake
checking for pandoc... /usr/bin/pandoc
configure: Using /usr/bin/STAR as STAR executable.
checking for hisat2... /usr/bin/hisat2
checking for hisat2-build... /usr/bin/hisat2-build
checking for multiqc... /usr/bin/multiqc
checking for fastp... /usr/bin/fastp
configure: Using /usr/bin/salmon as salmon executable.
checking for R... /usr/bin/R
checking for Rscript... /usr/bin/Rscript
checking for bamCoverage... /usr/bin/bamCoverage
checking for megadepth... /usr/bin/megadepth
checking R package rmarkdown ... yes
checking R package knitr ... yes
checking R package ggplot2 ... yes
checking R package ggrepel ... yes
checking R package DESeq2 ... yes
checking R package DT ... yes
checking R package pheatmap ... yes
checking R package corrplot ... yes
checking R package reshape2 ... yes
checking R package plotly ... yes
checking R package scales ... yes
checking R package crosstalk ... yes
checking R package gprofiler2 ... yes
checking R package ggpubr ... yes
checking R package rtracklayer ... yes
checking R package SummarizedExperiment ... yes
checking R package tximport ... yes
checking R package rjson ... yes
checking for samtools... /usr/bin/samtools
configure: Environment variables will be captured.
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating META
config.status: creating etc/settings.yaml
config.status: creating scripts/deseqReport.Rmd
config.status: creating Makefile
config.status: creating qsub-template.sh
config.status: creating test.sh
config.status: creating tests/test_hisat2/test.sh
config.status: creating tests/test_salmon/test_salmon_index.sh
config.status: creating tests/test_salmon/test_salmon_quant.sh
config.status: creating tests/test_salmon_counts/test.sh
config.status: creating tests/test_hisat2_counts/test.sh
config.status: creating tests/test_multiqc/test.sh
config.status: creating tests/test_deseq_reports/test.sh
config.status: creating tests/test_genome_coverage/test.sh
config.status: creating pigx-rnaseq
make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0'
dh_auto_build
make -j15
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'
rm -f debian/pigx-rnaseq.debhelper.log
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/pigx-rnaseq-0.1.0'
ln -sf /usr/share/javascript/jquery/jquery.min.js scripts/
#/usr/bin/make -j2 check VERBOSE=1
./test.sh
Commencing snakemake run submission locally
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads
--------------------------------- ------- ------------- -------------
all 1 1 1
check_annotation_files 1 1 1
collate_read_counts 1 1 1
count_reads 6 1 1
counts_from_SALMON 1 1 1
coverage_megadepth 6 1 1
hisat2_index 1 1 1
hisat2_map 6 1 1
index_bam 6 1 1
multiqc 1 1 1
norm_counts_deseq 1 1 1
report1 1 1 1
report2 1 1 1
report3 1 1 1
salmon_index 1 1 1
salmon_quant 6 1 1
translate_sample_sheet_for_report 1 1 1
trim_qc_reads_pe 4 1 1
trim_qc_reads_se 2 1 1
total 48 1 1
Select jobs to execute...
[Fri Apr 14 10:19:52 2023]
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
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]
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
log: /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep1.log
jobid: 5
reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz
wildcards: sample=HBR_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/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]
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
jobid: 24
reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv
resources: tmpdir=/tmp
/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]
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
log: /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep3.log
jobid: 15
reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz
wildcards: sample=UHR_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/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]
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
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]
rule check_annotation_files:
input: /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta, /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta, /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf
output: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv
log: /build/pigx-rnaseq-0.1.0/tests/output/logs/check_annotation_files.log
jobid: 1
reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv
resources: tmpdir=/tmp
/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//validate_input_annotation.R /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta /build/pigx-rnaseq-0.1.0/tests/output >> /build/pigx-rnaseq-0.1.0/tests/output/logs/check_annotation_files.log 2>&1
[Fri Apr 14 10:19:53 2023]
Finished job 24.
1 of 48 steps (2%) done
Select jobs to execute...
[Fri Apr 14 10:19:53 2023]
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
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]
Finished job 5.
2 of 48 steps (4%) done
Select jobs to execute...
[Fri Apr 14 10:19:54 2023]
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
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]
Finished job 7.
3 of 48 steps (6%) done
[Fri Apr 14 10:19:55 2023]
Finished job 15.
4 of 48 steps (8%) done
[Fri Apr 14 10:19:55 2023]
Finished job 9.
5 of 48 steps (10%) done
[Fri Apr 14 10:19:55 2023]
Finished job 13.
6 of 48 steps (12%) done
[Fri Apr 14 10:19:56 2023]
Finished job 11.
7 of 48 steps (15%) done
[Fri Apr 14 10:20:16 2023]
Finished job 1.
8 of 48 steps (17%) done
Select jobs to execute...
[Fri Apr 14 10:20:16 2023]
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
log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_index.log
jobid: 4
reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv
resources: tmpdir=/tmp, mem_mb=5000, mem_mib=4769
/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]
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
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]
Finished job 17.
9 of 48 steps (19%) done
Select jobs to execute...
[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_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
wildcards: sample=UHR_Rep3
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_Rep3_Aligned.out.sam -U /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep3.log 2>&1
/usr/bin/samtools view -bh /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.out.sam | /usr/bin/samtools sort -o /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/logs/hisat2/samtools.hisat2.UHR_Rep3.log 2>&1
rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_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/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
wildcards: sample=HBR_Rep3
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/HBR_Rep3_Aligned.out.sam -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 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep3.log 2>&1
/usr/bin/samtools view -bh /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.out.sam | /usr/bin/samtools sort -o /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/logs/hisat2/samtools.hisat2.HBR_Rep3.log 2>&1
rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_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_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
wildcards: sample=UHR_Rep1
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_Rep1_Aligned.out.sam -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 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep1.log 2>&1
/usr/bin/samtools view -bh /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.out.sam | /usr/bin/samtools sort -o /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/logs/hisat2/samtools.hisat2.UHR_Rep1.log 2>&1
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]
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
wildcards: sample=HBR_Rep1
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/HBR_Rep1_Aligned.out.sam -U /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep1.log 2>&1
/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
/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]
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
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]
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
wildcards: sample=HBR_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/HBR_Rep2_Aligned.out.sam -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 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep2.log 2>&1
/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.
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
/usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log 2>&1
[Fri Apr 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
/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
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_Rep3_Aligned.sortedByCoord.out.bam
output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai
log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep3.log
jobid: 31
reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam
wildcards: sample=HBR_Rep3
resources: tmpdir=/tmp, mem_mb=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
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
/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 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
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 Apr 14 10:20:23 2023]
Finished job 31.
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/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
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]
Finished job 18.
23 of 48 steps (48%) 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]
rule coverage_megadepth:
input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai
output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw
log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log
jobid: 41
reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai
wildcards: sample=HBR_Rep3
resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2
/usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep3.log 2>&1
[Fri Apr 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
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
Select jobs to execute...
[Fri Apr 14 10:20:23 2023]
Finished job 41.
25 of 48 steps (52%) done
[Fri Apr 14 10:20:24 2023]
rule count_reads:
input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai
output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv
log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log
jobid: 34
reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai
wildcards: sample=UHR_Rep2
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep2 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log 2>&1
[Fri Apr 14 10:20:26 2023]
Finished job 4.
26 of 48 steps (54%) done
Select jobs to execute...
[Fri Apr 14 10:20:26 2023]
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
log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep2.log
jobid: 29
reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /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=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]
Finished job 29.
27 of 48 steps (56%) done
Select jobs to execute...
[Fri Apr 14 10:20:26 2023]
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
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]
Finished job 40.
28 of 48 steps (58%) done
Select jobs to execute...
[Fri Apr 14 10:20:27 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_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
wildcards: sample=HBR_Rep3
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
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
Select jobs to execute...
[Fri Apr 14 10:20:31 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_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
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
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
Select jobs to execute...
[Fri Apr 14 10:20:36 2023]
rule salmon_quant:
input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz
output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf
log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log
jobid: 14
reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin
wildcards: sample=UHR_Rep3
resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723
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/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
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
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
/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
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 Apr 14 10:20:56 2023]
Finished job 26.
34 of 48 steps (71%) 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
wildcards: sample=UHR_Rep1
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
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
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
Select jobs to execute...
[Fri Apr 14 10:21:03 2023]
rule counts_from_SALMON:
input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv
output: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv
log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log
jobid: 23
reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.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
resources: tmpdir=/tmp, mem_mb=200, mem_mib=191
/usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//counts_matrix_from_SALMON.R /build/pigx-rnaseq-0.1.0/tests/output/salmon_output /build/pigx-rnaseq-0.1.0/tests/output/feature_counts /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log 2>&1
[Fri Apr 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
/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.
40 of 48 steps (83%) done
Select jobs to execute...
[Fri Apr 14 10:21:20 2023]
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
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]
Finished job 25.
42 of 48 steps (88%) done
Select jobs to execute...
[Fri Apr 14 10:21:21 2023]
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
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]
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
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]
Finished job 38.
44 of 48 steps (92%) done
[Fri Apr 14 10:23:04 2023]
Finished job 47.
45 of 48 steps (94%) done
[Fri Apr 14 10:23:04 2023]
Finished job 46.
46 of 48 steps (96%) done
[Fri Apr 14 10:23:08 2023]
Finished job 45.
47 of 48 steps (98%) done
Select jobs to execute...
[Fri Apr 14 10:23:08 2023]
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
resources: tmpdir=/tmp
[Fri Apr 14 10:23:08 2023]
Finished job 0.
48 of 48 steps (100%) done
Complete log: .snakemake/log/2023-04-14T101948.877977.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
- /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
make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0'
create-stamp debian/debhelper-build-stamp
dh_prep
rm -f -- debian/pigx-rnaseq.substvars
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[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/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 -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'
make[2]: Leaving directory '/build/pigx-rnaseq-0.1.0'
make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0'
dh_installdocs
install -m0755 -d debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq
install -m0755 -d debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq
cp --reflink=auto -a ./README.md debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq
cp --reflink=auto -a ./CONTRIBUTING debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq
chmod -R u\+rw,go=rX debian/pigx-rnaseq/usr/share/doc
install -p -m0644 debian/copyright debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq/copyright
dh_installchangelogs
install -m0755 -d debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq
install -p -m0644 debian/.debhelper/generated/pigx-rnaseq/dh_installchangelogs.dch.trimmed debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq/changelog.Debian
dh_installman
install -m0755 -d debian/pigx-rnaseq/usr/share/man/man1/
install -p -m0644 ./debian/pigx-rnaseq.1 debian/pigx-rnaseq/usr/share/man/man1/pigx-rnaseq.1
man-recode --to-code UTF-8 --suffix .dh-new debian/pigx-rnaseq/usr/share/man/man1/pigx-rnaseq.1
mv debian/pigx-rnaseq/usr/share/man/man1/pigx-rnaseq.1.dh-new debian/pigx-rnaseq/usr/share/man/man1/pigx-rnaseq.1
chmod 0644 -- debian/pigx-rnaseq/usr/share/man/man1/pigx-rnaseq.1
dh_perl
dh_link
dh_strip_nondeterminism
Using 1670955795 as canonical time
Normalizing debian/pigx-rnaseq/usr/share/pigx_rnaseq/Logo_PiGx.png using File::StripNondeterminism::handlers::png
dh_compress
cd debian/pigx-rnaseq
chmod a-x usr/share/doc/pigx-rnaseq/changelog.Debian usr/share/man/man1/pigx-rnaseq.1
gzip -9nf usr/share/doc/pigx-rnaseq/changelog.Debian usr/share/man/man1/pigx-rnaseq.1
cd '/build/pigx-rnaseq-0.1.0'
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/pigx-rnaseq-0.1.0'
dh_fixperms
find debian/pigx-rnaseq ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/pigx-rnaseq/usr/share/doc -type f -a -true -a ! -regex 'debian/pigx-rnaseq/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/pigx-rnaseq/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/pigx-rnaseq/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/pigx-rnaseq -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/pigx-rnaseq/usr/bin debian/pigx-rnaseq/usr/libexec -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
find debian/pigx-rnaseq/usr/libexec/pigx_rnaseq -name "*.R" | xargs -r chmod -x
find debian/pigx-rnaseq/usr/libexec/pigx_rnaseq -name "*.Rmd" | xargs -r chmod -x
find debian/pigx-rnaseq/usr/libexec/pigx_rnaseq -name "*.py" | xargs -r chmod -x
make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0'
dh_missing
dh_installdeb
install -m0755 -d debian/pigx-rnaseq/DEBIAN
dh_gencontrol
install -m0755 -d debian/pigx-rnaseq/DEBIAN
echo misc:Depends= >> debian/pigx-rnaseq.substvars
echo misc:Pre-Depends= >> debian/pigx-rnaseq.substvars
dpkg-gencontrol -ppigx-rnaseq -ldebian/changelog -Tdebian/pigx-rnaseq.substvars -Pdebian/pigx-rnaseq
chmod 0644 -- debian/pigx-rnaseq/DEBIAN/control
dh_md5sums
install -m0755 -d debian/pigx-rnaseq/DEBIAN
cd debian/pigx-rnaseq >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/pigx-rnaseq/DEBIAN/md5sums
dh_builddeb
dpkg-deb --root-owner-group --build debian/pigx-rnaseq ..
dpkg-deb: building package 'pigx-rnaseq' in '../pigx-rnaseq_0.1.0-1.1_all.deb'.
dpkg-genbuildinfo --build=binary -O../pigx-rnaseq_0.1.0-1.1_amd64.buildinfo
dpkg-genchanges --build=binary -O../pigx-rnaseq_0.1.0-1.1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
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
Fri Apr 14 22:23:41 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net.
Fri Apr 14 22:23:41 UTC 2023 I: Preparing to do remote build '2' on ionos15-amd64.debian.net.
Fri Apr 14 22:32:23 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
Fri Apr 14 22:32:24 UTC 2023 I: pigx-rnaseq_0.1.0-1.1_amd64.changes:
Format: 1.8
Date: Tue, 13 Dec 2022 18:23:15 +0000
Source: pigx-rnaseq
Binary: pigx-rnaseq
Architecture: all
Version: 0.1.0-1.1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Bastian Germann <bage@debian.org>
Description:
pigx-rnaseq - pipeline for checkpointed and distributed RNA-seq analyses
Changes:
pigx-rnaseq (0.1.0-1.1) unstable; urgency=medium
.
* Non-maintainer upload.
* Drop citeproc dependency (no longer required).
Checksums-Sha1:
f37f945f2af0651c939d52aabb88c938ef497e7a 61244 pigx-rnaseq_0.1.0-1.1_all.deb
dfab733cb54d05fed4bc2eae40c714990d3b5c0f 24995 pigx-rnaseq_0.1.0-1.1_amd64.buildinfo
Checksums-Sha256:
32b5f61115e9fbe559bf2f2dc316127579029f6a4309457906c100956c9ee553 61244 pigx-rnaseq_0.1.0-1.1_all.deb
b26428bafd86f7f362cb2b9166d4f9f025480223b3fb70ddbee7f2553ce6ff5e 24995 pigx-rnaseq_0.1.0-1.1_amd64.buildinfo
Files:
c498fc408d04299178397f05965119df 61244 science optional pigx-rnaseq_0.1.0-1.1_all.deb
721f42df537cfef7063287a48bcbe4f5 24995 science optional pigx-rnaseq_0.1.0-1.1_amd64.buildinfo
Fri Apr 14 22:32:25 UTC 2023 I: diffoscope 240 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dSllwiae/pigx-rnaseq_0.1.0-1.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dSllwiae/pigx-rnaseq_0.1.0-1.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dSllwiae/pigx-rnaseq_0.1.0-1.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dSllwiae/b1/pigx-rnaseq_0.1.0-1.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.dSllwiae/b2/pigx-rnaseq_0.1.0-1.1_amd64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.498s)
0.498s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.022s)
0.021s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.001s)
0.001s 1 call specialize
Fri Apr 14 22:34:14 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists.
Fri Apr 14 22:34:14 UTC 2023 I: pigx-rnaseq from bookworm built successfully and reproducibly on amd64.
Fri Apr 14 22:34:21 UTC 2023 I: Submitting .buildinfo files to external archives:
Fri Apr 14 22:34:21 UTC 2023 I: Submitting 28K b1/pigx-rnaseq_0.1.0-1.1_amd64.buildinfo.asc
Fri Apr 14 22:34:28 UTC 2023 I: Submitting 28K b2/pigx-rnaseq_0.1.0-1.1_amd64.buildinfo.asc
Fri Apr 14 22:34:36 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Fri Apr 14 22:34:36 UTC 2023 I: Done submitting .buildinfo files.
Fri Apr 14 22:34:36 UTC 2023 I: Removing signed pigx-rnaseq_0.1.0-1.1_amd64.buildinfo.asc files:
removed './b1/pigx-rnaseq_0.1.0-1.1_amd64.buildinfo.asc'
removed './b2/pigx-rnaseq_0.1.0-1.1_amd64.buildinfo.asc'