I: pbuilder: network access will be disabled during build I: Current time: Fri May 17 18:46:44 +14 2024 I: pbuilder-time-stamp: 1715921204 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration 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 Wed Dec 14 08:32:19 2022 +14 gpgv: using RSA key 406220C8B8552802378CCE411F5C7A8B45564314 gpgv: issuer "bage@debian.org" gpgv: Can't check signature: No public key 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/2740028/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2740028/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2740028/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME='pbuilder2' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ead8c3767a4246579c64c1040d309ab3' LANG='C' LANGUAGE='et_EE:et' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2740028' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dSllwiae/pbuilderrc_mH5i --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dSllwiae/b2 --logfile b2/build.log --extrapackages usrmerge pigx-rnaseq_0.1.0-1.1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux i-capture-the-hostname 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 13 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 2023 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 2023 more -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed lrwxrwxrwx 1 root root 4 Jan 6 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 2023 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/2740028/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team 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: adwaita-icon-theme{a} at-spi2-common{a} autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} coinor-cbc{a} coinor-libcbc3{a} coinor-libcgl1{a} coinor-libclp1{a} coinor-libcoinutils3v5{a} coinor-libosi1v5{a} cutadapt{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} fastp{a} fastqc{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-font-awesome{a} fonts-glyphicons-halflings{a} fonts-lyx{a} fonts-mathjax{a} gettext{a} gettext-base{a} gir1.2-glib-2.0{a} git{a} git-man{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} hisat2{a} intltool-debian{a} java-common{a} javascript-common{a} libaec0{a} libapache-pom-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasound2{a} libasound2-data{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbigwig0{a} libblas3{a} 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} libhts3{a} libhtscodecs2{a} libhtsjdk-java{a} libhwloc15{a} libice6{a} libicu72{a} libimagequant0{a} libisal2{a} libjbig0{a} libjbzip2-java{a} libjemalloc2{a} libjpeg62-turbo{a} libjs-bootstrap{a} libjs-bootstrap4{a} libjs-d3{a} libjs-es5-shim{a} libjs-highlight.js{a} libjs-jquery{a} libjs-jquery-datatables{a} libjs-jquery-datatables-extensions{a} libjs-jquery-metadata{a} libjs-jquery-selectize.js{a} libjs-jquery-tablesorter{a} libjs-jquery-ui{a} libjs-json{a} libjs-mathjax{a} libjs-microplugin.js{a} libjs-modernizr{a} libjs-popper.js{a} libjs-prettify{a} libjs-sifter.js{a} libjs-sphinxdoc{a} libjs-twitter-bootstrap-datepicker{a} libjs-underscore{a} libjson-perl{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm15{a} liblua5.3-0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmjson-java{a} libncbi-ngs3{a} libncbi-vdb3{a} libncurses6{a} libnghttp2-14{a} libngs-java{a} libngs-jni{a} libnlopt0{a} libnspr4{a} libnss3{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librhino-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsis-base-java{a} libsis-base-jni{a} libsis-jhdf5-java{a} libsis-jhdf5-jni{a} libsm6{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libsodium23{a} libssh2-1{a} libstaden-read14{a} libsub-override-perl{a} libsz2{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libuv1{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxml2{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libxt6{a} libxtst6{a} libxxf86vm1{a} libyaml-0-2{a} libz3-4{a} littler{a} m4{a} man-db{a} media-types{a} megadepth{a} multiqc{a} ncbi-vdb-data{a} node-bootstrap-sass{a} node-html5shiv{a} node-normalize.css{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} pandoc{a} pandoc-data{a} pigz{a} po-debconf{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-adal{a} python3-aiohttp{a} python3-aiosignal{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-async-timeout{a} python3-attr{a} python3-avro{a} python3-azure{a} python3-azure-storage{a} python3-babel{a} python3-bcrypt{a} python3-beniget{a} python3-blinker{a} python3-boto3{a} python3-botocore{a} python3-brotli{a} python3-certifi{a} python3-cffi-backend{a} python3-chardet{a} python3-charset-normalizer{a} python3-click{a} python3-colorama{a} python3-coloredlogs{a} python3-colormath{a} python3-configargparse{a} python3-connection-pool{a} python3-contourpy{a} python3-cryptography{a} python3-cutadapt{a} python3-cycler{a} python3-dateutil{a} python3-datrie{a} python3-decorator{a} python3-deeptools{a} python3-deeptoolsintervals{a} python3-dev{a} python3-distutils{a} python3-dnaio{a} python3-docutils{a} python3-fastjsonschema{a} python3-fonttools{a} python3-frozenlist{a} python3-fs{a} python3-future{a} python3-gast{a} python3-gi{a} python3-git{a} python3-gitdb{a} python3-htseq{a} python3-humanfriendly{a} python3-idna{a} python3-imagesize{a} python3-isodate{a} python3-jinja2{a} python3-jmespath{a} python3-jsonschema{a} python3-jupyter-core{a} python3-jwt{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-lzstring{a} python3-markdown{a} python3-markdown-it{a} python3-markupsafe{a} python3-marshmallow{a} python3-matplotlib{a} python3-mdurl{a} python3-minimal{a} python3-mpmath{a} python3-msal{a} python3-msal-extensions{a} python3-msrest{a} python3-msrestazure{a} python3-multidict{a} python3-nacl{a} python3-nbformat{a} python3-networkx{a} python3-numpy{a} python3-numpydoc{a} python3-oauthlib{a} python3-packaging{a} python3-paramiko{a} python3-pbr{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-plotly{a} python3-ply{a} python3-portalocker{a} python3-psutil{a} python3-pulp{a} python3-py{a} python3-py2bit{a} python3-pybigwig{a} python3-pygments{a} python3-pyparsing{a} python3-pyrsistent{a} python3-pysam{a} python3-pythran{a} python3-ratelimiter{a} python3-requests{a} python3-requests-oauthlib{a} python3-retry{a} python3-rich{a} python3-rich-click{a} python3-roman{a} python3-ruamel.yaml{a} python3-ruamel.yaml.clib{a} python3-s3transfer{a} python3-scipy{a} python3-setuptools{a} python3-simplejson{a} python3-six{a} python3-smart-open{a} python3-smmap{a} python3-snowballstemmer{a} python3-spectra{a} python3-sphinx{a} python3-stopit{a} python3-strictyaml{a} python3-sympy{a} python3-tabulate{a} python3-tenacity{a} python3-throttler{a} python3-tk{a} python3-toposort{a} python3-tqdm{a} python3-traitlets{a} python3-typing-extensions{a} python3-tz{a} python3-uamqp{a} python3-ufolib2{a} python3-urllib3{a} python3-wrapt{a} python3-xopen{a} python3-yaml{a} python3-yarl{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} r-base-core{a} r-bioc-annotate{a} r-bioc-annotationdbi{a} r-bioc-biobase{a} r-bioc-biocgenerics{a} r-bioc-biocio{a} r-bioc-biocparallel{a} r-bioc-biostrings{a} r-bioc-delayedarray{a} r-bioc-deseq2{a} r-bioc-geneplotter{a} r-bioc-genomeinfodb{a} r-bioc-genomeinfodbdata{a} r-bioc-genomicalignments{a} r-bioc-genomicranges{a} r-bioc-iranges{a} r-bioc-keggrest{a} r-bioc-matrixgenerics{a} r-bioc-rhtslib{a} r-bioc-rsamtools{a} r-bioc-rtracklayer{a} r-bioc-s4vectors{a} r-bioc-summarizedexperiment{a} r-bioc-tximport{a} r-bioc-xvector{a} r-bioc-zlibbioc{a} r-cran-abind{a} r-cran-askpass{a} r-cran-backports{a} r-cran-base64enc{a} r-cran-bh{a} r-cran-bit{a} r-cran-bit64{a} r-cran-bitops{a} r-cran-blob{a} r-cran-boot{a} r-cran-brio{a} r-cran-broom{a} r-cran-bslib{a} r-cran-cachem{a} r-cran-callr{a} r-cran-car{a} r-cran-cardata{a} r-cran-caret{a} r-cran-cellranger{a} r-cran-class{a} r-cran-cli{a} r-cran-clipr{a} r-cran-clock{a} r-cran-codetools{a} r-cran-colorspace{a} r-cran-colourpicker{a} r-cran-commonmark{a} r-cran-conquer{a} r-cran-corrplot{a} r-cran-cowplot{a} r-cran-cpp11{a} r-cran-crayon{a} r-cran-crosstalk{a} r-cran-curl{a} r-cran-data.table{a} r-cran-dbi{a} r-cran-desc{a} r-cran-diffobj{a} r-cran-digest{a} r-cran-dplyr{a} r-cran-dt{a} r-cran-e1071{a} r-cran-ellipsis{a} r-cran-evaluate{a} r-cran-fansi{a} r-cran-farver{a} r-cran-fastmap{a} r-cran-fontawesome{a} r-cran-forcats{a} r-cran-foreach{a} r-cran-foreign{a} r-cran-formatr{a} r-cran-fs{a} r-cran-futile.logger{a} r-cran-futile.options{a} r-cran-future{a} r-cran-future.apply{a} r-cran-generics{a} r-cran-ggplot2{a} r-cran-ggpubr{a} r-cran-ggrepel{a} r-cran-ggsci{a} r-cran-ggsignif{a} r-cran-globals{a} r-cran-glue{a} r-cran-gower{a} r-cran-gprofiler2{a} r-cran-gridextra{a} r-cran-gtable{a} r-cran-hardhat{a} r-cran-haven{a} r-cran-highr{a} r-cran-hms{a} r-cran-htmltools{a} r-cran-htmlwidgets{a} r-cran-httpuv{a} r-cran-httr{a} r-cran-ipred{a} r-cran-isoband{a} r-cran-iterators{a} r-cran-jquerylib{a} r-cran-jsonlite{a} r-cran-kernsmooth{a} r-cran-knitr{a} r-cran-labeling{a} r-cran-lambda.r{a} r-cran-later{a} r-cran-lattice{a} r-cran-lava{a} r-cran-lazyeval{a} r-cran-lifecycle{a} r-cran-listenv{a} r-cran-littler{a} r-cran-lme4{a} r-cran-locfit{a} r-cran-lubridate{a} r-cran-magrittr{a} r-cran-maptools{a} r-cran-mass{a} r-cran-matrix{a} r-cran-matrixmodels{a} r-cran-matrixstats{a} r-cran-memoise{a} r-cran-mgcv{a} r-cran-mime{a} r-cran-miniui{a} r-cran-minqa{a} r-cran-modelmetrics{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-nloptr{a} r-cran-nnet{a} r-cran-numderiv{a} r-cran-openssl{a} r-cran-openxlsx{a} r-cran-parallelly{a} r-cran-pbkrtest{a} r-cran-pheatmap{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-pkgload{a} r-cran-plogr{a} r-cran-plotly{a} r-cran-plyr{a} r-cran-png{a} r-cran-polynom{a} r-cran-praise{a} r-cran-prettyunits{a} r-cran-proc{a} r-cran-processx{a} r-cran-prodlim{a} r-cran-progress{a} r-cran-progressr{a} r-cran-promises{a} r-cran-proxy{a} r-cran-ps{a} r-cran-purrr{a} r-cran-quantreg{a} r-cran-r6{a} r-cran-rappdirs{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rcpparmadillo{a} r-cran-rcppeigen{a} r-cran-rcurl{a} r-cran-readr{a} r-cran-readxl{a} r-cran-recipes{a} r-cran-rematch{a} r-cran-rematch2{a} r-cran-reshape2{a} r-cran-restfulr{a} r-cran-rio{a} r-cran-rjson{a} r-cran-rlang{a} r-cran-rmarkdown{a} r-cran-rpart{a} r-cran-rprojroot{a} r-cran-rsqlite{a} r-cran-rstatix{a} r-cran-sass{a} r-cran-scales{a} r-cran-shiny{a} r-cran-shinyjs{a} r-cran-snow{a} r-cran-sourcetools{a} r-cran-sp{a} r-cran-sparsem{a} r-cran-squarem{a} r-cran-statmod{a} r-cran-stringi{a} r-cran-stringr{a} r-cran-survival{a} r-cran-sys{a} r-cran-testthat{a} r-cran-tibble{a} r-cran-tidyr{a} r-cran-tidyselect{a} r-cran-timechange{a} r-cran-timedate{a} r-cran-tinytex{a} r-cran-tzdb{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-vroom{a} r-cran-waldo{a} r-cran-withr{a} r-cran-xfun{a} r-cran-xml{a} r-cran-xtable{a} r-cran-yaml{a} r-cran-zip{a} readline-common{a} salmon{a} samtools{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} snakemake{a} sphinx-common{a} tk8.6-blt2.5{a} trim-galore{a} ucf{a} unicode-data{a} unzip{a} x11-common{a} xdg-utils{a} xml-core{a} zip{a} zlib1g-dev{a} 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. Need to get 576 MB of archives. After unpacking 2664 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 pigz amd64 2.6-1 [64.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 11 http://deb.debian.org/debian bookworm/main 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http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] 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 8s (68.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) 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. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 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. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21537 files and directories currently installed.) 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. Preparing to unpack .../036-autopoint_0.21-12_all.deb ... 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. Preparing to unpack .../046-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../047-libx11-data_2%3a1.8.4-2_all.deb ... Unpacking libx11-data (2:1.8.4-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../048-libx11-6_2%3a1.8.4-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.4-2) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../049-libxrender1_1%3a0.9.10-1.1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../050-libxft2_2.3.6-1_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1) ... Selecting previously unselected package libxext6:amd64. 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Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libwebpdemux2:amd64 (1.2.4-0.1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-9) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... Setting up libtbbbind-2-5:amd64 (2021.8.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up coinor-libcoinutils3v5:amd64 (2.11.4+repack1-2) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (2.17.1.1-1.1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-4) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up libjs-jquery-metadata (12-4) ... Setting up shared-mime-info (2.2-1) ... Setting up ucf (3.0043+nmu1) ... Setting up gir1.2-glib-2.0:amd64 (1.74.0-3) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up coinor-libosi1v5:amd64 (0.108.6+repack1-2) ... Setting up libcommons-lang3-java (3.12.0-2) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up xml-core (0.18+nmu1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libcurl4:amd64 (7.88.1-8) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.8-9) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-5) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (3.24.37-2) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libngs-jni:amd64 (3.0.3+dfsg-5) ... Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-8) ... Setting up libtbb12:amd64 (2021.8.0-1) ... Setting up libbigwig0:amd64 (0.4.7+dfsg-3) ... Setting up libpaper-utils (1.1.29) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up adwaita-icon-theme (43-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up coinor-libclp1:amd64 (1.17.6-3) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up sphinx-common (5.3.0-4) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up git (1:2.39.2-1.1) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libcups2:amd64 (2.4.2-3) ... Setting up libsis-base-java (18.09~pre1+git20180928.45fbd31+dfsg-3) ... Setting up libhdf5-103-1:amd64 (1.10.8+repack1-1) ... Setting up libsis-jhdf5-jni (19.04.1+dfsg-3) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up coinor-libcgl1:amd64 (0.60.3+repack1-4) ... Setting up libngs-java:amd64 (3.0.3+dfsg-5) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libstaden-read14:amd64 (1.14.15-1) ... Setting up libhtsjdk-java (3.0.4+dfsg-2) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up coinor-libcbc3:amd64 (2.10.8+ds1-1) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libsis-jhdf5-java (19.04.1+dfsg-3) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-psutil (5.9.4-1+b1) ... Setting up python3-multidict (6.0.4-1+b1) ... Setting up python3-tz (2022.7.1-3) ... Setting up samtools (1.16.1-1) ... Setting up python3-frozenlist (1.3.3-1+b1) ... Setting up python3-aiosignal (1.3.1-1) ... Setting up python3-ratelimiter (1.2.0.post0-4) ... Setting up python3-async-timeout (4.0.2-1) ... Setting up python3-six (1.16.0-4) ... Setting up salmon (1.10.1+ds1-1+b1) ... Setting up python3-simplejson (3.18.3-1) ... Setting up python3-isodate (0.6.1-1) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.0-1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up coinor-cbc (2.10.8+ds1-1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-humanfriendly (10.0-3) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up python3-avro (1.11.1+dfsg-2) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-jmespath (1.0.1-1) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-mdurl (0.1.2-1) ... Setting up python3-gi (3.42.2-3+b1) ... Setting up python3-cycler (0.11.0-1) ... Setting up r-base-core (4.2.2.20221110-2) ... Creating config file /etc/R/Renviron with new version Setting up python3-connection-pool (0.0.3-2) ... Setting up r-cran-crayon (1.5.2-1) ... Setting up r-cran-squarem (2021.1-1) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up megadepth (1.2.0-4) ... Setting up r-cran-gtable (0.3.1+dfsg-1) ... Setting up python3-idna (3.3-1) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up python3-wrapt (1.14.1-2+b2) ... Setting up python3-markdown (3.4.1-2) ... Setting up python3-throttler (1.2.2-2) ... Setting up r-cran-sourcetools (0.1.7-1-1) ... Setting up r-cran-futile.options (1.0.1-3) ... Setting up python3-typing-extensions (4.4.0-1) ... Setting up r-cran-lattice (0.20-45-3) ... Setting up r-cran-ps (1.7.2-1) ... Setting up r-cran-nlme (3.1.162-1) ... Setting up r-cran-farver (2.1.1-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up r-cran-formatr (1.14-1) ... Setting up python3-markdown-it (2.1.0-5) ... Setting up python3-fastjsonschema (2.16.3-2) ... Setting up r-cran-zip (2.2.2-1+b1) ... Setting up r-cran-xml (3.99-0.13-1) ... Setting up python3-pyrsistent:amd64 (0.18.1-1+b3) ... Setting up hisat2 (2.2.1-4+b2) ... Setting up r-cran-viridislite (0.4.1-1) ... Setting up r-cran-locfit (1.5-9.7-1) ... Setting up python3-lxml:amd64 (4.9.2-1+b1) ... Setting up python3-traitlets (5.5.0-1) ... Setting up python3-portalocker (2.2.1-1) ... Setting up r-cran-sparsem (1.81-1) ... Setting up r-cran-statmod (1.5.0-1) ... Setting up r-cran-nnet (7.3-18-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-py2bit (0.3.1-1+b2) ... Setting up r-cran-lazyeval (0.2.2-1+b1) ... Setting up python3-datrie:amd64 (0.8.2-4+b1) ... Setting up r-cran-clipr (0.8.0-1) ... Setting up r-cran-polynom (1.4-1+dfsg-1) ... Setting up r-cran-commonmark (1.8.1-1) ... Setting up r-cran-proxy (0.4-27-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up r-cran-numderiv (2016.8-1.1-3) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-yarl (1.8.2-1+b1) ... Setting up python3-smmap (5.0.0-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-rappdirs (0.3.3-1) ... Setting up r-bioc-genomeinfodbdata (1.2.9-1) ... Setting up python3-cffi-backend:amd64 (1.15.1-5+b1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-blinker (1.5-1) ... Setting up r-cran-littler (0.3.17-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up python3-toposort (1.9-1) ... Setting up python3-configargparse (1.5.3-1) ... Setting up python3-sympy (1.11.1-1) ... Setting up r-cran-fs (1.6.1+dfsg-1) ... Setting up r-cran-rcpp (1.0.10-1) ... Setting up python3-attr (22.2.0-1) ... Setting up r-cran-curl (5.0.0+dfsg-1) ... Setting up r-cran-codetools (0.2-19-1) ... Setting up r-cran-brio (1.1.3-1+b1) ... Setting up r-cran-boot (1.3-28.1-1) ... Setting up r-cran-diffobj (0.3.5-1+b1) ... Setting up r-cran-rematch (1.0.1-3) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up r-bioc-biocgenerics (0.44.0-2) ... Setting up r-cran-rlang (1.0.6-1) ... Setting up r-cran-matrixstats (0.63.0-1) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up r-cran-listenv (0.9.0+dfsg-1) ... Setting up littler (0.3.17-1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up r-bioc-matrixgenerics (1.10.0-1) ... Setting up python3-jwt (2.6.0-1) ... Setting up r-cran-xfun (0.37+dfsg-1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up r-cran-sys (3.4.1-1) ... Setting up python3-deeptoolsintervals (0.1.9-3+b6) ... Setting up python3-colorama (0.4.6-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up r-cran-plogr (0.2.0-3) ... Setting up r-cran-withr (2.5.0-1) ... Setting up r-cran-backports (1.4.1-1) ... Setting up python3-pbr (5.10.0-2) ... Setting up python3-pulp (2.6.0+dfsg-1) ... Setting up r-cran-processx (3.8.0-1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up r-cran-mime (0.12-1+b1) ... Setting up r-cran-praise (1.0.0-4) ... Setting up python3-alabaster (0.7.12-1) ... Setting up r-cran-generics (0.1.3-1) ... Setting up r-cran-base64enc (0.1-3-3) ... Setting up r-cran-iterators (1.0.14-1) ... Setting up r-cran-abind (1.4-5-2) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up r-cran-digest (0.6.31-1) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up r-cran-yaml (2.3.7-1) ... Setting up python3-tenacity (8.2.1-1) ... Setting up python3-bcrypt (3.2.2-1) ... Setting up python3-ply (3.11-5) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up python3-tqdm (4.64.1-1) ... Setting up r-cran-gower (1.0.1-1) ... Setting up r-cran-evaluate (0.20-1) ... Setting up r-cran-dbi (1.1.3-1) ... Setting up r-cran-timedate (4022.108-1) ... Setting up python3-ruamel.yaml.clib:amd64 (0.2.7-1+b2) ... Setting up r-cran-highr (0.10+dfsg-1) ... Setting up r-cran-foreach (1.5.2-1) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (1.0.4-1) ... Setting up r-cran-cardata (3.0.5-1) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-aiohttp (3.8.4-1) ... Setting up python3-marshmallow (3.18.0-1) ... Setting up r-cran-mass (7.3-58.2-1) ... Setting up python3-tabulate (0.8.9-1) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-yaml (6.0-3+b2) ... Setting up python3-tk:amd64 (3.11.2-2) ... Setting up r-cran-snow (1:0.4.4-2) ... Setting up python3-gitdb (4.0.9-2) ... Setting up python3-uamqp (1.5.3-1+b4) ... Setting up python3-click (8.1.3-2) ... Setting up r-cran-data.table (1.14.8+dfsg-1) ... Setting up r-cran-glue (1.6.2-1) ... Setting up r-cran-foreign (0.8.84-1) ... Setting up r-cran-bit (4.0.5-1) ... Setting up python3-networkx (2.8.8-1) ... Setting up r-cran-xtable (1:1.8-4-2) ... Setting up r-cran-cli (3.6.0-1) ... Setting up r-cran-lifecycle (1.0.3+dfsg-1) ... Setting up r-cran-bitops (1.0-7-1) ... Setting up r-cran-rprojroot (2.0.3-1) ... Setting up r-cran-bit64 (4.0.5-1) ... Setting up r-cran-progressr (0.13.0-1) ... Setting up r-bioc-zlibbioc (1.44.0+dfsg-1) ... Setting up python3-fs (2.4.16-2) ... Setting up r-cran-askpass (1.1-2) ... Setting up r-cran-fastmap (1.1.1-1) ... Setting up python3-beniget (0.4.1-3) ... Setting up r-cran-png (0.1-8-1) ... Setting up r-bioc-biobase (2.58.0-2) ... Setting up r-cran-jsonlite (1.8.4+dfsg-1) ... Setting up r-cran-corrplot (0.92-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-xopen (1.7.0-2) ... Setting up r-cran-sp (1:1.6-0+dfsg-1) ... Setting up r-cran-utf8 (1.2.3-1) ... Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up r-cran-parallelly (1.34.0-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up r-cran-stringi (1.7.12-1) ... Setting up python3-jsonschema (4.10.3-1) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up r-cran-cpp11 (0.4.3-1) ... Setting up r-cran-plyr (1.8.8-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up python3-cryptography (38.0.4-3) ... Setting up r-bioc-s4vectors (0.36.1-1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up python3-git (3.1.30-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up r-cran-gridextra (2.3-3) ... Setting up python3-retry (0.9.2-2) ... Setting up r-cran-later (1.3.0+dfsg-1+b1) ... Setting up r-cran-matrix (1.5-3-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-colormath (3.0.0-4) ... Setting up python3-pybigwig (0.3.18+dfsg-1+b3) ... Setting up r-cran-tinytex (0.44-1) ... Setting up r-bioc-tximport (1.26.1+dfsg-1) ... Setting up r-cran-kernsmooth (2.23-20-1) ... Setting up r-cran-knitr (1.42+dfsg-1) ... Setting up python3-ruamel.yaml (0.17.21-1) ... Setting up r-cran-mgcv (1.8-41-1) ... Setting up python3-adal (1.2.7-2) ... Setting up python3-stopit (1.1.2-2) ... Setting up r-cran-cachem (1.0.7-1) ... Setting up python3-contourpy (1.0.7-1+b1) ... Setting up r-cran-rcpparmadillo (0.12.0.1.0-1) ... Setting up r-bioc-iranges (2.32.0-1) ... Setting up r-cran-rjson (0.2.21-1) ... Setting up r-cran-tzdb (0.3.0-1) ... Setting up python3-future (0.18.2-6) ... update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode Setting up python3-lzstring (1.0.4-2) ... Setting up r-cran-globals (0.16.2-1) ... Setting up r-cran-rcurl (1.98-1.10+dfsg-1) ... Setting up r-cran-maptools (1:1.1-6+dfsg-1) ... Setting up r-cran-restfulr (0.0.15-1) ... Setting up python3-htseq (1.99.2-1+b3) ... Setting up r-cran-vctrs (0.5.2-1) ... Setting up python3-jupyter-core (4.12.0-1) ... Setting up python3-nacl (1.5.0-2) ... Setting up r-bioc-delayedarray (0.24.0+dfsg-1) ... Setting up r-cran-rcppeigen (0.3.3.9.3-1) ... Setting up python3-dnaio (0.10.0-1+b1) ... Setting up r-cran-pillar (1.8.1+dfsg-1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up r-cran-ellipsis (0.3.2-2) ... Setting up r-cran-minqa (1.2.5-1) ... Setting up r-cran-openssl (2.0.5+dfsg-1) ... Setting up r-cran-stringr (1.5.0-1) ... Setting up r-cran-class (7.3-21-1) ... Setting up r-bioc-biocparallel (1.32.5-1) ... Setting up r-cran-modelmetrics (1.2.2.2-1+b1) ... Setting up r-cran-callr (3.7.3-2) ... Setting up python3-spectra (0.0.11-4) ... Setting up r-cran-openxlsx (4.2.5.2-1) ... Setting up python3-rich (13.3.1-1) ... Setting up r-cran-matrixmodels (0.5-1-1) ... Setting up r-bioc-rhtslib (2.0.0+dfsg-1) ... Setting up r-cran-desc (1.4.2-1) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-tibble (3.1.8+dfsg-1) ... Setting up r-cran-clock (0.6.1-2) ... Setting up python3-msal (1.21.0-1) ... Setting up r-cran-proc (1.18.0-1+b1) ... Setting up python3-msal-extensions (1.0.0-2) ... Setting up r-cran-survival (3.5-3-1) ... Setting up python3-nbformat (5.5.0-1) ... Setting up r-bioc-biocio (1.8.0+dfsg-1) ... Setting up r-cran-future (1.31.0+dfsg-1) ... Setting up r-cran-forcats (1.0.0-1) ... Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... Setting up r-cran-reshape2 (1.4.4-2) ... Setting up python3-strictyaml (1.6.1-3) ... Setting up r-cran-future.apply (1.10.0+dfsg-1) ... Setting up python3-oauthlib (3.2.2-1) ... Setting up python3-cutadapt (4.2-1+b1) ... Setting up r-bioc-genomeinfodb (1.34.9-1) ... Setting up r-cran-timechange (0.2.0-1) ... Setting up r-cran-httr (1.4.5+dfsg-1) ... Setting up python3-botocore (1.29.27+repack-1) ... Setting up r-cran-hms (1.1.2-1) ... Setting up r-cran-scales (1.2.1-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-lava (1.7.2.1+dfsg-1) ... Setting up r-cran-promises (1.2.0.1+dfsg-1) ... Setting up r-cran-purrr (1.0.1-1) ... Setting up r-cran-e1071 (1.7-13-1) ... Setting up r-cran-blob (1.2.3-1) ... Setting up python3-plotly (5.4.1+dfsg-1) ... Setting up r-cran-htmltools (0.5.4-1) ... Setting up r-bioc-xvector (0.38.0-1) ... Setting up python3-rich-click (1.6.0-1) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up r-cran-hardhat (1.2.0+dfsg-1) ... Setting up r-cran-sass (0.4.5+dfsg-1) ... Setting up r-cran-dplyr (1.0.10-1) ... Setting up python3-paramiko (2.12.0-2) ... Setting up r-cran-rsqlite (2.2.20-1) ... Setting up r-cran-progress (1.2.2-2) ... Setting up python3-requests-oauthlib (1.3.0+ds-1) ... Setting up r-cran-pheatmap (1.0.12-2) ... Setting up r-cran-lubridate (1.9.2+dfsg-1) ... Setting up r-cran-pkgload (1.3.2-1) ... Setting up r-cran-vroom (1.6.1-1) ... Setting up r-cran-prodlim (2019.11.13-1+b1) ... Setting up python3-scipy (1.10.1-2) ... Setting up r-cran-ggplot2 (3.4.1+dfsg-1) ... Setting up r-cran-ggsignif (0.6.4-1) ... Setting up r-bioc-genomicranges (1.50.2+dfsg-1) ... Setting up cutadapt (4.2-1) ... Setting up r-cran-cellranger (1.1.0-3) ... Setting up r-cran-httpuv (1.6.9+dfsg-1) ... Setting up r-cran-rematch2 (2.1.2-2) ... Setting up python3-s3transfer (0.6.0-1) ... Setting up r-cran-rpart (4.1.19-1) ... Setting up r-bioc-biostrings (2.66.0-1) ... Setting up r-cran-fontawesome (0.5.0-1) ... Setting up r-cran-ggsci (2.9-3) ... Setting up r-cran-ipred (0.9-13-1) ... Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... Setting up python3-msrest (0.6.21-2) ... 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 Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/2740028/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/2740028/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/pigx-rnaseq-0.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pigx-rnaseq_0.1.0-1.1_source.changes dpkg-buildpackage: info: source package pigx-rnaseq dpkg-buildpackage: info: source version 0.1.0-1.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Bastian Germann 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... /usr/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 -j16 make[1]: Entering directory '/build/pigx-rnaseq-0.1.0' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0' 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: /usr/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 May 17 18:53:40 2024] rule trim_qc_reads_pe: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz, /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.json log: /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep2.log jobid: 7 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz --in2 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz --out1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz --out2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -h /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.html -j /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep2.pe.fastp.json >> /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep2.log 2>&1 [Fri May 17 18:53:40 2024] rule trim_qc_reads_se: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep1.se.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep1.se.fastp.json 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 May 17 18:53:40 2024] rule translate_sample_sheet_for_report: input: /build/pigx-rnaseq-0.1.0/tests/sample_sheet.csv output: /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv 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 May 17 18:53:40 2024] rule trim_qc_reads_se: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep3.se.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep3.se.fastp.json 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 May 17 18:53:40 2024] rule trim_qc_reads_pe: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz, /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.json log: /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep3.log jobid: 9 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz --in2 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz --out1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz --out2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -h /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.html -j /build/pigx-rnaseq-0.1.0/tests/output/QC/HBR_Rep3.pe.fastp.json >> /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.HBR_Rep3.log 2>&1 [Fri May 17 18:53:40 2024] rule check_annotation_files: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta, /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta, /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf output: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv log: /build/pigx-rnaseq-0.1.0/tests/output/logs/check_annotation_files.log jobid: 1 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv resources: tmpdir=/tmp /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//validate_input_annotation.R /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta /build/pigx-rnaseq-0.1.0/tests/output >> /build/pigx-rnaseq-0.1.0/tests/output/logs/check_annotation_files.log 2>&1 [Fri May 17 18:53:41 2024] Finished job 24. 1 of 48 steps (2%) done Select jobs to execute... [Fri May 17 18:53:41 2024] rule trim_qc_reads_pe: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz, /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.json log: /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep2.log jobid: 13 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz --in2 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz --out1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz --out2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -h /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.html -j /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep2.pe.fastp.json >> /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep2.log 2>&1 [Fri May 17 18:53:41 2024] Finished job 5. 2 of 48 steps (4%) done Select jobs to execute... [Fri May 17 18:53:41 2024] rule trim_qc_reads_pe: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz, /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.html, /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.json log: /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep1.log jobid: 11 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/fastp --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz --in2 /build/pigx-rnaseq-0.1.0/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz --out1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz --out2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -h /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.html -j /build/pigx-rnaseq-0.1.0/tests/output/QC/UHR_Rep1.pe.fastp.json >> /build/pigx-rnaseq-0.1.0/tests/output/logs/trim_reads.UHR_Rep1.log 2>&1 [Fri May 17 18:53:41 2024] Finished job 7. 3 of 48 steps (6%) done [Fri May 17 18:53:41 2024] Finished job 15. 4 of 48 steps (8%) done [Fri May 17 18:53:41 2024] Finished job 9. 5 of 48 steps (10%) done [Fri May 17 18:53:42 2024] Finished job 13. 6 of 48 steps (12%) done [Fri May 17 18:53:42 2024] Finished job 11. 7 of 48 steps (15%) done [Fri May 17 18:53:53 2024] Finished job 1. 8 of 48 steps (17%) done Select jobs to execute... [Fri May 17 18:53:53 2024] rule salmon_index: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.cdna.fasta, /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin 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 May 17 18:53:53 2024] rule hisat2_index: input: /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta, /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2_index.log jobid: 17 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv resources: tmpdir=/tmp, mem_mb=32000, mem_mib=30518 /usr/bin/hisat2-build -f -p 2 --large-index /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.fasta /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2_index.log 2>&1 [Fri May 17 18:53:56 2024] Finished job 17. 9 of 48 steps (19%) done Select jobs to execute... [Fri May 17 18:53:56 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep3.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep3.log jobid: 22 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /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 May 17 18:53:56 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep3.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep3.log jobid: 19 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /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 May 17 18:53:56 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep1.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep1.log jobid: 20 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /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 May 17 18:53:56 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep1.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep1.log jobid: 16 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /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 May 17 18:53:56 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep2.log jobid: 21 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /usr/bin/hisat2 --fast -x /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index -p 2 -q -S /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam -1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_UHR_Rep2.log 2>&1 /usr/bin/samtools view -bh /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam | /usr/bin/samtools sort -o /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.UHR_Rep2.log 2>&1 rm /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.out.sam [Fri May 17 18:53:56 2024] Finished job 16. 10 of 48 steps (21%) done Select jobs to execute... [Fri May 17 18:53:56 2024] rule hisat2_map: input: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/hisat2_map_HBR_Rep2.log, /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/samtools.hisat2.HBR_Rep2.log jobid: 18 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.1.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.6.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.8.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.2.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.5.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.4.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.3.ht2l, /build/pigx-rnaseq-0.1.0/tests/output/hisat2_index/GRCm38_index.7.ht2l wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=8000, mem_mib=7630 /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 May 17 18:53:56 2024] Finished job 22. 11 of 48 steps (23%) done [Fri May 17 18:53:56 2024] Finished job 4. 12 of 48 steps (25%) done [Fri May 17 18:53:56 2024] Finished job 19. 13 of 48 steps (27%) done Select jobs to execute... [Fri May 17 18:53:56 2024] rule salmon_quant: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log jobid: 3 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 [Fri May 17 18:53:56 2024] rule salmon_quant: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log jobid: 10 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 [Fri May 17 18:53:56 2024] rule salmon_quant: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log jobid: 6 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 [Fri May 17 18:53:56 2024] Finished job 20. 14 of 48 steps (29%) done Select jobs to execute... [Fri May 17 18:53:56 2024] rule index_bam: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai 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 May 17 18:53:56 2024] Finished job 21. 15 of 48 steps (31%) done Select jobs to execute... [Fri May 17 18:53:56 2024] rule index_bam: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep3.log jobid: 37 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep3.log 2>&1 [Fri May 17 18:53:56 2024] Finished job 31. 16 of 48 steps (33%) done Select jobs to execute... [Fri May 17 18:53:56 2024] rule index_bam: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_HBR_Rep1.log jobid: 27 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=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 May 17 18:53:56 2024] Finished job 37. 17 of 48 steps (35%) done Select jobs to execute... [Fri May 17 18:53:56 2024] rule count_reads: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep3.count_reads.log jobid: 36 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep3 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep3.count_reads.log 2>&1 [Fri May 17 18:53:56 2024] Finished job 27. 18 of 48 steps (38%) done [Fri May 17 18:53:56 2024] Finished job 18. 19 of 48 steps (40%) done Select jobs to execute... [Fri May 17 18:53:56 2024] rule coverage_megadepth: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw 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 May 17 18:53:56 2024] rule index_bam: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep1.log jobid: 33 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=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 Select jobs to execute... [Fri May 17 18:53:56 2024] Finished job 33. 20 of 48 steps (42%) done [Fri May 17 18:53:56 2024] rule count_reads: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep1.count_reads.log jobid: 26 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep1 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep1.count_reads.log 2>&1 [Fri May 17 18:53:56 2024] Finished job 41. 21 of 48 steps (44%) done Select jobs to execute... [Fri May 17 18:53:56 2024] rule index_bam: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai 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 May 17 18:53:56 2024] Finished job 29. 22 of 48 steps (46%) done Select jobs to execute... [Fri May 17 18:53:56 2024] rule coverage_megadepth: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log jobid: 40 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep2.log 2>&1 [Fri May 17 18:53:56 2024] Finished job 40. 23 of 48 steps (48%) done Select jobs to execute... [Fri May 17 18:53:56 2024] rule salmon_quant: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log jobid: 8 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... /usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep2.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep2.log 2>&1 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... /usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep1.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep1.log 2>&1 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... /usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -r /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep1.trimmed.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep1.log 2>&1 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... /usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/HBR_Rep3.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_HBR_Rep3.log 2>&1 [Fri May 17 18:53:58 2024] Finished job 6. 24 of 48 steps (50%) done Select jobs to execute... [Fri May 17 18:53:58 2024] rule count_reads: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep1.count_reads.log jobid: 32 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep1 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep1.count_reads.log 2>&1 [Fri May 17 18:53:58 2024] Finished job 10. 25 of 48 steps (52%) done Select jobs to execute... [Fri May 17 18:53:59 2024] rule salmon_quant: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log jobid: 12 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 [Fri May 17 18:53:59 2024] Finished job 3. 26 of 48 steps (54%) done Select jobs to execute... [Fri May 17 18:53:59 2024] rule coverage_megadepth: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log jobid: 39 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai wildcards: sample=HBR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.HBR_Rep1.log 2>&1 [Fri May 17 18:53:59 2024] Finished job 39. 27 of 48 steps (56%) done Select jobs to execute... [Fri May 17 18:53:59 2024] rule salmon_quant: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin, /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz output: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log jobid: 14 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz, /build/pigx-rnaseq-0.1.0/tests/output/salmon_index/pos.bin wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 [Fri May 17 18:53:59 2024] Finished job 8. 28 of 48 steps (58%) done Select jobs to execute... [Fri May 17 18:53:59 2024] rule count_reads: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep3.count_reads.log jobid: 30 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai wildcards: sample=HBR_Rep3 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep3 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep3.count_reads.log 2>&1 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... /usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -r /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep3.trimmed.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep3.log 2>&1 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 6 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6000, mem_mib=5723 Select jobs to execute... /usr/bin/salmon quant -i /build/pigx-rnaseq-0.1.0/tests/output/salmon_index -l A -p 8 -1 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R1.fq.gz -2 /build/pigx-rnaseq-0.1.0/tests/output/trimmed_reads/UHR_Rep2.trimmed.R2.fq.gz -o /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_quant_UHR_Rep2.log 2>&1 [Fri May 17 18:54:01 2024] Finished job 12. 29 of 48 steps (60%) done Select jobs to execute... [Fri May 17 18:54:01 2024] rule index_bam: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai log: /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep2.log jobid: 35 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/samtools index /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/pigx-rnaseq-0.1.0/tests/output/logs/samtools_index_UHR_Rep2.log 2>&1 [Fri May 17 18:54:01 2024] Finished job 35. 30 of 48 steps (62%) done Select jobs to execute... [Fri May 17 18:54:01 2024] rule coverage_megadepth: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log jobid: 43 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep2.log 2>&1 [Fri May 17 18:54:01 2024] Finished job 43. 31 of 48 steps (65%) done Select jobs to execute... [Fri May 17 18:54:01 2024] rule coverage_megadepth: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log jobid: 42 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai wildcards: sample=UHR_Rep1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep1.log 2>&1 [Fri May 17 18:54:01 2024] Finished job 14. 32 of 48 steps (67%) done Select jobs to execute... [Fri May 17 18:54:01 2024] rule multiqc: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html log: /build/pigx-rnaseq-0.1.0/tests/output/logs/multiqc.hisat2.log jobid: 2 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf resources: tmpdir=/tmp, mem_mb=500, mem_mib=477 /usr/bin/multiqc -f -o /build/pigx-rnaseq-0.1.0/tests/output/multiqc /build/pigx-rnaseq-0.1.0/tests/output >> /build/pigx-rnaseq-0.1.0/tests/output/logs/multiqc.hisat2.log 2>&1 [Fri May 17 18:54:01 2024] Finished job 42. 33 of 48 steps (69%) done Select jobs to execute... [Fri May 17 18:54:01 2024] rule counts_from_SALMON: input: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log jobid: 23 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/pigx-rnaseq-0.1.0/tests/output/salmon_output/HBR_Rep3/quant.sf resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//counts_matrix_from_SALMON.R /build/pigx-rnaseq-0.1.0/tests/output/salmon_output /build/pigx-rnaseq-0.1.0/tests/output/feature_counts /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/salmon_import_counts.log 2>&1 [Fri May 17 18:54:11 2024] Finished job 2. 34 of 48 steps (71%) done Select jobs to execute... [Fri May 17 18:54:11 2024] rule coverage_megadepth: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log jobid: 44 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai wildcards: sample=UHR_Rep3 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815, threads=2 /usr/bin/megadepth /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3_Aligned.sortedByCoord.out.bam --threads 2 --bigwig --prefix /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/coverage_megadepth.UHR_Rep3.log 2>&1 [Fri May 17 18:54:11 2024] Finished job 44. 35 of 48 steps (73%) done Select jobs to execute... [Fri May 17 18:54:11 2024] rule count_reads: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log jobid: 34 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam wildcards: sample=UHR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R UHR_Rep2 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/UHR_Rep2.count_reads.log 2>&1 [Fri May 17 18:54:16 2024] Finished job 26. 36 of 48 steps (75%) done Select jobs to execute... [Fri May 17 18:54:16 2024] rule count_reads: input: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep2.count_reads.log jobid: 28 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai wildcards: sample=HBR_Rep2 resources: tmpdir=/tmp, mem_mb=6000, mem_mib=5723 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts//count_reads.R HBR_Rep2 /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/HBR_Rep2.count_reads.log 2>&1 [Fri May 17 18:54:16 2024] Finished job 36. 37 of 48 steps (77%) done [Fri May 17 18:54:18 2024] Finished job 32. 38 of 48 steps (79%) done [Fri May 17 18:54:19 2024] Finished job 30. 39 of 48 steps (81%) done [Fri May 17 18:54:21 2024] Finished job 23. 40 of 48 steps (83%) done Select jobs to execute... [Fri May 17 18:54:21 2024] rule report2: input: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log jobid: 46 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv wildcards: analysis=analysis1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts/runDeseqReport.R --logo=/build/pigx-rnaseq-0.1.0/images/Logo_PiGx.png --prefix='analysis1.salmon.transcripts' --reportFile=/build/pigx-rnaseq-0.1.0/scripts/deseqReport.Rmd --countDataFile=/build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv --colDataFile=/build/pigx-rnaseq-0.1.0/tests/output/colData.tsv --gtfFile=/build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/pigx-rnaseq-0.1.0/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.transcripts.log 2>&1 [Fri May 17 18:54:21 2024] rule report3: input: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html log: /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.genes.log jobid: 47 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv wildcards: analysis=analysis1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts/runDeseqReport.R --logo=/build/pigx-rnaseq-0.1.0/images/Logo_PiGx.png --prefix='analysis1.salmon.genes' --reportFile=/build/pigx-rnaseq-0.1.0/scripts/deseqReport.Rmd --countDataFile=/build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv --colDataFile=/build/pigx-rnaseq-0.1.0/tests/output/colData.tsv --gtfFile=/build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/pigx-rnaseq-0.1.0/tests/output/report/salmon --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/pigx-rnaseq-0.1.0/tests/output/logs/salmon/analysis1.report.salmon.genes.log 2>&1 [Fri May 17 18:54:28 2024] Finished job 34. 41 of 48 steps (85%) done [Fri May 17 18:54:36 2024] Finished job 28. 42 of 48 steps (88%) done Select jobs to execute... [Fri May 17 18:54:36 2024] rule collate_read_counts: input: /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv output: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/collate_read_counts.log jobid: 25 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep1.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep2.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep2.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/HBR_Rep3.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep3.read_counts.csv, /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2/UHR_Rep1.read_counts.csv resources: tmpdir=/tmp, mem_mb=200, mem_mib=191 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts/collate_read_counts.R /build/pigx-rnaseq-0.1.0/tests/output/mapped_reads/hisat2 /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/collate_read_counts.log 2>&1 [Fri May 17 18:54:36 2024] Finished job 25. 43 of 48 steps (90%) done Select jobs to execute... [Fri May 17 18:54:36 2024] rule norm_counts_deseq: input: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/norm_counts_deseq.log jobid: 38 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv resources: tmpdir=/tmp, mem_mb=1000, mem_mib=954 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts/norm_counts_deseq.R /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2 >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/norm_counts_deseq.log 2>&1 [Fri May 17 18:54:36 2024] rule report1: input: /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv output: /build/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html log: /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/analysis1.report.log jobid: 45 reason: Missing output files: /build/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html; Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/colData.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv wildcards: analysis=analysis1 resources: tmpdir=/tmp, mem_mb=4000, mem_mib=3815 /usr/bin/Rscript --vanilla /build/pigx-rnaseq-0.1.0/scripts/runDeseqReport.R --logo=/build/pigx-rnaseq-0.1.0/images/Logo_PiGx.png --prefix='analysis1' --reportFile=/build/pigx-rnaseq-0.1.0/scripts/deseqReport.Rmd --countDataFile=/build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv --colDataFile=/build/pigx-rnaseq-0.1.0/tests/output/colData.tsv --gtfFile=/build/pigx-rnaseq-0.1.0/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/pigx-rnaseq-0.1.0/tests/output/report/hisat2 --organism='' --description='This analysis is part of the pigx-rnaseq build-time tests.' --selfContained='True' >> /build/pigx-rnaseq-0.1.0/tests/output/logs/hisat2/analysis1.report.log 2>&1 [Fri May 17 18:54:50 2024] Finished job 38. 44 of 48 steps (92%) done [Fri May 17 18:55:03 2024] Finished job 47. 45 of 48 steps (94%) done [Fri May 17 18:55:04 2024] Finished job 46. 46 of 48 steps (96%) done [Fri May 17 18:55:15 2024] Finished job 45. 47 of 48 steps (98%) done Select jobs to execute... [Fri May 17 18:55:15 2024] localrule all: input: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv, /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html jobid: 0 reason: Input files updated by another job: /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep1.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/hisat2/counts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep3.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.transcripts.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep2.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_size_factors.txt, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep1.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/raw_counts/salmon/counts_from_SALMON.genes.tsv, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/UHR_Rep3.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/salmon/TPM_counts_from_SALMON.transcripts.tsv, /build/pigx-rnaseq-0.1.0/tests/output/bigwig_files/hisat2/megadepth/HBR_Rep2.all.bw, /build/pigx-rnaseq-0.1.0/tests/output/report/salmon/analysis1.salmon.genes.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/report/hisat2/analysis1.deseq.report.html, /build/pigx-rnaseq-0.1.0/tests/output/feature_counts/normalized/hisat2/deseq_normalized_counts.tsv resources: tmpdir=/tmp [Fri May 17 18:55:15 2024] Finished job 0. 48 of 48 steps (100%) done Complete log: .snakemake/log/2024-05-17T185340.014054.snakemake.log The following files have been generated: - /build/pigx-rnaseq-0.1.0/tests/output/input_annotation_stats.tsv - /build/pigx-rnaseq-0.1.0/tests/output/multiqc/multiqc_report.html - /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 -j16 install DESTDIR=/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/pigx-rnaseq-0.1.0' make[2]: Entering directory '/build/pigx-rnaseq-0.1.0' /usr/bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /usr/bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' /usr/bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/bin' /usr/bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /usr/bin/mkdir -p '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/pigx_rnaseq' /usr/bin/install -c snakefile.py qsub-template.sh '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /usr/bin/install -c pigx-rnaseq '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/bin' /usr/bin/install -c scripts/runDeseqReport.R scripts/translate_sample_sheet_for_report.R scripts/deseqReport.Rmd scripts/counts_matrix_from_SALMON.R scripts/validate_input.py scripts/norm_counts_deseq.R scripts/count_reads.R scripts/collate_read_counts.R scripts/validate_input_annotation.R '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' /usr/bin/install -c -m 644 etc/sample_sheet.csv.example etc/settings.yaml etc/pretty.txt images/Logo_PiGx.png '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/pigx_rnaseq' /usr/bin/install -c -m 644 README.md '/build/pigx-rnaseq-0.1.0/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' make[2]: Leaving directory '/build/pigx-rnaseq-0.1.0' make[1]: Leaving directory '/build/pigx-rnaseq-0.1.0' dh_installdocs 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: user script /srv/workspace/pbuilder/2740028/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2740028/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2740028 and its subdirectories I: Current time: Fri May 17 18:55:23 +14 2024 I: pbuilder-time-stamp: 1715921723