I: pbuilder: network access will be disabled during build I: Current time: Sat Jan 6 20:01:50 -12 2024 I: pbuilder-time-stamp: 1704614510 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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_0.0.10+ds-2.dsc] I: copying [./pigx-rnaseq_0.0.10+ds.orig.tar.xz] I: copying [./pigx-rnaseq_0.0.10+ds-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.dSzvDw30/trustedkeys.kbx': General error gpgv: Signature made Fri Oct 23 14:13:09 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pigx-rnaseq_0.0.10+ds-2.dsc dpkg-source: info: extracting pigx-rnaseq in pigx-rnaseq-0.0.10+ds dpkg-source: info: unpacking pigx-rnaseq_0.0.10+ds.orig.tar.xz dpkg-source: info: unpacking pigx-rnaseq_0.0.10+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying latencyWait.patch dpkg-source: info: applying notSelfContained.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/476780/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=12 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='595823d678184422a2222c786ebf230c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='476780' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.UR3y8s4j/pbuilderrc_ipSd --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UR3y8s4j/b1 --logfile b1/build.log pigx-rnaseq_0.0.10+ds-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.104:3128' I: uname -a Linux codethink02-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Mar 27 2022 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 64856 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 182496 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 93744 Apr 10 2022 gzip -rwxr-xr-x 1 root root 18440 Nov 7 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 157864 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jan 20 2022 more -rwsr-xr-x 1 root root 51360 Jan 20 2022 mount -rwxr-xr-x 1 root root 14496 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Dec 7 09:24 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jan 20 2022 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jan 20 2022 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 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 5898 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 8049 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/476780/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: arm64 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), pandoc-citeproc, python3-all, python3-deeptools, multiqc, python3-htseq, r-cran-locfit, r-bioc-deseq2, r-bioc-tximport, r-cran-data.table, r-cran-rlang, r-cran-rmarkdown, r-cran-ggplot2, r-cran-ggrepel, r-cran-dt (>= 0.15+dfsg-2), r-cran-pheatmap, r-cran-corrplot, r-cran-reshape2, r-cran-plotly, r-cran-scales, r-cran-crosstalk, r-cran-gprofiler, r-bioc-summarizedexperiment, r-bioc-rtracklayer, r-cran-rjson, trim-galore, snakemake, fastqc, samtools, rna-star, salmon, libjs-jquery-datatables, libjs-jquery-tablesorter dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 17734 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 pandoc-citeproc; however: Package pandoc-citeproc 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 multiqc; however: Package multiqc is not installed. pbuilder-satisfydepends-dummy depends on python3-htseq; however: Package python3-htseq 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-bioc-deseq2; however: Package r-bioc-deseq2 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-data.table; however: Package r-cran-data.table 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-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-dt (>= 0.15+dfsg-2); however: Package r-cran-dt 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-corrplot; however: Package r-cran-corrplot 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-plotly; however: Package r-cran-plotly is not installed. pbuilder-satisfydepends-dummy depends on r-cran-scales; however: Package r-cran-scales 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-gprofiler; however: Package r-cran-gprofiler 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-rtracklayer; however: Package r-bioc-rtracklayer is not installed. pbuilder-satisfydepends-dummy depends on r-cran-rjson; however: Package r-cran-rjson is not installed. pbuilder-satisfydepends-dummy depends on trim-galore; however: Package trim-galore is not installed. pbuilder-satisfydepends-dummy depends on snakemake; however: Package snakemake is not installed. pbuilder-satisfydepends-dummy depends on fastqc; however: Package fastqc is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on rna-star; however: Package rna-star is not installed. pbuilder-satisfydepends-dummy depends on salmon; however: Package salmon 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. 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: ant{a} ant-optional{a} autoconf{a} automake{a} autopoint{a} autotools-dev{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} fastqc{a} file{a} fontconfig{a} fontconfig-config{a} fonts-font-awesome{a} fonts-glyphicons-halflings{a} fonts-lato{a} fonts-lyx{a} fonts-mathjax{a} gettext{a} gettext-base{a} git{a} git-man{a} groff-base{a} intltool-debian{a} java-common{a} libactivation-java{a} libaec0{a} libaopalliance-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasound2{a} libasound2-data{a} libatinject-jsr330-api-java{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbibutils7{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} libc-ares2{a} libcairo2{a} libcdi-api-java{a} libcmark-gfm-extensions0{a} libcmark-gfm0{a} libcodemodel-java{a} libcommons-cli-java{a} libcommons-codec-java{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} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libedit2{a} libelf1{a} liberror-perl{a} libexpat1{a} libfastinfoset-java{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} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgfortran5{a} libghc-pandoc-citeproc-data{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libguava-java{a} libguice-java{a} libharfbuzz0b{a} libhdf5-103-1{a} libhts3{a} libhtscodecs2{a} libhtsjdk-java{a} libhttpclient-java{a} libhttpcore-java{a} libice6{a} libicu67{a} libimagequant0{a} libistack-commons-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjbig0{a} libjbzip2-java{a} libjemalloc2{a} libjpeg62-turbo{a} libjs-bootstrap{a} libjs-d3{a} libjs-d3-format{a} libjs-es5-shim{a} libjs-highlight.js{a} libjs-inherits{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-prettify{a} libjs-sifter.js{a} libjs-sphinxdoc{a} libjs-sprintf-js{a} libjs-twitter-bootstrap-datepicker{a} libjs-underscore{a} libjs-util{a} libjsoup-java{a} libjsr305-java{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.4-2{a} libllvm11{a} libmagic-mgc{a} libmagic1{a} libmaven-file-management-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmd0{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libngs-java{a} libngs-sdk-dev{a} libngs-sdk2{a} libnode72{a} libnotify-bin{a} libnotify4{a} libnspr4{a} libnss3{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libplexus-archiver-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-component-annotations-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16{a} libpsl5{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librelaxng-datatype-java{a} librngom-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsigsegv2{a} libsis-base-java{a} libsis-base-jni{a} libsis-jhdf5-java{a} libsis-jhdf5-jni{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsm6{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1{a} libstaden-read14{a} libstax-ex-java{a} libstreambuffer-java{a} libsub-override-perl{a} libsz2{a} libtbb2{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff5{a} libtk8.6{a} libtool{a} libtxw2-java{a} libuchardet0{a} libuv1{a} libvulkan1{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwebp6{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-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxss1{a} libxt6{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libyaml-0-2{a} libz3-4{a} littler{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} mocha{a} multiqc{a} node-ansi-colors{a} node-ansi-regex{a} node-ansi-styles{a} node-anymatch{a} node-argparse{a} node-assert{a} node-async-each{a} node-balanced-match{a} node-binary-extensions{a} node-brace-expansion{a} node-braces{a} node-browser-stdout{a} node-camelcase{a} node-chalk{a} node-chokidar{a} node-cliui{a} node-clone{a} node-color-convert{a} node-color-name{a} node-commander{a} node-d3{a} node-d3-array{a} node-d3-axis{a} node-d3-brush{a} node-d3-chord{a} node-d3-collection{a} node-d3-color{a} node-d3-contour{a} node-d3-dispatch{a} node-d3-drag{a} node-d3-dsv{a} node-d3-ease{a} node-d3-fetch{a} node-d3-force{a} node-d3-format{a} node-d3-geo{a} node-d3-hierarchy{a} node-d3-interpolate{a} node-d3-path{a} node-d3-polygon{a} node-d3-quadtree{a} node-d3-queue{a} node-d3-random{a} node-d3-scale{a} node-d3-scale-chromatic{a} node-d3-selection{a} node-d3-shape{a} node-d3-time{a} node-d3-time-format{a} node-d3-timer{a} node-d3-transition{a} node-d3-voronoi{a} node-d3-zoom{a} node-dagre-d3-renderer{a} node-dagre-layout{a} node-debug{a} node-decamelize{a} node-defaults{a} node-diff{a} node-end-of-stream{a} node-escape-string-regexp{a} node-esprima{a} node-execa{a} node-fill-range{a} node-find-up{a} node-fs.realpath{a} node-get-caller-file{a} node-get-stream{a} node-glob{a} node-glob-parent{a} node-graceful-fs{a} node-graphlibrary{a} node-growl{a} node-has-flag{a} node-he{a} node-highlight.js{a} node-html5shiv{a} node-iconv-lite{a} node-inflight{a} node-inherits{a} node-invert-kv{a} node-is-binary-path{a} node-is-buffer{a} node-is-extglob{a} node-is-glob{a} node-is-number{a} node-is-plain-obj{a} node-is-stream{a} node-isexe{a} node-js-yaml{a} node-kind-of{a} node-lcid{a} node-locate-path{a} node-lodash{a} node-mem{a} node-merge-stream{a} node-mimic-fn{a} node-minimatch{a} node-ms{a} node-normalize-path{a} node-normalize.css{a} node-npm-run-path{a} node-object-assign{a} node-once{a} node-os-locale{a} node-p-limit{a} node-p-locate{a} node-path-dirname{a} node-path-exists{a} node-path-is-absolute{a} node-pump{a} node-randombytes{a} node-readdirp{a} node-repeat-string{a} node-require-directory{a} node-require-main-filename{a} node-rw{a} node-safe-buffer{a} node-serialize-javascript{a} node-set-blocking{a} node-set-immediate-shim{a} node-shebang-command{a} node-shebang-regex{a} node-signal-exit{a} node-sprintf-js{a} node-string-width{a} node-strip-ansi{a} node-strip-json-comments{a} node-supports-color{a} node-to-regex-range{a} node-util{a} node-wcwidth.js{a} node-which{a} node-which-module{a} node-wide-align{a} node-wrap-ansi{a} node-wrappy{a} node-y18n{a} node-yargs{a} node-yargs-parser{a} nodejs{a} openjdk-11-jre{a} openjdk-11-jre-headless{a} openssl{a} pandoc{a} pandoc-citeproc{a} pandoc-data{a} pigz{a} po-debconf{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-appdirs{a} python3-attr{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-click{a} python3-colorama{a} python3-coloredlogs{a} python3-colormath{a} python3-configargparse{a} python3-cutadapt{a} python3-cycler{a} python3-dateutil{a} python3-datrie{a} python3-decorator{a} python3-deeptools{a} python3-deeptoolsintervals{a} python3-distutils{a} python3-dnaio{a} python3-docutils{a} python3-future{a} python3-git{a} python3-gitdb{a} python3-htseq{a} python3-humanfriendly{a} python3-idna{a} python3-imagesize{a} python3-importlib-metadata{a} python3-ipython-genutils{a} python3-jinja2{a} python3-jsonschema{a} python3-jupyter-core{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lzstring{a} python3-markdown{a} python3-markupsafe{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-nbformat{a} python3-networkx{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pil{a} python3-pkg-resources{a} python3-plotly{a} python3-psutil{a} python3-pulp{a} python3-py2bit{a} python3-pybigwig{a} python3-pygments{a} python3-pyparsing{a} python3-pyrsistent{a} python3-pysam{a} python3-ratelimiter{a} python3-requests{a} python3-retrying{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-simplejson{a} python3-six{a} python3-smmap{a} python3-snowballstemmer{a} python3-spectra{a} python3-sphinx{a} python3-toposort{a} python3-traitlets{a} python3-tz{a} python3-urllib3{a} python3-wrapt{a} python3-xopen{a} python3-yaml{a} python3-zipp{a} python3.9{a} python3.9-minimal{a} r-base-core{a} r-bioc-annotate{a} r-bioc-annotationdbi{a} r-bioc-biobase{a} r-bioc-biocgenerics{a} r-bioc-biocparallel{a} r-bioc-biostrings{a} r-bioc-delayedarray{a} r-bioc-deseq2{a} r-bioc-genefilter{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-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-askpass{a} r-cran-assertthat{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-brio{a} r-cran-cachem{a} r-cran-callr{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-colourpicker{a} r-cran-commonmark{a} r-cran-corrplot{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-ellipsis{a} r-cran-evaluate{a} r-cran-fansi{a} r-cran-farver{a} r-cran-fastmap{a} r-cran-formatr{a} r-cran-futile.logger{a} r-cran-futile.options{a} r-cran-generics{a} r-cran-ggplot2{a} r-cran-ggrepel{a} r-cran-glue{a} r-cran-gprofiler{a} r-cran-gtable{a} r-cran-highr{a} r-cran-htmltools{a} r-cran-htmlwidgets{a} r-cran-httpuv{a} r-cran-httr{a} r-cran-isoband{a} r-cran-jsonlite{a} r-cran-knitr{a} r-cran-labeling{a} r-cran-lambda.r{a} r-cran-later{a} r-cran-lattice{a} r-cran-lazyeval{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-locfit{a} r-cran-magrittr{a} r-cran-markdown{a} r-cran-mass{a} r-cran-matrix{a} r-cran-matrixstats{a} r-cran-memoise{a} r-cran-mgcv{a} r-cran-mime{a} r-cran-miniui{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-openssl{a} r-cran-pheatmap{a} r-cran-pillar{a} r-cran-pkgbuild{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-praise{a} r-cran-prettyunits{a} r-cran-processx{a} r-cran-promises{a} r-cran-ps{a} r-cran-purrr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rcpparmadillo{a} r-cran-rcurl{a} r-cran-rematch2{a} r-cran-reshape2{a} r-cran-rjson{a} r-cran-rlang{a} r-cran-rmarkdown{a} r-cran-rprojroot{a} r-cran-rsqlite{a} r-cran-rstudioapi{a} r-cran-scales{a} r-cran-shiny{a} r-cran-shinyjs{a} r-cran-snow{a} r-cran-sourcetools{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-tinytex{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{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} readline-common{a} rna-star{a} salmon{a} samtools{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} snakemake{a} sphinx-common{a} sphinx-rtd-theme-common{a} trim-galore{a} ttf-bitstream-vera{a} tzdata{a} ucf{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 awesome cinnamon curl cwltool dbus dunst fonts-dejavu-extra gnome-flashback gnome-shell graphicsmagick-imagemagick-compat imagemagick imagemagick-6.q16 javascript-common less libarchive-cpio-perl libatk-wrapper-java-jni libfile-mimeinfo-perl libgdk-pixbuf2.0-bin libglib2.0-data libgpm2 libjansi-java libjs-filesaver libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lxqt-notificationd lynx mate-notification-daemon mesa-vulkan-drivers node-clipboard nodejs-doc notification-daemon notify-osd openssh-client phosh plasma-workspace publicsuffix python3-azure-storage python3-biopython python3-boto3 python3-botocore python3-dropbox python3-flask python3-ftputil python3-gdal python3-irodsclient python3-jarabe python3-kubernetes python3-olefile python3-pydot python3-pygraphviz python3-tk python3-yappi r-base-dev r-bioc-glmgampoi r-bioc-go.db r-bioc-shortread r-cran-abind r-cran-batchjobs r-cran-batchtools r-cran-class r-cran-cliapp r-cran-codetools r-cran-dbitest r-cran-dbplyr r-cran-decor r-cran-domc r-cran-doparallel r-cran-dygraphs r-cran-future r-cran-ggthemes r-cran-hexbin r-cran-hms r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-maptools r-cran-mockery r-cran-mockr r-cran-png r-cran-quantreg r-cran-rmpi r-cran-rsclient r-cran-runit r-cran-sf r-cran-sodium r-cran-sp r-cran-testit r-cran-tikzdevice r-cran-vdiffr r-cran-webutils r-cran-xml2 r-doc-html r-recommended texlive-xetex wget x11-utils x11-xserver-utils xdg-user-dirs xfce4-notifyd 0 packages upgraded, 685 newly installed, 0 to remove and 0 not upgraded. Need to get 463 MB of archives. After unpacking 1698 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8+deb11u1 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 fonts-lato all 2.0-2.1 [2696 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 node-normalize.css all 8.0.1-3 [12.5 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 pigz arm64 2.6-1 [56.2 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2+deb11u5 [84.1 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 mailcap all 3.69 [31.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 mime-support all 3.66 [10.9 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 tzdata all 2021a-1+deb11u10 [286 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 sgml-base all 1.30 [15.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1w-0+deb11u1 [837 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3+deb11u1 [273 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3+deb11u1 [123 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3+deb11u1 [69.2 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 ucf all 3.0043 [74.0 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libnspr4 arm64 2:4.29-1 [105 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libnss3 arm64 2:3.61-1+deb11u3 [1209 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 ca-certificates-java all 20190909+deb11u1 [15.9 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 java-common all 0.72 [14.5 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libavahi-common-data arm64 0.8-5+deb11u2 [124 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libavahi-common3 arm64 0.8-5+deb11u2 [57.5 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libdbus-1-3 arm64 1.12.28-0+deb11u1 [213 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libavahi-client3 arm64 0.8-5+deb11u2 [61.0 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libcups2 arm64 2.3.3op2-3+deb11u6 [334 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 liblcms2-2 arm64 2.12~rc1-2 [140 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libfreetype6 arm64 2.10.4+dfsg-1+deb11u1 [393 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libasound2-data all 1.2.4-1.1 [38.2 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libasound2 arm64 1.2.4-1.1 [326 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libharfbuzz0b arm64 2.7.4-1 [1445 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libpcsclite1 arm64 1.9.1-1 [59.5 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 openjdk-11-jre-headless arm64 11.0.20+8-1~deb11u1 [37.3 MB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 default-jre-headless arm64 2:1.11-72 [10.9 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 ant all 1.10.9-4 [2118 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 ant-optional all 1.10.9-4 [381 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libblas3 arm64 3.9.0-3+deb11u1 [100 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 liblapack3 arm64 3.9.0-3+deb11u1 [1538 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 coinor-libcoinutils3v5 arm64 2.11.4+repack1-1 [417 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 coinor-libosi1v5 arm64 0.108.6+repack1-2 [229 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 coinor-libclp1 arm64 1.17.5+repack1-1 [777 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 coinor-libcgl1 arm64 0.60.3+repack1-2 [354 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 coinor-libcbc3 arm64 2.10.5+ds1-3 [610 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 coinor-cbc arm64 2.10.5+ds1-3 [14.7 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 python3-xopen all 1.1.0-1 [12.0 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 python3-dnaio arm64 0.5.0-1 [84.7 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 python3-cutadapt arm64 3.2-2 [120 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 cutadapt all 3.2-2 [22.3 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 90 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7+deb11u4 [629 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 95 http://deb.debian.org/debian bullseye/main arm64 libglvnd0 arm64 1.3.2-1 [44.3 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 98 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1+deb11u1 [106 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 libxcb1 arm64 1.14-3 [138 kB] Get: 101 http://deb.debian.org/debian bullseye/main arm64 libx11-data all 2:1.7.2-1+deb11u1 [311 kB] Get: 102 http://deb.debian.org/debian bullseye/main arm64 libx11-6 arm64 2:1.7.2-1+deb11u1 [749 kB] Get: 103 http://deb.debian.org/debian bullseye/main arm64 libdrm-common all 2.4.104-1 [14.9 kB] Get: 104 http://deb.debian.org/debian bullseye/main arm64 libdrm2 arm64 2.4.104-1 [41.3 kB] Get: 105 http://deb.debian.org/debian bullseye/main arm64 libglapi-mesa arm64 20.3.5-1 [96.7 kB] Get: 106 http://deb.debian.org/debian bullseye/main arm64 libx11-xcb1 arm64 2:1.7.2-1+deb11u1 [203 kB] Get: 107 http://deb.debian.org/debian bullseye/main arm64 libxcb-dri2-0 arm64 1.14-3 [103 kB] Get: 108 http://deb.debian.org/debian bullseye/main arm64 libxcb-dri3-0 arm64 1.14-3 [102 kB] Get: 109 http://deb.debian.org/debian bullseye/main arm64 libxcb-glx0 arm64 1.14-3 [118 kB] Get: 110 http://deb.debian.org/debian bullseye/main arm64 libxcb-present0 arm64 1.14-3 [101 kB] Get: 111 http://deb.debian.org/debian bullseye/main arm64 libxcb-shm0 arm64 1.14-3 [101 kB] Get: 112 http://deb.debian.org/debian bullseye/main arm64 libxcb-sync1 arm64 1.14-3 [105 kB] Get: 113 http://deb.debian.org/debian bullseye/main arm64 libxcb-xfixes0 arm64 1.14-3 [105 kB] Get: 114 http://deb.debian.org/debian bullseye/main arm64 libxdamage1 arm64 1:1.1.5-2 [15.7 kB] Get: 115 http://deb.debian.org/debian bullseye/main arm64 libxext6 arm64 2:1.3.3-1.1 [51.6 kB] Get: 116 http://deb.debian.org/debian bullseye/main arm64 libxfixes3 arm64 1:5.0.3-2 [22.1 kB] Get: 117 http://deb.debian.org/debian bullseye/main arm64 libxshmfence1 arm64 1.3-1 [8712 B] Get: 118 http://deb.debian.org/debian bullseye/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get: 119 http://deb.debian.org/debian bullseye/main arm64 libdrm-amdgpu1 arm64 2.4.104-1 [28.0 kB] Get: 120 http://deb.debian.org/debian bullseye/main arm64 libdrm-nouveau2 arm64 2.4.104-1 [26.1 kB] Get: 121 http://deb.debian.org/debian bullseye/main arm64 libdrm-radeon1 arm64 2.4.104-1 [29.3 kB] Get: 122 http://deb.debian.org/debian bullseye/main arm64 libedit2 arm64 3.1-20191231-2+b1 [92.1 kB] Get: 123 http://deb.debian.org/debian bullseye/main arm64 libz3-4 arm64 4.8.10-1 [6117 kB] Get: 124 http://deb.debian.org/debian bullseye/main arm64 libllvm11 arm64 1:11.0.1-2 [14.7 MB] Get: 125 http://deb.debian.org/debian bullseye/main arm64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get: 126 http://deb.debian.org/debian bullseye/main arm64 libsensors5 arm64 1:3.6.0-7 [51.2 kB] Get: 127 http://deb.debian.org/debian bullseye/main arm64 libvulkan1 arm64 1.2.162.0-1 [95.7 kB] Get: 128 http://deb.debian.org/debian bullseye/main arm64 libgl1-mesa-dri arm64 20.3.5-1 [6552 kB] Get: 129 http://deb.debian.org/debian bullseye/main arm64 libglx-mesa0 arm64 20.3.5-1 [186 kB] Get: 130 http://deb.debian.org/debian bullseye/main arm64 libglx0 arm64 1.3.2-1 [32.0 kB] Get: 131 http://deb.debian.org/debian bullseye/main arm64 libgl1 arm64 1.3.2-1 [91.4 kB] Get: 132 http://deb.debian.org/debian bullseye/main arm64 libgif7 arm64 5.1.9-2 [45.0 kB] Get: 133 http://deb.debian.org/debian bullseye/main arm64 libxi6 arm64 2:1.7.10-1 [81.7 kB] Get: 134 http://deb.debian.org/debian bullseye/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB] Get: 135 http://deb.debian.org/debian bullseye/main arm64 x11-common all 1:7.7+22 [252 kB] Get: 136 http://deb.debian.org/debian bullseye/main arm64 libxtst6 arm64 2:1.2.3-1 [26.7 kB] Get: 137 http://deb.debian.org/debian bullseye/main arm64 openjdk-11-jre arm64 11.0.20+8-1~deb11u1 [182 kB] Get: 138 http://deb.debian.org/debian bullseye/main arm64 default-jre arm64 2:1.11-72 [1044 B] Get: 139 http://deb.debian.org/debian bullseye/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 140 http://deb.debian.org/debian bullseye/main arm64 docutils-common all 0.16+dfsg-4 [129 kB] Get: 141 http://deb.debian.org/debian bullseye/main arm64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 142 http://deb.debian.org/debian bullseye/main arm64 libjbzip2-java all 0.9.1-5 [42.6 kB] Get: 143 http://deb.debian.org/debian bullseye/main arm64 libapache-pom-java all 18-1 [4676 B] Get: 144 http://deb.debian.org/debian bullseye/main arm64 libcommons-parent-java all 43-1 [10.8 kB] Get: 145 http://deb.debian.org/debian bullseye/main arm64 libcommons-compress-java all 1.20-1 [574 kB] Get: 146 http://deb.debian.org/debian bullseye/main arm64 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 147 http://deb.debian.org/debian bullseye/main arm64 libcommons-jexl2-java all 2.1.1-5 [256 kB] Get: 148 http://deb.debian.org/debian bullseye/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 149 http://deb.debian.org/debian bullseye/main arm64 libargs4j-java all 2.33-1.1 [137 kB] Get: 150 http://deb.debian.org/debian bullseye/main arm64 libjaxen-java all 1.1.6-4 [214 kB] Get: 151 http://deb.debian.org/debian bullseye/main arm64 libdom4j-java all 2.1.3-1 [310 kB] Get: 152 http://deb.debian.org/debian bullseye/main arm64 libcommons-io-java all 2.8.0-1 [279 kB] Get: 153 http://deb.debian.org/debian bullseye/main arm64 libmaven-shared-utils-java all 3.3.0-1+deb11u1 [149 kB] Get: 154 http://deb.debian.org/debian bullseye/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 155 http://deb.debian.org/debian bullseye/main arm64 libcommons-cli-java all 1.4-2 [57.3 kB] Get: 156 http://deb.debian.org/debian bullseye/main arm64 libcommons-lang3-java all 3.11-1 [550 kB] Get: 157 http://deb.debian.org/debian bullseye/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 158 http://deb.debian.org/debian bullseye/main arm64 libaopalliance-java all 20070526-6 [9048 B] Get: 159 http://deb.debian.org/debian bullseye/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 160 http://deb.debian.org/debian bullseye/main arm64 libguava-java all 29.0-6 [2419 kB] Get: 161 http://deb.debian.org/debian bullseye/main arm64 libguice-java all 4.2.3-2 [1435 kB] Get: 162 http://deb.debian.org/debian bullseye/main arm64 libmaven-parent-java all 31-2 [5100 B] Get: 163 http://deb.debian.org/debian bullseye/main arm64 libplexus-utils2-java all 3.3.0-1 [250 kB] Get: 164 http://deb.debian.org/debian bullseye/main arm64 libwagon-provider-api-java all 3.3.4-1 [50.2 kB] Get: 165 http://deb.debian.org/debian bullseye/main arm64 libmaven-resolver-java all 1.4.2-3 [556 kB] Get: 166 http://deb.debian.org/debian bullseye/main arm64 libplexus-cipher-java all 1.8-2 [15.0 kB] Get: 167 http://deb.debian.org/debian bullseye/main arm64 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 168 http://deb.debian.org/debian bullseye/main arm64 libplexus-component-annotations-java all 2.1.0-1 [7620 B] Get: 169 http://deb.debian.org/debian bullseye/main arm64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 170 http://deb.debian.org/debian bullseye/main arm64 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 171 http://deb.debian.org/debian bullseye/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 172 http://deb.debian.org/debian bullseye/main arm64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 173 http://deb.debian.org/debian bullseye/main arm64 libslf4j-java all 1.7.30-1 [144 kB] Get: 174 http://deb.debian.org/debian bullseye/main arm64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 175 http://deb.debian.org/debian bullseye/main arm64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 176 http://deb.debian.org/debian bullseye/main arm64 libmaven3-core-java all 3.6.3-5 [1538 kB] Get: 177 http://deb.debian.org/debian bullseye/main arm64 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 178 http://deb.debian.org/debian bullseye/main arm64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 179 http://deb.debian.org/debian bullseye/main arm64 libplexus-io-java all 3.2.0-1.1 [65.0 kB] Get: 180 http://deb.debian.org/debian bullseye/main arm64 libsnappy1v5 arm64 1.1.8-1 [17.2 kB] Get: 181 http://deb.debian.org/debian bullseye/main arm64 libsnappy-jni arm64 1.1.8.3-1 [7056 B] Get: 182 http://deb.debian.org/debian bullseye/main arm64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 183 http://deb.debian.org/debian bullseye/main arm64 libxz-java all 1.8-2 [141 kB] Get: 184 http://deb.debian.org/debian bullseye/main arm64 libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 185 http://deb.debian.org/debian bullseye/main arm64 libhttpcore-java all 4.4.14-1 [631 kB] Get: 186 http://deb.debian.org/debian bullseye/main arm64 libcommons-codec-java all 1.15-1 [292 kB] Get: 187 http://deb.debian.org/debian bullseye/main arm64 libhttpclient-java all 4.5.13-2 [1233 kB] Get: 188 http://deb.debian.org/debian bullseye/main arm64 libjsoup-java all 1.10.2-2 [350 kB] Get: 189 http://deb.debian.org/debian bullseye/main arm64 libwagon-http-java all 3.3.4-1 [53.9 kB] Get: 190 http://deb.debian.org/debian bullseye/main arm64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 191 http://deb.debian.org/debian bullseye/main arm64 libcodemodel-java all 2.6+jaxb2.3.0.1-10 [163 kB] Get: 192 http://deb.debian.org/debian bullseye/main arm64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 193 http://deb.debian.org/debian bullseye/main arm64 librngom-java all 2.3.0.1-10 [288 kB] Get: 194 http://deb.debian.org/debian bullseye/main arm64 libxsom-java all 2.3.0.1-10 [396 kB] Get: 195 http://deb.debian.org/debian bullseye/main arm64 libtxw2-java all 2.3.0.1-10 [134 kB] Get: 196 http://deb.debian.org/debian bullseye/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 197 http://deb.debian.org/debian bullseye/main arm64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 198 http://deb.debian.org/debian bullseye/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 199 http://deb.debian.org/debian bullseye/main arm64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 200 http://deb.debian.org/debian bullseye/main arm64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 201 http://deb.debian.org/debian bullseye/main arm64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 202 http://deb.debian.org/debian bullseye/main arm64 libjaxb-java all 2.3.0.1-10 [1954 kB] Get: 203 http://deb.debian.org/debian bullseye/main arm64 libngs-sdk2 arm64 2.10.9-1 [45.5 kB] Get: 204 http://deb.debian.org/debian bullseye/main arm64 libngs-sdk-dev arm64 2.10.9-1 [91.9 kB] Get: 205 http://deb.debian.org/debian bullseye/main arm64 libngs-java arm64 2.10.9-1 [80.4 kB] Get: 206 http://deb.debian.org/debian bullseye/main arm64 libhtsjdk-java all 2.23.0+dfsg-2 [1607 kB] Get: 207 http://deb.debian.org/debian bullseye/main arm64 libfindbin-libs-perl all 2.190.02-1 [30.3 kB] Get: 208 http://deb.debian.org/debian bullseye/main arm64 libsis-base-jni arm64 18.09~pre1+git20180928.45fbd31+dfsg-3 [13.1 kB] Get: 209 http://deb.debian.org/debian bullseye/main arm64 libsis-base-java all 18.09~pre1+git20180928.45fbd31+dfsg-3 [97.8 kB] Get: 210 http://deb.debian.org/debian bullseye/main arm64 libaec0 arm64 1.0.4-1 [19.8 kB] Get: 211 http://deb.debian.org/debian bullseye/main arm64 libsz2 arm64 1.0.4-1 [6736 B] Get: 212 http://deb.debian.org/debian bullseye/main arm64 libhdf5-103-1 arm64 1.10.6+repack-4+deb11u1 [1032 kB] Get: 213 http://deb.debian.org/debian bullseye/main arm64 libsis-jhdf5-jni arm64 19.04.0+dfsg-4 [95.8 kB] Get: 214 http://deb.debian.org/debian bullseye/main arm64 libsis-jhdf5-java all 19.04.0+dfsg-4 [1491 kB] Get: 215 http://deb.debian.org/debian bullseye/main arm64 fastqc all 0.11.9+dfsg-4 [390 kB] Get: 216 http://deb.debian.org/debian bullseye/main arm64 fontconfig arm64 2.13.1-4.2 [416 kB] Get: 217 http://deb.debian.org/debian bullseye/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 218 http://deb.debian.org/debian bullseye/main arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-2 [164 kB] Get: 219 http://deb.debian.org/debian bullseye/main arm64 fonts-lyx all 2.3.6-1 [205 kB] Get: 220 http://deb.debian.org/debian bullseye/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 221 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1+deb11u1 [69.4 kB] Get: 222 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1+deb11u1 [105 kB] Get: 223 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3+deb11u1 [222 kB] Get: 224 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 225 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 226 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 227 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 228 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+deb11u9 [323 kB] Get: 229 http://deb.debian.org/debian bullseye/main arm64 liberror-perl all 0.17029-1 [31.0 kB] Get: 230 http://deb.debian.org/debian bullseye/main arm64 git-man all 1:2.30.2-1+deb11u2 [1828 kB] Get: 231 http://deb.debian.org/debian bullseye/main arm64 git arm64 1:2.30.2-1+deb11u2 [5423 kB] Get: 232 http://deb.debian.org/debian bullseye/main arm64 libbibutils7 arm64 6.10-2 [358 kB] Get: 233 http://deb.debian.org/debian bullseye/main arm64 libbigwig0 arm64 0.4.4+dfsg-2 [25.7 kB] Get: 234 http://deb.debian.org/debian bullseye/main arm64 libboost1.74-dev arm64 1.74.0-9 [9534 kB] Get: 235 http://deb.debian.org/debian bullseye/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] Get: 236 http://deb.debian.org/debian bullseye/main arm64 libboost-filesystem1.74.0 arm64 1.74.0-9 [278 kB] Get: 237 http://deb.debian.org/debian bullseye/main arm64 libboost-program-options1.74.0 arm64 1.74.0-9 [344 kB] Get: 238 http://deb.debian.org/debian bullseye/main arm64 libc-ares2 arm64 1.17.1-1+deb11u3 [100.0 kB] Get: 239 http://deb.debian.org/debian bullseye/main arm64 libpixman-1-0 arm64 0.40.0-1.1~deb11u1 [445 kB] Get: 240 http://deb.debian.org/debian bullseye/main arm64 libxcb-render0 arm64 1.14-3 [111 kB] Get: 241 http://deb.debian.org/debian bullseye/main arm64 libcairo2 arm64 1.16.0-5 [648 kB] Get: 242 http://deb.debian.org/debian bullseye/main arm64 libcmark-gfm0 arm64 0.29.0.gfm.0-6 [108 kB] Get: 243 http://deb.debian.org/debian bullseye/main arm64 libcmark-gfm-extensions0 arm64 0.29.0.gfm.0-6 [45.4 kB] Get: 244 http://deb.debian.org/debian bullseye/main arm64 libcurl4 arm64 7.74.0-1.3+deb11u9 [326 kB] Get: 245 http://deb.debian.org/debian bullseye/main arm64 libdatrie1 arm64 0.2.13-1 [42.1 kB] Get: 246 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 247 http://deb.debian.org/debian bullseye/main arm64 libfribidi0 arm64 1.0.8-2+deb11u1 [64.9 kB] Get: 248 http://deb.debian.org/debian bullseye/main arm64 libgdk-pixbuf2.0-common all 2.42.2+dfsg-1+deb11u1 [320 kB] Get: 249 http://deb.debian.org/debian bullseye/main arm64 shared-mime-info arm64 2.0-1 [700 kB] Get: 250 http://deb.debian.org/debian bullseye/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB] Get: 251 http://deb.debian.org/debian bullseye/main arm64 libwebp6 arm64 0.6.1-2.1+deb11u2 [244 kB] Get: 252 http://deb.debian.org/debian bullseye/main arm64 libtiff5 arm64 4.2.0-1+deb11u4 [278 kB] Get: 253 http://deb.debian.org/debian bullseye/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.2+dfsg-1+deb11u1 [136 kB] Get: 254 http://deb.debian.org/debian bullseye/main arm64 libghc-pandoc-citeproc-data all 0.17.0.1-1 [80.3 kB] Get: 255 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 256 http://deb.debian.org/debian bullseye/main arm64 libhtscodecs2 arm64 0.5-3 [48.3 kB] Get: 257 http://deb.debian.org/debian bullseye/main arm64 libice6 arm64 2:1.0.10-1 [55.6 kB] Get: 258 http://deb.debian.org/debian bullseye/main arm64 libimagequant0 arm64 2.12.2-1.1 [30.3 kB] Get: 259 http://deb.debian.org/debian bullseye/main arm64 libjemalloc2 arm64 5.2.1-3 [192 kB] Get: 260 http://deb.debian.org/debian bullseye/main arm64 libjs-bootstrap all 3.4.1+dfsg-2 [173 kB] Get: 261 http://deb.debian.org/debian bullseye/main arm64 libjs-d3 all 3.5.17-4 [132 kB] Get: 262 http://deb.debian.org/debian bullseye/main arm64 libjs-d3-format all 1:1.4.1-3 [16.9 kB] Get: 263 http://deb.debian.org/debian bullseye/main arm64 libjs-es5-shim all 4.5.15-1 [43.6 kB] Get: 264 http://deb.debian.org/debian bullseye/main arm64 libjs-highlight.js all 9.18.5+dfsg1-1 [397 kB] Get: 265 http://deb.debian.org/debian bullseye/main arm64 libjs-inherits all 2.0.4-1 [3228 B] Get: 266 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 267 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery-datatables all 1.10.21+dfsg-2+deb11u1 [138 kB] Get: 268 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery-datatables-extensions all 0.0+git20150910.28fd64e+dfsg-5 [648 kB] Get: 269 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery-metadata all 12-3 [7660 B] Get: 270 http://deb.debian.org/debian bullseye/main arm64 libjs-sifter.js all 0.6.0+dfsg-1 [12.1 kB] Get: 271 http://deb.debian.org/debian bullseye/main arm64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B] Get: 272 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB] Get: 273 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-1 [185 kB] Get: 274 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 275 http://deb.debian.org/debian bullseye/main arm64 libjs-json all 0~20190826+~1.0.5-2 [20.5 kB] Get: 276 http://deb.debian.org/debian bullseye/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 277 http://deb.debian.org/debian bullseye/main arm64 libjs-modernizr all 2.6.2+ds1-4 [47.1 kB] Get: 278 http://deb.debian.org/debian bullseye/main arm64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB] Get: 279 http://deb.debian.org/debian bullseye/main arm64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 280 http://deb.debian.org/debian bullseye/main arm64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 281 http://deb.debian.org/debian bullseye/main arm64 libjs-sprintf-js all 1.1.2+ds1-2 [12.3 kB] Get: 282 http://deb.debian.org/debian bullseye/main arm64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB] Get: 283 http://deb.debian.org/debian bullseye/main arm64 libuv1 arm64 1.40.0-2 [126 kB] Get: 284 http://deb.debian.org/debian bullseye/main arm64 libnode72 arm64 12.22.12~dfsg-1~deb11u4 [7694 kB] Get: 285 http://deb.debian.org/debian bullseye/main arm64 nodejs arm64 12.22.12~dfsg-1~deb11u4 [148 kB] Get: 286 http://deb.debian.org/debian bullseye/main arm64 node-inherits all 2.0.4-1 [4204 B] Get: 287 http://deb.debian.org/debian bullseye/main arm64 libjs-util all 0.10.3-4 [9620 B] Get: 288 http://deb.debian.org/debian bullseye/main arm64 liblbfgsb0 arm64 3.0+dfsg.3-9 [24.5 kB] Get: 289 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2+deb11u2 [93.1 kB] Get: 290 http://deb.debian.org/debian bullseye/main arm64 libnotify4 arm64 0.7.9-3 [23.0 kB] Get: 291 http://deb.debian.org/debian bullseye/main arm64 libnotify-bin arm64 0.7.9-3 [14.2 kB] Get: 292 http://deb.debian.org/debian bullseye/main arm64 libthai-data all 0.1.28-3 [170 kB] Get: 293 http://deb.debian.org/debian bullseye/main arm64 libthai0 arm64 0.1.28-3 [53.0 kB] Get: 294 http://deb.debian.org/debian bullseye/main arm64 libpango-1.0-0 arm64 1.46.2-3 [183 kB] Get: 295 http://deb.debian.org/debian bullseye/main arm64 libpangoft2-1.0-0 arm64 1.46.2-3 [59.4 kB] Get: 296 http://deb.debian.org/debian bullseye/main arm64 libpangocairo-1.0-0 arm64 1.46.2-3 [48.6 kB] Get: 297 http://deb.debian.org/debian bullseye/main arm64 libpaper1 arm64 1.1.28+b1 [21.4 kB] Get: 298 http://deb.debian.org/debian bullseye/main arm64 libpaper-utils arm64 1.1.28+b1 [18.3 kB] Get: 299 http://deb.debian.org/debian bullseye/main arm64 libpython3.9 arm64 3.9.2-1 [1556 kB] Get: 300 http://deb.debian.org/debian bullseye/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get: 301 http://deb.debian.org/debian bullseye/main arm64 libstaden-read14 arm64 1.14.13-4 [251 kB] Get: 302 http://deb.debian.org/debian bullseye/main arm64 libtbb2 arm64 2020.3-1 [131 kB] Get: 303 http://deb.debian.org/debian bullseye/main arm64 libtcl8.6 arm64 8.6.11+dfsg-1 [964 kB] Get: 304 http://deb.debian.org/debian bullseye/main arm64 libxft2 arm64 2.3.2-2 [51.3 kB] Get: 305 http://deb.debian.org/debian bullseye/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB] Get: 306 http://deb.debian.org/debian bullseye/main arm64 libtk8.6 arm64 8.6.11-2 [738 kB] Get: 307 http://deb.debian.org/debian bullseye/main arm64 libwebpdemux2 arm64 0.6.1-2.1+deb11u2 [87.6 kB] Get: 308 http://deb.debian.org/debian bullseye/main arm64 libwebpmux3 arm64 0.6.1-2.1+deb11u2 [96.7 kB] Get: 309 http://deb.debian.org/debian bullseye/main arm64 libxt6 arm64 1:1.2.0-1 [176 kB] Get: 310 http://deb.debian.org/debian bullseye/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get: 311 http://deb.debian.org/debian bullseye/main arm64 zip arm64 3.0-12 [228 kB] Get: 312 http://deb.debian.org/debian bullseye/main arm64 unzip arm64 6.0-26+deb11u1 [165 kB] Get: 313 http://deb.debian.org/debian bullseye/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 314 http://deb.debian.org/debian bullseye/main arm64 r-base-core arm64 4.0.4-1 [24.9 MB] Get: 315 http://deb.debian.org/debian bullseye/main arm64 r-cran-littler arm64 0.3.12-1 [95.1 kB] Get: 316 http://deb.debian.org/debian bullseye/main arm64 littler all 0.3.12-1 [15.6 kB] Get: 317 http://deb.debian.org/debian bullseye/main arm64 node-ansi-colors all 4.1.1-2 [13.2 kB] Get: 318 http://deb.debian.org/debian bullseye/main arm64 node-browser-stdout all 1.3.1-2 [3268 B] Get: 319 http://deb.debian.org/debian bullseye/main arm64 node-camelcase all 6.2.0-2 [5512 B] Get: 320 http://deb.debian.org/debian bullseye/main arm64 node-color-name all 1.1.4+~1.1.1-1 [5788 B] Get: 321 http://deb.debian.org/debian bullseye/main arm64 node-color-convert all 1.9.3-1 [10.2 kB] Get: 322 http://deb.debian.org/debian bullseye/main arm64 node-ansi-styles all 4.2.1-1 [7600 B] Get: 323 http://deb.debian.org/debian bullseye/main arm64 node-escape-string-regexp all 4.0.0-1 [4116 B] Get: 324 http://deb.debian.org/debian bullseye/main arm64 node-has-flag all 4.0.0-1 [4076 B] Get: 325 http://deb.debian.org/debian bullseye/main arm64 node-supports-color all 8.1.0+~7.2.0-1 [6736 B] Get: 326 http://deb.debian.org/debian bullseye/main arm64 node-chalk all 4.1.0-1 [15.0 kB] Get: 327 http://deb.debian.org/debian bullseye/main arm64 node-is-extglob all 2.1.1-1 [4128 B] Get: 328 http://deb.debian.org/debian bullseye/main arm64 node-is-glob all 4.0.1-1 [6312 B] Get: 329 http://deb.debian.org/debian bullseye/main arm64 node-binary-extensions all 2.2.0-1 [4352 B] Get: 330 http://deb.debian.org/debian bullseye/main arm64 node-is-binary-path all 2.1.0-1 [3432 B] Get: 331 http://deb.debian.org/debian bullseye/main arm64 node-normalize-path all 3.0.0-2 [5752 B] Get: 332 http://deb.debian.org/debian bullseye/main arm64 node-anymatch all 3.1.1+~2.2.2-1 [28.5 kB] Get: 333 http://deb.debian.org/debian bullseye/main arm64 node-graceful-fs all 4.2.4+repack-1 [13.1 kB] Get: 334 http://deb.debian.org/debian bullseye/main arm64 node-set-immediate-shim all 2.0.0-1 [3600 B] Get: 335 http://deb.debian.org/debian bullseye/main arm64 node-readdirp all 3.5.0-2 [11.3 kB] Get: 336 http://deb.debian.org/debian bullseye/main arm64 node-async-each all 1.0.3-1 [4024 B] Get: 337 http://deb.debian.org/debian bullseye/main arm64 node-is-buffer all 2.0.5-1 [4048 B] Get: 338 http://deb.debian.org/debian bullseye/main arm64 node-kind-of all 6.0.3+dfsg-1 [10.0 kB] Get: 339 http://deb.debian.org/debian bullseye/main arm64 node-is-number all 7.0.0-1.1 [5860 B] Get: 340 http://deb.debian.org/debian bullseye/main arm64 node-repeat-string all 1.6.1-1 [5180 B] Get: 341 http://deb.debian.org/debian bullseye/main arm64 node-to-regex-range all 5.0.1-2 [10.2 kB] Get: 342 http://deb.debian.org/debian bullseye/main arm64 node-fill-range all 7.0.1-2 [7872 B] Get: 343 http://deb.debian.org/debian bullseye/main arm64 node-braces all 3.0.2+~3.0.0-1 [20.6 kB] Get: 344 http://deb.debian.org/debian bullseye/main arm64 node-path-is-absolute all 2.0.0-1 [3864 B] Get: 345 http://deb.debian.org/debian bullseye/main arm64 node-path-dirname all 1.0.2-1.1 [3972 B] Get: 346 http://deb.debian.org/debian bullseye/main arm64 node-glob-parent all 5.1.1+~5.1.0-2 [6672 B] Get: 347 http://deb.debian.org/debian bullseye/main arm64 node-chokidar all 3.4.3-3 [32.0 kB] Get: 348 http://deb.debian.org/debian bullseye/main arm64 node-ms all 2.1.3+~cs0.7.31-1 [5612 B] Get: 349 http://deb.debian.org/debian bullseye/main arm64 node-debug all 4.3.1+~cs4.1.5-1 [17.3 kB] Get: 350 http://deb.debian.org/debian bullseye/main arm64 node-decamelize all 4.0.0-1 [3944 B] Get: 351 http://deb.debian.org/debian bullseye/main arm64 node-diff all 4.0.2~dfsg-2 [65.0 kB] Get: 352 http://deb.debian.org/debian bullseye/main arm64 node-p-limit all 3.1.0+~cs2.3.0-1 [6904 B] Get: 353 http://deb.debian.org/debian bullseye/main arm64 node-p-locate all 5.0.0-1 [5080 B] Get: 354 http://deb.debian.org/debian bullseye/main arm64 node-path-exists all 4.0.0-2 [3840 B] Get: 355 http://deb.debian.org/debian bullseye/main arm64 node-locate-path all 6.0.0-1 [5264 B] Get: 356 http://deb.debian.org/debian bullseye/main arm64 node-find-up all 5.0.0-1 [5840 B] Get: 357 http://deb.debian.org/debian bullseye/main arm64 node-fs.realpath all 1.0.0-1.1 [5780 B] Get: 358 http://deb.debian.org/debian bullseye/main arm64 node-wrappy all 1.0.2-1.1 [3352 B] Get: 359 http://deb.debian.org/debian bullseye/main arm64 node-once all 1.4.0-3 [4344 B] Get: 360 http://deb.debian.org/debian bullseye/main arm64 node-inflight all 1.0.6-1.1 [3568 B] Get: 361 http://deb.debian.org/debian bullseye/main arm64 node-balanced-match all 1.0.0-1 [4528 B] Get: 362 http://deb.debian.org/debian bullseye/main arm64 node-brace-expansion all 2.0.0-1 [7184 B] Get: 363 http://deb.debian.org/debian bullseye/main arm64 node-minimatch all 3.0.4+~3.0.3-1+deb11u2 [16.1 kB] Get: 364 http://deb.debian.org/debian bullseye/main arm64 node-glob all 7.1.6+~7.1.3-1 [129 kB] Get: 365 http://deb.debian.org/debian bullseye/main arm64 node-growl all 1.10.5-2 [7356 B] Get: 366 http://deb.debian.org/debian bullseye/main arm64 node-he all 1.2.0-1 [36.7 kB] Get: 367 http://deb.debian.org/debian bullseye/main arm64 node-is-plain-obj all 3.0.0-1 [3916 B] Get: 368 http://deb.debian.org/debian bullseye/main arm64 node-sprintf-js all 1.1.2+ds1-2 [1836 B] Get: 369 http://deb.debian.org/debian bullseye/main arm64 node-argparse all 2.0.1-1 [34.5 kB] Get: 370 http://deb.debian.org/debian bullseye/main arm64 node-esprima all 4.0.1+ds+~4.0.2-2 [69.0 kB] Get: 371 http://deb.debian.org/debian bullseye/main arm64 node-js-yaml all 3.14.1+dfsg+~3.12.6-2 [44.8 kB] Get: 372 http://deb.debian.org/debian bullseye/main arm64 node-safe-buffer all 5.2.1+~cs2.1.2-1 [15.5 kB] Get: 373 http://deb.debian.org/debian bullseye/main arm64 node-randombytes all 2.1.0-1 [4104 B] Get: 374 http://deb.debian.org/debian bullseye/main arm64 node-serialize-javascript all 5.0.1-2 [11.5 kB] Get: 375 http://deb.debian.org/debian bullseye/main arm64 node-strip-json-comments all 3.1.1-1 [5168 B] Get: 376 http://deb.debian.org/debian bullseye/main arm64 node-isexe all 2.0.0-5 [4632 B] Get: 377 http://deb.debian.org/debian bullseye/main arm64 node-which all 2.0.2+~cs1.3.2-1 [8436 B] Get: 378 http://deb.debian.org/debian bullseye/main arm64 node-ansi-regex all 5.0.1-1~deb11u1 [4704 B] Get: 379 http://deb.debian.org/debian bullseye/main arm64 node-strip-ansi all 6.0.0-2 [4044 B] Get: 380 http://deb.debian.org/debian bullseye/main arm64 node-clone all 2.1.2-2 [8132 B] Get: 381 http://deb.debian.org/debian bullseye/main arm64 node-defaults all 1.0.3-2 [3612 B] Get: 382 http://deb.debian.org/debian bullseye/main arm64 node-wcwidth.js all 1.0.0-1.1 [6652 B] Get: 383 http://deb.debian.org/debian bullseye/main arm64 node-string-width all 4.2.0-1 [9716 B] Get: 384 http://deb.debian.org/debian bullseye/main arm64 node-wide-align all 1.1.3-1 [3896 B] Get: 385 http://deb.debian.org/debian bullseye/main arm64 node-require-directory all 2.1.1-1.1 [5596 B] Get: 386 http://deb.debian.org/debian bullseye/main arm64 node-get-caller-file all 1.0.2-1.1 [3056 B] Get: 387 http://deb.debian.org/debian bullseye/main arm64 node-set-blocking all 2.0.0-1.1 [4036 B] Get: 388 http://deb.debian.org/debian bullseye/main arm64 node-require-main-filename all 2.0.0-1 [4108 B] Get: 389 http://deb.debian.org/debian bullseye/main arm64 node-wrap-ansi all 4.0.0-2 [5540 B] Get: 390 http://deb.debian.org/debian bullseye/main arm64 node-cliui all 4.1.0-2 [7964 B] Get: 391 http://deb.debian.org/debian bullseye/main arm64 node-which-module all 2.0.0-1 [3792 B] Get: 392 http://deb.debian.org/debian bullseye/main arm64 node-end-of-stream all 1.4.4-1 [4356 B] Get: 393 http://deb.debian.org/debian bullseye/main arm64 node-pump all 3.0.0-4 [4936 B] Get: 394 http://deb.debian.org/debian bullseye/main arm64 node-get-stream all 6.0.0-1 [7172 B] Get: 395 http://deb.debian.org/debian bullseye/main arm64 node-is-stream all 2.0.0-1 [4004 B] Get: 396 http://deb.debian.org/debian bullseye/main arm64 node-merge-stream all 2.0.0+~1.1.2-1 [5036 B] Get: 397 http://deb.debian.org/debian bullseye/main arm64 node-mimic-fn all 3.1.0-1 [5180 B] Get: 398 http://deb.debian.org/debian bullseye/main arm64 node-npm-run-path all 2.0.2-2 [4412 B] Get: 399 http://deb.debian.org/debian bullseye/main arm64 node-shebang-regex all 3.0.0-1 [3352 B] Get: 400 http://deb.debian.org/debian bullseye/main arm64 node-shebang-command all 1.2.0-1.1 [3132 B] Get: 401 http://deb.debian.org/debian bullseye/main arm64 node-signal-exit all 3.0.3-1 [6172 B] Get: 402 http://deb.debian.org/debian bullseye/main arm64 node-execa all 4.1.0+dfsg+~cs19.3.6-5 [28.1 kB] Get: 403 http://deb.debian.org/debian bullseye/main arm64 node-invert-kv all 3.0.1-1 [3904 B] Get: 404 http://deb.debian.org/debian bullseye/main arm64 node-lcid all 3.1.1-1 [5280 B] Get: 405 http://deb.debian.org/debian bullseye/main arm64 node-mem all 1.1.0-1.1 [4308 B] Get: 406 http://deb.debian.org/debian bullseye/main arm64 node-os-locale all 5.0.0-1 [4876 B] Get: 407 http://deb.debian.org/debian bullseye/main arm64 node-y18n all 4.0.0-4 [6256 B] Get: 408 http://deb.debian.org/debian bullseye/main arm64 node-yargs-parser all 18.1.3+~15.0.0-1 [24.0 kB] Get: 409 http://deb.debian.org/debian bullseye/main arm64 node-yargs all 15.3.1+repack-2 [109 kB] Get: 410 http://deb.debian.org/debian bullseye/main arm64 mocha all 8.2.1+ds1+~cs29.4.27-3 [157 kB] Get: 411 http://deb.debian.org/debian bullseye/main arm64 python3-colorama all 0.4.4-1 [28.5 kB] Get: 412 http://deb.debian.org/debian bullseye/main arm64 python3-click all 7.1.2-1 [75.7 kB] Get: 413 http://deb.debian.org/debian bullseye/main arm64 python3-humanfriendly all 9.1-1 [84.6 kB] Get: 414 http://deb.debian.org/debian bullseye/main arm64 python3-coloredlogs all 7.3-2 [28.0 kB] Get: 415 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 416 http://deb.debian.org/debian bullseye/main arm64 python3-future all 0.18.2-5 [349 kB] Get: 417 http://deb.debian.org/debian bullseye/main arm64 python3-markupsafe arm64 1.1.1-1+b3 [15.2 kB] Get: 418 http://deb.debian.org/debian bullseye/main arm64 python3-jinja2 all 2.11.3-1 [114 kB] Get: 419 http://deb.debian.org/debian bullseye/main arm64 python3-lzstring all 1.0.4-1.1 [5456 B] Get: 420 http://deb.debian.org/debian bullseye/main arm64 python3-markdown all 3.3.4-1 [71.4 kB] Get: 421 http://deb.debian.org/debian bullseye/main arm64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 422 http://deb.debian.org/debian bullseye/main arm64 python3-six all 1.16.0-2 [17.5 kB] Get: 423 http://deb.debian.org/debian bullseye/main arm64 python3-dateutil all 2.8.1-6 [79.2 kB] Get: 424 http://deb.debian.org/debian bullseye/main arm64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 425 http://deb.debian.org/debian bullseye/main arm64 python3-numpy arm64 1:1.19.5-1 [3196 kB] Get: 426 http://deb.debian.org/debian bullseye/main arm64 python3-cycler all 0.10.0-3 [8084 B] Get: 427 http://deb.debian.org/debian bullseye/main arm64 python3-kiwisolver arm64 1.3.1-1+b1 [51.6 kB] Get: 428 http://deb.debian.org/debian bullseye/main arm64 python3-pil arm64 8.1.2+dfsg-0.3+deb11u1 [429 kB] Get: 429 http://deb.debian.org/debian bullseye/main arm64 python3-matplotlib arm64 3.3.4-1 [4109 kB] Get: 430 http://deb.debian.org/debian bullseye/main arm64 python3-decorator all 4.4.2-2 [15.8 kB] Get: 431 http://deb.debian.org/debian bullseye/main arm64 python3-networkx all 2.5+ds-2 [900 kB] Get: 432 http://deb.debian.org/debian bullseye/main arm64 python3-certifi all 2020.6.20-1 [151 kB] Get: 433 http://deb.debian.org/debian bullseye/main arm64 python3-chardet all 4.0.0-1 [99.0 kB] Get: 434 http://deb.debian.org/debian bullseye/main arm64 python3-idna all 2.10-1 [37.4 kB] Get: 435 http://deb.debian.org/debian bullseye/main arm64 python3-urllib3 all 1.26.5-1~exp1 [114 kB] Get: 436 http://deb.debian.org/debian bullseye/main arm64 python3-requests all 2.25.1+dfsg-2 [69.3 kB] Get: 437 http://deb.debian.org/debian bullseye/main arm64 python3-simplejson arm64 3.17.2-1 [60.6 kB] Get: 438 http://deb.debian.org/debian bullseye/main arm64 python3-colormath all 3.0.0-1.1 [35.3 kB] Get: 439 http://deb.debian.org/debian bullseye/main arm64 python3-spectra all 0.0.11-2 [16.4 kB] Get: 440 http://deb.debian.org/debian bullseye/main arm64 python3-yaml arm64 5.3.1-5 [118 kB] Get: 441 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 442 http://deb.debian.org/debian bullseye/main arm64 multiqc all 1.9+dfsg-3 [554 kB] Get: 443 http://deb.debian.org/debian bullseye/main arm64 node-object-assign all 4.1.1-3 [4460 B] Get: 444 http://deb.debian.org/debian bullseye/main arm64 node-util all 0.10.3-4 [2960 B] Get: 445 http://deb.debian.org/debian bullseye/main arm64 node-assert all 1.5.0-1 [8892 B] Get: 446 http://deb.debian.org/debian bullseye/main arm64 node-commander all 6.2.1-2 [38.3 kB] Get: 447 http://deb.debian.org/debian bullseye/main arm64 node-d3-array all 1.2.4-3 [19.2 kB] Get: 448 http://deb.debian.org/debian bullseye/main arm64 node-d3-axis all 1.0.12-3 [10.1 kB] Get: 449 http://deb.debian.org/debian bullseye/main arm64 node-d3-dispatch all 1.0.6-2 [7856 B] Get: 450 http://deb.debian.org/debian bullseye/main arm64 node-d3-selection all 1.4.0-6 [30.7 kB] Get: 451 http://deb.debian.org/debian bullseye/main arm64 node-d3-drag all 1.2.5-2 [13.9 kB] Get: 452 http://deb.debian.org/debian bullseye/main arm64 node-d3-color all 1.2.8-2 [15.0 kB] Get: 453 http://deb.debian.org/debian bullseye/main arm64 node-d3-interpolate all 1.4.0-2 [18.5 kB] Get: 454 http://deb.debian.org/debian bullseye/main arm64 node-d3-ease all 1.0.5-3 [9932 B] Get: 455 http://deb.debian.org/debian bullseye/main arm64 node-d3-timer all 1.0.10-1 [8608 B] Get: 456 http://deb.debian.org/debian bullseye/main arm64 node-d3-transition all 1.3.2-3 [22.2 kB] Get: 457 http://deb.debian.org/debian bullseye/main arm64 node-d3-brush all 1.1.5-2 [181 kB] Get: 458 http://deb.debian.org/debian bullseye/main arm64 node-d3-path all 1.0.9-2 [8212 B] Get: 459 http://deb.debian.org/debian bullseye/main arm64 node-d3-chord all 1.0.6-3 [10.0 kB] Get: 460 http://deb.debian.org/debian bullseye/main arm64 node-d3-collection all 1.0.7-3 [11.7 kB] Get: 461 http://deb.debian.org/debian bullseye/main arm64 node-d3-contour all 1.3.2-4 [13.6 kB] Get: 462 http://deb.debian.org/debian bullseye/main arm64 node-iconv-lite all 0.5.1-3 [128 kB] Get: 463 http://deb.debian.org/debian bullseye/main arm64 node-d3-queue all 3.0.7-11 [9828 B] Get: 464 http://deb.debian.org/debian bullseye/main arm64 node-rw all 1.3.3-2 [7096 B] Get: 465 http://deb.debian.org/debian bullseye/main arm64 node-d3-dsv all 1.1.1-5 [14.5 kB] Get: 466 http://deb.debian.org/debian bullseye/main arm64 node-d3-fetch all 1.2.0-1 [7344 B] Get: 467 http://deb.debian.org/debian bullseye/main arm64 node-d3-quadtree all 1.0.7-2 [13.1 kB] Get: 468 http://deb.debian.org/debian bullseye/main arm64 node-d3-force all 1.2.1-2 [368 kB] Get: 469 http://deb.debian.org/debian bullseye/main arm64 node-d3-format all 1:1.4.1-3 [9004 B] Get: 470 http://deb.debian.org/debian bullseye/main arm64 node-d3-geo all 1.11.9-4 [53.6 kB] Get: 471 http://deb.debian.org/debian bullseye/main arm64 node-d3-hierarchy all 1.1.8-3 [28.6 kB] Get: 472 http://deb.debian.org/debian bullseye/main arm64 node-d3-polygon all 1.0.5-3 [7396 B] Get: 473 http://deb.debian.org/debian bullseye/main arm64 node-d3-random all 1.1.2-3 [7184 B] Get: 474 http://deb.debian.org/debian bullseye/main arm64 node-d3-time all 1.0.11-4 [14.6 kB] Get: 475 http://deb.debian.org/debian bullseye/main arm64 node-d3-time-format all 2.1.3-3 [18.9 kB] Get: 476 http://deb.debian.org/debian bullseye/main arm64 node-d3-scale all 2.2.2-3 [31.5 kB] Get: 477 http://deb.debian.org/debian bullseye/main arm64 node-d3-scale-chromatic all 1.5.0-2 [18.5 kB] Get: 478 http://deb.debian.org/debian bullseye/main arm64 node-d3-shape all 1.3.7-2 [40.4 kB] Get: 479 http://deb.debian.org/debian bullseye/main arm64 node-d3-voronoi all 1.1.4-3 [17.1 kB] Get: 480 http://deb.debian.org/debian bullseye/main arm64 node-d3-zoom all 1.8.3-2 [20.1 kB] Get: 481 http://deb.debian.org/debian bullseye/main arm64 node-d3 all 5.16.0-4 [208 kB] Get: 482 http://deb.debian.org/debian bullseye/main arm64 node-lodash all 4.17.21+dfsg+~cs8.31.173-1 [385 kB] Get: 483 http://deb.debian.org/debian bullseye/main arm64 node-graphlibrary all 2.2.0+really2.1.8+dfsg-3 [53.2 kB] Get: 484 http://deb.debian.org/debian bullseye/main arm64 node-dagre-layout all 0.8.8+really0.8.5+dfsg-4 [42.4 kB] Get: 485 http://deb.debian.org/debian bullseye/main arm64 node-dagre-d3-renderer all 0.6.4+dfsg-3 [601 kB] Get: 486 http://deb.debian.org/debian bullseye/main arm64 node-highlight.js all 9.18.5+dfsg1-1 [333 kB] Get: 487 http://deb.debian.org/debian bullseye/main arm64 node-html5shiv all 3.7.3+dfsg-3 [12.9 kB] Get: 488 http://deb.debian.org/debian bullseye/main arm64 pandoc-data all 2.9.2.1-1+deb11u1 [377 kB] Get: 489 http://deb.debian.org/debian bullseye/main arm64 pandoc arm64 2.9.2.1-1+deb11u1 [22.8 MB] Get: 490 http://deb.debian.org/debian bullseye/main arm64 pandoc-citeproc arm64 0.17.0.1-1+b2 [17.6 MB] Get: 491 http://deb.debian.org/debian bullseye/main arm64 python-babel-localedata all 2.8.0+dfsg.1-7 [4997 kB] Get: 492 http://deb.debian.org/debian bullseye/main arm64 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get: 493 http://deb.debian.org/debian bullseye/main arm64 python3-all arm64 3.9.2-3 [1056 B] Get: 494 http://deb.debian.org/debian bullseye/main arm64 python3-appdirs all 1.4.4-1 [12.7 kB] Get: 495 http://deb.debian.org/debian bullseye/main arm64 python3-attr all 20.3.0-1 [52.9 kB] Get: 496 http://deb.debian.org/debian bullseye/main arm64 python3-tz all 2021.1-1 [34.8 kB] Get: 497 http://deb.debian.org/debian bullseye/main arm64 python3-babel all 2.8.0+dfsg.1-7 [100 kB] Get: 498 http://deb.debian.org/debian bullseye/main arm64 python3-configargparse all 1.2.3-1 [25.2 kB] Get: 499 http://deb.debian.org/debian bullseye/main arm64 python3-datrie arm64 0.8.2-1+b1 [88.0 kB] Get: 500 http://deb.debian.org/debian bullseye/main arm64 python3-deeptoolsintervals arm64 0.1.9-3+b2 [49.9 kB] Get: 501 http://deb.debian.org/debian bullseye/main arm64 sphinx-common all 3.4.3-2 [578 kB] Get: 502 http://deb.debian.org/debian bullseye/main arm64 python3-roman all 2.0.0-5 [9064 B] Get: 503 http://deb.debian.org/debian bullseye/main arm64 python3-docutils all 0.16+dfsg-4 [384 kB] Get: 504 http://deb.debian.org/debian bullseye/main arm64 python3-imagesize all 1.2.0-2 [5824 B] Get: 505 http://deb.debian.org/debian bullseye/main arm64 python3-packaging all 20.9-2 [33.5 kB] Get: 506 http://deb.debian.org/debian bullseye/main arm64 python3-pygments all 2.7.1+dfsg-2.1 [657 kB] Get: 507 http://deb.debian.org/debian bullseye/main arm64 python3-snowballstemmer all 2.1.0-1 [58.7 kB] Get: 508 http://deb.debian.org/debian bullseye/main arm64 python3-sphinx all 3.4.3-2 [545 kB] Get: 509 http://deb.debian.org/debian bullseye/main arm64 python3-numpydoc all 1.1.0-3 [40.0 kB] Get: 510 http://deb.debian.org/debian bullseye/main arm64 python3-ipython-genutils all 0.2.0-4 [21.4 kB] Get: 511 http://deb.debian.org/debian bullseye/main arm64 python3-more-itertools all 4.2.0-3 [42.7 kB] Get: 512 http://deb.debian.org/debian bullseye/main arm64 python3-zipp all 1.0.0-3 [6060 B] Get: 513 http://deb.debian.org/debian bullseye/main arm64 python3-importlib-metadata all 1.6.0-2 [10.3 kB] Get: 514 http://deb.debian.org/debian bullseye/main arm64 python3-setuptools all 52.0.0-4 [366 kB] Get: 515 http://deb.debian.org/debian bullseye/main arm64 python3-pyrsistent arm64 0.15.5-1+b3 [58.2 kB] Get: 516 http://deb.debian.org/debian bullseye/main arm64 python3-jsonschema all 3.2.0-3 [46.3 kB] Get: 517 http://deb.debian.org/debian bullseye/main arm64 python3-traitlets all 5.0.5-1 [84.4 kB] Get: 518 http://deb.debian.org/debian bullseye/main arm64 python3-jupyter-core all 4.7.1-1+deb11u1 [44.2 kB] Get: 519 http://deb.debian.org/debian bullseye/main arm64 python3-nbformat all 5.1.2-1 [51.6 kB] Get: 520 http://deb.debian.org/debian bullseye/main arm64 python3-retrying all 1.3.3-4 [8876 B] Get: 521 http://deb.debian.org/debian bullseye/main arm64 python3-plotly all 4.14.3+dfsg-1 [2450 kB] Get: 522 http://deb.debian.org/debian bullseye/main arm64 python3-py2bit arm64 0.3.0-6+b1 [17.9 kB] Get: 523 http://deb.debian.org/debian bullseye/main arm64 python3-pybigwig arm64 0.3.17-1+b4 [39.5 kB] Get: 524 http://deb.debian.org/debian bullseye/main arm64 python3-pysam arm64 0.15.4+ds-3+b2 [1386 kB] Get: 525 http://deb.debian.org/debian bullseye/main arm64 python3-scipy arm64 1.6.0-2 [11.6 MB] Get: 526 http://deb.debian.org/debian bullseye/main arm64 python3-deeptools all 3.5.0-1 [158 kB] Get: 527 http://deb.debian.org/debian bullseye/main arm64 python3-smmap all 4.0.0-1 [21.0 kB] Get: 528 http://deb.debian.org/debian bullseye/main arm64 python3-gitdb all 4.0.5-1 [46.5 kB] Get: 529 http://deb.debian.org/debian bullseye/main arm64 python3-git all 3.1.14-1 [119 kB] Get: 530 http://deb.debian.org/debian bullseye/main arm64 python3-htseq arm64 0.13.5-1 [202 kB] Get: 531 http://deb.debian.org/debian bullseye/main arm64 python3-psutil arm64 5.8.0-1 [184 kB] Get: 532 http://deb.debian.org/debian bullseye/main arm64 python3-pulp all 1.6.0+dfsg1-5 [54.0 kB] Get: 533 http://deb.debian.org/debian bullseye/main arm64 python3-ratelimiter arm64 1.2.0.post0-1 [5504 B] Get: 534 http://deb.debian.org/debian bullseye/main arm64 python3-toposort all 1.6-1 [7620 B] Get: 535 http://deb.debian.org/debian bullseye/main arm64 python3-wrapt arm64 1.12.1-4+b1 [38.4 kB] Get: 536 http://deb.debian.org/debian bullseye/main arm64 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get: 537 http://deb.debian.org/debian bullseye/main arm64 r-bioc-biobase arm64 2.50.0-1 [2228 kB] Get: 538 http://deb.debian.org/debian bullseye/main arm64 r-bioc-s4vectors arm64 0.28.1-1 [2023 kB] Get: 539 http://deb.debian.org/debian bullseye/main arm64 r-bioc-iranges arm64 2.24.1-1 [2198 kB] Get: 540 http://deb.debian.org/debian bullseye/main arm64 r-cran-dbi all 1.1.1-1 [619 kB] Get: 541 http://deb.debian.org/debian bullseye/main arm64 r-cran-bit arm64 4.0.4+dfsg-1 [417 kB] Get: 542 http://deb.debian.org/debian bullseye/main arm64 r-cran-bit64 arm64 4.0.5-1 [467 kB] Get: 543 http://deb.debian.org/debian bullseye/main arm64 r-cran-rlang arm64 0.4.10-1 [1177 kB] Get: 544 http://deb.debian.org/debian bullseye/main arm64 r-cran-ellipsis arm64 0.3.1-1 [31.7 kB] Get: 545 http://deb.debian.org/debian bullseye/main arm64 r-cran-digest arm64 0.6.27-1 [185 kB] Get: 546 http://deb.debian.org/debian bullseye/main arm64 r-cran-glue arm64 1.4.2-1 [138 kB] Get: 547 http://deb.debian.org/debian bullseye/main arm64 r-cran-vctrs arm64 0.3.6-1 [1094 kB] Get: 548 http://deb.debian.org/debian bullseye/main arm64 r-cran-blob all 1.2.1-2 [49.1 kB] Get: 549 http://deb.debian.org/debian bullseye/main arm64 r-cran-fastmap arm64 1.1.0-1 [63.9 kB] Get: 550 http://deb.debian.org/debian bullseye/main arm64 r-cran-cachem arm64 1.0.3-1 [61.5 kB] Get: 551 http://deb.debian.org/debian bullseye/main arm64 r-cran-memoise all 2.0.0-1 [52.9 kB] Get: 552 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 553 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgkitten all 0.2.1-1 [26.5 kB] Get: 554 http://deb.debian.org/debian bullseye/main arm64 r-cran-rcpp arm64 1.0.6-1 [2020 kB] Get: 555 http://deb.debian.org/debian bullseye/main arm64 r-cran-bh all 1.74.0-1 [5196 B] Get: 556 http://deb.debian.org/debian bullseye/main arm64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get: 557 http://deb.debian.org/debian bullseye/main arm64 r-cran-rsqlite arm64 2.2.3-1 [973 kB] Get: 558 http://deb.debian.org/debian bullseye/main arm64 r-bioc-annotationdbi all 1.52.0-1 [4707 kB] Get: 559 http://deb.debian.org/debian bullseye/main arm64 r-cran-xml arm64 3.99-0.5-1 [1722 kB] Get: 560 http://deb.debian.org/debian bullseye/main arm64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get: 561 http://deb.debian.org/debian bullseye/main arm64 r-cran-curl arm64 4.3+dfsg-1+b1 [150 kB] Get: 562 http://deb.debian.org/debian bullseye/main arm64 r-cran-jsonlite arm64 1.7.2+dfsg-1 [445 kB] Get: 563 http://deb.debian.org/debian bullseye/main arm64 r-cran-mime arm64 0.9-1+b1 [35.4 kB] Get: 564 http://deb.debian.org/debian bullseye/main arm64 r-cran-sys arm64 3.4-1 [42.5 kB] Get: 565 http://deb.debian.org/debian bullseye/main arm64 r-cran-askpass arm64 1.1-2 [22.2 kB] Get: 566 http://deb.debian.org/debian bullseye/main arm64 r-cran-openssl arm64 1.4.3+dfsg-2 [374 kB] Get: 567 http://deb.debian.org/debian bullseye/main arm64 r-cran-r6 all 2.5.0-1 [104 kB] Get: 568 http://deb.debian.org/debian bullseye/main arm64 r-cran-httr all 1.4.2-1 [478 kB] Get: 569 http://deb.debian.org/debian bullseye/main arm64 r-bioc-annotate all 1.68.0+dfsg-1 [2103 kB] Get: 570 http://deb.debian.org/debian bullseye/main arm64 r-cran-formatr all 1.7-2 [151 kB] Get: 571 http://deb.debian.org/debian bullseye/main arm64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get: 572 http://deb.debian.org/debian bullseye/main arm64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get: 573 http://deb.debian.org/debian bullseye/main arm64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get: 574 http://deb.debian.org/debian bullseye/main arm64 r-cran-snow all 1:0.4.3-2 [109 kB] Get: 575 http://deb.debian.org/debian bullseye/main arm64 r-bioc-biocparallel arm64 1.24.1-1 [1139 kB] Get: 576 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2+deb11u2 [189 kB] Get: 577 http://deb.debian.org/debian bullseye/main arm64 r-bioc-zlibbioc all 1.36.0+dfsg-1 [8824 B] Get: 578 http://deb.debian.org/debian bullseye/main arm64 r-bioc-xvector arm64 0.30.0-1 [617 kB] Get: 579 http://deb.debian.org/debian bullseye/main arm64 r-cran-crayon all 1.4.0-1 [143 kB] Get: 580 http://deb.debian.org/debian bullseye/main arm64 r-bioc-biostrings arm64 2.58.0-1 [14.2 MB] Get: 581 http://deb.debian.org/debian bullseye/main arm64 r-cran-lattice arm64 0.20-41-1+b1 [1164 kB] Get: 582 http://deb.debian.org/debian bullseye/main arm64 r-cran-matrix arm64 1.3-2-1 [3559 kB] Get: 583 http://deb.debian.org/debian bullseye/main arm64 r-cran-matrixstats arm64 0.58.0-3 [584 kB] Get: 584 http://deb.debian.org/debian bullseye/main arm64 r-bioc-matrixgenerics all 1.2.1-4 [288 kB] Get: 585 http://deb.debian.org/debian bullseye/main arm64 r-bioc-delayedarray arm64 0.16.1+dfsg-1 [1797 kB] Get: 586 http://deb.debian.org/debian bullseye/main arm64 r-cran-bitops arm64 1.0-6-5 [23.5 kB] Get: 587 http://deb.debian.org/debian bullseye/main arm64 r-cran-rcurl arm64 1.98-1.2-1+b1 [787 kB] Get: 588 http://deb.debian.org/debian bullseye/main arm64 r-bioc-genomeinfodbdata all 1.2.4-1 [10.7 MB] Get: 589 http://deb.debian.org/debian bullseye/main arm64 r-bioc-genomeinfodb all 1.26.2-2 [3905 kB] Get: 590 http://deb.debian.org/debian bullseye/main arm64 r-bioc-genomicranges arm64 1.42.0+dfsg-1 [1855 kB] Get: 591 http://deb.debian.org/debian bullseye/main arm64 r-bioc-summarizedexperiment all 1.20.0+dfsg-1 [1955 kB] Get: 592 http://deb.debian.org/debian bullseye/main arm64 r-cran-survival arm64 3.2-7-1 [7617 kB] Get: 593 http://deb.debian.org/debian bullseye/main arm64 r-bioc-genefilter arm64 1.72.1-1 [1152 kB] Get: 594 http://deb.debian.org/debian bullseye/main arm64 r-cran-locfit arm64 1.5-9.4-2+b1 [492 kB] Get: 595 http://deb.debian.org/debian bullseye/main arm64 r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB] Get: 596 http://deb.debian.org/debian bullseye/main arm64 r-bioc-geneplotter all 1.68.0-1 [1551 kB] Get: 597 http://deb.debian.org/debian bullseye/main arm64 r-cran-gtable all 0.3.0+dfsg-2 [163 kB] Get: 598 http://deb.debian.org/debian bullseye/main arm64 r-cran-brio arm64 1.1.1-1 [31.0 kB] Get: 599 http://deb.debian.org/debian bullseye/main arm64 r-cran-ps arm64 1.5.0-1 [275 kB] Get: 600 http://deb.debian.org/debian bullseye/main arm64 r-cran-processx arm64 3.4.5-1 [294 kB] Get: 601 http://deb.debian.org/debian bullseye/main arm64 r-cran-callr all 3.5.1-1 [386 kB] Get: 602 http://deb.debian.org/debian bullseye/main arm64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get: 603 http://deb.debian.org/debian bullseye/main arm64 r-cran-cli all 2.3.0-1 [480 kB] Get: 604 http://deb.debian.org/debian bullseye/main arm64 r-cran-rprojroot all 2.0.2-1 [114 kB] Get: 605 http://deb.debian.org/debian bullseye/main arm64 r-cran-desc all 1.2.0-3 [301 kB] Get: 606 http://deb.debian.org/debian bullseye/main arm64 r-cran-evaluate all 0.14-2 [81.1 kB] Get: 607 http://deb.debian.org/debian bullseye/main arm64 r-cran-lifecycle all 0.2.0-2 [93.2 kB] Get: 608 http://deb.debian.org/debian bullseye/main arm64 r-cran-magrittr arm64 2.0.1-1 [198 kB] Get: 609 http://deb.debian.org/debian bullseye/main arm64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get: 610 http://deb.debian.org/debian bullseye/main arm64 r-cran-withr all 2.4.1-1 [210 kB] Get: 611 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgbuild all 1.2.0-1 [146 kB] Get: 612 http://deb.debian.org/debian bullseye/main arm64 r-cran-rstudioapi all 0.13-1 [262 kB] Get: 613 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgload arm64 1.1.0-1 [168 kB] Get: 614 http://deb.debian.org/debian bullseye/main arm64 r-cran-praise all 1.0.0-4 [20.1 kB] Get: 615 http://deb.debian.org/debian bullseye/main arm64 r-cran-diffobj arm64 0.3.2-1 [1069 kB] Get: 616 http://deb.debian.org/debian bullseye/main arm64 r-cran-fansi arm64 0.4.2-1 [340 kB] Get: 617 http://deb.debian.org/debian bullseye/main arm64 r-cran-utf8 arm64 1.1.4-2 [131 kB] Get: 618 http://deb.debian.org/debian bullseye/main arm64 r-cran-pillar all 1.4.7-1 [227 kB] Get: 619 http://deb.debian.org/debian bullseye/main arm64 r-cran-tibble arm64 3.0.6+dfsg-1 [416 kB] Get: 620 http://deb.debian.org/debian bullseye/main arm64 r-cran-rematch2 all 2.1.2-2 [46.3 kB] Get: 621 http://deb.debian.org/debian bullseye/main arm64 r-cran-waldo all 0.2.3-2 [79.3 kB] Get: 622 http://deb.debian.org/debian bullseye/main arm64 r-cran-testthat arm64 3.0.1-1 [1439 kB] Get: 623 http://deb.debian.org/debian bullseye/main arm64 r-cran-isoband arm64 0.2.3-2 [2062 kB] Get: 624 http://deb.debian.org/debian bullseye/main arm64 r-cran-mass arm64 7.3-53.1-1 [1114 kB] Get: 625 http://deb.debian.org/debian bullseye/main arm64 r-cran-nlme arm64 3.1.152-1 [2238 kB] Get: 626 http://deb.debian.org/debian bullseye/main arm64 r-cran-mgcv arm64 1.8-34-1 [2978 kB] Get: 627 http://deb.debian.org/debian bullseye/main arm64 r-cran-farver arm64 2.0.3-1+b1 [1380 kB] Get: 628 http://deb.debian.org/debian bullseye/main arm64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get: 629 http://deb.debian.org/debian bullseye/main arm64 r-cran-colorspace arm64 2.0-0+dfsg-1 [1683 kB] Get: 630 http://deb.debian.org/debian bullseye/main arm64 r-cran-munsell all 0.5.0-2 [236 kB] Get: 631 http://deb.debian.org/debian bullseye/main arm64 r-cran-viridislite all 0.3.0-4 [59.2 kB] Get: 632 http://deb.debian.org/debian bullseye/main arm64 r-cran-scales all 1.1.1-1 [557 kB] Get: 633 http://deb.debian.org/debian bullseye/main arm64 r-cran-ggplot2 all 3.3.3+dfsg-1 [3158 kB] Get: 634 http://deb.debian.org/debian bullseye/main arm64 r-cran-rcpparmadillo arm64 0.10.2.1.0-1 [1142 kB] Get: 635 http://deb.debian.org/debian bullseye/main arm64 r-bioc-deseq2 arm64 1.30.1+dfsg-1 [1282 kB] Get: 636 http://deb.debian.org/debian bullseye/main arm64 r-bioc-rhtslib arm64 1.22.0+dfsg-1 [993 kB] Get: 637 http://deb.debian.org/debian bullseye/main arm64 r-bioc-rsamtools arm64 2.6.0-1 [3625 kB] Get: 638 http://deb.debian.org/debian bullseye/main arm64 r-bioc-genomicalignments arm64 1.26.0-1 [2195 kB] Get: 639 http://deb.debian.org/debian bullseye/main arm64 r-bioc-rtracklayer arm64 1.50.0-1 [7455 kB] Get: 640 http://deb.debian.org/debian bullseye/main arm64 r-bioc-tximport all 1.18.0+dfsg-1 [86.2 kB] Get: 641 http://deb.debian.org/debian bullseye/main arm64 r-cran-base64enc arm64 0.1-3-3 [27.8 kB] Get: 642 http://deb.debian.org/debian bullseye/main arm64 r-cran-htmltools arm64 0.5.1.1-1 [241 kB] Get: 643 http://deb.debian.org/debian bullseye/main arm64 r-cran-yaml arm64 2.2.1-1+b1 [97.0 kB] Get: 644 http://deb.debian.org/debian bullseye/main arm64 r-cran-htmlwidgets all 1.5.3+dfsg-1 [124 kB] Get: 645 http://deb.debian.org/debian bullseye/main arm64 r-cran-later arm64 1.1.0.1+dfsg-1 [112 kB] Get: 646 http://deb.debian.org/debian bullseye/main arm64 r-cran-promises arm64 1.1.1+dfsg-1 [171 kB] Get: 647 http://deb.debian.org/debian bullseye/main arm64 r-cran-httpuv arm64 1.5.5+dfsg-1 [470 kB] Get: 648 http://deb.debian.org/debian bullseye/main arm64 r-cran-sourcetools arm64 0.1.7-3 [44.5 kB] Get: 649 http://deb.debian.org/debian bullseye/main arm64 r-cran-commonmark arm64 1.7-2 [100.0 kB] Get: 650 http://deb.debian.org/debian bullseye/main arm64 r-cran-shiny all 1.5.0+dfsg-2 [3599 kB] Get: 651 http://deb.debian.org/debian bullseye/main arm64 r-cran-miniui all 0.1.1.1-3 [35.9 kB] Get: 652 http://deb.debian.org/debian bullseye/main arm64 r-cran-shinyjs all 2.0.0-1 [1028 kB] Get: 653 http://deb.debian.org/debian bullseye/main arm64 r-cran-colourpicker all 1.1.0+dfsg-1 [1727 kB] Get: 654 http://deb.debian.org/debian bullseye/main arm64 r-cran-corrplot all 0.84-3 [103 kB] Get: 655 http://deb.debian.org/debian bullseye/main arm64 r-cran-cpp11 all 0.2.6-1 [144 kB] Get: 656 http://deb.debian.org/debian bullseye/main arm64 r-cran-lazyeval arm64 0.2.2-1+b1 [143 kB] Get: 657 http://deb.debian.org/debian bullseye/main arm64 r-cran-crosstalk all 1.1.1+dfsg-2 [167 kB] Get: 658 http://deb.debian.org/debian bullseye/main arm64 r-cran-data.table arm64 1.13.6+dfsg-1 [1701 kB] Get: 659 http://deb.debian.org/debian bullseye/main arm64 r-cran-generics all 0.1.0-1 [73.5 kB] Get: 660 http://deb.debian.org/debian bullseye/main arm64 r-cran-purrr arm64 0.3.4-1+b1 [396 kB] Get: 661 http://deb.debian.org/debian bullseye/main arm64 r-cran-tidyselect arm64 1.1.0+dfsg-1 [191 kB] Get: 662 http://deb.debian.org/debian bullseye/main arm64 r-cran-dplyr arm64 1.0.4-1 [1142 kB] Get: 663 http://deb.debian.org/debian bullseye/main arm64 r-cran-dt all 0.17+dfsg-3 [209 kB] Get: 664 http://deb.debian.org/debian bullseye/main arm64 r-cran-ggrepel arm64 0.9.1-1 [369 kB] Get: 665 http://deb.debian.org/debian bullseye/main arm64 r-cran-plyr arm64 1.8.6-2 [828 kB] Get: 666 http://deb.debian.org/debian bullseye/main arm64 r-cran-gprofiler all 0.7.0-2 [42.6 kB] Get: 667 http://deb.debian.org/debian bullseye/main arm64 r-cran-highr all 0.8+dfsg-2 [40.1 kB] Get: 668 http://deb.debian.org/debian bullseye/main arm64 r-cran-xfun arm64 0.20-1 [288 kB] Get: 669 http://deb.debian.org/debian bullseye/main arm64 r-cran-markdown arm64 1.1+dfsg-1+b1 [123 kB] Get: 670 http://deb.debian.org/debian bullseye/main arm64 r-cran-stringi arm64 1.5.3-1 [705 kB] Get: 671 http://deb.debian.org/debian bullseye/main arm64 r-cran-stringr all 1.4.0-2 [199 kB] Get: 672 http://deb.debian.org/debian bullseye/main arm64 r-cran-knitr all 1.31+dfsg-1 [833 kB] Get: 673 http://deb.debian.org/debian bullseye/main arm64 r-cran-pheatmap all 1.0.12-2 [77.9 kB] Get: 674 http://deb.debian.org/debian bullseye/main arm64 r-cran-tidyr arm64 1.1.2-1 [782 kB] Get: 675 http://deb.debian.org/debian bullseye/main arm64 r-cran-plotly all 4.9.3+dfsg-2 [3266 kB] Get: 676 http://deb.debian.org/debian bullseye/main arm64 r-cran-reshape2 arm64 1.4.4-2 [110 kB] Get: 677 http://deb.debian.org/debian bullseye/main arm64 r-cran-rjson arm64 0.2.20-2 [126 kB] Get: 678 http://deb.debian.org/debian bullseye/main arm64 r-cran-tinytex all 0.29-1 [118 kB] Get: 679 http://deb.debian.org/debian bullseye/main arm64 r-cran-rmarkdown all 2.6+dfsg-1 [2160 kB] Get: 680 http://deb.debian.org/debian bullseye/main arm64 rna-star arm64 2.7.8a+dfsg-2 [646 kB] Get: 681 http://deb.debian.org/debian bullseye/main arm64 sphinx-rtd-theme-common all 0.5.1+dfsg-1 [995 kB] Get: 682 http://deb.debian.org/debian bullseye/main arm64 salmon arm64 1.4.0+ds1-1+b4 [2046 kB] Get: 683 http://deb.debian.org/debian bullseye/main arm64 samtools arm64 1.11-1 [526 kB] Get: 684 http://deb.debian.org/debian bullseye/main arm64 snakemake all 5.24.1-2 [6107 kB] Get: 685 http://deb.debian.org/debian bullseye/main arm64 trim-galore all 0.6.6-1 [17.8 MB] Fetched 463 MB in 15s (31.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17734 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_arm64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package fonts-lato. Preparing to unpack .../05-fonts-lato_2.0-2.1_all.deb ... Unpacking fonts-lato (2.0-2.1) ... Selecting previously unselected package node-normalize.css. Preparing to unpack .../06-node-normalize.css_8.0.1-3_all.deb ... Unpacking node-normalize.css (8.0.1-3) ... Selecting previously unselected package pigz. Preparing to unpack .../07-pigz_2.6-1_arm64.deb ... Unpacking pigz (2.6-1) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../08-libpython3.9-minimal_3.9.2-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../09-libexpat1_2.2.10-2+deb11u5_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../10-python3.9-minimal_3.9.2-1_arm64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:arm64 (3.9.2-1) ... Setting up libexpat1:arm64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 18653 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.9.2-3_arm64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../02-mailcap_3.69_all.deb ... Unpacking mailcap (3.69) ... Selecting previously unselected package mime-support. Preparing to unpack .../03-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package tzdata. Preparing to unpack .../04-tzdata_2021a-1+deb11u10_all.deb ... Unpacking tzdata (2021a-1+deb11u10) ... Selecting previously unselected package libmpdec3:arm64. Preparing to unpack .../05-libmpdec3_2.5.1-1_arm64.deb ... Unpacking libmpdec3:arm64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../06-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../07-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:arm64. Preparing to unpack .../08-libpython3.9-stdlib_3.9.2-1_arm64.deb ... Unpacking libpython3.9-stdlib:arm64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../09-python3.9_3.9.2-1_arm64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../10-libpython3-stdlib_3.9.2-3_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 20960 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_arm64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.30_all.deb ... Unpacking sgml-base (1.30) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_1.1.1w-0+deb11u1_arm64.deb ... Unpacking openssl (1.1.1w-0+deb11u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.39-3+deb11u1_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3+deb11u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../006-libmagic1_1%3a5.39-3+deb11u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3+deb11u1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.39-3+deb11u1_arm64.deb ... Unpacking file (1:5.39-3+deb11u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../009-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libnspr4:arm64. Preparing to unpack .../010-libnspr4_2%3a4.29-1_arm64.deb ... Unpacking libnspr4:arm64 (2:4.29-1) ... Selecting previously unselected package libnss3:arm64. Preparing to unpack .../011-libnss3_2%3a3.61-1+deb11u3_arm64.deb ... Unpacking libnss3:arm64 (2:3.61-1+deb11u3) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../012-ca-certificates-java_20190909+deb11u1_all.deb ... Unpacking ca-certificates-java (20190909+deb11u1) ... Selecting previously unselected package java-common. Preparing to unpack .../013-java-common_0.72_all.deb ... Unpacking java-common (0.72) ... Selecting previously unselected package libavahi-common-data:arm64. Preparing to unpack .../014-libavahi-common-data_0.8-5+deb11u2_arm64.deb ... Unpacking libavahi-common-data:arm64 (0.8-5+deb11u2) ... Selecting previously unselected package libavahi-common3:arm64. Preparing to unpack .../015-libavahi-common3_0.8-5+deb11u2_arm64.deb ... Unpacking libavahi-common3:arm64 (0.8-5+deb11u2) ... Selecting previously unselected package libdbus-1-3:arm64. Preparing to unpack .../016-libdbus-1-3_1.12.28-0+deb11u1_arm64.deb ... Unpacking libdbus-1-3:arm64 (1.12.28-0+deb11u1) ... Selecting previously unselected package libavahi-client3:arm64. Preparing to unpack .../017-libavahi-client3_0.8-5+deb11u2_arm64.deb ... Unpacking libavahi-client3:arm64 (0.8-5+deb11u2) ... Selecting previously unselected package libcups2:arm64. Preparing to unpack .../018-libcups2_2.3.3op2-3+deb11u6_arm64.deb ... Unpacking libcups2:arm64 (2.3.3op2-3+deb11u6) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../019-liblcms2-2_2.12~rc1-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.12~rc1-2) ... 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Setting up libdbus-1-3:arm64 (1.12.28-0+deb11u1) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up libfribidi0:arm64 (1.0.8-2+deb11u1) ... Setting up libimagequant0:arm64 (2.12.2-1.1) ... Setting up libplexus-interpolation-java (1.26-1) ... Setting up libjs-d3 (3.5.17-4) ... Setting up libpng16-16:arm64 (1.6.37-3) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libxz-java (1.8-2) ... Setting up libtcl8.6:arm64 (8.6.11+dfsg-1) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:arm64 (0.6.1-2.1+deb11u2) ... Setting up libjbzip2-java (0.9.1-5) ... Setting up libngs-sdk-dev:arm64 (2.10.9-1) ... Setting up libpcsclite1:arm64 (1.9.1-1) ... Setting up libsensors5:arm64 (1:3.6.0-7) ... Setting up libcmark-gfm0:arm64 (0.29.0.gfm.0-6) ... Setting up libactivation-java (1.2.0-2) ... Setting up libglapi-mesa:arm64 (20.3.5-1) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libgfortran5:arm64 (10.2.1-6) ... Setting up libvulkan1:arm64 (1.2.162.0-1) ... Setting up libgif7:arm64 (5.1.9-2) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libmd0:arm64 (1.0.3-3) ... Setting up libjs-highlight.js (9.18.5+dfsg1-1) ... Setting up libjs-d3-format (1:1.4.1-3) ... Setting up sensible-utils (0.0.14) ... Setting up libxshmfence1:arm64 (1.3-1) ... Setting up libjsoup-java (1.10.2-2) ... Setting up pigz (2.6-1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libasound2:arm64 (1.2.4-1.1) ... Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up node-esprima (4.0.1+ds+~4.0.2-2) ... Setting up libsub-override-perl (0.09-2) ... Setting up libplexus-sec-dispatcher-java (1.4-4) ... Setting up git-man (1:2.30.2-1+deb11u2) ... Setting up libthai-data (0.1.28-3) ... Setting up libssh2-1:arm64 (1.9.0-2) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up sgml-base (1.30) ... Setting up libjs-prettify (2015.12.04+dfsg-1.1) ... Setting up libboost-dev:arm64 (1.74.0.3) ... Setting up libtiff5:arm64 (4.2.0-1+deb11u4) ... Setting up libhttpcore-java (4.4.14-1) ... Setting up pandoc-data (2.9.2.1-1+deb11u1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libngs-java:arm64 (2.10.9-1) ... Setting up librelaxng-datatype-java (1.0+ds1-3.1) ... Setting up python-matplotlib-data (3.3.4-1) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libwebpmux3:arm64 (0.6.1-2.1+deb11u2) ... Setting up libbsd0:arm64 (0.11.3-1+deb11u1) ... Setting up node-normalize.css (8.0.1-3) ... Setting up libdrm-common (2.4.104-1) ... Setting up mailcap (3.69) ... Setting up libcdi-api-java (1.2-3) ... Setting up libelf1:arm64 (0.183-1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (0.5.1+dfsg-1) ... Setting up node-is-buffer (2.0.5-1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libargs4j-java (2.33-1.1) ... Setting up libsz2:arm64 (1.0.4-1) ... Setting up libjs-bootstrap (3.4.1+dfsg-2) ... Setting up node-is-plain-obj (3.0.0-1) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... Setting up libjs-jquery-datatables-extensions (0.0+git20150910.28fd64e+dfsg-5) ... Setting up libdom4j-java (2.1.3-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up r-cran-bh (1.74.0-1) ... Setting up libwagon-provider-api-java (3.3.4-1) ... Setting up libice6:arm64 (2:1.0.10-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up liblapack3:arm64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libxcb-xfixes0:arm64 (1.14-3) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15) ... Setting up libxcb-render0:arm64 (1.14-3) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libxcb-glx0:arm64 (1.14-3) ... Setting up libwebpdemux2:arm64 (0.6.1-2.1+deb11u2) ... Setting up libmaven-parent-java (31-2) ... Setting up libedit2:arm64 (3.1-20191231-2+b1) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Setting up libcommons-parent-java (43-1) ... Setting up libavahi-common3:arm64 (0.8-5+deb11u2) ... Setting up libcommons-logging-java (1.2-2) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3+deb11u1) ... Setting up m4 (1.4.18-5) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3+deb11u9) ... Setting up libnss3:arm64 (2:3.61-1+deb11u3) ... Setting up libxcb-shm0:arm64 (1.14-3) ... Setting up libbigwig0:arm64 (0.4.4+dfsg-2) ... Setting up libcmark-gfm-extensions0:arm64 (0.29.0.gfm.0-6) ... Setting up libnode72:arm64 (12.22.12~dfsg-1~deb11u4) ... Setting up libjs-jquery-datatables (1.10.21+dfsg-2+deb11u1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxcb-present0:arm64 (1.14-3) ... Setting up libcommons-jexl2-java (2.1.1-5) ... Setting up coinor-libcoinutils3v5 (2.11.4+repack1-1) ... Setting up libthai0:arm64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libmaven-resolver-java (1.4.2-3) ... Setting up libllvm11:arm64 (1:11.0.1-2) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Setting up pandoc (2.9.2.1-1+deb11u1) ... Setting up libfreetype6:arm64 (2.10.4+dfsg-1+deb11u1) ... Setting up libguava-java (29.0-6) ... Setting up libxcb-sync1:arm64 (1.14-3) ... Setting up libjs-jquery-metadata (12-3) ... Setting up shared-mime-info (2.0-1) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up ucf (3.0043) ... Setting up git (1:2.30.2-1+deb11u2) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up coinor-libosi1v5:arm64 (0.108.6+repack1-2) ... Setting up libcommons-lang3-java (3.11-1) ... Setting up autoconf (2.69-14) ... Setting up libxcb-dri2-0:arm64 (1.14-3) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up librngom-java (2.3.0.1-10) ... Setting up libdrm2:arm64 (2.4.104-1) ... Setting up libhdf5-103-1:arm64 (1.10.6+repack-4+deb11u1) ... Setting up dwz (0.13+20210201-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-1) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up libcurl4:arm64 (7.74.0-1.3+deb11u9) ... Setting up libx11-6:arm64 (2:1.7.2-1+deb11u1) ... Setting up libharfbuzz0b:arm64 (2.7.4-1) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.2+dfsg-1+deb11u1) ... Setting up libsis-jhdf5-jni (19.04.0+dfsg-4) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libxsom-java (2.3.0.1-10) ... Setting up libstaden-read14:arm64 (1.14.13-4) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up libavahi-client3:arm64 (0.8-5+deb11u2) ... Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.3-9) ... Setting up libdrm-amdgpu1:arm64 (2.4.104-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxcb-dri3-0:arm64 (1.14-3) ... Setting up libpaper1:arm64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libx11-xcb1:arm64 (2:1.7.2-1+deb11u1) ... Setting up pandoc-citeproc (0.17.0.1-1+b2) ... Setting up libhts3:arm64 (1.11-4) ... Setting up libdrm-nouveau2:arm64 (2.4.104-1) ... Setting up libxdamage1:arm64 (1:1.1.5-2) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up libcommons-compress-java (1.20-1) ... Setting up libcommons-io-java (2.8.0-1) ... Setting up libdrm-radeon1:arm64 (2.4.104-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libgl1-mesa-dri:arm64 (20.3.5-1) ... Setting up libxext6:arm64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up nodejs (12.22.12~dfsg-1~deb11u4) ... update-alternatives: using /usr/bin/nodejs to provide /usr/bin/js (js) in auto mode Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up rna-star (2.7.8a+dfsg-2) ... Setting up libguice-java (4.2.3-2) ... Setting up node-argparse (2.0.1-1) ... Setting up node-d3-path (1.0.9-2) ... Setting up node-he (1.2.0-1) ... Setting up samtools (1.11-1) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b2) ... Setting up node-clone (2.1.2-2) ... Setting up node-has-flag (4.0.0-1) ... Setting up salmon (1.4.0+ds1-1+b4) ... Setting up dh-autoreconf (20) ... Setting up node-inherits (2.0.4-1) ... Setting up node-path-is-absolute (2.0.0-1) ... Setting up node-iconv-lite (0.5.1-3) ... Setting up node-safe-buffer (5.2.1+~cs2.1.2-1) ... Setting up node-d3-polygon (1.0.5-3) ... Setting up libpython3.9:arm64 (3.9.2-1) ... Setting up node-y18n (4.0.0-4) ... Setting up node-d3-quadtree (1.0.7-2) ... Setting up libxfixes3:arm64 (1:5.0.3-2) ... Setting up node-balanced-match (1.0.0-1) ... Setting up node-brace-expansion (2.0.0-1) ... Setting up libnotify4:arm64 (0.7.9-3) ... Setting up coinor-libclp1 (1.17.5+repack1-1) ... Setting up sphinx-common (3.4.3-2) ... Setting up node-set-blocking (2.0.0-1.1) ... Setting up node-repeat-string (1.6.1-1) ... Setting up node-d3-collection (1.0.7-3) ... Setting up node-signal-exit (3.0.3-1) ... Setting up node-randombytes (2.1.0-1) ... Setting up libxt6:arm64 (1:1.2.0-1) ... Setting up node-wrappy (1.0.2-1.1) ... Setting up node-d3-voronoi (1.1.4-3) ... Setting up node-require-directory (2.1.1-1.1) ... Setting up node-d3-dispatch (1.0.6-2) ... Setting up node-d3-time (1.0.11-4) ... Setting up libnotify-bin (0.7.9-3) ... Setting up libcups2:arm64 (2.3.3op2-3+deb11u6) ... Setting up node-defaults (1.0.3-2) ... Setting up libsis-base-java (18.09~pre1+git20180928.45fbd31+dfsg-3) ... Setting up node-commander (6.2.1-2) ... Setting up node-d3-array (1.2.4-3) ... Setting up libhttpclient-java (4.5.13-2) ... Setting up node-graceful-fs (4.2.4+repack-1) ... Setting up node-merge-stream (2.0.0+~1.1.2-1) ... Setting up node-binary-extensions (2.2.0-1) ... Setting up node-mimic-fn (3.1.0-1) ... Setting up node-path-dirname (1.0.2-1.1) ... Setting up libwagon-http-java (3.3.4-1) ... Setting up libmaven-shared-utils-java (3.3.0-1+deb11u1) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libfontconfig1:arm64 (2.13.1-4.2) ... Setting up node-minimatch (3.0.4+~3.0.3-1+deb11u2) ... Setting up coinor-libcgl1 (0.60.3+repack1-2) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up node-d3-geo (1.11.9-4) ... Setting up node-set-immediate-shim (2.0.0-1) ... Setting up node-js-yaml (3.14.1+dfsg+~3.12.6-2) ... Setting up node-npm-run-path (2.0.2-2) ... Setting up node-color-convert (1.9.3-1) ... Setting up node-lodash (4.17.21+dfsg+~cs8.31.173-1) ... Setting up node-d3-random (1.1.2-3) ... Setting up node-async-each (1.0.3-1) ... Setting up python3.9 (3.9.2-1) ... Setting up node-is-extglob (2.1.1-1) ... Setting up node-ms (2.1.3+~cs0.7.31-1) ... Setting up node-shebang-command (1.2.0-1.1) ... Setting up node-ansi-colors (4.1.1-2) ... Setting up node-fs.realpath (1.0.0-1.1) ... Setting up node-diff (4.0.2~dfsg-2) ... Setting up coinor-libcbc3:arm64 (2.10.5+ds1-3) ... Setting up node-d3-timer (1.0.10-1) ... Setting up node-highlight.js (9.18.5+dfsg1-1) ... Setting up node-object-assign (4.1.1-3) ... Setting up node-is-glob (4.0.1-1) ... Setting up node-d3-color (1.2.8-2) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.2-2) ... Setting up node-d3-interpolate (1.4.0-2) ... Setting up node-d3-queue (3.0.7-11) ... Setting up node-mem (1.1.0-1.1) ... Setting up libplexus-io-java (3.2.0-1.1) ... Setting up libglx-mesa0:arm64 (20.3.5-1) ... Setting up node-supports-color (8.1.0+~7.2.0-1) ... Setting up node-invert-kv (3.0.1-1) ... Setting up node-d3-format (1:1.4.1-3) ... Setting up node-p-limit (3.1.0+~cs2.3.0-1) ... Setting up node-ansi-regex (5.0.1-1~deb11u1) ... Setting up node-d3-hierarchy (1.1.8-3) ... Setting up node-d3-ease (1.0.5-3) ... Setting up libxi6:arm64 (2:1.7.10-1) ... Setting up node-strip-json-comments (3.1.1-1) ... Setting up libglx0:arm64 (1.3.2-1) ... Setting up node-once (1.4.0-3) ... Setting up node-browser-stdout (1.3.1-2) ... Setting up libmaven3-core-java (3.6.3-5) ... Setting up node-get-caller-file (1.0.2-1.1) ... Setting up node-require-main-filename (2.0.0-1) ... Setting up node-d3-time-format (2.1.3-3) ... Setting up libsis-jhdf5-java (19.04.0+dfsg-4) ... Setting up node-d3-scale-chromatic (1.5.0-2) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up node-serialize-javascript (5.0.1-2) ... Setting up libxtst6:arm64 (2:1.2.3-1) ... Setting up node-isexe (2.0.0-5) ... Setting up libtk8.6:arm64 (8.6.11-2) ... Setting up libpango-1.0-0:arm64 (1.46.2-3) ... Setting up node-path-exists (4.0.0-2) ... Setting up node-d3-chord (1.0.6-3) ... Setting up node-escape-string-regexp (4.0.0-1) ... Setting up node-p-locate (5.0.0-1) ... Setting up node-which-module (2.0.0-1) ... Setting up node-decamelize (4.0.0-1) ... Setting up node-normalize-path (3.0.0-2) ... Setting up node-kind-of (6.0.3+dfsg-1) ... Setting up node-growl (1.10.5-2) ... Setting up debhelper (13.3.4) ... Setting up node-d3-selection (1.4.0-6) ... Setting up python3 (3.9.2-3) ... Setting up node-is-binary-path (2.1.0-1) ... Setting up node-debug (4.3.1+~cs4.1.5-1) ... Setting up libjs-util (0.10.3-4) ... Setting up node-camelcase (6.2.0-2) ... Setting up node-d3-axis (1.0.12-3) ... Setting up node-d3-shape (1.3.7-2) ... Setting up python3-markupsafe (1.1.1-1+b3) ... Setting up libcairo2:arm64 (1.16.0-5) ... Setting up node-yargs-parser (18.1.3+~15.0.0-1) ... Setting up python3-psutil (5.8.0-1) ... Setting up python3-tz (2021.1-1) ... Setting up python3-ratelimiter (1.2.0.post0-1) ... Setting up node-wcwidth.js (1.0.0-1.1) ... Setting up python3-six (1.16.0-2) ... Setting up python3-simplejson (3.17.2-1) ... Setting up python3-pil:arm64 (8.1.2+dfsg-0.3+deb11u1) ... Setting up node-locate-path (6.0.0-1) ... Setting up python3-roman (2.0.0-5) ... Setting up node-d3-drag (1.2.5-2) ... Setting up python3-decorator (4.4.2-2) ... Setting up python3-jinja2 (2.11.3-1) ... Setting up node-rw (1.3.3-2) ... Setting up libgl1:arm64 (1.3.2-1) ... Setting up coinor-cbc (2.10.5+ds1-3) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-humanfriendly (9.1-1) ... Setting up node-ansi-styles (4.2.1-1) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-snowballstemmer (2.1.0-1) ... Setting up node-d3-scale (2.2.2-3) ... Setting up python3-cycler (0.10.0-3) ... Setting up node-strip-ansi (6.0.0-2) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up python3-idna (2.10-1) ... Setting up python3-wrapt (1.12.1-4+b1) ... Setting up node-chalk (4.1.0-1) ... Setting up node-which (2.0.2+~cs1.3.2-1) ... Setting up node-lcid (3.1.1-1) ... Setting up node-d3-force (1.2.1-2) ... Setting up node-d3-contour (1.3.2-4) ... Setting up python3-urllib3 (1.26.5-1~exp1) ... Setting up python3-pyrsistent:arm64 (0.15.5-1+b3) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up node-inflight (1.0.6-1.1) ... Setting up node-glob-parent (5.1.1+~5.1.0-2) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up python3-dateutil (2.8.1-6) ... Setting up python3-py2bit (0.3.0-6+b1) ... Setting up python3-datrie:arm64 (0.8.2-1+b1) ... Setting up node-d3-dsv (1.1.1-5) ... Setting up libpangoft2-1.0-0:arm64 (1.46.2-3) ... Setting up node-anymatch (3.1.1+~2.2.2-1) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-coloredlogs (7.3-2) ... Setting up node-d3-transition (1.3.2-3) ... Setting up python3-appdirs (1.4.4-1) ... Setting up python3-smmap (4.0.0-1) ... Setting up libpangocairo-1.0-0:arm64 (1.46.2-3) ... Setting up node-string-width (4.2.0-1) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up python3-toposort (1.6-1) ... Setting up python3-more-itertools (4.2.0-3) ... Setting up python3-configargparse (1.2.3-1) ... Setting up python3-attr (20.3.0-1) ... Setting up node-is-number (7.0.0-1.1) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up node-end-of-stream (1.4.4-1) ... Setting up python3-setuptools (52.0.0-4) ... Setting up node-pump (3.0.0-4) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-deeptoolsintervals (0.1.9-3+b2) ... Setting up python3-colorama (0.4.4-1) ... Setting up python3-ipython-genutils (0.2.0-4) ... Setting up python3-pulp (1.6.0+dfsg1-5) ... /usr/lib/python3/dist-packages/pulp/pulp.py:700: SyntaxWarning: "is" with a literal. Did you mean "=="? if other is 0: return self /usr/lib/python3/dist-packages/pulp/pulp.py:720: SyntaxWarning: "is" with a literal. Did you mean "=="? if other is 0: return self Setting up python3-alabaster (0.7.8-1.1) ... Setting up node-d3-zoom (1.8.3-2) ... Setting up python3-retrying (1.3.3-4) ... Setting up node-find-up (5.0.0-1) ... Setting up python3-all (3.9.2-3) ... Setting up python3-yaml (5.3.1-5) ... Setting up node-d3-fetch (1.2.0-1) ... Setting up node-util (0.10.3-4) ... Setting up python3-gitdb (4.0.5-1) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-click (7.1.2-1) ... Setting up python3-networkx (2.5+ds-2) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up python3-xopen (1.1.0-1) ... Setting up python3-packaging (20.9-2) ... Setting up python3-chardet (4.0.0-1) ... Setting up node-wrap-ansi (4.0.0-2) ... Setting up node-glob (7.1.6+~7.1.3-1) ... Setting up node-readdirp (3.5.0-2) ... Setting up python3-git (3.1.14-1) ... Setting up node-get-stream (6.0.0-1) ... Setting up python3-requests (2.25.1+dfsg-2) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.4.0-1) ... Setting up r-cran-gtable (0.3.0+dfsg-2) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up python3-markdown (3.3.4-1) ... Setting up r-cran-sourcetools (0.1.7-3) ... Setting up r-cran-futile.options (1.0.1-3) ... Setting up r-cran-lattice (0.20-41-1+b1) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up r-cran-ps (1.5.0-1) ... Setting up r-cran-nlme (3.1.152-1) ... Setting up python3-colormath (3.0.0-1.1) ... Setting up r-cran-farver (2.0.3-1+b1) ... Setting up python3-pybigwig (0.3.17-1+b4) ... Setting up r-cran-formatr (1.7-2) ... Setting up node-assert (1.5.0-1) ... Setting up r-cran-xml (3.99-0.5-1) ... Setting up r-cran-viridislite (0.3.0-4) ... Setting up node-d3-brush (1.1.5-2) ... Setting up r-cran-locfit (1.5-9.4-2+b1) ... Setting up python3-traitlets (5.0.5-1) ... Setting up node-wide-align (1.1.3-1) ... Setting up r-cran-lazyeval (0.2.2-1+b1) ... Setting up r-cran-commonmark (1.7-2) ... Setting up r-cran-r6 (2.5.0-1) ... Setting up r-cran-pkgkitten (0.2.1-1) ... Setting up python3-future (0.18.2-5) ... 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 (1.0.4-1.1) ... Setting up r-cran-magrittr (2.0.1-1) ... Setting up python3-htseq (0.13.5-1) ... Setting up python3-jupyter-core (4.7.1-1+deb11u1) ... Setting up node-cliui (4.1.0-2) ... Setting up r-bioc-genomeinfodbdata (1.2.4-1) ... Setting up python3-dnaio (0.5.0-1) ... Setting up r-cran-littler (0.3.12-1) ... Setting up r-cran-rcpp (1.0.6-1) ... Setting up r-cran-curl (4.3+dfsg-1+b1) ... Setting up r-cran-brio (1.1.1-1) ... Setting up node-to-regex-range (5.0.1-2) ... Setting up r-cran-diffobj (0.3.2-1) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up r-bioc-biocgenerics (0.36.0-1) ... Setting up r-cran-rlang (0.4.10-1) ... Setting up r-cran-matrixstats (0.58.0-3) ... Setting up python3-scipy (1.6.0-2) ... Setting up r-cran-assertthat (0.2.1-2) ... Setting up python3-importlib-metadata (1.6.0-2) ... Setting up littler (0.3.12-1) ... Setting up node-execa (4.1.0+dfsg+~cs19.3.6-5) ... Setting up python3-spectra (0.0.11-2) ... Setting up r-bioc-matrixgenerics (1.2.1-4) ... Setting up r-cran-xfun (0.20-1) ... Setting up r-cran-sys (3.4-1) ... Setting up r-cran-plogr (0.2.0-3) ... Setting up r-cran-withr (2.4.1-1) ... Setting up r-cran-processx (3.4.5-1) ... Setting up r-cran-mime (0.9-1+b1) ... Setting up r-cran-praise (1.0.0-4) ... Setting up r-cran-generics (0.1.0-1) ... Setting up r-cran-base64enc (0.1-3-3) ... Setting up r-cran-digest (0.6.27-1) ... Setting up r-cran-yaml (2.2.1-1+b1) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-evaluate (0.14-2) ... Setting up r-cran-dbi (1.1.1-1) ... Setting up r-cran-highr (0.8+dfsg-2) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (0.4.2-1) ... Setting up r-cran-mass (7.3-53.1-1) ... Setting up r-cran-snow (1:0.4.3-2) ... Setting up node-d3 (5.16.0-4) ... Setting up r-cran-data.table (1.13.6+dfsg-1) ... Setting up r-cran-glue (1.4.2-1) ... Setting up node-os-locale (5.0.0-1) ... Setting up r-cran-bit (4.0.4+dfsg-1) ... Setting up r-cran-xtable (1:1.8-4-2) ... Setting up r-cran-cli (2.3.0-1) ... Setting up r-cran-lifecycle (0.2.0-2) ... Setting up r-cran-bitops (1.0-6-5) ... Setting up r-cran-rprojroot (2.0.2-1) ... Setting up r-cran-bit64 (4.0.5-1) ... Setting up r-bioc-zlibbioc (1.36.0+dfsg-1) ... Setting up r-cran-askpass (1.1-2) ... Setting up r-cran-fastmap (1.1.0-1) ... Setting up r-bioc-biobase (2.50.0-1) ... Setting up r-cran-jsonlite (1.7.2+dfsg-1) ... Setting up r-cran-corrplot (0.84-3) ... Setting up r-cran-rstudioapi (0.13-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.1.4-2) ... Setting up r-cran-colorspace (2.0-0+dfsg-1) ... Setting up r-cran-stringi (1.5.3-1) ... Setting up python3-cutadapt (3.2-2) ... Setting up r-cran-markdown (1.1+dfsg-1+b1) ... Setting up python3-jsonschema (3.2.0-3) ... Setting up r-cran-cpp11 (0.2.6-1) ... Setting up r-cran-plyr (1.8.6-2) ... Setting up r-cran-rcolorbrewer (1.1-2-3) ... Setting up r-bioc-s4vectors (0.28.1-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-purrr (0.3.4-1+b1) ... Setting up r-cran-later (1.1.0.1+dfsg-1) ... Setting up r-cran-matrix (1.3-2-1) ... Setting up r-cran-htmltools (0.5.1.1-1) ... Setting up r-cran-tinytex (0.29-1) ... Setting up r-bioc-tximport (1.18.0+dfsg-1) ... Setting up r-cran-mgcv (1.8-34-1) ... Setting up r-cran-cachem (1.0.3-1) ... Setting up r-cran-rcpparmadillo (0.10.2.1.0-1) ... Setting up r-bioc-iranges (2.24.1-1) ... Setting up r-cran-rjson (0.2.20-2) ... Setting up r-cran-rcurl (1.98-1.2-1+b1) ... Setting up r-bioc-delayedarray (0.16.1+dfsg-1) ... Setting up r-cran-ellipsis (0.3.1-1) ... Setting up multiqc (1.9+dfsg-3) ... /usr/lib/python3/dist-packages/multiqc/modules/custom_content/custom_content.py:71: SyntaxWarning: "is not" with a literal. Did you mean "!="? cust_mods[c_id]['config'].update( { k:v for k, v in f.items() if k is not 'data' } ) Setting up node-fill-range (7.0.1-2) ... Setting up r-cran-openssl (1.4.3+dfsg-2) ... Setting up node-yargs (15.3.1+repack-2) ... Setting up r-cran-stringr (1.4.0-2) ... Setting up r-bioc-biocparallel (1.24.1-1) ... Setting up r-cran-callr (3.5.1-1) ... Setting up r-cran-gprofiler (0.7.0-2) ... Setting up cutadapt (3.2-2) ... Setting up r-bioc-rhtslib (1.22.0+dfsg-1) ... Setting up r-cran-desc (1.2.0-3) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-survival (3.2-7-1) ... Setting up python3-nbformat (5.1.2-1) ... Setting up r-cran-htmlwidgets (1.5.3+dfsg-1) ... Setting up r-cran-reshape2 (1.4.4-2) ... Setting up r-bioc-genomeinfodb (1.26.2-2) ... Setting up r-cran-httr (1.4.2-1) ... Setting up r-cran-scales (1.1.1-1) ... Setting up r-cran-memoise (2.0.0-1) ... Setting up r-cran-promises (1.1.1+dfsg-1) ... Setting up python3-plotly (4.14.3+dfsg-1) ... Setting up r-bioc-xvector (0.30.0-1) ... Setting up r-cran-knitr (1.31+dfsg-1) ... Setting up r-cran-pkgbuild (1.2.0-1) ... Setting up node-braces (3.0.2+~3.0.0-1) ... Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... Setting up node-chokidar (3.4.3-3) ... Setting up r-cran-pheatmap (1.0.12-2) ... Setting up r-cran-pkgload (1.1.0-1) ... Setting up trim-galore (0.6.6-1) ... Setting up r-bioc-genomicranges (1.42.0+dfsg-1) ... Setting up r-cran-httpuv (1.5.5+dfsg-1) ... Setting up r-bioc-biostrings (2.58.0-1) ... Setting up r-cran-tibble (3.0.6+dfsg-1) ... Setting up r-cran-shiny (1.5.0+dfsg-2) ... Setting up r-cran-shinyjs (2.0.0-1) ... Setting up r-cran-tidyselect (1.1.0+dfsg-1) ... Setting up r-cran-miniui (0.1.1.1-3) ... Setting up r-cran-rmarkdown (2.6+dfsg-1) ... Setting up r-cran-blob (1.2.1-2) ... Setting up r-bioc-rsamtools (2.6.0-1) ... Setting up r-cran-dplyr (1.0.4-1) ... Setting up r-cran-rsqlite (2.2.3-1) ... Setting up mocha (8.2.1+ds1+~cs29.4.27-3) ... Setting up r-cran-crosstalk (1.1.1+dfsg-2) ... Setting up r-cran-dt (0.17+dfsg-3) ... Setting up r-bioc-summarizedexperiment (1.20.0+dfsg-1) ... Setting up r-bioc-annotationdbi (1.52.0-1) ... Setting up r-cran-rematch2 (2.1.2-2) ... Setting up node-graphlibrary (2.2.0+really2.1.8+dfsg-3) ... Setting up r-bioc-annotate (1.68.0+dfsg-1) ... Setting up r-cran-waldo (0.2.3-2) ... Setting up r-cran-tidyr (1.1.2-1) ... Setting up r-bioc-genefilter (1.72.1-1) ... Setting up r-bioc-genomicalignments (1.26.0-1) ... Setting up node-dagre-layout (0.8.8+really0.8.5+dfsg-4) ... Setting up r-bioc-geneplotter (1.68.0-1) ... Setting up r-bioc-rtracklayer (1.50.0-1) ... Setting up r-cran-testthat (3.0.1-1) ... Setting up r-cran-isoband (0.2.3-2) ... Setting up node-dagre-d3-renderer (0.6.4+dfsg-3) ... Setting up r-cran-ggplot2 (3.3.3+dfsg-1) ... Setting up r-bioc-deseq2 (1.30.1+dfsg-1) ... Setting up r-cran-colourpicker (1.1.0+dfsg-1) ... Setting up r-cran-ggrepel (0.9.1-1) ... Setting up r-cran-plotly (4.9.3+dfsg-2) ... Setting up default-jre-headless (2:1.11-72) ... Setting up openjdk-11-jre-headless:arm64 (11.0.20+8-1~deb11u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jre:arm64 (11.0.20+8-1~deb11u1) ... Setting up default-jre (2:1.11-72) ... Setting up ant (1.10.9-4) ... Setting up ca-certificates-java (20190909+deb11u1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up ant-optional (1.10.9-4) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10) ... Setting up libtxw2-java (2.3.0.1-10) ... Setting up libjaxb-java (2.3.0.1-10) ... Setting up libhtsjdk-java (2.23.0+dfsg-2) ... Setting up fastqc (0.11.9+dfsg-4) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.16+dfsg-4) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.16+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up snakemake (5.24.1-2) ... Setting up python3-sphinx (3.4.3-2) ... Setting up python3-numpydoc (1.1.0-3) ... Setting up python3-deeptools (3.5.0-1) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/pigx-rnaseq-0.0.10+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pigx-rnaseq_0.0.10+ds-2_source.changes dpkg-buildpackage: info: source package pigx-rnaseq dpkg-buildpackage: info: source version 0.0.10+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' dh_auto_clean install -d /build/reproducible-path/pigx-rnaseq-0.0.10\+ds/debian/.debhelper/generated/_source/home 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/reproducible-path/pigx-rnaseq-0.0.10+ds' 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 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 configure.ac:6: installing 'build-aux/install-sh' configure.ac:6: installing 'build-aux/missing' Makefile.am:16: warning: whitespace following trailing backslash 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 dh_auto_configure install -d /build/reproducible-path/pigx-rnaseq-0.0.10\+ds/debian/.debhelper/generated/_source/home ./configure --build=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking how to create a pax tar archive... gnutar checking whether make supports nested variables... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for a Python interpreter with version >= 3.5... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.9 checking for python3 platform... linux checking for python3 script directory... ${prefix}/lib/python3.9/site-packages checking for python3 extension module directory... ${exec_prefix}/lib/python3.9/site-packages checking python3 module: yaml... yes checking for gunzip... /bin/gunzip 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 checking for pandoc-citeproc... /usr/bin/pandoc-citeproc configure: Using /usr/bin/fastqc as fastqc executable. configure: Using /usr/bin/trim_galore as trim_galore executable. configure: Using /usr/bin/STAR as STAR executable. checking for multiqc... /usr/bin/multiqc checking for htseq-count... /usr/bin/htseq-count configure: Using /usr/bin/salmon as salmon executable. checking for R... /usr/bin/R checking for Rscript... /usr/bin/Rscript 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 gProfileR ... 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 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_trim_galore/test.sh config.status: creating tests/test_star/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_fastqc/test.sh config.status: creating tests/test_star_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 dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' ln -sf /usr/share/javascript/jquery/jquery.min.js scripts/ #/usr/bin/make -j2 check VERBOSE=1 ./test.sh Commencing snakemake run submission locally Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Job counts: count jobs 1 all 1 collate_read_counts 6 count_reads 1 counts_from_SALMON 6 fastqc 6 genomeCoverage 6 index_bam 1 multiqc 1 norm_counts_deseq 1 report1 1 report2 1 report3 1 salmon_index 6 salmon_quant 6 sort_bam 1 star_index 6 star_map 1 translate_sample_sheet_for_report 4 trim_galore_pe 2 trim_galore_se 59 [Sat Jan 6 20:04:38 2024] rule trim_galore_se: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep1.log jobid: 47 wildcards: sample=HBR_Rep1 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep1.read1.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep1.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1.read1_trimmed.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz [Sat Jan 6 20:04:49 2024] Finished job 47. 1 of 59 steps (2%) done [Sat Jan 6 20:04:49 2024] rule trim_galore_se: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep3.log jobid: 52 wildcards: sample=UHR_Rep3 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep3.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3.read1_trimmed.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz [Sat Jan 6 20:04:59 2024] Finished job 52. 2 of 59 steps (3%) done [Sat Jan 6 20:04:59 2024] rule trim_galore_pe: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep2.log jobid: 51 wildcards: sample=UHR_Rep2 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep2.read2.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep2.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2.read1_val_1.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2.read2_val_2.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz [Sat Jan 6 20:05:10 2024] Finished job 51. 3 of 59 steps (5%) done [Sat Jan 6 20:05:10 2024] rule trim_galore_pe: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep3.log jobid: 49 wildcards: sample=HBR_Rep3 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep3.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3.read1_val_1.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3.read2_val_2.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz [Sat Jan 6 20:05:21 2024] Finished job 49. 4 of 59 steps (7%) done [Sat Jan 6 20:05:21 2024] rule trim_galore_pe: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep1.log jobid: 50 wildcards: sample=UHR_Rep1 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/UHR_Rep1.read2.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_UHR_Rep1.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1.read1_val_1.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1.read2_val_2.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz [Sat Jan 6 20:05:32 2024] Finished job 50. 5 of 59 steps (8%) done [Sat Jan 6 20:05:32 2024] rule trim_galore_pe: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep2.log jobid: 48 wildcards: sample=HBR_Rep2 /usr/bin/trim_galore -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads --paired /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/trim_galore_HBR_Rep2.log 2>&1 && sleep 10 && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2.read1_val_1.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz && mv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2.read2_val_2.fq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz [Sat Jan 6 20:05:42 2024] Finished job 48. 6 of 59 steps (10%) done [Sat Jan 6 20:05:42 2024] rule translate_sample_sheet_for_report: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_sheet.csv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv jobid: 34 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//translate_sample_sheet_for_report.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_sheet.csv [Sat Jan 6 20:05:43 2024] Finished job 34. 7 of 59 steps (12%) done [Sat Jan 6 20:05:43 2024] rule salmon_index: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.cdna.fasta output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_index.log jobid: 2 /usr/bin/salmon index -t /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.cdna.fasta -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -p 8 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_index.log 2>&1 [Sat Jan 6 20:05:48 2024] Finished job 2. 8 of 59 steps (14%) done [Sat Jan 6 20:05:48 2024] rule star_index: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.fasta output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_index.log jobid: 1 /usr/bin/STAR --runMode genomeGenerate --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --genomeFastaFiles /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.fasta --sjdbGTFfile /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_index.log 2>&1 [Sat Jan 6 20:06:00 2024] Finished job 1. 9 of 59 steps (15%) done [Sat Jan 6 20:06:00 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep1.log jobid: 56 wildcards: sample=UHR_Rep1 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep1.log 2>&1 [Sat Jan 6 20:06:00 2024] Finished job 56. 10 of 59 steps (17%) done [Sat Jan 6 20:06:00 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep3.log jobid: 58 wildcards: sample=UHR_Rep3 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep3.log 2>&1 [Sat Jan 6 20:06:01 2024] Finished job 58. 11 of 59 steps (19%) done [Sat Jan 6 20:06:01 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep3.log jobid: 55 wildcards: sample=HBR_Rep3 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep3.log 2>&1 [Sat Jan 6 20:06:02 2024] Finished job 55. 12 of 59 steps (20%) done [Sat Jan 6 20:06:02 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep2.log jobid: 57 wildcards: sample=UHR_Rep2 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_UHR_Rep2.log 2>&1 [Sat Jan 6 20:06:02 2024] Finished job 57. 13 of 59 steps (22%) done [Sat Jan 6 20:06:03 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep1.log jobid: 53 wildcards: sample=HBR_Rep1 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep1.log 2>&1 [Sat Jan 6 20:06:03 2024] Finished job 53. 14 of 59 steps (24%) done [Sat Jan 6 20:06:03 2024] rule star_map: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep2.log jobid: 54 wildcards: sample=HBR_Rep2 /usr/bin/STAR --runThreadN 2 --genomeDir /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index --readFilesIn /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz --readFilesCommand '/bin/gunzip -c' --outSAMtype BAM Unsorted --outFileNamePrefix /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_ >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/star_map_HBR_Rep2.log 2>&1 [Sat Jan 6 20:06:04 2024] Finished job 54. 15 of 59 steps (25%) done [Sat Jan 6 20:06:04 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep3.log jobid: 24 wildcards: sample=HBR_Rep3 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep3.log 2>&1 [Sat Jan 6 20:06:04 2024] Finished job 24. 16 of 59 steps (27%) done [Sat Jan 6 20:06:04 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep2.log jobid: 23 wildcards: sample=HBR_Rep2 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep2.log 2>&1 [Sat Jan 6 20:06:04 2024] Finished job 23. 17 of 59 steps (29%) done [Sat Jan 6 20:06:04 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep3.log jobid: 27 wildcards: sample=UHR_Rep3 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep3.log 2>&1 [Sat Jan 6 20:06:04 2024] Finished job 27. 18 of 59 steps (31%) done [Sat Jan 6 20:06:04 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep1.log jobid: 22 wildcards: sample=HBR_Rep1 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_HBR_Rep1.log 2>&1 [Sat Jan 6 20:06:04 2024] Finished job 22. 19 of 59 steps (32%) done [Sat Jan 6 20:06:04 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep2_Aligned.sortedByCoord.out_fastqc.zip log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep2.log jobid: 29 wildcards: sample=HBR_Rep2 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep2.log 2>&1 [Sat Jan 6 20:06:07 2024] Finished job 29. 20 of 59 steps (34%) done [Sat Jan 6 20:06:07 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep1.log jobid: 25 wildcards: sample=UHR_Rep1 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep1.log 2>&1 [Sat Jan 6 20:06:07 2024] Finished job 25. 21 of 59 steps (36%) done [Sat Jan 6 20:06:07 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep1_Aligned.sortedByCoord.out_fastqc.zip log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep1.log jobid: 31 wildcards: sample=UHR_Rep1 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep1.log 2>&1 [Sat Jan 6 20:06:11 2024] Finished job 31. 22 of 59 steps (37%) done [Sat Jan 6 20:06:11 2024] rule sort_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep2.log jobid: 26 wildcards: sample=UHR_Rep2 /usr/bin/samtools sort -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_sort_UHR_Rep2.log 2>&1 [Sat Jan 6 20:06:11 2024] Finished job 26. 23 of 59 steps (39%) done [Sat Jan 6 20:06:11 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep1_Aligned.sortedByCoord.out_fastqc.zip log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep1.log jobid: 28 wildcards: sample=HBR_Rep1 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep1.log 2>&1 [Sat Jan 6 20:06:16 2024] Finished job 28. 24 of 59 steps (41%) done [Sat Jan 6 20:06:16 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep2.log jobid: 20 wildcards: sample=UHR_Rep2 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R1.fastq.gz -2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep2_R2.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep2.log 2>&1 [Sat Jan 6 20:06:18 2024] Finished job 20. 25 of 59 steps (42%) done [Sat Jan 6 20:06:18 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep1.log jobid: 16 wildcards: sample=HBR_Rep1 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep1_R.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep1.log 2>&1 [Sat Jan 6 20:06:19 2024] Finished job 16. 26 of 59 steps (44%) done [Sat Jan 6 20:06:19 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep2.log jobid: 17 wildcards: sample=HBR_Rep2 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R1.fastq.gz -2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep2_R2.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep2.log 2>&1 [Sat Jan 6 20:06:22 2024] Finished job 17. 27 of 59 steps (46%) done [Sat Jan 6 20:06:22 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep3.log jobid: 21 wildcards: sample=UHR_Rep3 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -r /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep3_R.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep3.log 2>&1 [Sat Jan 6 20:06:23 2024] Finished job 21. 28 of 59 steps (47%) done [Sat Jan 6 20:06:23 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep1.log jobid: 19 wildcards: sample=UHR_Rep1 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R1.fastq.gz -2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/UHR_Rep1_R2.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_UHR_Rep1.log 2>&1 [Sat Jan 6 20:06:25 2024] Finished job 19. 29 of 59 steps (49%) done [Sat Jan 6 20:06:25 2024] rule salmon_quant: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.genes.sf log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep3.log jobid: 18 wildcards: sample=HBR_Rep3 Job counts: count jobs 1 salmon_quant 1 /usr/bin/salmon quant -i /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index -l A -p 8 -1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R1.fastq.gz -2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/trimmed_reads/HBR_Rep3_R2.fastq.gz -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3 --seqBias --gcBias -g /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_quant_HBR_Rep3.log 2>&1 [Sat Jan 6 20:06:27 2024] Finished job 18. 30 of 59 steps (51%) done [Sat Jan 6 20:06:27 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep3.log jobid: 43 wildcards: sample=HBR_Rep3 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep3.log 2>&1 [Sat Jan 6 20:06:27 2024] Finished job 43. 31 of 59 steps (53%) done [Sat Jan 6 20:06:27 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep3.log jobid: 46 wildcards: sample=UHR_Rep3 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep3.log 2>&1 [Sat Jan 6 20:06:27 2024] Finished job 46. 32 of 59 steps (54%) done [Sat Jan 6 20:06:27 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep2.log jobid: 42 wildcards: sample=HBR_Rep2 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep2.log 2>&1 [Sat Jan 6 20:06:27 2024] Finished job 42. 33 of 59 steps (56%) done [Sat Jan 6 20:06:27 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep2.log jobid: 45 wildcards: sample=UHR_Rep2 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep2.log 2>&1 [Sat Jan 6 20:06:27 2024] Finished job 45. 34 of 59 steps (58%) done [Sat Jan 6 20:06:27 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep1.log jobid: 41 wildcards: sample=HBR_Rep1 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_HBR_Rep1.log 2>&1 [Sat Jan 6 20:06:28 2024] Finished job 41. 35 of 59 steps (59%) done [Sat Jan 6 20:06:28 2024] rule index_bam: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep1.log jobid: 44 wildcards: sample=UHR_Rep1 /usr/bin/samtools index /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/samtools_index_UHR_Rep1.log 2>&1 [Sat Jan 6 20:06:28 2024] Finished job 44. 36 of 59 steps (61%) done [Sat Jan 6 20:06:28 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep2_Aligned.sortedByCoord.out_fastqc.zip log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep2.log jobid: 32 wildcards: sample=UHR_Rep2 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep2.log 2>&1 [Sat Jan 6 20:06:30 2024] Finished job 32. 37 of 59 steps (63%) done [Sat Jan 6 20:06:30 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep3_Aligned.sortedByCoord.out_fastqc.zip log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep3.log jobid: 30 wildcards: sample=HBR_Rep3 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_HBR_Rep3.log 2>&1 [Sat Jan 6 20:06:33 2024] Finished job 30. 38 of 59 steps (64%) done [Sat Jan 6 20:06:33 2024] rule fastqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep3_Aligned.sortedByCoord.out_fastqc.zip log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep3.log jobid: 33 wildcards: sample=UHR_Rep3 /usr/bin/fastqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc -f bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/fastqc_UHR_Rep3.log 2>&1 [Sat Jan 6 20:06:38 2024] Finished job 33. 39 of 59 steps (66%) done [Sat Jan 6 20:06:38 2024] rule multiqc: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep1_Aligned.sortedByCoord.out_fastqc.zip, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep2_Aligned.sortedByCoord.out_fastqc.zip, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/HBR_Rep3_Aligned.sortedByCoord.out_fastqc.zip, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep1_Aligned.sortedByCoord.out_fastqc.zip, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep2_Aligned.sortedByCoord.out_fastqc.zip, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/fastqc/UHR_Rep3_Aligned.sortedByCoord.out_fastqc.zip output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/multiqc/multiqc_report.html log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/multiqc.log jobid: 3 /usr/bin/multiqc -o /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/multiqc /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/multiqc.log 2>&1 [Sat Jan 6 20:06:45 2024] Finished job 3. 40 of 59 steps (68%) done [Sat Jan 6 20:06:45 2024] rule counts_from_SALMON: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/HBR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep1/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep2/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output/UHR_Rep3/quant.genes.sf, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.genes.tsv log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_import_counts.log jobid: 4 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//counts_matrix_from_SALMON.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_output /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/salmon_import_counts.log 2>&1 [Sat Jan 6 20:06:55 2024] Finished job 4. 41 of 59 steps (69%) done [Sat Jan 6 20:06:55 2024] rule report3: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.genes.deseq.report.html log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.salmon.genes.log jobid: 15 wildcards: analysis=analysis1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/images/Logo_PiGx.png --prefix='analysis1.salmon.genes' --reportFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report --organism='' --selfContained=FALSE >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.salmon.genes.log 2>&1 [Sat Jan 6 20:07:18 2024] Finished job 15. 42 of 59 steps (71%) done [Sat Jan 6 20:07:18 2024] rule report2: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.transcripts.deseq.report.html log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.salmon.transcripts.log jobid: 14 wildcards: analysis=analysis1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/images/Logo_PiGx.png --prefix='analysis1.salmon.transcripts' --reportFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report --organism='' >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.salmon.transcripts.log 2>&1 [Sat Jan 6 20:07:37 2024] Finished job 14. 43 of 59 steps (73%) done [Sat Jan 6 20:07:37 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep1.count_reads.log jobid: 35 wildcards: sample=HBR_Rep1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R HBR_Rep1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep1.count_reads.log 2>&1 [Sat Jan 6 20:07:46 2024] Finished job 35. 44 of 59 steps (75%) done [Sat Jan 6 20:07:46 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep2.count_reads.log jobid: 39 wildcards: sample=UHR_Rep2 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R UHR_Rep2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep2.count_reads.log 2>&1 [Sat Jan 6 20:07:55 2024] Finished job 39. 45 of 59 steps (76%) done [Sat Jan 6 20:07:55 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep1.count_reads.log jobid: 38 wildcards: sample=UHR_Rep1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R UHR_Rep1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep1.count_reads.log 2>&1 [Sat Jan 6 20:08:03 2024] Finished job 38. 46 of 59 steps (78%) done [Sat Jan 6 20:08:03 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep3.count_reads.log jobid: 37 wildcards: sample=HBR_Rep3 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R HBR_Rep3 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep3.count_reads.log 2>&1 [Sat Jan 6 20:08:12 2024] Finished job 37. 47 of 59 steps (80%) done [Sat Jan 6 20:08:12 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep3.count_reads.log jobid: 40 wildcards: sample=UHR_Rep3 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R UHR_Rep3 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf True Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/UHR_Rep3.count_reads.log 2>&1 [Sat Jan 6 20:08:21 2024] Finished job 40. 48 of 59 steps (81%) done [Sat Jan 6 20:08:21 2024] rule count_reads: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2.read_counts.csv log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep2.count_reads.log jobid: 36 wildcards: sample=HBR_Rep2 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//count_reads.R HBR_Rep2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf False Union True unspecific exon gene_id 2000000 >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/HBR_Rep2.count_reads.log 2>&1 [Sat Jan 6 20:08:29 2024] Finished job 36. 49 of 59 steps (83%) done [Sat Jan 6 20:08:29 2024] rule collate_read_counts: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2.read_counts.csv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3.read_counts.csv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/collate_read_counts.log jobid: 5 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/collate_read_counts.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/collate_read_counts.log 2>&1 [Sat Jan 6 20:08:29 2024] Finished job 5. 50 of 59 steps (85%) done [Sat Jan 6 20:08:29 2024] rule norm_counts_deseq: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_normalized_counts.tsv log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/norm_counts_deseq.log jobid: 6 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/norm_counts_deseq.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/norm_counts_deseq.log 2>&1 [Sat Jan 6 20:08:36 2024] Finished job 6. 51 of 59 steps (86%) done [Sat Jan 6 20:08:36 2024] rule report1: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.star.deseq.report.html log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.star.log jobid: 13 wildcards: analysis=analysis1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/runDeseqReport.R --logo=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/images/Logo_PiGx.png --prefix='analysis1.star' --reportFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts/deseqReport.Rmd --countDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv --colDataFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/colData.tsv --gtfFile=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/sample_data/sample.gtf --caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates='' --workdir=/build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report --organism='' >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/analysis1.report.star.log 2>&1 [Sat Jan 6 20:08:55 2024] Finished job 13. 52 of 59 steps (88%) done [Sat Jan 6 20:08:55 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.reverse.bigwig log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep1.log jobid: 10 wildcards: sample=UHR_Rep1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam UHR_Rep1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep1.log 2>&1 [Sat Jan 6 20:09:02 2024] Finished job 10. 53 of 59 steps (90%) done [Sat Jan 6 20:09:02 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.reverse.bigwig log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep3.log jobid: 9 wildcards: sample=HBR_Rep3 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam HBR_Rep3 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep3.log 2>&1 [Sat Jan 6 20:09:09 2024] Finished job 9. 54 of 59 steps (92%) done [Sat Jan 6 20:09:09 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.reverse.bigwig log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep3.log jobid: 12 wildcards: sample=UHR_Rep3 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam UHR_Rep3 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep3.log 2>&1 [Sat Jan 6 20:09:16 2024] Finished job 12. 55 of 59 steps (93%) done [Sat Jan 6 20:09:16 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.reverse.bigwig log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep2.log jobid: 8 wildcards: sample=HBR_Rep2 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam HBR_Rep2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep2.log 2>&1 [Sat Jan 6 20:09:23 2024] Finished job 8. 56 of 59 steps (95%) done [Sat Jan 6 20:09:23 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.reverse.bigwig log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep1.log jobid: 7 wildcards: sample=HBR_Rep1 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam HBR_Rep1 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_HBR_Rep1.log 2>&1 [Sat Jan 6 20:09:33 2024] Finished job 7. 57 of 59 steps (97%) done [Sat Jan 6 20:09:33 2024] rule genomeCoverage: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam.bai output: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.reverse.bigwig log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep2.log jobid: 11 wildcards: sample=UHR_Rep2 /usr/bin/Rscript --vanilla /build/reproducible-path/pigx-rnaseq-0.0.10+ds/scripts//export_bigwig.R /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam UHR_Rep2 /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files >> /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/logs/genomeCoverage_UHR_Rep2.log 2>&1 [Sat Jan 6 20:09:43 2024] Finished job 11. 58 of 59 steps (98%) done [Sat Jan 6 20:09:43 2024] localrule all: input: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/multiqc/multiqc_report.html, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.transcripts.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.genes.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.forward.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.reverse.bigwig, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.star.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.transcripts.deseq.report.html, /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.genes.deseq.report.html jobid: 0 [Sat Jan 6 20:09:43 2024] Finished job 0. 59 of 59 steps (100%) done Complete log: /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/.snakemake/log/2024-01-06T200438.351172.snakemake.log The following files have been generated: - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/star_index/SAindex - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/salmon_index/pos.bin - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/multiqc/multiqc_report.html - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_SALMON.genes.tsv - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.transcripts.tsv - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/TPM_counts_from_SALMON.genes.tsv - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/raw_counts/counts_from_star.tsv - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/feature_counts/normalized/deseq_size_factors.txt - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.forward.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.forward.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.forward.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.forward.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.forward.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.forward.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep1.reverse.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep2.reverse.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/HBR_Rep3.reverse.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep1.reverse.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep2.reverse.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/bigwig_files/UHR_Rep3.reverse.bigwig - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.star.deseq.report.html - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.transcripts.deseq.report.html - /build/reproducible-path/pigx-rnaseq-0.0.10+ds/tests/output/report/analysis1.salmon.genes.deseq.report.html make[1]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' 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/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' dh_auto_install install -d /build/reproducible-path/pigx-rnaseq-0.0.10\+ds/debian/pigx-rnaseq make -j12 install DESTDIR=/build/reproducible-path/pigx-rnaseq-0.0.10\+ds/debian/pigx-rnaseq AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' make[3]: Entering directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' /bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' /usr/bin/install -c pigx_rnaseq.py qsub-template.sh '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq' /bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/bin' /bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /bin/mkdir -p '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/share/pigx_rnaseq' /usr/bin/install -c scripts/runDeseqReport.R scripts/translate_sample_sheet_for_report.R scripts/deseqReport.Rmd scripts/counts_matrix_from_SALMON.R scripts/validate_input.py scripts/export_bigwig.R scripts/norm_counts_deseq.R scripts/count_reads.R scripts/collate_read_counts.R '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/libexec/pigx_rnaseq/scripts' /usr/bin/install -c -m 644 README.md '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/share/doc/pigx_rnaseq' /usr/bin/install -c pigx-rnaseq '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/bin' /usr/bin/install -c -m 644 etc/sample_sheet.csv.example etc/settings.yaml etc/pretty.txt images/Logo_PiGx.png '/build/reproducible-path/pigx-rnaseq-0.0.10+ds/debian/pigx-rnaseq/usr/share/pigx_rnaseq' make[3]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' make[2]: Leaving directory '/build/reproducible-path/pigx-rnaseq-0.0.10+ds' find debian/pigx-rnaseq/usr/libexec/pigx_rnaseq -name "*.R"|xargs -r chmod -x 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/reproducible-path/pigx-rnaseq-0.0.10+ds' dh_installdocs install -d debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq install -d debian/.debhelper/generated/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 -p -m0644 debian/changelog debian/pigx-rnaseq/usr/share/doc/pigx-rnaseq/changelog.Debian dh_installman install -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 1603460552 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/reproducible-path/pigx-rnaseq-0.0.10+ds' 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 -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_installdeb install -d debian/pigx-rnaseq/DEBIAN dh_gencontrol 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 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_0.0.10+ds-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pigx-rnaseq_0.0.10+ds-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/476780 and its subdirectories I: Current time: Sat Jan 6 20:09:47 -12 2024 I: pbuilder-time-stamp: 1704614987