Sat Jul 10 02:31:33 UTC 2021 I: starting to build paleomix/bullseye/arm64 on jenkins on '2021-07-10 02:31' Sat Jul 10 02:31:33 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_28/32833/console.log Sat Jul 10 02:31:33 UTC 2021 I: Downloading source for bullseye/paleomix=1.3.2-1 --2021-07-10 02:31:33-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/paleomix/paleomix_1.3.2-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2297 (2.2K) Saving to: ‘paleomix_1.3.2-1.dsc’ 0K .. 100% 169M=0s 2021-07-10 02:31:33 (169 MB/s) - ‘paleomix_1.3.2-1.dsc’ saved [2297/2297] Sat Jul 10 02:31:33 UTC 2021 I: paleomix_1.3.2-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: paleomix Binary: paleomix Architecture: any Version: 1.3.2-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://geogenetics.ku.dk/publications/paleomix Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/paleomix Vcs-Git: https://salsa.debian.org/med-team/paleomix.git Testsuite: autopkgtest Testsuite-Triggers: python3-nose, python3-pytest Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-pytest , python3-coloredlogs , python3-configargparse , python3-ruamel.yaml , python3-pysam , python3-setproctitle , default-jre-headless , bowtie2, rsync, examl, picard-tools Package-List: paleomix deb science optional arch=any Checksums-Sha1: f39ce96ae924161ad8e816dba5d58164579db92e 1135803 paleomix_1.3.2.orig.tar.gz 0f3fde1716d43b0bcf646a5a1dc1c20ce9c802e4 10240 paleomix_1.3.2-1.debian.tar.xz Checksums-Sha256: abd26f7064822db967ab51bdcfc5a200c5cf3b739fc2777776fa1df52902d07e 1135803 paleomix_1.3.2.orig.tar.gz 367407d6ea8b1157eb837ec5f8c519e6a5e0103adf84b80b1c91e675ee2e9dbd 10240 paleomix_1.3.2-1.debian.tar.xz Files: 5b9adb473de3deb08c1651ed2b162566 1135803 paleomix_1.3.2.orig.tar.gz c0e7b4e16478f341c4e893523bab27f3 10240 paleomix_1.3.2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAl+hIB0ACgkQeTz2fo8N EdqZfg/+Prj8rRTScMG1QRah4aqOmVkIwL9MLlnWyR+RzciUjCJ0y1g4Ia6+lr0s PYk+v21n37Rgpe7p/2ouQ8RrnRlxkw1SMQyJACqyQ9z5sPD80aByqljS8LdRvysj fb/3KlkWHkc3aZzVQjiPj+NeLdL6VpnBrFYO42NMpFdXhEiNVZhjqyfY8Nlle5EK 5bqL6vrvLQedOzeGWFssHfprgQlicwyJ94/v21lTq3eSILwdIQblUIgGtXc6pFT2 qbmzkDRsS4btOQdSw7m/P52MnHm1qbpoRaBE90scwEG8stOovCG0TzdXrLJzkHFl NDpf6PdzZn3HcgfG3ZXdH6bOq0S4YLsOsk4doSvg5LeW6TUYnjY4PDlsu492zuS4 x6H6C4O1pYt2/Z3mRvMYwow/DZIRr3J3LzQGs1/oo3I1Fd4KDZLSZ1Gdmy+lh3G+ c5oOnRAM6ljnMysplq7VS0Q7gof7z6G/cFQoNe7Fk0LSZdilhNhE6u5lMwp4oy/j hqLVozenWL05tZI6o3M0r63vQNFFc6R6G/q+iFtgfWOYyEKR5MzNLPgyA22/ZAiV c64MxCpqtiuhK1j8m4BLVR7z8aTRYOhRAB5e3Odwac3PwpRqHR3mvJTtnDrV7y// cZmH1thL7T+JmnPQPdJpTywE3x5jJEeKEiBaTp5/cCocnIV3/dE= =uNfp -----END PGP SIGNATURE----- Sat Jul 10 02:31:33 UTC 2021 I: Checking whether the package is not for us Sat Jul 10 02:31:33 UTC 2021 I: Starting 1st build on remote node codethink15-arm64.debian.net. Sat Jul 10 02:31:33 UTC 2021 I: Preparing to do remote build '1' on codethink15-arm64.debian.net. Sat Jul 10 02:33:47 UTC 2021 I: Deleting $TMPDIR on codethink15-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Aug 11 20:54:35 -12 2022 I: pbuilder-time-stamp: 1660294475 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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 [paleomix_1.3.2-1.dsc] I: copying [./paleomix_1.3.2.orig.tar.gz] I: copying [./paleomix_1.3.2-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.IfEvKapU/trustedkeys.kbx': General error gpgv: Signature made Mon Nov 2 21:17:17 2020 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./paleomix_1.3.2-1.dsc dpkg-source: info: extracting paleomix in paleomix-1.3.2 dpkg-source: info: unpacking paleomix_1.3.2.orig.tar.gz dpkg-source: info: unpacking paleomix_1.3.2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying xfail_command_tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5680/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='5680' 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/tmp.UN6kMFMRYE/pbuilderrc_5cSK --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.UN6kMFMRYE/b1 --logfile b1/build.log paleomix_1.3.2-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink15-arm64 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 21 2021 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 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 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 161960 Feb 7 2021 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 Feb 7 2021 more -rwsr-xr-x 1 root root 51360 Feb 7 2021 mount -rwxr-xr-x 1 root root 14496 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 2021 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 Aug 10 03:47 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 Feb 7 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 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 Feb 7 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/5680/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), dh-python, python3, python3-setuptools, python3-pytest, python3-coloredlogs, python3-configargparse, python3-ruamel.yaml, python3-pysam, python3-setproctitle, default-jre-headless, bowtie2, rsync, examl, picard-tools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 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 dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-coloredlogs; however: Package python3-coloredlogs is not installed. pbuilder-satisfydepends-dummy depends on python3-configargparse; however: Package python3-configargparse is not installed. pbuilder-satisfydepends-dummy depends on python3-ruamel.yaml; however: Package python3-ruamel.yaml is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-setproctitle; however: Package python3-setproctitle is not installed. pbuilder-satisfydepends-dummy depends on default-jre-headless; however: Package default-jre-headless is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on rsync; however: Package rsync is not installed. pbuilder-satisfydepends-dummy depends on examl; however: Package examl is not installed. pbuilder-satisfydepends-dummy depends on picard-tools; however: Package picard-tools 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} bowtie2{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} examl{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} java-common{a} libactivation-java{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} libbarclay-java{a} libbrotli1{a} libbsd0{a} libcbor0{a} libcdi-api-java{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} 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} libevent-core-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfastinfoset-java{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libgatk-native-bindings-java{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgif7{a} libgkl-java{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libguava-java{a} libguice-java{a} libharfbuzz0b{a} libhts3{a} libhtsjdk-java{a} libhttpclient-java{a} libhttpcore-java{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu67{a} libistack-commons-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjoptsimple-java{a} libjpeg62-turbo{a} libjsoup-java{a} libjsr305-java{a} liblcms2-2{a} libldap-2.4-2{a} liblightcouch-java{a} libllvm11{a} liblog4j2-java{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} libmongodb-java{a} libmpdec3{a} libnghttp2-14{a} libngs-java{a} libngs-sdk-dev{a} libngs-sdk2{a} libnl-3-200{a} libnl-route-3-200{a} libnspr4{a} libnss3{a} libnuma1{a} libopenmpi3{a} libpciaccess0{a} libpcsclite1{a} libpicard-java{a} libpipeline1{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} libpmix2{a} libpng16-16{a} libpopt0{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} librdmacm1{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} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1{a} libstax-ex-java{a} libstreambuffer-java{a} libsub-override-perl{a} libtool{a} libtxw2-java{a} libuchardet0{a} libucx0{a} libvulkan1{a} libwagon-http-java{a} libwagon-provider-api-java{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-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxnvctrl0{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} media-types{a} ocl-icd-libopencl1{a} openjdk-11-jre{a} openjdk-11-jre-headless{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} picard-tools{a} po-debconf{a} python3{a} python3-attr{a} python3-coloredlogs{a} python3-configargparse{a} python3-distutils{a} python3-humanfriendly{a} python3-importlib-metadata{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pyparsing{a} python3-pysam{a} python3-pytest{a} python3-ruamel.yaml{a} python3-ruamel.yaml.clib{a} python3-setproctitle{a} python3-setuptools{a} python3-six{a} python3-toml{a} python3-zipp{a} python3.9{a} python3.9-minimal{a} readline-common{a} rsync{a} sensible-utils{a} ucf{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus fonts-dejavu-extra libarchive-cpio-perl libatk-wrapper-java-jni libglib2.0-data libjansi-java libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx mesa-vulkan-drivers publicsuffix python3-pygments r-base-core shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 253 newly installed, 0 to remove and 0 not upgraded. Need to get 145 MB of archives. After unpacking 502 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 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 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libpopt0 arm64 1.18-2 [48.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 rsync arm64 3.2.3-4 [316 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1k-1 [829 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 libedit2 arm64 3.1-20191231-2+b1 [92.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 libcbor0 arm64 0.5.0+dfsg-2 [20.1 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 libfido2-1 arm64 1.6.0-2 [50.2 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 openssh-client arm64 1:8.4p1-5 [892 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 ucf all 3.0043 [74.0 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libnspr4 arm64 2:4.29-1 [105 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libnss3 arm64 2:3.61-1 [1210 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 ca-certificates-java all 20190909 [15.7 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 java-common all 0.72 [14.5 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libavahi-common-data arm64 0.8-5 [123 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libavahi-common3 arm64 0.8-5 [57.1 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libdbus-1-3 arm64 1.12.20-2 [208 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libavahi-client3 arm64 0.8-5 [60.6 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libcups2 arm64 2.3.3op2-3+deb11u1 [334 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 liblcms2-2 arm64 2.12~rc1-2 [140 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libfreetype6 arm64 2.10.4+dfsg-1 [393 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libasound2-data all 1.2.4-1.1 [38.2 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libasound2 arm64 1.2.4-1.1 [326 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libharfbuzz0b arm64 2.7.4-1 [1445 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libpcsclite1 arm64 1.9.1-1 [59.5 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 openjdk-11-jre-headless arm64 11.0.11+9-1 [36.4 MB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 default-jre-headless arm64 2:1.11-72 [10.9 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 ant all 1.10.9-4 [2118 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 ant-optional all 1.10.9-4 [381 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 bowtie2 arm64 2.4.2-2+b3 [1264 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 libglvnd0 arm64 1.3.2-1 [44.3 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 libxcb1 arm64 1.14-3 [138 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 libx11-data all 2:1.7.1-1 [310 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 libx11-6 arm64 2:1.7.1-1 [747 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 libdrm-common all 2.4.104-1 [14.9 kB] Get: 90 http://deb.debian.org/debian bullseye/main arm64 libdrm2 arm64 2.4.104-1 [41.3 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 libglapi-mesa arm64 20.3.4-1 [96.7 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 libx11-xcb1 arm64 2:1.7.1-1 [203 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 libxcb-dri2-0 arm64 1.14-3 [103 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 libxcb-dri3-0 arm64 1.14-3 [102 kB] Get: 95 http://deb.debian.org/debian bullseye/main arm64 libxcb-glx0 arm64 1.14-3 [118 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 libxcb-present0 arm64 1.14-3 [101 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 libxcb-shm0 arm64 1.14-3 [101 kB] Get: 98 http://deb.debian.org/debian bullseye/main arm64 libxcb-sync1 arm64 1.14-3 [105 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 libxcb-xfixes0 arm64 1.14-3 [105 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 libxdamage1 arm64 1:1.1.5-2 [15.7 kB] Get: 101 http://deb.debian.org/debian bullseye/main arm64 libxext6 arm64 2:1.3.3-1.1 [51.6 kB] Get: 102 http://deb.debian.org/debian bullseye/main arm64 libxfixes3 arm64 1:5.0.3-2 [22.1 kB] Get: 103 http://deb.debian.org/debian bullseye/main arm64 libxshmfence1 arm64 1.3-1 [8712 B] Get: 104 http://deb.debian.org/debian bullseye/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get: 105 http://deb.debian.org/debian bullseye/main arm64 libdrm-amdgpu1 arm64 2.4.104-1 [28.0 kB] Get: 106 http://deb.debian.org/debian bullseye/main arm64 libdrm-nouveau2 arm64 2.4.104-1 [26.1 kB] Get: 107 http://deb.debian.org/debian bullseye/main arm64 libdrm-radeon1 arm64 2.4.104-1 [29.3 kB] Get: 108 http://deb.debian.org/debian bullseye/main arm64 libz3-4 arm64 4.8.10-1 [6117 kB] Get: 109 http://deb.debian.org/debian bullseye/main arm64 libllvm11 arm64 1:11.0.1-2 [14.7 MB] Get: 110 http://deb.debian.org/debian bullseye/main arm64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get: 111 http://deb.debian.org/debian bullseye/main arm64 libsensors5 arm64 1:3.6.0-7 [51.2 kB] Get: 112 http://deb.debian.org/debian bullseye/main arm64 libvulkan1 arm64 1.2.162.0-1 [95.7 kB] Get: 113 http://deb.debian.org/debian bullseye/main arm64 libgl1-mesa-dri arm64 20.3.4-1 [6552 kB] Get: 114 http://deb.debian.org/debian bullseye/main arm64 libglx-mesa0 arm64 20.3.4-1 [186 kB] Get: 115 http://deb.debian.org/debian bullseye/main arm64 libglx0 arm64 1.3.2-1 [32.0 kB] Get: 116 http://deb.debian.org/debian bullseye/main arm64 libgl1 arm64 1.3.2-1 [91.4 kB] Get: 117 http://deb.debian.org/debian bullseye/main arm64 libgif7 arm64 5.1.9-2 [45.0 kB] Get: 118 http://deb.debian.org/debian bullseye/main arm64 libxi6 arm64 2:1.7.10-1 [81.7 kB] Get: 119 http://deb.debian.org/debian bullseye/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB] Get: 120 http://deb.debian.org/debian bullseye/main arm64 x11-common all 1:7.7+22 [252 kB] Get: 121 http://deb.debian.org/debian bullseye/main arm64 libxtst6 arm64 2:1.2.3-1 [26.7 kB] Get: 122 http://deb.debian.org/debian bullseye/main arm64 openjdk-11-jre arm64 11.0.11+9-1 [165 kB] Get: 123 http://deb.debian.org/debian bullseye/main arm64 default-jre arm64 2:1.11-72 [1044 B] Get: 124 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 125 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 126 http://deb.debian.org/debian bullseye/main arm64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 127 http://deb.debian.org/debian bullseye/main arm64 libevent-core-2.1-7 arm64 2.1.12-stable-1 [132 kB] Get: 128 http://deb.debian.org/debian bullseye/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-1 [57.2 kB] Get: 129 http://deb.debian.org/debian bullseye/main arm64 libnl-3-200 arm64 3.4.0-1+b1 [60.6 kB] Get: 130 http://deb.debian.org/debian bullseye/main arm64 libnl-route-3-200 arm64 3.4.0-1+b1 [149 kB] Get: 131 http://deb.debian.org/debian bullseye/main arm64 libibverbs1 arm64 33.2-1 [56.1 kB] Get: 132 http://deb.debian.org/debian bullseye/main arm64 ibverbs-providers arm64 33.2-1 [235 kB] Get: 133 http://deb.debian.org/debian bullseye/main arm64 librdmacm1 arm64 33.2-1 [65.3 kB] Get: 134 http://deb.debian.org/debian bullseye/main arm64 libfabric1 arm64 1.11.0-2 [389 kB] Get: 135 http://deb.debian.org/debian bullseye/main arm64 libhwloc15 arm64 2.4.1+dfsg-1 [131 kB] Get: 136 http://deb.debian.org/debian bullseye/main arm64 libpciaccess0 arm64 0.16-1 [52.9 kB] Get: 137 http://deb.debian.org/debian bullseye/main arm64 libxnvctrl0 arm64 460.73.01-1 [26.7 kB] Get: 138 http://deb.debian.org/debian bullseye/main arm64 ocl-icd-libopencl1 arm64 2.2.14-2 [41.5 kB] Get: 139 http://deb.debian.org/debian bullseye/main arm64 libhwloc-plugins arm64 2.4.1+dfsg-1 [21.1 kB] Get: 140 http://deb.debian.org/debian bullseye/main arm64 libpmix2 arm64 4.0.0-4 [513 kB] Get: 141 http://deb.debian.org/debian bullseye/main arm64 libnuma1 arm64 2.0.12-1+b1 [25.8 kB] Get: 142 http://deb.debian.org/debian bullseye/main arm64 libucx0 arm64 1.10.1~rc1+really.1.10.0-1 [567 kB] Get: 143 http://deb.debian.org/debian bullseye/main arm64 libopenmpi3 arm64 4.1.0-10 [2152 kB] Get: 144 http://deb.debian.org/debian bullseye/main arm64 openmpi-common all 4.1.0-10 [179 kB] Get: 145 http://deb.debian.org/debian bullseye/main arm64 openmpi-bin arm64 4.1.0-10 [237 kB] Get: 146 http://deb.debian.org/debian bullseye/main arm64 examl arm64 3.0.22-1+b4 [799 kB] Get: 147 http://deb.debian.org/debian bullseye/main arm64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 148 http://deb.debian.org/debian bullseye/main arm64 libaopalliance-java all 20070526-6 [9048 B] Get: 149 http://deb.debian.org/debian bullseye/main arm64 libapache-pom-java all 18-1 [4676 B] Get: 150 http://deb.debian.org/debian bullseye/main arm64 libargs4j-java all 2.33-1.1 [137 kB] Get: 151 http://deb.debian.org/debian bullseye/main arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 152 http://deb.debian.org/debian bullseye/main arm64 libfreemarker-java all 2.3.23-11 [1221 kB] Get: 153 http://deb.debian.org/debian bullseye/main arm64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get: 154 http://deb.debian.org/debian bullseye/main arm64 libcommons-parent-java all 43-1 [10.8 kB] Get: 155 http://deb.debian.org/debian bullseye/main arm64 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 156 http://deb.debian.org/debian bullseye/main arm64 libgoogle-gson-java all 2.8.6-1 [225 kB] Get: 157 http://deb.debian.org/debian bullseye/main arm64 libcommons-codec-java all 1.15-1 [292 kB] Get: 158 http://deb.debian.org/debian bullseye/main arm64 libhttpcore-java all 4.4.14-1 [631 kB] Get: 159 http://deb.debian.org/debian bullseye/main arm64 libhttpclient-java all 4.5.13-2 [1233 kB] Get: 160 http://deb.debian.org/debian bullseye/main arm64 liblightcouch-java all 0.0.6-1.1 [65.2 kB] Get: 161 http://deb.debian.org/debian bullseye/main arm64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 162 http://deb.debian.org/debian bullseye/main arm64 libslf4j-java all 1.7.30-1 [144 kB] Get: 163 http://deb.debian.org/debian bullseye/main arm64 liblog4j2-java all 2.13.3-1 [1979 kB] Get: 164 http://deb.debian.org/debian bullseye/main arm64 libbarclay-java all 2.1.0-3.1 [116 kB] Get: 165 http://deb.debian.org/debian bullseye/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 166 http://deb.debian.org/debian bullseye/main arm64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 167 http://deb.debian.org/debian bullseye/main arm64 libjaxen-java all 1.1.6-4 [214 kB] Get: 168 http://deb.debian.org/debian bullseye/main arm64 libdom4j-java all 2.1.3-1 [310 kB] Get: 169 http://deb.debian.org/debian bullseye/main arm64 libcommons-io-java all 2.8.0-1 [279 kB] Get: 170 http://deb.debian.org/debian bullseye/main arm64 libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get: 171 http://deb.debian.org/debian bullseye/main arm64 libcommons-cli-java all 1.4-2 [57.3 kB] Get: 172 http://deb.debian.org/debian bullseye/main arm64 libcommons-lang3-java all 3.11-1 [550 kB] Get: 173 http://deb.debian.org/debian bullseye/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 174 http://deb.debian.org/debian bullseye/main arm64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 175 http://deb.debian.org/debian bullseye/main arm64 libguava-java all 29.0-6 [2419 kB] Get: 176 http://deb.debian.org/debian bullseye/main arm64 libguice-java all 4.2.3-2 [1435 kB] Get: 177 http://deb.debian.org/debian bullseye/main arm64 libmaven-parent-java all 31-2 [5100 B] Get: 178 http://deb.debian.org/debian bullseye/main arm64 libplexus-utils2-java all 3.3.0-1 [250 kB] Get: 179 http://deb.debian.org/debian bullseye/main arm64 libwagon-provider-api-java all 3.3.4-1 [50.2 kB] Get: 180 http://deb.debian.org/debian bullseye/main arm64 libmaven-resolver-java all 1.4.2-3 [556 kB] Get: 181 http://deb.debian.org/debian bullseye/main arm64 libplexus-cipher-java all 1.8-2 [15.0 kB] Get: 182 http://deb.debian.org/debian bullseye/main arm64 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 183 http://deb.debian.org/debian bullseye/main arm64 libplexus-component-annotations-java all 2.1.0-1 [7620 B] Get: 184 http://deb.debian.org/debian bullseye/main arm64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 185 http://deb.debian.org/debian bullseye/main arm64 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 186 http://deb.debian.org/debian bullseye/main arm64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 187 http://deb.debian.org/debian bullseye/main arm64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 188 http://deb.debian.org/debian bullseye/main arm64 libmaven3-core-java all 3.6.3-5 [1538 kB] Get: 189 http://deb.debian.org/debian bullseye/main arm64 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 190 http://deb.debian.org/debian bullseye/main arm64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 191 http://deb.debian.org/debian bullseye/main arm64 libcommons-compress-java all 1.20-1 [574 kB] Get: 192 http://deb.debian.org/debian bullseye/main arm64 libplexus-io-java all 3.2.0-1.1 [65.0 kB] Get: 193 http://deb.debian.org/debian bullseye/main arm64 libsnappy1v5 arm64 1.1.8-1 [17.2 kB] Get: 194 http://deb.debian.org/debian bullseye/main arm64 libsnappy-jni arm64 1.1.8.3-1 [7056 B] Get: 195 http://deb.debian.org/debian bullseye/main arm64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 196 http://deb.debian.org/debian bullseye/main arm64 libxz-java all 1.8-2 [141 kB] Get: 197 http://deb.debian.org/debian bullseye/main arm64 libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 198 http://deb.debian.org/debian bullseye/main arm64 libjsoup-java all 1.10.2-2 [350 kB] Get: 199 http://deb.debian.org/debian bullseye/main arm64 libwagon-http-java all 3.3.4-1 [53.9 kB] Get: 200 http://deb.debian.org/debian bullseye/main arm64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 201 http://deb.debian.org/debian bullseye/main arm64 libcodemodel-java all 2.6+jaxb2.3.0.1-10 [163 kB] Get: 202 http://deb.debian.org/debian bullseye/main arm64 libcommons-jexl2-java all 2.1.1-5 [256 kB] Get: 203 http://deb.debian.org/debian bullseye/main arm64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 204 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 205 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 206 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 207 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 208 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 209 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 210 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 211 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB] Get: 212 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 213 http://deb.debian.org/debian bullseye/main arm64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 214 http://deb.debian.org/debian bullseye/main arm64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 215 http://deb.debian.org/debian bullseye/main arm64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 216 http://deb.debian.org/debian bullseye/main arm64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 217 http://deb.debian.org/debian bullseye/main arm64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 218 http://deb.debian.org/debian bullseye/main arm64 libxsom-java all 2.3.0.1-10 [396 kB] Get: 219 http://deb.debian.org/debian bullseye/main arm64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 220 http://deb.debian.org/debian bullseye/main arm64 libgatk-native-bindings-java all 1.0.0-2.1 [7344 B] Get: 221 http://deb.debian.org/debian bullseye/main arm64 libgkl-java all 0.8.7+dfsg-1 [998 kB] Get: 222 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 223 http://deb.debian.org/debian bullseye/main arm64 librngom-java all 2.3.0.1-10 [288 kB] Get: 224 http://deb.debian.org/debian bullseye/main arm64 libtxw2-java all 2.3.0.1-10 [134 kB] Get: 225 http://deb.debian.org/debian bullseye/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 226 http://deb.debian.org/debian bullseye/main arm64 libjaxb-java all 2.3.0.1-10 [1954 kB] Get: 227 http://deb.debian.org/debian bullseye/main arm64 libngs-sdk2 arm64 2.10.9-1 [45.5 kB] Get: 228 http://deb.debian.org/debian bullseye/main arm64 libngs-sdk-dev arm64 2.10.9-1 [91.9 kB] Get: 229 http://deb.debian.org/debian bullseye/main arm64 libngs-java arm64 2.10.9-1 [80.4 kB] Get: 230 http://deb.debian.org/debian bullseye/main arm64 libhtsjdk-java all 2.23.0+dfsg-2 [1607 kB] Get: 231 http://deb.debian.org/debian bullseye/main arm64 libpicard-java all 2.24.1+dfsg-1 [1617 kB] Get: 232 http://deb.debian.org/debian bullseye/main arm64 picard-tools all 2.24.1+dfsg-1 [313 kB] Get: 233 http://deb.debian.org/debian bullseye/main arm64 python3-attr all 20.3.0-1 [52.9 kB] Get: 234 http://deb.debian.org/debian bullseye/main arm64 python3-humanfriendly all 9.1-1 [84.6 kB] Get: 235 http://deb.debian.org/debian bullseye/main arm64 python3-coloredlogs all 7.3-2 [28.0 kB] Get: 236 http://deb.debian.org/debian bullseye/main arm64 python3-configargparse all 1.2.3-1 [25.2 kB] Get: 237 http://deb.debian.org/debian bullseye/main arm64 python3-six all 1.16.0-1 [17.1 kB] Get: 238 http://deb.debian.org/debian bullseye/main arm64 python3-more-itertools all 4.2.0-3 [42.7 kB] Get: 239 http://deb.debian.org/debian bullseye/main arm64 python3-zipp all 1.0.0-3 [6060 B] Get: 240 http://deb.debian.org/debian bullseye/main arm64 python3-importlib-metadata all 1.6.0-2 [10.3 kB] Get: 241 http://deb.debian.org/debian bullseye/main arm64 python3-iniconfig all 1.1.1-1 [6308 B] Get: 242 http://deb.debian.org/debian bullseye/main arm64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 243 http://deb.debian.org/debian bullseye/main arm64 python3-packaging all 20.9-2 [33.5 kB] Get: 244 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 245 http://deb.debian.org/debian bullseye/main arm64 python3-pluggy all 0.13.0-6 [22.3 kB] Get: 246 http://deb.debian.org/debian bullseye/main arm64 python3-py all 1.10.0-1 [94.2 kB] Get: 247 http://deb.debian.org/debian bullseye/main arm64 python3-pysam arm64 0.15.4+ds-3+b2 [1386 kB] Get: 248 http://deb.debian.org/debian bullseye/main arm64 python3-toml all 0.10.1-1 [15.9 kB] Get: 249 http://deb.debian.org/debian bullseye/main arm64 python3-pytest all 6.0.2-2 [211 kB] Get: 250 http://deb.debian.org/debian bullseye/main arm64 python3-ruamel.yaml.clib arm64 0.2.2-1+b2 [108 kB] Get: 251 http://deb.debian.org/debian bullseye/main arm64 python3-ruamel.yaml all 0.16.12-2 [110 kB] Get: 252 http://deb.debian.org/debian bullseye/main arm64 python3-setproctitle arm64 1.2.1-1+b1 [16.6 kB] Get: 253 http://deb.debian.org/debian bullseye/main arm64 python3-setuptools all 52.0.0-4 [366 kB] Fetched 145 MB in 5s (29.0 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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../5-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 .../6-libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-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) ... 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 ... 20513 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:arm64. Preparing to unpack .../2-libmpdec3_2.5.1-1_arm64.deb ... Unpacking libmpdec3:arm64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../4-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:arm64. Preparing to unpack .../5-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 .../6-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 .../7-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 ... 20934 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 libpopt0:arm64. Preparing to unpack .../001-libpopt0_1.18-2_arm64.deb ... Unpacking libpopt0:arm64 (1.18-2) ... Selecting previously unselected package rsync. 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Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libmd0:arm64. Preparing to unpack .../010-libmd0_1.0.3-3_arm64.deb ... Unpacking libmd0:arm64 (1.0.3-3) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../011-libbsd0_0.11.3-1_arm64.deb ... Unpacking libbsd0:arm64 (0.11.3-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../012-libedit2_3.1-20191231-2+b1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20191231-2+b1) ... Selecting previously unselected package libcbor0:arm64. Preparing to unpack .../013-libcbor0_0.5.0+dfsg-2_arm64.deb ... Unpacking libcbor0:arm64 (0.5.0+dfsg-2) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../014-libfido2-1_1.6.0-2_arm64.deb ... Unpacking libfido2-1:arm64 (1.6.0-2) ... 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Selecting previously unselected package libavahi-common-data:arm64. Preparing to unpack .../021-libavahi-common-data_0.8-5_arm64.deb ... Unpacking libavahi-common-data:arm64 (0.8-5) ... Selecting previously unselected package libavahi-common3:arm64. Preparing to unpack .../022-libavahi-common3_0.8-5_arm64.deb ... Unpacking libavahi-common3:arm64 (0.8-5) ... Selecting previously unselected package libdbus-1-3:arm64. Preparing to unpack .../023-libdbus-1-3_1.12.20-2_arm64.deb ... Unpacking libdbus-1-3:arm64 (1.12.20-2) ... Selecting previously unselected package libavahi-client3:arm64. Preparing to unpack .../024-libavahi-client3_0.8-5_arm64.deb ... Unpacking libavahi-client3:arm64 (0.8-5) ... Selecting previously unselected package libcups2:arm64. Preparing to unpack .../025-libcups2_2.3.3op2-3+deb11u1_arm64.deb ... Unpacking libcups2:arm64 (2.3.3op2-3+deb11u1) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../026-liblcms2-2_2.12~rc1-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.12~rc1-2) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../027-libjpeg62-turbo_1%3a2.0.6-4_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.0.6-4) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../028-libbrotli1_1.0.9-2+b2_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../029-libpng16-16_1.6.37-3_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.37-3) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../030-libfreetype6_2.10.4+dfsg-1_arm64.deb ... Unpacking libfreetype6:arm64 (2.10.4+dfsg-1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../031-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../032-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../033-libfontconfig1_2.13.1-4.2_arm64.deb ... Unpacking libfontconfig1:arm64 (2.13.1-4.2) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../034-libasound2-data_1.2.4-1.1_all.deb ... Unpacking libasound2-data (1.2.4-1.1) ... Selecting previously unselected package libasound2:arm64. Preparing to unpack .../035-libasound2_1.2.4-1.1_arm64.deb ... Unpacking libasound2:arm64 (1.2.4-1.1) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../036-libglib2.0-0_2.66.8-1_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.66.8-1) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../037-libgraphite2-3_1.3.14-1_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../038-libharfbuzz0b_2.7.4-1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (2.7.4-1) ... Selecting previously unselected package libpcsclite1:arm64. Preparing to unpack .../039-libpcsclite1_1.9.1-1_arm64.deb ... Unpacking libpcsclite1:arm64 (1.9.1-1) ... Selecting previously unselected package openjdk-11-jre-headless:arm64. Preparing to unpack .../040-openjdk-11-jre-headless_11.0.11+9-1_arm64.deb ... Unpacking openjdk-11-jre-headless:arm64 (11.0.11+9-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../041-default-jre-headless_2%3a1.11-72_arm64.deb ... Unpacking default-jre-headless (2:1.11-72) ... Selecting previously unselected package ant. Preparing to unpack .../042-ant_1.10.9-4_all.deb ... Unpacking ant (1.10.9-4) ... Selecting previously unselected package ant-optional. Preparing to unpack .../043-ant-optional_1.10.9-4_all.deb ... Unpacking ant-optional (1.10.9-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../044-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../045-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../046-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../047-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../048-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../049-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package bowtie2. 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Setting up libmaven-resolver-java (1.4.2-3) ... Setting up libllvm11:arm64 (1:11.0.1-2) ... Setting up libfreetype6:arm64 (2.10.4+dfsg-1) ... Setting up libguava-java (29.0-6) ... Setting up libxcb-sync1:arm64 (1.14-3) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up ucf (3.0043) ... 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 (1.11.0-1) ... Setting up librngom-java (2.3.0.1-10) ... Setting up libdrm2:arm64 (2.4.104-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libx11-6:arm64 (2:1.7.1-1) ... Setting up libharfbuzz0b:arm64 (2.7.4-1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libxsom-java (2.3.0.1-10) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libavahi-client3:arm64 (0.8-5) ... Setting up rsync (3.2.3-4) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... 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 libx11-xcb1:arm64 (2:1.7.1-1) ... Setting up libibverbs1:arm64 (33.2-1) ... 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 ibverbs-providers:arm64 (33.2-1) ... 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 openssh-client (1:8.4p1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libgl1-mesa-dri:arm64 (20.3.4-1) ... Setting up libxext6:arm64 (2:1.3.3-1.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libguice-java (4.2.3-2) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b2) ... Setting up libxnvctrl0:arm64 (460.73.01-1) ... Setting up dh-autoreconf (20) ... Setting up libxfixes3:arm64 (1:5.0.3-2) ... Setting up libcups2:arm64 (2.3.3op2-3+deb11u1) ... Setting up libhttpclient-java (4.5.13-2) ... Setting up liblightcouch-java (0.0.6-1.1) ... Setting up libwagon-http-java (3.3.4-1) ... Setting up libmaven-shared-utils-java (3.3.0-1) ... Setting up libfontconfig1:arm64 (2.13.1-4.2) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up python3.9 (3.9.2-1) ... Setting up librdmacm1:arm64 (33.2-1) ... Setting up libucx0:arm64 (1.10.1~rc1+really.1.10.0-1) ... Setting up libplexus-io-java (3.2.0-1.1) ... Setting up libglx-mesa0:arm64 (20.3.4-1) ... Setting up libxi6:arm64 (2:1.7.10-1) ... Setting up libglx0:arm64 (1.3.2-1) ... Setting up libmaven3-core-java (3.6.3-5) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up libxtst6:arm64 (2:1.2.3-1) ... Setting up liblog4j2-java (2.13.3-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libhwloc-plugins:arm64 (2.4.1+dfsg-1) ... Setting up bowtie2 (2.4.2-2+b3) ... Setting up python3-six (1.16.0-1) ... Setting up libgl1:arm64 (1.3.2-1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-humanfriendly (9.1-1) ... Setting up python3-setproctitle:arm64 (1.2.1-1+b1) ... Setting up python3-toml (0.10.1-1) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-coloredlogs (7.3-2) ... Setting up libbarclay-java (2.1.0-3.1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up python3-more-itertools (4.2.0-3) ... Setting up python3-configargparse (1.2.3-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up python3-iniconfig (1.1.1-1) ... Setting up python3-attr (20.3.0-1) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-py (1.10.0-1) ... Setting up libpmix2:arm64 (4.0.0-4) ... Setting up libopenmpi3:arm64 (4.1.0-10) ... Setting up python3-ruamel.yaml.clib:arm64 (0.2.2-1+b2) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-packaging (20.9-2) ... Setting up python3-ruamel.yaml (0.16.12-2) ... Setting up openmpi-bin (4.1.0-10) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up python3-importlib-metadata (1.6.0-2) ... Setting up examl (3.0.22-1+b4) ... Setting up python3-pluggy (0.13.0-6) ... Setting up python3-pytest (6.0.2-2) ... Setting up default-jre-headless (2:1.11-72) ... Setting up openjdk-11-jre-headless:arm64 (11.0.11+9-1) ... 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 (11.0.11+9-1) ... Setting up default-jre (2:1.11-72) ... Setting up ant (1.10.9-4) ... Setting up ca-certificates-java (20190909) ... 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 libpicard-java (2.24.1+dfsg-1) ... Setting up picard-tools (2.24.1+dfsg-1) ... Processing triggers for libc-bin (2.31-12) ... 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/paleomix-1.3.2/ && 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 > ../paleomix_1.3.2-1_source.changes dpkg-buildpackage: info: source package paleomix dpkg-buildpackage: info: source version 1.3.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/paleomix-1.3.2/.pybuild/cpython3_3.9/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix copying paleomix/yaml.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix copying paleomix/pipeline.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix copying paleomix/nodegraph.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix copying paleomix/node.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix copying paleomix/main.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix copying paleomix/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools copying paleomix/tools/vcf_to_fasta.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools copying paleomix/tools/vcf_filter.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools copying paleomix/tools/validate_fastq.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools copying paleomix/tools/rmdup_collapsed.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools copying paleomix/tools/gtf_to_bed.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools copying paleomix/tools/factory.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools copying paleomix/tools/dupcheck.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools copying paleomix/tools/depths.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools copying paleomix/tools/coverage.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools copying paleomix/tools/cleanup.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools copying paleomix/tools/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources copying paleomix/resources/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines copying paleomix/pipelines/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/validation.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/sequences.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/samtools.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/raxml.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/picard.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/phylip.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/newick.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/mapdamage.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/mafft.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/formats.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/examl.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/commands.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/bwa.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/bowtie2.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/bedtools.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/adapterremoval.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes copying paleomix/nodes/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/versions.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/vcfwrap.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/vcffilter.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/utilities.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/timer.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/text.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/testing.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/system.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/sequences.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/sampling.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/rtools.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/procs.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/makefile.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/logging.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/fileutils.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/bedtools.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/bamfiles.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/argparse.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common copying paleomix/common/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd copying paleomix/atomiccmd/sets.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd copying paleomix/atomiccmd/pprint.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd copying paleomix/atomiccmd/command.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd copying paleomix/atomiccmd/builder.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd copying paleomix/atomiccmd/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/coverage.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/common.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/bam_stats creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/pipeline.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/database.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/config.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/common.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_tped.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_mito.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_db.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/pipeline.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/mkfile.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/makefile.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/example.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/config.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/trim_pipeline.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/pipeline.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/paths.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/nodes.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/mkfile.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/makefile.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/config.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/summary.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/report.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/nuclear.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/mitochondria.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/common.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/admixture.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/phylo.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/msa.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/genotype.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/target.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/summary.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/statistics.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/sample.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/reads.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/prefix.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/library.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/lane.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats copying paleomix/common/formats/phylip.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats copying paleomix/common/formats/newick.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats copying paleomix/common/formats/msa.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats copying paleomix/common/formats/fastq.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats copying paleomix/common/formats/fasta.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats copying paleomix/common/formats/_graph.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats copying paleomix/common/formats/_common.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats copying paleomix/common/formats/__init__.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats running egg_info creating paleomix.egg-info writing paleomix.egg-info/PKG-INFO writing dependency_links to paleomix.egg-info/dependency_links.txt writing entry points to paleomix.egg-info/entry_points.txt writing requirements to paleomix.egg-info/requires.txt writing top-level names to paleomix.egg-info/top_level.txt writing manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'paleomix/yaml/CHANGES' warning: no files found matching 'paleomix/yaml/LICENSE' warning: no files found matching 'paleomix/yaml/PKG-INFO' warning: no files found matching 'paleomix/yaml/README' warning: no files found matching 'pylint.conf' writing manifest file 'paleomix.egg-info/SOURCES.txt' creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline copying paleomix/resources/examples/bam_pipeline/makefile.yaml -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_04.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_01.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_02.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_03.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_04.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_01.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_02.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_03.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_01.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_02.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_03.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_01.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_02.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_03.fastq.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.truncated.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.singleton.truncated.gz -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/prefixes copying paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/prefixes creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/setup.sh -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/makefile.yaml -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/bonobo.fasta -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/chimpanzee.fasta -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/gorilla.fasta -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta.fai -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/sumatran_orangutan.fasta -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/white_handed_gibbon.fasta -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/phylogeny copying paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/reports creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/reports/zonkey copying paleomix/resources/reports/zonkey/report.css -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/reports/zonkey creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/common copying paleomix/resources/rscripts/common/requires.r -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/common creating /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/admixture.r -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/coverage.r -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/pca.r -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/tinytree.r -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/treemix.r -> /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/zonkey debian/rules override_dh_auto_test make[1]: Entering directory '/build/paleomix-1.3.2' PATH=/build/paleomix-1.3.2/bin/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test I: pybuild pybuild:284: cp -a README.rst /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build; I: pybuild base:232: cd /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build; python3.9 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.9.2, pytest-6.0.2, py-1.10.0, pluggy-0.13.0 rootdir: /build/paleomix-1.3.2, configfile: setup.cfg collected 1494 items tests/node_test.py ..................................................... [ 3%] ......................................... [ 6%] tests/nodegraph_test.py ......... [ 6%] tests/atomiccmd_test/builder_test.py ................................... [ 9%] ...................................................... [ 12%] tests/atomiccmd_test/command_test.py ................................... [ 15%] ........................................................................ [ 20%] ................ [ 21%] tests/atomiccmd_test/pprint_test.py .................................... [ 23%] .. [ 23%] tests/atomiccmd_test/sets_test.py ...................................... [ 26%] ............ [ 26%] tests/common_tests/bedtools_test.py ............................... [ 29%] tests/common_tests/fileutils_test.py ................................... [ 31%] ...................................................................... [ 36%] tests/common_tests/makefile_test.py .................................... [ 38%] ........................................................................ [ 43%] ........................................................................ [ 48%] ........................................................................ [ 52%] ........................................................................ [ 57%] ............................... [ 59%] tests/common_tests/sampling_test.py ........................ [ 61%] tests/common_tests/sequences_test.py ................................... [ 63%] ............... [ 64%] tests/common_tests/text_test.py ....................................... [ 67%] tests/common_tests/utilities_test.py ................................... [ 69%] ........................................................................ [ 74%] .. [ 74%] tests/common_tests/versions_test.py .................................... [ 77%] ............................................................ [ 81%] tests/common_tests/formats_tests/fasta_test.py ......................... [ 82%] ............. [ 83%] tests/common_tests/formats_tests/fastq_test.py ......................... [ 85%] ........... [ 86%] tests/common_tests/formats_tests/msa_test.py ........................... [ 87%] ................... [ 89%] tests/common_tests/formats_tests/newick_test.py ........................ [ 90%] ........................................................................ [ 95%] ...... [ 95%] tests/common_tests/formats_tests/phylip_test.py ........ [ 96%] tests/tools_test/factory_test.py xXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX [ 99%] XXXXXXXXXXXXX [100%] ================= 1442 passed, 1 xfailed, 51 xpassed in 36.48s ================= make[1]: Leaving directory '/build/paleomix-1.3.2' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/paleomix-1.3.2/debian/paleomix running install running build running build_py running egg_info writing paleomix.egg-info/PKG-INFO writing dependency_links to paleomix.egg-info/dependency_links.txt writing entry points to paleomix.egg-info/entry_points.txt writing requirements to paleomix.egg-info/requires.txt writing top-level names to paleomix.egg-info/top_level.txt reading manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'paleomix/yaml/CHANGES' warning: no files found matching 'paleomix/yaml/LICENSE' warning: no files found matching 'paleomix/yaml/PKG-INFO' warning: no files found matching 'paleomix/yaml/README' warning: no files found matching 'pylint.conf' writing manifest file 'paleomix.egg-info/SOURCES.txt' running install_lib creating /build/paleomix-1.3.2/debian/paleomix/usr creating /build/paleomix-1.3.2/debian/paleomix/usr/lib creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9 creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/README.rst -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/__pycache__/pipeline.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/__pycache__/main.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/__pycache__/yaml.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/__pycache__/nodegraph.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/__pycache__/node.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/__pycache__ creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd/__pycache__/sets.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd/__pycache__/builder.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd/__pycache__/pprint.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd/__pycache__/command.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd/builder.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd/command.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd/pprint.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/atomiccmd/sets.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/vcfwrap.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/vcffilter.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/timer.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/bamfiles.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/argparse.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/rtools.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/logging.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/system.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/text.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/sequences.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/sampling.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/makefile.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/testing.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/bedtools.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/versions.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/procs.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/utilities.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/fileutils.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__pycache__ creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/__pycache__/phylip.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/__pycache__/_graph.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/__pycache__/newick.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/__pycache__/msa.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/__pycache__/fastq.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/__pycache__/fasta.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/__pycache__/_common.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/_common.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/_graph.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/fasta.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/fastq.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/msa.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/newick.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/formats/phylip.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/argparse.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/bamfiles.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/bedtools.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/fileutils.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/logging.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/makefile.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/procs.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/rtools.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/sampling.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/sequences.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/system.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/testing.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/text.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/timer.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/utilities.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/vcffilter.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/vcfwrap.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/common/versions.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/newick.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/examl.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/phylip.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/raxml.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/formats.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/mafft.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/sequences.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/bedtools.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/commands.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/mapdamage.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/picard.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/adapterremoval.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/validation.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/bowtie2.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/bwa.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/samtools.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/adapterremoval.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/bedtools.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/bowtie2.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/bwa.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/commands.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/examl.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/formats.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/mafft.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/mapdamage.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/newick.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/phylip.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/picard.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/raxml.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/samtools.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/sequences.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodes/validation.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/__pycache__ creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/__pycache__/trim_pipeline.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/__pycache__/mkfile.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/__pycache__/config.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/__pycache__/nodes.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/__pycache__/makefile.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/__pycache__/pipeline.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/__pycache__/paths.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/__pycache__ creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/__pycache__/summary.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/__pycache__/statistics.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/__pycache__/target.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/__pycache__/prefix.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/__pycache__/sample.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/__pycache__/library.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/__pycache__/lane.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/__pycache__/reads.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/lane.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/library.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/prefix.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/reads.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/sample.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/statistics.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/summary.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/parts/target.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/config.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/makefile.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/mkfile.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/nodes.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/paths.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/pipeline.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/bam/trim_pipeline.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/__pycache__/makefile.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/__pycache__/config.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/__pycache__/mkfile.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/__pycache__/example.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/__pycache__/pipeline.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/__pycache__ creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts/__pycache__/phylo.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts/__pycache__/msa.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts/__pycache__/genotype.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts/genotype.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts/msa.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/parts/phylo.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/config.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/example.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/makefile.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/mkfile.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/phylo/pipeline.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/__pycache__/build_tped.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/__pycache__/build_mito.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/__pycache__/build_db.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/__pycache__/common.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/__pycache__/database.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/__pycache__/config.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/__pycache__/pipeline.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/__pycache__ creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/__pycache__/summary.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/__pycache__/admixture.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/__pycache__/report.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/__pycache__/nuclear.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/__pycache__/mitochondria.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/__pycache__/common.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/admixture.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/common.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/mitochondria.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/nuclear.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/report.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/parts/summary.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/build_db.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/build_mito.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/build_tped.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/common.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/config.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/database.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/zonkey/pipeline.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipelines/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/__pycache__ creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/rscripts creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/zonkey/treemix.r -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/zonkey/tinytree.r -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/zonkey/pca.r -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/zonkey/coverage.r -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/zonkey/admixture.r -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/rscripts/zonkey creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/rscripts/common copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/rscripts/common/requires.r -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/rscripts/common creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/reports creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/reports/zonkey copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/reports/zonkey/report.css -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/reports/zonkey creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/white_handed_gibbon.fasta -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/sumatran_orangutan.fasta -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta.fai -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/gorilla.fasta -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/chimpanzee.fasta -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/bonobo.fasta -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/alignment/makefile.yaml -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/phylo_pipeline/setup.sh -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/prefixes copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/prefixes creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.singleton.truncated.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.truncated.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_03.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_02.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_01.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_03.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_02.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_01.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_03.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_02.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_01.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_04.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_03.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_02.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_01.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_04.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/examples/bam_pipeline/makefile.yaml -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/bam_pipeline copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/resources/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/__pycache__/validate_fastq.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/__pycache__/vcf_to_fasta.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/__pycache__/vcf_filter.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/__pycache__/rmdup_collapsed.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/__pycache__/depths.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/__pycache__/coverage.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/__pycache__/cleanup.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/__pycache__/factory.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/__pycache__ creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/bam_stats creating /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/bam_stats/__pycache__/common.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/bam_stats/__pycache__/coverage.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/bam_stats/__pycache__/__init__.cpython-39.pyc -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/bam_stats/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/bam_stats/common.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/bam_stats/coverage.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/cleanup.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/coverage.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/depths.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/dupcheck.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/factory.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/gtf_to_bed.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/rmdup_collapsed.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/validate_fastq.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/vcf_filter.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/tools/vcf_to_fasta.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/__init__.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/main.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/node.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/nodegraph.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/pipeline.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix copying /build/paleomix-1.3.2/.pybuild/cpython3_3.9/build/paleomix/yaml.py -> /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd/builder.py to builder.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd/command.py to command.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd/pprint.py to pprint.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/atomiccmd/sets.py to sets.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/_common.py to _common.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/_graph.py to _graph.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/fasta.py to fasta.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/fastq.py to fastq.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/msa.py to msa.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/newick.py to newick.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/formats/phylip.py to phylip.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/argparse.py to argparse.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/bamfiles.py to bamfiles.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/bedtools.py to bedtools.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/fileutils.py to fileutils.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/logging.py to logging.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/makefile.py to makefile.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/procs.py to procs.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/rtools.py to rtools.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/sampling.py to sampling.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/sequences.py to sequences.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/system.py to system.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/testing.py to testing.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/text.py to text.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/timer.py to timer.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/utilities.py to utilities.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/vcffilter.py to vcffilter.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/vcfwrap.py to vcfwrap.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/common/versions.py to versions.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/adapterremoval.py to adapterremoval.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/bedtools.py to bedtools.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/bowtie2.py to bowtie2.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/bwa.py to bwa.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/commands.py to commands.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/examl.py to examl.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/formats.py to formats.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/mafft.py to mafft.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/mapdamage.py to mapdamage.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/newick.py to newick.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/phylip.py to phylip.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/picard.py to picard.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/raxml.py to raxml.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/samtools.py to samtools.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/sequences.py to sequences.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodes/validation.py to validation.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/lane.py to lane.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/library.py to library.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/prefix.py to prefix.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/reads.py to reads.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/sample.py to sample.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/statistics.py to statistics.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/summary.py to summary.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/parts/target.py to target.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/config.py to config.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/makefile.py to makefile.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/mkfile.py to mkfile.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/nodes.py to nodes.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/paths.py to paths.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/pipeline.py to pipeline.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/bam/trim_pipeline.py to trim_pipeline.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts/genotype.py to genotype.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts/msa.py to msa.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/parts/phylo.py to phylo.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/config.py to config.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/example.py to example.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/makefile.py to makefile.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/mkfile.py to mkfile.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/phylo/pipeline.py to pipeline.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/admixture.py to admixture.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/common.py to common.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/mitochondria.py to mitochondria.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/nuclear.py to nuclear.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/report.py to report.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/parts/summary.py to summary.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/build_db.py to build_db.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/build_mito.py to build_mito.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/build_tped.py to build_tped.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/common.py to common.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/config.py to config.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/database.py to database.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/zonkey/pipeline.py to pipeline.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipelines/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py to synthesize_reads.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/resources/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/bam_stats/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/bam_stats/common.py to common.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/bam_stats/coverage.py to coverage.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/cleanup.py to cleanup.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/coverage.py to coverage.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/depths.py to depths.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/dupcheck.py to dupcheck.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/factory.py to factory.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/gtf_to_bed.py to gtf_to_bed.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/rmdup_collapsed.py to rmdup_collapsed.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/validate_fastq.py to validate_fastq.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/vcf_filter.py to vcf_filter.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/tools/vcf_to_fasta.py to vcf_to_fasta.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/__init__.py to __init__.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/main.py to main.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/node.py to node.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/nodegraph.py to nodegraph.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/pipeline.py to pipeline.cpython-39.pyc byte-compiling /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix/yaml.py to yaml.cpython-39.pyc running install_egg_info Copying paleomix.egg-info to /build/paleomix-1.3.2/debian/paleomix/usr/lib/python3.9/dist-packages/paleomix-1.3.2.egg-info Skipping SOURCES.txt running install_scripts Installing paleomix script to /build/paleomix-1.3.2/debian/paleomix/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/paleomix-1.3.2' dh_install find debian -name LICENSE -delete find debian -name README.rst -delete make[1]: Leaving directory '/build/paleomix-1.3.2' debian/rules override_dh_installdocs make[1]: Entering directory '/build/paleomix-1.3.2' dh_installdocs # since tests dir contains empty files which are used afterwards for # testing and dh_installdocs is ignoring empty files we need to make # sure all files are really copied rsync -a -v tests debian/paleomix/usr/share/doc/paleomix sending incremental file list tests/atomiccmd_test/ tests/common_tests/ tests/common_tests/formats_tests/ tests/data/ tests/data/empty_file_1 tests/data/empty_file_2 sent 932 bytes received 76 bytes 2,016.00 bytes/sec total size is 334,736 speedup is 332.08 # test runner is seeking for paleomix modules in source - we use inside the installed package ### sed -i 's:(find paleomix -mindepth 1:(find /usr/lib/python*/dist-packages/paleomix -mindepth 1:' debian/*/usr/share/doc/*/tests/run #echo "====== Also empty files belong to the docs ======" #find debian -name "empty_file*" #find debian -name "timestamp_*" #echo "====== Hope something was printed between these lines ====" # # This test tries to execute setup.sh which does not work outside source directory find debian/paleomix/usr/share/doc/ -name fileutils_test.py -delete find debian/paleomix/usr/share/doc/ -name setup.h -delete make[1]: Leaving directory '/build/paleomix-1.3.2' dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/paleomix-1.3.2' dh_python3 --verbose --shebang=/usr/bin/python3 D: dh_python3 dh_python3:161: version: 4.20201102+nmu1 D: dh_python3 dh_python3:162: argv: ['/usr/bin/dh_python3', '--verbose', '--shebang=/usr/bin/python3'] D: dh_python3 dh_python3:163: options: {'guess_deps': True, 'skip_private': False, 'verbose': True, 'arch': None, 'package': None, 'no_package': None, 'compile_all': False, 'vrange': None, 'regexpr': None, 'accept_upstream_versions': False, 'depends': None, 'depends_section': None, 'recommends': None, 'recommends_section': None, 'suggests': None, 'suggests_section': None, 'requires': None, 'shebang': '/usr/bin/python3', 'ignore_shebangs': False, 'clean_dbg_pkg': True, 'no_ext_rename': False, 'no_shebang_rewrite': False, 'O': None} D: dh_python3 dh_python3:164: args: [] D: dh_python3 dh_python3:165: supported Python versions: 3.9 (default=3.9) D: dh_python3 debhelper:152: source=paleomix, binary packages=['paleomix'] D: dh_python3 dh_python3:183: processing package paleomix... D: dh_python3 fs:49: moving files from debian/paleomix/usr/lib/python3.9/dist-packages to debian/paleomix/usr/lib/python3/dist-packages/ I: dh_python3 tools:114: replacing shebang in debian/paleomix/usr/bin/paleomix D: dh_python3 fs:260: package paleomix details = {'requires.txt': {'debian/paleomix/usr/lib/python3/dist-packages/paleomix-1.3.2.egg-info/requires.txt'}, 'egg-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package paleomix D: dh_python3 pydist:142: trying to find dependency for coloredlogs>=10.0 (python=None) D: dh_python3 pydist:142: trying to find dependency for configargparse>=0.13.0 (python=None) D: dh_python3 pydist:142: trying to find dependency for pysam>=0.10.0 (python=None) D: dh_python3 pydist:142: trying to find dependency for ruamel.yaml>=0.16.0 (python=None) D: dh_python3 pydist:142: trying to find dependency for setproctitle>=1.1.0 (python=None) D: dh_python3 depends:275: D={'python3-coloredlogs', 'python3-setproctitle', 'python3:any', 'python3-ruamel.yaml', 'python3-pysam', 'python3-configargparse'}; R=[]; S=[]; E=[], B=[]; RT=[] make[1]: Leaving directory '/build/paleomix-1.3.2' dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/paleomix-1.3.2' dh_fixperms for rs in `find debian -iname "*.r"` ; do \ if head -n 1 $rs | grep -q '^#!/usr/bin/.*Rscript' ; then \ chmod +x $rs ; \ else \ chmod -x $rs ; \ fi ; \ done make[1]: Leaving directory '/build/paleomix-1.3.2' dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'paleomix' in '../paleomix_1.3.2-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../paleomix_1.3.2-1_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: including full 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/5680 and its subdirectories I: Current time: Thu Aug 11 20:56:46 -12 2022 I: pbuilder-time-stamp: 1660294606 Sat Jul 10 02:33:48 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink16-arm64.debian.net. Sat Jul 10 02:33:48 UTC 2021 I: Preparing to do remote build '2' on codethink16-arm64.debian.net. Sat Jul 10 02:36:29 UTC 2021 I: Deleting $TMPDIR on codethink16-arm64.debian.net. Sat Jul 10 02:36:29 UTC 2021 I: paleomix_1.3.2-1_arm64.changes: Format: 1.8 Date: Mon, 02 Nov 2020 18:42:32 +0100 Source: paleomix Binary: paleomix Architecture: arm64 Version: 1.3.2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: paleomix - pipelines and tools for the processing of ancient and modern HTS Changes: paleomix (1.3.2-1) unstable; urgency=medium . * Team upload. * New upstream version * Removed python3_in_shebang.patch as upstream now uses #!/usr/bin/python3. * Refreshed xfail_command_tests.patch. * Removed compressed-duplicate from lintian overrides, as it is now unused. Checksums-Sha1: f68a61907c2ccdb250c40d11f5742ac5db0ea5c0 11851 paleomix_1.3.2-1_arm64.buildinfo 1352e3139759b67fb7b755b583e169c824da2115 982540 paleomix_1.3.2-1_arm64.deb Checksums-Sha256: c0ae08c088a2659e359b7f3d6c332148c4a5bc9dfaf7e8ad9a51e678d93de89a 11851 paleomix_1.3.2-1_arm64.buildinfo 77e28289d0f0754552b8ebaa2df8ec700dc651832c85aaf10fcb9a68ac8e1acf 982540 paleomix_1.3.2-1_arm64.deb Files: 2930c0d4590f02a83c4df5c38bb7a8d1 11851 science optional paleomix_1.3.2-1_arm64.buildinfo 04725829a5fa51348b28a4edfea448b0 982540 science optional paleomix_1.3.2-1_arm64.deb Sat Jul 10 02:36:31 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.UN6kMFMRYE/paleomix_1.3.2-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.UN6kMFMRYE/paleomix_1.3.2-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.UN6kMFMRYE/paleomix_1.3.2-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.UN6kMFMRYE/b1/paleomix_1.3.2-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.UN6kMFMRYE/b2/paleomix_1.3.2-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.237s) 0.237s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.023s) 0.023s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sat Jul 10 02:36:32 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sat Jul 10 02:36:32 UTC 2021 I: paleomix from bullseye built successfully and reproducibly on arm64. Sat Jul 10 02:36:34 UTC 2021 I: Submitting .buildinfo files to external archives: Sat Jul 10 02:36:34 UTC 2021 I: Submitting 16K b1/paleomix_1.3.2-1_arm64.buildinfo.asc Sat Jul 10 02:36:35 UTC 2021 I: Submitting 16K b2/paleomix_1.3.2-1_arm64.buildinfo.asc Sat Jul 10 02:36:36 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Jul 10 02:36:36 UTC 2021 I: Done submitting .buildinfo files. Sat Jul 10 02:36:36 UTC 2021 I: Removing signed paleomix_1.3.2-1_arm64.buildinfo.asc files: removed './b1/paleomix_1.3.2-1_arm64.buildinfo.asc' removed './b2/paleomix_1.3.2-1_arm64.buildinfo.asc'