Fri Jan 6 00:25:42 UTC 2023 I: starting to build cnvkit/bullseye/amd64 on jenkins on '2023-01-06 00:25' Fri Jan 6 00:25:42 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_29/7365/console.log Fri Jan 6 00:25:42 UTC 2023 I: Downloading source for bullseye/cnvkit=0.9.8-1 --2023-01-06 00:25:42-- http://cdn-fastly.deb.debian.org/debian/pool/main/c/cnvkit/cnvkit_0.9.8-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2324 (2.3K) [text/prs.lines.tag] Saving to: ‘cnvkit_0.9.8-1.dsc’ 0K .. 100% 167M=0s 2023-01-06 00:25:42 (167 MB/s) - ‘cnvkit_0.9.8-1.dsc’ saved [2324/2324] Fri Jan 6 00:25:42 UTC 2023 I: cnvkit_0.9.8-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: cnvkit Binary: cnvkit Architecture: amd64 arm64 ppc64el Version: 0.9.8-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Steffen Moeller , Olivier Sallou Homepage: http://cnvkit.readthedocs.org Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/cnvkit Vcs-Git: https://salsa.debian.org/med-team/cnvkit.git Testsuite: autopkgtest Testsuite-Triggers: poppler-utils Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-pyfaidx, help2man, python3-biopython, python3-pandas, python3-numpy, python3-pysam, python3-scipy, python3-matplotlib, python3-pyvcf, python3-future, python3-pomegranate, r-bioc-dnacopy, poppler-utils Package-List: cnvkit deb science optional arch=amd64,arm64,ppc64el Checksums-Sha1: d5c593a40b820c01ec59c0ba34c828e8eb681553 23667917 cnvkit_0.9.8.orig.tar.gz 8022930b47d4e65aaf4b018757c407d079ab608f 6184 cnvkit_0.9.8-1.debian.tar.xz Checksums-Sha256: 57e3081fd12c402abbc448851fda741795f23e68416c2564d9c09930bd56eef8 23667917 cnvkit_0.9.8.orig.tar.gz aa13357cf280637ab385d272951b727fd321bd8930cbda7d6d84a501dab8e653 6184 cnvkit_0.9.8-1.debian.tar.xz Files: 9e09f37f86147b92b87a18fffbe92a24 23667917 cnvkit_0.9.8.orig.tar.gz 4d307af14817257ae436bb0d30f0c35d 6184 cnvkit_0.9.8-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl/vW0wACgkQPCZ2P2xn 5uL3ow/+OD9rSFzw/R1rZ1QkH703sIy+2ljydEmXjzsdROumGCjGrMuyQFSKX69t ma1TRvinTOMvOIuxVTqUAyb1FhLH7y39NslLgCVz6E2Ikb/vgae+/Qrwg9u31E1R b8Z/tmyngagaUEDhftIZy8VAQZqzRiJiy6Xx1O017ntiFq58SIncCgYm8w/Vw7JM Y7PDytsMsFWwVviB03xjcs7OdeqBRhuI4+BMGg2PG7Rn+zWKk4F2H4/Qs8Yoyu5A CqAGhrERYGTeB5LQUl+JG0ObB3URwpZX9GEWlcmESDDAXSmjH8z2REK4+SdWureY 64m0OTD1FWDY6HBs+ISEoNpZIIbdCcl3ojjEXriZlHSqmZK65X3Gqm2eGRq4Scln Jk+hSEHOaT9Ivuyp2je530DdzKVKYEa2aaOrzn9M4B2S6i1EA8dEwOhA3mAt/8WV x+xWw7qlT98YWpt7E9U27+/wG+YT09MdI1c9Irg/qPjr+tndcG+3WOyS/bw0cveq RWin4CcpGR/PjaarUTHvjJZQ0ICueaAfLoGjcmyc1wThsR0XKnFpGKHRZcL/uLPE AuIEPpXPaPGXH3rVeU+SsUF6XQOBepF61C8q6mCV80C6XfQv0deMZCQS9x+34xRC LHLPJc41eOODgDIlTZheZut4tYG0+4Ia0E2ozVGrP22kKua55rw= =WBTa -----END PGP SIGNATURE----- Fri Jan 6 00:25:42 UTC 2023 I: Checking whether the package is not for us Fri Jan 6 00:25:42 UTC 2023 I: Starting 1st build on remote node ionos11-amd64.debian.net. Fri Jan 6 00:25:42 UTC 2023 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Fri Jan 6 00:31:00 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 5 12:25:44 -12 2023 I: pbuilder-time-stamp: 1672964744 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [cnvkit_0.9.8-1.dsc] I: copying [./cnvkit_0.9.8.orig.tar.gz] I: copying [./cnvkit_0.9.8-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.6NAPyt_z/trustedkeys.kbx': General error gpgv: Signature made Fri Jan 1 05:26:36 2021 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cnvkit_0.9.8-1.dsc dpkg-source: info: extracting cnvkit in cnvkit-0.9.8 dpkg-source: info: unpacking cnvkit_0.9.8.orig.tar.gz dpkg-source: info: unpacking cnvkit_0.9.8-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-py-ext dpkg-source: info: applying python3compat.patch dpkg-source: info: applying spelling dpkg-source: info: applying controldir I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/931345/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b46cc588656b4c1f9495d375de649039' 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='931345' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.S84apGfa/pbuilderrc_RaDQ --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.S84apGfa/b1 --logfile b1/build.log cnvkit_0.9.8-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 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 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Dec 20 21:25 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/931345/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-pyfaidx, help2man, python3-biopython, python3-pandas, python3-numpy, python3-pysam, python3-scipy, python3-matplotlib, python3-pyvcf, python3-future, python3-pomegranate, r-bioc-dnacopy, poppler-utils dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19704 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-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pyvcf; however: Package python3-pyvcf is not installed. pbuilder-satisfydepends-dummy depends on python3-future; however: Package python3-future is not installed. pbuilder-satisfydepends-dummy depends on python3-pomegranate; however: Package python3-pomegranate is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-dnacopy; however: Package r-bioc-dnacopy is not installed. pbuilder-satisfydepends-dummy depends on poppler-utils; however: Package poppler-utils 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: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcurl3-gnutls{a} libcurl4{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhts3{a} libice6{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.4-2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpoppler102{a} libprocps8{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libssh2-1{a} libsub-override-perl{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff5{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libxt6{a} libyaml-0-2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} openssl{a} po-debconf{a} poppler-utils{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-biopython{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-distutils{a} python3-future{a} python3-joblib{a} python3-kiwisolver{a} python3-lib2to3{a} python3-matplotlib{a} python3-minimal{a} python3-networkx{a} python3-numpy{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-pomegranate{a} python3-pyfaidx{a} python3-pyparsing{a} python3-pysam{a} python3-reportlab{a} python3-reportlab-accel{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-tz{a} python3-vcf{a} python3-yaml{a} python3.9{a} python3.9-minimal{a} r-base-core{a} r-bioc-biocgenerics{a} r-bioc-dnacopy{a} readline-common{a} sensible-utils{a} ttf-bitstream-vera{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx ncbi-blast+ poppler-data psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-gdal python3-html5lib python3-jinja2 python3-lxml python3-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-psutil python3-pydot python3-pygraphviz python3-pytest python3-renderpm python3-simplejson python3-tables python3-tk python3-xlwt r-base-dev r-cran-runit r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 162 newly installed, 0 to remove and 0 not upgraded. Need to get 112 MB of archives. After unpacking 390 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 mailcap all 3.69 [31.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 mime-support all 3.66 [10.9 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1n-0+deb11u3 [853 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u3 [693 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 fonts-lyx all 2.3.6-1 [205 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 help2man amd64 1.48.1 [190 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u3 [342 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u3 [345 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 liblbfgsb0 amd64 3.0+dfsg.3-9 [28.5 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libnspr4 amd64 2:4.29-1 [112 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libnss3 amd64 2:3.61-1+deb11u2 [1306 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libopenjp2-7 amd64 2.4.0-3 [172 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1 [258 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u1 [289 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 libpoppler102 amd64 20.09.0-3.1+deb11u1 [1676 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 libwebpdemux2 amd64 0.6.1-2.1 [87.7 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 libwebpmux3 amd64 0.6.1-2.1 [97.6 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 poppler-utils amd64 20.09.0-3.1+deb11u1 [189 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 python3-all amd64 3.9.2-3 [1056 B] Get: 131 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 python3-reportlab-accel amd64 3.5.59-2 [39.1 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 python3-pil amd64 8.1.2+dfsg-0.3+deb11u1 [445 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 python3-reportlab all 3.5.59-2 [575 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 python3-biopython amd64 1.78+dfsg-4 [1402 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 python3-cycler all 0.10.0-3 [8084 B] Get: 139 http://deb.debian.org/debian bullseye/main amd64 python3-dateutil all 2.8.1-6 [79.2 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 python3-decorator all 4.4.2-2 [15.8 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 python3-future all 0.18.2-5 [349 kB] Get: 142 http://deb.debian.org/debian bullseye/main amd64 python3-joblib all 0.17.0-4 [213 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 python3-kiwisolver amd64 1.3.1-1+b1 [55.7 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 python3-matplotlib amd64 3.3.4-1 [4163 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 python3-networkx all 2.5+ds-2 [900 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 python3-tz all 2021.1-1 [34.8 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 python3-pandas-lib amd64 1.1.5+dfsg-2 [3287 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 python3-pandas all 1.1.5+dfsg-2 [2096 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 python3-scipy amd64 1.6.0-2 [12.3 MB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 python3-yaml amd64 5.3.1-5 [138 kB] Get: 152 http://deb.debian.org/debian bullseye/main amd64 python3-pomegranate amd64 0.13.5-1 [2482 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 python3-pyfaidx all 0.5.9.2-1 [26.4 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 python3-pysam amd64 0.15.4+ds-3+b2 [1536 kB] Get: 155 http://deb.debian.org/debian bullseye/main amd64 python3-setuptools all 52.0.0-4 [366 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 python3-vcf amd64 0.6.8+git20170215.476169c-7+b3 [42.5 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 zip amd64 3.0-12 [232 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26+deb11u1 [172 kB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 r-bioc-dnacopy amd64 1.64.0-1 [420 kB] Fetched 112 MB in 2s (50.9 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 ... 19704 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../5-liblocale-gettext-perl_1.07-4+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../6-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../7-libexpat1_2.2.10-2+deb11u5_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.9-minimal. 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Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up zip (3.0-12) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.2-1) ... Setting up libnspr4:amd64 (2:4.29-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20201114-2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libfribidi0:amd64 (1.0.8-2+deb11u1) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up libtcl8.6:amd64 (8.6.11+dfsg-1) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:amd64 (0.6.1-2.1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... 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Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15) ... Setting up libxcb-render0:amd64 (1.14-3) ... Setting up libwebpdemux2:amd64 (0.6.1-2.1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u3) ... Setting up libnss3:amd64 (2:3.61-1+deb11u2) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u3) ... Setting up libx11-6:amd64 (2:1.7.2-1) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-9) ... 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 libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libhts3:amd64 (1.11-4) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up python3.9 (3.9.2-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up python3-tz (2021.1-1) ... Setting up python3-six (1.16.0-2) ... Setting up python3-pil:amd64 (8.1.2+dfsg-0.3+deb11u1) ... Setting up python3-decorator (4.4.2-2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-reportlab-accel:amd64 (3.5.59-2) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up python3-reportlab (3.5.59-2) ... Setting up libpoppler102:amd64 (20.09.0-3.1+deb11u1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up poppler-utils (20.09.0-3.1+deb11u1) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... 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-pyfaidx (0.5.9.2-1) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up python3-setuptools (52.0.0-4) ... Setting up python3-joblib (0.17.0-4) ... Setting up python3-all (3.9.2-3) ... Setting up python3-yaml (5.3.1-5) ... Setting up python3-networkx (2.5+ds-2) ... Setting up python3-vcf (0.6.8+git20170215.476169c-7+b3) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-future (0.18.2-5) ... update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode Setting up python3-biopython (1.78+dfsg-4) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up r-bioc-biocgenerics (0.36.0-1) ... Setting up python3-scipy (1.6.0-2) ... Setting up python3-pomegranate (0.13.5-1) ... Setting up python3-pandas-lib:amd64 (1.1.5+dfsg-2) ... Setting up python3-pandas (1.1.5+dfsg-2) ... Setting up r-bioc-dnacopy (1.64.0-1) ... Processing triggers for libc-bin (2.31-13+deb11u5) ... 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. 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/cnvkit-0.9.8/ && 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 > ../cnvkit_0.9.8-1_source.changes dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.8-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/cnvkit-0.9.8' cd test && /usr/bin/make clean || /bin/true make[2]: Entering directory '/build/cnvkit-0.9.8/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/build/cnvkit-0.9.8/test' if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi dh_auto_clean I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it rm -rf test/p2-20-metrics.tsv test/p2-5_5-metrics.tsv test/p2-9_2-metrics.tsv rm -rf test/build CNVkit.egg-info make[1]: Leaving directory '/build/cnvkit-0.9.8' 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 debian/rules override_dh_auto_build make[1]: Entering directory '/build/cnvkit-0.9.8' [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted build if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ mv ${script} cnvkit-${script%%.py}; \ done; \ fi dh_auto_build I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/commands.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/vary.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/target.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/smoothing.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/segmetrics.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/segfilters.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/scatter.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/samutil.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/rna.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/reports.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/reference.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/plots.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/params.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/parallel.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/metrics.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/importers.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/import_rna.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/heatmap.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/fix.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/export.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/diagram.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/descriptives.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/coverage.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/core.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cnary.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cmdutil.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cluster.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/call.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/bintest.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/batch.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/autobin.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/antitarget.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/access.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/_version.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/__init__.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib creating /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/none.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation creating /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/subtract.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/subdivide.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/rangelabel.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/merge.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/intersect.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/gary.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/combiners.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/chromsort.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/__init__.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome creating /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfio.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/util.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/textcoord.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/tab.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/seqdict.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/seg.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/picard.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/gff.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/genepred.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/bedio.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/__init__.py -> /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio running build_scripts creating build creating build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/cnvkit -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-skg_convert -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-reference2targets -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-guess_baits -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-cnv_updater -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.9 copying and adjusting /build/cnvkit-0.9.8/scripts/cnvkit-cnv_annotate -> build/scripts-3.9 copying /build/cnvkit-0.9.8/scripts/snpfilter.sh -> build/scripts-3.9 changing mode of build/scripts-3.9/cnvkit from 644 to 755 changing mode of build/scripts-3.9/cnvkit-skg_convert from 644 to 755 changing mode of build/scripts-3.9/cnvkit-reference2targets from 644 to 755 changing mode of build/scripts-3.9/cnvkit-guess_baits from 644 to 755 changing mode of build/scripts-3.9/cnvkit-cnv_updater from 644 to 755 changing mode of build/scripts-3.9/cnvkit-cnv_expression_correlate from 644 to 755 changing mode of build/scripts-3.9/cnvkit-cnv_annotate from 644 to 755 cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py make[1]: Leaving directory '/build/cnvkit-0.9.8' debian/rules override_dh_auto_test make[1]: Entering directory '/build/cnvkit-0.9.8' cd test && /usr/bin/make -j15 make[2]: Entering directory '/build/cnvkit-0.9.8/test' python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7hakm8jq because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xo2baud8 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-yld6gnn8 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3wjczax3 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xh2kp01l because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-sogxkrpk because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wldtprjl because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-sre15q01 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-p0wy30tt because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-t4ewxr8b because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-p38ce6g5 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lw0zp9kq because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-29_b75a8 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xlshlwu1 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-njj2w36e because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Created directory build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn Matplotlib created a temporary config/cache directory at /tmp/matplotlib-d_x1od88 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Number of target and antitarget files: 3, 3 No FASTA reference genome provided; skipping GC, RM calculations Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female Loading build/p2-20_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-5_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-9_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-20_5.antitargetcoverage.cnn Correcting for GC bias... Loading build/p2-5_5.antitargetcoverage.cnn Correcting for GC bias... Loading build/p2-9_5.antitargetcoverage.cnn Correcting for GC bias... Calculating average bin coverages Calculating bin spreads Targets: 338 (5.0858%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 " chr1:2435319-2436685 log2=-0.709 spread=0.503 ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 " chr1:120611883-120612051 log2=0.070 spread=0.050 NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 " chr1:156842391-156842479 log2=-0.398 spread=0.290 MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 " chr1:183481886-183481951 log2=-0.040 spread=0.119 CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 " chr1:243800859-243801066 log2=0.023 spread=0.063 MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 " chr2:25536716-25536891 log2=0.702 spread=0.033 MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 REL chr2:61108881-61109061 log2=1.026 spread=0.559 " chr2:61128072-61128256 log2=0.115 spread=0.173 " chr2:61145275-61145462 log2=0.014 spread=0.099 CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 " chr2:128095237-128095425 log2=0.215 spread=0.212 METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 " chr3:97160189-97160367 log2=-0.050 spread=0.191 ATR chr3:142254935-142255077 log2=0.024 spread=0.027 " chr3:142286854-142287031 log2=-0.076 spread=0.116 GAK chr4:896278-896357 log2=-1.505 spread=1.261 FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 " chr4:1803044-1803507 log2=-0.073 spread=0.117 " chr4:1808792-1809022 log2=0.252 spread=0.108 CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 " chr4:178514600-178514725 log2=-0.098 spread=0.096 TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 " chr5:1295312-1295381 log2=-0.690 spread=0.462 CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 " chr5:25519857-25520034 log2=-0.015 spread=0.095 RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 " chr5:38962338-38962525 log2=0.005 spread=0.019 " chr5:38966685-38966862 log2=0.006 spread=0.165 " chr5:38978620-38978763 log2=0.040 spread=0.030 " chr5:39074133-39074327 log2=-0.158 spread=0.139 CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 " chr5:51030131-51030313 log2=-0.034 spread=0.192 MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 " chr5:56168412-56168590 log2=0.479 spread=0.038 CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 " chr5:86637023-86637168 log2=0.054 spread=0.111 " chr5:86642414-86642592 log2=0.254 spread=0.162 " chr5:86648912-86649096 log2=0.092 spread=0.062 " chr5:86670598-86670778 log2=0.222 spread=0.198 MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 APC chr5:112101965-112102138 log2=0.104 spread=0.217 NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 " chr5:170837567-170837631 log2=0.085 spread=0.349 FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 " chr5:180046203-180046404 log2=-1.531 spread=0.722 " chr5:180076418-180076603 log2=-2.224 spread=1.416 TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 " chr6:31939599-31940313 log2=-19.582 spread=0.181 STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 " chr6:31946632-31946824 log2=-20.052 spread=0.088 " chr6:31947142-31947366 log2=-20.114 spread=0.066 " chr6:31948176-31948360 log2=-19.982 spread=0.149 " chr6:31948382-31948612 log2=-19.757 spread=0.165 " chr6:31948730-31949253 log2=-20.048 spread=0.014 NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 " chr6:32164046-32164227 log2=-19.755 spread=0.189 " chr6:32164652-32164888 log2=-19.984 spread=0.154 " chr6:32165021-32165403 log2=-19.625 spread=0.196 " chr6:32166163-32166545 log2=-20.043 spread=0.072 " chr6:32166648-32166962 log2=-3.514 spread=5.742 " chr6:32168554-32168821 log2=-19.601 spread=0.197 " chr6:32168844-32169306 log2=-19.683 spread=0.166 " chr6:32169801-32170391 log2=-19.405 spread=0.205 " chr6:32171492-32171691 log2=-20.095 spread=0.101 " chr6:32171861-32172198 log2=-3.141 spread=7.288 " chr6:32178478-32178749 log2=-19.927 spread=0.164 " chr6:32180197-32180441 log2=-10.902 spread=9.532 " chr6:32180544-32180722 log2=-19.675 spread=0.186 " chr6:32180857-32181062 log2=-19.562 spread=0.227 " chr6:32181411-32181646 log2=-19.966 spread=0.171 " chr6:32181832-32182066 log2=-19.961 spread=0.172 " chr6:32182948-32183194 log2=-19.935 spread=0.168 " chr6:32184667-32185079 log2=-19.923 spread=0.165 " chr6:32185720-32185919 log2=-19.707 spread=0.197 " chr6:32187317-32187601 log2=-19.765 spread=0.173 " chr6:32187871-32188094 log2=-19.660 spread=0.188 " chr6:32188127-32188451 log2=-19.622 spread=0.169 " chr6:32188481-32188693 log2=-19.902 spread=0.132 " chr6:32188704-32189133 log2=-19.501 spread=0.193 " chr6:32190258-32190616 log2=-19.570 spread=0.209 " chr6:32190724-32190908 log2=-19.540 spread=0.232 " chr6:32191570-32191668 log2=-19.773 spread=0.178 " chr6:32191676-32191753 log2=-19.374 spread=0.201 FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 " chr6:128316545-128316699 log2=-0.070 spread=0.050 MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 " chr6:157099442-157099991 log2=-0.846 spread=0.504 " chr6:157100042-157100634 log2=-1.570 spread=0.825 IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 " chr7:98491365-98491541 log2=0.209 spread=0.153 " chr7:98493314-98493496 log2=0.389 spread=0.207 SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 " chr7:128829048-128829358 log2=-0.474 spread=0.315 BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 " chr7:140484736-140484912 log2=0.081 spread=0.150 " chr7:140487956-140488430 log2=-0.089 spread=0.142 " chr7:140493336-140493442 log2=-0.340 spread=0.283 " chr7:140624315-140624540 log2=-0.497 spread=0.342 TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 WRN chr8:30925752-30925890 log2=0.120 spread=0.158 " chr8:30941153-30941335 log2=0.079 spread=0.294 " chr8:30942625-30942802 log2=0.044 spread=0.247 " chr8:30947918-30948092 log2=0.151 spread=0.124 " chr8:31000128-31000252 log2=-0.099 spread=0.098 " chr8:31001006-31001182 log2=-0.002 spread=0.062 GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 " chr8:37698557-37699898 log2=-0.612 spread=0.029 ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 " chr8:48845528-48845758 log2=0.056 spread=0.196 " chr8:48866846-48867043 log2=-0.067 spread=0.097 " chr8:48868369-48868526 log2=-0.239 spread=0.174 " chr8:48872485-48872722 log2=-0.636 spread=0.464 CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 " chr9:2101491-2101640 log2=0.244 spread=0.104 JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 " chr9:5067014-5067883 log2=0.146 spread=0.089 " chr9:5068184-5070306 log2=0.133 spread=0.092 " chr9:5076944-5077152 log2=0.046 spread=0.137 PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 " chr9:21986759-21986899 log2=0.058 spread=0.175 LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 " chr9:87425375-87425452 log2=0.494 spread=0.066 PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 " chr9:139250747-139251032 log2=-0.223 spread=0.273 " chr9:139252418-139252703 log2=-0.512 spread=0.264 NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 " chr9:139417262-139417677 log2=-0.173 spread=0.191 " chr9:139440110-139440287 log2=-1.257 spread=0.500 MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 CGH chr10:22505654-22505837 log2=0.072 spread=0.107 RET chr10:43572644-43572830 log2=-1.376 spread=1.092 " chr10:43600360-43600677 log2=-0.341 spread=0.222 PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 " chr10:89685254-89685374 log2=0.244 spread=0.259 TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 " chr10:93579008-93579121 log2=0.166 spread=0.220 SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 " chr10:112679716-112679934 log2=-0.008 spread=0.028 CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 " chr11:94170270-94170454 log2=0.095 spread=0.285 YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 ATM chr11:108153392-108153639 log2=0.113 spread=0.136 " chr11:108164020-108164234 log2=-0.056 spread=0.040 " chr11:108217986-108218135 log2=0.359 spread=0.277 MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 " chr12:25391004-25391186 log2=0.368 spread=0.128 DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 " chr12:51206782-51207287 log2=-0.012 spread=0.101 PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 " chr13:26970356-26970536 log2=0.137 spread=0.121 FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 " chr13:32903506-32903689 log2=0.019 spread=0.232 " chr13:32918645-32918823 log2=0.158 spread=0.114 " chr13:32920899-32921077 log2=0.014 spread=0.247 RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 " chr13:48919164-48919369 log2=0.025 spread=0.094 " chr13:48921877-48922044 log2=0.106 spread=0.147 " chr13:48923026-48923204 log2=0.360 spread=0.016 " chr13:48938965-48939147 log2=0.084 spread=0.356 " chr13:48941578-48941767 log2=0.238 spread=0.212 " chr13:48947486-48947665 log2=0.025 spread=0.126 " chr13:48954166-48954251 log2=0.061 spread=0.273 " chr13:49037815-49038005 log2=0.063 spread=0.062 " chr13:49047410-49047589 log2=0.053 spread=0.170 CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 " chr13:85527771-85527948 log2=0.007 spread=0.222 GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 " chr13:110438332-110438432 log2=-3.643 spread=2.325 CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 " chr14:20291466-20291612 log2=0.697 spread=0.248 NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 " chr14:36989195-36989373 log2=0.023 spread=0.162 SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 " chr14:50619741-50619923 log2=0.003 spread=0.272 " chr14:50697856-50698044 log2=0.277 spread=0.334 MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 " chr14:71275790-71275923 log2=-2.815 spread=1.938 TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 CGH chr15:20870700-20870881 log2=1.102 spread=0.611 " chr15:38544477-38545455 log2=-0.348 spread=0.179 SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 " chr15:41803968-41804185 log2=-2.202 spread=0.188 " chr15:41804261-41804494 log2=-0.402 spread=0.392 NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 " chr16:2611404-2611585 log2=-5.171 spread=1.963 " chr16:2611721-2611943 log2=-11.810 spread=9.172 " chr16:2615504-2615725 log2=-20.113 spread=0.007 " chr16:2616307-2616486 log2=-20.054 spread=0.072 " chr16:2631267-2631414 log2=-20.009 spread=0.061 " chr16:2631583-2631734 log2=-20.089 spread=0.090 " chr16:2633363-2633616 log2=-20.101 spread=0.089 CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 CGH chr16:31526705-31526886 log2=0.057 spread=0.074 CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 " chr16:50826460-50826650 log2=0.239 spread=0.204 CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 " chr16:60005694-60005857 log2=-0.366 spread=0.298 CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 " chr17:12011053-12011253 log2=0.028 spread=0.232 NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 " chr17:29496854-29497046 log2=0.226 spread=0.193 RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 " chr17:30519172-30519355 log2=0.163 spread=0.289 " chr17:30525911-30526093 log2=-0.157 spread=0.046 ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 " chr19:2210351-2210545 log2=-0.860 spread=0.261 " chr19:2226130-2227152 log2=-0.113 spread=0.120 GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 " chr19:15311544-15311749 log2=-1.887 spread=1.202 JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 " chr19:33792774-33793010 log2=-1.781 spread=0.127 " chr19:33793014-33793356 log2=-0.541 spread=0.385 CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 " chr19:45873698-45873881 log2=-0.522 spread=0.327 BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 " chr21:36265140-36265318 log2=0.042 spread=0.039 CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 " chr22:29115325-29115465 log2=0.055 spread=0.390 SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 " chrX:1317372-1317594 log2=-21.121 spread=0.049 " chrX:1321225-1321435 log2=-20.851 spread=0.196 " chrX:1325274-1325530 log2=-21.121 spread=0.011 " chrX:1327651-1327830 log2=-21.000 spread=0.029 " chrX:1331391-1331576 log2=-21.018 spread=0.052 KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 " chrX:123185143-123185290 log2=-1.018 spread=0.062 " chrX:123202378-123202544 log2=-0.959 spread=0.103 FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 " chrY:9008607-9008759 log2=-1.012 spread=0.097 " chrY:13131970-13132039 log2=-1.004 spread=0.074 " chrY:19506485-19506650 log2=-1.018 spread=0.034 " chrY:21033918-21034071 log2=-1.013 spread=0.057 " chrY:28463435-28463622 log2=-0.952 spread=0.039 " chrY:28514033-28514208 log2=-0.992 spread=0.026 Antitargets: 108 (0.8597%) bins failed filters Wrote build/reference-picard.cnn with 19209 regions python3 ../cnvkit.py fix build/p2-5_5.targetcoverage.cnn build/p2-5_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-5_5.cnr python3 ../cnvkit.py fix build/p2-9_2.targetcoverage.cnn build/p2-9_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-9_2.cnr python3 ../cnvkit.py fix build/p2-20_1.targetcoverage.cnn build/p2-20_1.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_1.cnr python3 ../cnvkit.py fix build/p2-20_2.targetcoverage.cnn build/p2-20_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_2.cnr python3 ../cnvkit.py fix build/p2-20_3.targetcoverage.cnn build/p2-20_3.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_3.cnr python3 ../cnvkit.py fix build/p2-20_4.targetcoverage.cnn build/p2-20_4.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_4.cnr python3 ../cnvkit.py fix build/p2-20_5.targetcoverage.cnn build/p2-20_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_5.cnr Matplotlib created a temporary config/cache directory at /tmp/matplotlib-mrnsmr8c because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1k8fcway because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9sgeljs5 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-b2ob5k4_ because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zo6o8prv because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fl4_13kb because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-w8u0g781 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Processing target: p2-20_5 Processing target: p2-20_3 Keeping 6308 of 6646 bins Processing target: p2-20_4 Processing target: p2-5_5 Correcting for GC bias... Correcting for density bias... Keeping 6308 of 6646 bins Processing target: p2-9_2 Keeping 6308 of 6646 bins Processing antitarget: p2-20_5 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Correcting for GC bias... Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_4 Keeping 6308 of 6646 bins Correcting for density bias... Keeping 12455 of 12563 bins Processing antitarget: p2-5_5 Correcting for GC bias... Processing antitarget: p2-20_3 Correcting for GC bias... Correcting for density bias... Keeping 12455 of 12563 bins WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... Processing antitarget: p2-9_2 Keeping 12455 of 12563 bins WARNING: Skipping correction for RepeatMasker bias Processing target: p2-20_1 Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Keeping 12455 of 12563 bins Keeping 12455 of 12563 bins Processing target: p2-20_2 Keeping 6308 of 6646 bins Targets are 2.60 x more variable than antitargets Targets are 1.43 x more variable than antitargets Correcting for GC bias... Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias WARNING: Skipping correction for RepeatMasker bias Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Correcting for GC bias... Correcting for density bias... Targets are 1.75 x more variable than antitargets Processing antitarget: p2-20_1 Processing antitarget: p2-20_2 Wrote build/p2-20_5.cnr with 18763 regions Wrote build/p2-20_4.cnr with 18763 regions Targets are 1.14 x more variable than antitargets Keeping 12455 of 12563 bins Antitargets are 1.08 x more variable than targets python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns Correcting for GC bias... python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns Wrote build/p2-9_2.cnr with 18763 regions WARNING: Skipping correction for RepeatMasker bias Keeping 12455 of 12563 bins Correcting for GC bias... python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus Targets are 1.14 x more variable than antitargets python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt Wrote build/p2-5_5.cnr with 18763 regions WARNING: Skipping correction for RepeatMasker bias Wrote build/p2-20_3.cnr with 18763 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf Targets are 1.09 x more variable than antitargets Wrote build/p2-20_1.cnr with 18763 regions Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0j66q4mu because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-nyqnl59v because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote build/p2-20_2.cnr with 18763 regions Matplotlib created a temporary config/cache directory at /tmp/matplotlib-naka41bj because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-08a_uaa1 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-cztr82rx because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-5zrcrwtv because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf python3 ../cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt python3 ../cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ribrwm35 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-oreu0r__ because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-19xn4v6l because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wdvm4jxz because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-86vu7tmp because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rswfken2 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-enu9iynd because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2wdznea8 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-sa2h2j2g because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-9_2 as female Selected test sample NA12882 and control sample NA12878 Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Loaded 3654 records; skipped: 514 somatic, 394 depth Kept 2631 heterozygous of 3654 VCF records Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Treating sample p2-5_5 as female Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Treating sample p2-20_1 as female Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Wrote p2-9_2.nexus Treating sample p2-20_2 as female Dropped 1 / 949 bins on chromosome chr6 Placed 705 variants into 18763 bins Wrote p2-9_2.nexus-ogt Wrote p2-all.cdt Wrote p2-all-jtv.txt Dropped 11 / 49 bins on chromosome chrY Dropped 27 / 49 bins on chromosome chrY Dropped 8 / 49 bins on chromosome chrY Dropped 8 / 49 bins on chromosome chrY Dropped 7 / 49 bins on chromosome chrY Wrote build/p2-20_3.cns with 74 regions Wrote build/p2-9_2.cns with 107 regions Wrote build/p2-5_5.cns with 71 regions Wrote build/p2-20_4.cns with 137 regions python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns Dropped 6 / 49 bins on chromosome chrY python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -t --y-min=-2.5 -o p2-9_2-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c 'chr9:150000-45000000' -o p2-9_2-chr9p-scatter.pdf Dropped 6 / 49 bins on chromosome chrY python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -g SMARCA2,PTPRD -w 4e6 -o p2-9_2-SMARCA2-PTPRD-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -l regions.bed -o p2-9_2-bed_regions-scatter.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf Wrote build/p2-20_2.cns with 125 regions python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf Wrote build/p2-20_5.cns with 129 regions Wrote build/p2-20_1.cns with 117 regions Matplotlib created a temporary config/cache directory at /tmp/matplotlib-bu52qg0q because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-o9e58u0k because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7kt3ch28 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-q7x7j13w because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-8gb0ybeg because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-u6fsxt7v because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wxdls6pt because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-owo102de because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-20_1-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-51u239xp because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns build/p2-9_2.cnr -t 0.3 -o p2-9_2-both-diagram.pdf Treating sample p2-20_3 as female Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2cboedyj because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_3.call.cns with 74 regions python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns build/p2-20_1.cnr -t 0.3 -o p2-20_1-both-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-mkwqgi11 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Wrote p2-5_5-cbs-diagram.pdf Showing 1480 probes and 0 selected genes in region chr1 Wrote p2-20_2-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns build/p2-20_2.cnr -t 0.3 -o p2-20_2-both-diagram.pdf Showing 201 probes and 0 selected genes in region chr21 Showing 330 probes and 13 selected genes in region chr9:149999-45000000 python3 ../cnvkit.py heatmap build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -y -o heatmap-picard.pdf Wrote p2-9_2-diagram.pdf Showing 179 probes and 2 selected genes in region chr9:0-14504268 Wrote p2-5_5-diagram.pdf Detected file format: bed Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 Treating sample p2-9_2 as female Treating sample p2-20_2 as female python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xej88al_ because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt Wrote p2-9_2-chr21-scatter.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2_cc6kjl because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tysczoog because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-20_2-cbs-diagram.pdf Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 Wrote p2-9_2-cbs-diagram.pdf Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf Wrote p2-9_2-chr1-scatter.pdf Wrote p2-9_2-chr9p-scatter.pdf python3 ../cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt python3 ../cnvkit.py export seg build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-all.seg python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2lei0lcy because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns Smoothing overshot at 3 / 97 indices: (-19.887157566382854, -3.337830278732133) vs. original (-19.2826, -0.27873000000000003) Treating sample p2-5_5 as female Matplotlib created a temporary config/cache directory at /tmp/matplotlib-413g5bt0 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-afm11ryd because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-4rqwnagf because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-nq_ewa9k because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2bf9jvk2 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-pg5fcjc0 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_2 as female Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ibdn3kvl because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-e6lj8_i4 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-9_2 as female Treating sample p2-20_1 as female Treating sample p2-9_2 as female Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qjq53cgv because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Treating sample p2-9_2 as female Treating sample p2-20_1 as female Treating sample p2-20_2 as female Treating sample p2-20_3 as female Treating sample p2-20_4 as female Treating sample p2-20_5 as female Treating sample p2-9_2 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-9_2.call.cns with 107 regions python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns Wrote p2-all.seg python3 ../cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf Treating sample p2-20_1 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_1.call.cns with 117 regions Found 15 gene breakpoints Wrote p2-9_2-breaks.txt Treating sample p2-20_2 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_2.call.cns with 125 regions Treating sample p2-5_5 as female Rescaling sample with purity 0.65, ploidy 2 python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input Wrote build/p2-5_5.call.cns with 71 regions Wrote gender-picard.txt python3 ../cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ --mean --median --mode --t-test \ --stdev --mad --mse --iqr --bivar \ --ci --pi --sem --smooth-bootstrap python3 ../cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ --ci -b 50 -a 0.5 python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv Treating sample p2-20_4 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_4.call.cns with 137 regions python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv Matplotlib created a temporary config/cache directory at /tmp/matplotlib-amhxsm8d because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-43iv2nn5 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv Wrote p2-9_2-scatter.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qnf0h1wn because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-nkhi4qea because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qp9f5dni because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-h5z_lrvp because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py scatter -s build/p2-5_5.cns build/p2-5_5.cnr -t --y-min=-2.5 -o p2-5_5-scatter.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-edrh53dr because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Found 53 gene-level gains and losses Wrote p2-9_2-genemetrics.txt Treating sample p2-20_5 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_5.call.cns with 129 regions Treating sample p2-9_2.call as female Matplotlib created a temporary config/cache directory at /tmp/matplotlib-hgbfyo6h because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote heatmap-picard.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-i3yc3gv5 because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py export bed build/p2-5_5.call.cns build/p2-9_2.call.cns build/p2-20_1.call.cns build/p2-20_2.call.cns build/p2-20_3.call.cns build/p2-20_4.call.cns build/p2-20_5.call.cns -y --show variant -o p2-all.bed Wrote p2-9_2.vcf Wrote p2-5_5-metrics.tsv Wrote p2-5_5-segmetrics.cns with 71 regions Wrote p2-9_2-metrics.tsv Wrote p2-9_2.theta2.input Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9ec_x21b because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-31_6f4nm because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-20-metrics.tsv Treating sample p2-5_5.call as female Treating sample p2-9_2.call as female Treating sample p2-20_1.call as female Treating sample p2-20_2.call as female Treating sample p2-20_3.call as female Treating sample p2-20_4.call as female Treating sample p2-20_5.call as female Wrote p2-all.bed Treating sample p2-20_1 as female Wrote p2-20_1-cbs-diagram.pdf Wrote p2-9_2-segmetrics.cns with 107 regions Wrote p2-5_5-scatter.pdf which pdfunite && pdfunite p2-5_5-scatter.pdf p2-9_2-scatter.pdf p2-9_2-chr1-scatter.pdf p2-9_2-chr21-scatter.pdf p2-9_2-chr9p-scatter.pdf p2-9_2-SMARCA2-PTPRD-scatter.pdf p2-9_2-bed_regions-scatter.pdf all-scatters.pdf || touch all-scatters.pdf /usr/bin/pdfunite Wrote p2-5_5-both-diagram.pdf Wrote p2-9_2-both-diagram.pdf Wrote p2-20_2-both-diagram.pdf Wrote p2-20_1-both-diagram.pdf which pdfunite && pdfunite p2-5_5-diagram.pdf p2-9_2-diagram.pdf p2-20_1-diagram.pdf p2-20_2-diagram.pdf p2-5_5-cbs-diagram.pdf p2-9_2-cbs-diagram.pdf p2-20_1-cbs-diagram.pdf p2-20_2-cbs-diagram.pdf p2-5_5-both-diagram.pdf p2-9_2-both-diagram.pdf p2-20_1-both-diagram.pdf p2-20_2-both-diagram.pdf all-diagrams.pdf || touch all-diagrams.pdf /usr/bin/pdfunite make[2]: Leaving directory '/build/cnvkit-0.9.8/test' cd test && /usr/bin/make -j15 clean || /bin/true make[2]: Entering directory '/build/cnvkit-0.9.8/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/build/cnvkit-0.9.8/test' rm -Rf test/build test/*.tsv make[1]: Leaving directory '/build/cnvkit-0.9.8' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/cnvkit-0.9.8' [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted install if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ mv ${script} cnvkit-${script%%.py}; \ done; \ fi dh_auto_install I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/cnvkit-0.9.8/debian/cnvkit running install running build running build_py running build_scripts running install_lib creating /build/cnvkit-0.9.8/debian/cnvkit/usr creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9 creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/__init__.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/bedio.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/genepred.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/gff.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/picard.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/seg.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/seqdict.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/tab.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/textcoord.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/util.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/vcfio.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/vcfsimple.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/__init__.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/chromsort.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/combiners.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/gary.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/intersect.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/merge.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/rangelabel.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/subdivide.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/subtract.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib creating /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/__init__.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/cbs.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/flasso.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/haar.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/hmm.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/none.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/__init__.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/_version.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/access.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/antitarget.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/autobin.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/batch.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/bintest.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/call.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cluster.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cmdutil.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cnary.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/core.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/coverage.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/descriptives.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/diagram.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/export.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/fix.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/heatmap.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/import_rna.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/importers.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/metrics.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/parallel.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/params.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/plots.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/reference.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/reports.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/rna.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/samutil.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/scatter.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segfilters.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmetrics.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/smoothing.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/target.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/vary.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/commands.py -> /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/bedio.py to bedio.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/genepred.py to genepred.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/gff.py to gff.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/picard.py to picard.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/seg.py to seg.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/seqdict.py to seqdict.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/tab.py to tab.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/textcoord.py to textcoord.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/util.py to util.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/vcfio.py to vcfio.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/vcfsimple.py to vcfsimple.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/chromsort.py to chromsort.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/combiners.py to combiners.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/gary.py to gary.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/intersect.py to intersect.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/merge.py to merge.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/rangelabel.py to rangelabel.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/subdivide.py to subdivide.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/subtract.py to subtract.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/cbs.py to cbs.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/flasso.py to flasso.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/haar.py to haar.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/hmm.py to hmm.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/none.py to none.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/_version.py to _version.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/access.py to access.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/antitarget.py to antitarget.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/autobin.py to autobin.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/batch.py to batch.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/bintest.py to bintest.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/call.py to call.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cluster.py to cluster.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cmdutil.py to cmdutil.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cnary.py to cnary.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/core.py to core.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/coverage.py to coverage.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/descriptives.py to descriptives.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/diagram.py to diagram.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/export.py to export.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/fix.py to fix.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/heatmap.py to heatmap.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/import_rna.py to import_rna.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/importers.py to importers.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/metrics.py to metrics.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/parallel.py to parallel.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/params.py to params.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/plots.py to plots.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/reference.py to reference.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/reports.py to reports.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/rna.py to rna.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/samutil.py to samutil.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/scatter.py to scatter.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segfilters.py to segfilters.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmetrics.py to segmetrics.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/smoothing.py to smoothing.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/target.py to target.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/vary.py to vary.cpython-39.pyc byte-compiling /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/commands.py to commands.cpython-39.pyc running install_egg_info running egg_info creating CNVkit.egg-info writing CNVkit.egg-info/PKG-INFO writing dependency_links to CNVkit.egg-info/dependency_links.txt writing requirements to CNVkit.egg-info/requires.txt writing top-level names to CNVkit.egg-info/top_level.txt writing manifest file 'CNVkit.egg-info/SOURCES.txt' reading manifest file 'CNVkit.egg-info/SOURCES.txt' writing manifest file 'CNVkit.egg-info/SOURCES.txt' Copying CNVkit.egg-info to /build/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/CNVkit-0.9.8.egg-info Skipping SOURCES.txt running install_scripts creating /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/snpfilter.sh -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_annotate -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_expression_correlate -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_updater -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-guess_baits -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-reference2targets -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-skg_convert -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit -> /build/cnvkit-0.9.8/debian/cnvkit/usr/bin changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/snpfilter.sh to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-guess_baits to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-reference2targets to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-skg_convert to 755 changing mode of /build/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit to 755 help2man --no-info --version-option=version \ --name="a command-line toolkit for copy number analysis." \ ./cnvkit > debian/cnvkit.1 PYTHONPATH=$PYTHONPATH:. debian/genmanpages.py 0.9.8 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ep60tkta because the default path (/nonexistent/first-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. cd scripts && PYTHONPATH=../ help2man --no-info \ --version-string=0.9.8 --help-option='-h' \ ./cnvkit-reference2targets --name='Extract target and antitarget BED files from a CNVkit reference file.' \ > ../debian/cnvkit-reference2targets.1; cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py make[1]: Leaving directory '/build/cnvkit-0.9.8' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild 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 'cnvkit' in '../cnvkit_0.9.8-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../cnvkit_0.9.8-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/931345 and its subdirectories I: Current time: Thu Jan 5 12:31:00 -12 2023 I: pbuilder-time-stamp: 1672965060 Fri Jan 6 00:31:01 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Fri Jan 6 00:31:01 UTC 2023 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Fri Jan 6 00:34:43 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Fri Jan 6 00:34:43 UTC 2023 I: cnvkit_0.9.8-1_amd64.changes: Format: 1.8 Date: Fri, 01 Jan 2021 16:17:10 +0100 Source: cnvkit Binary: cnvkit Architecture: amd64 Version: 0.9.8-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: cnvkit - Copy number variant detection from targeted DNA sequencing Closes: 962743 Changes: cnvkit (0.9.8-1) unstable; urgency=medium . [ Steffen Moeller ] * Added symbolic link from /usr/lib/debian-med/bin/cnvkit.py to /usr/bin/cnvkit.py . bcbio explicitly looks in /usr/bin, though. . [ Michael R. Crusoe ] * New upstream version * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * debian/control: mips64el is not supported by upstream, remove it Closes: #962743 Checksums-Sha1: 4589a292e5d2b9202789913aa92e6f838d134467 9098 cnvkit_0.9.8-1_amd64.buildinfo e69926df9dc8426666f5047c84cdc8804547f64c 15426700 cnvkit_0.9.8-1_amd64.deb Checksums-Sha256: a17832d162afc94c34674eec6025a2578359ead5eefe3fae5c11f2a5a39ffd7d 9098 cnvkit_0.9.8-1_amd64.buildinfo 3cf402dc6e221dc422ddc5047fd1ff6028251b6aeef46cc4fb886ad82c581f21 15426700 cnvkit_0.9.8-1_amd64.deb Files: 88af72758da2b24f8b1acc074b4b0e1b 9098 science optional cnvkit_0.9.8-1_amd64.buildinfo b450dc7d39842d03e71ea16a83e6fecf 15426700 science optional cnvkit_0.9.8-1_amd64.deb Fri Jan 6 00:34:44 UTC 2023 I: diffoscope 228 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.S84apGfa/cnvkit_0.9.8-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.S84apGfa/cnvkit_0.9.8-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.S84apGfa/cnvkit_0.9.8-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.S84apGfa/b1/cnvkit_0.9.8-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.S84apGfa/b2/cnvkit_0.9.8-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.392s) 0.392s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.149s) 0.149s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Fri Jan 6 00:34:46 UTC 2023 I: diffoscope 228 found no differences in the changes files, and a .buildinfo file also exists. Fri Jan 6 00:34:46 UTC 2023 I: cnvkit from bullseye built successfully and reproducibly on amd64. Fri Jan 6 00:34:47 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Jan 6 00:34:47 UTC 2023 I: Submitting 12K b1/cnvkit_0.9.8-1_amd64.buildinfo.asc Fri Jan 6 00:34:48 UTC 2023 I: Submitting 12K b2/cnvkit_0.9.8-1_amd64.buildinfo.asc Fri Jan 6 00:34:49 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Jan 6 00:34:49 UTC 2023 I: Done submitting .buildinfo files. Fri Jan 6 00:34:49 UTC 2023 I: Removing signed cnvkit_0.9.8-1_amd64.buildinfo.asc files: removed './b1/cnvkit_0.9.8-1_amd64.buildinfo.asc' removed './b2/cnvkit_0.9.8-1_amd64.buildinfo.asc'