https://launchpad.net/ubuntu/+source/cnvkit/0.9.7-1/+build/19392522 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy01-amd64-018 4.4.0-179-generic #209-Ubuntu SMP Fri Apr 24 17:48:44 UTC 2020 x86_64 Buildd toolchain package versions: launchpad-buildd_189 python-lpbuildd_189 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.9 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 1 Jun 23:11:37 ntpdate[1910]: adjust time server 10.211.37.1 offset -0.032087 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19392522 --image-type chroot /home/buildd/filecache-default/7f6882774d93a6ce12d34cd2f4e4b83a707bcc6e Creating target for build PACKAGEBUILD-19392522 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19392522 Starting target for build PACKAGEBUILD-19392522 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19392522 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19392522 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19392522 Updating target for build PACKAGEBUILD-19392522 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [268 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [119 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main amd64 Packages [971 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [507 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe amd64 Packages [8731 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5180 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 Packages [52.0 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [27.7 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 Packages [502 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [302 kB] Fetched 16.8 MB in 2s (7276 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files binutils binutils-common binutils-x86-64-linux-gnu bsdutils bzip2 ca-certificates cpp-9 dash debconf debianutils e2fsprogs fdisk g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip libacl1 libapparmor1 libapt-pkg6.0 libasan5 libatomic1 libbinutils libblkid1 libbz2-1.0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdevmapper1.02.1 libext2fs2 libfdisk1 libgcc-9-dev libgcc-s1 libgomp1 libidn2-0 libitm1 libkmod2 liblsan0 libmount1 libncurses6 libncursesw6 libperl5.30 libprocps8 libquadmath0 libseccomp2 libsmartcols1 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 libunistring2 libuuid1 linux-libc-dev login logsave make mount ncurses-base ncurses-bin passwd perl perl-base perl-modules-5.30 procps systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata util-linux 86 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 56.6 MB of archives. After this operation, 529 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main amd64 libcrypt-dev amd64 1:4.4.15-1ubuntu1 [104 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main amd64 libcrypt1 amd64 1:4.4.15-1ubuntu1 [78.2 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main amd64 base-files amd64 11ubuntu7 [60.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 bsdutils amd64 1:2.35.1-5ubuntu2 [86.8 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main amd64 debianutils amd64 4.11 [85.6 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main amd64 perl-modules-5.30 all 5.30.2-1 [2740 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main amd64 libperl5.30 amd64 5.30.2-1 [3952 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main amd64 perl amd64 5.30.2-1 [224 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main amd64 perl-base amd64 5.30.2-1 [1513 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 bzip2 amd64 1.0.8-3 [33.4 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libbz2-1.0 amd64 1.0.8-3 [32.3 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main amd64 debconf all 1.5.74 [121 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main amd64 dash amd64 0.5.10.2-7 [86.3 kB] Get:14 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 gzip amd64 1.10-2ubuntu1 [95.0 kB] Get:15 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 login amd64 1:4.8.1-1ubuntu6 [221 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main amd64 ncurses-bin amd64 6.2-1 [172 kB] Get:17 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libblkid1 amd64 2.35.1-5ubuntu2 [133 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libuuid1 amd64 2.35.1-5ubuntu2 [22.2 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libfdisk1 amd64 2.35.1-5ubuntu2 [171 kB] Get:20 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libmount1 amd64 2.35.1-5ubuntu2 [145 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main amd64 libncurses6 amd64 6.2-1 [101 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main amd64 libncursesw6 amd64 6.2-1 [132 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main amd64 libtinfo6 amd64 6.2-1 [87.1 kB] Get:24 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libsmartcols1 amd64 2.35.1-5ubuntu2 [95.7 kB] Get:25 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 fdisk amd64 2.35.1-5ubuntu2 [123 kB] Get:26 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 util-linux amd64 2.35.1-5ubuntu2 [1050 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main amd64 ncurses-base all 6.2-1 [18.7 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main amd64 sysvinit-utils amd64 2.96-3ubuntu1 [20.6 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main amd64 libatomic1 amd64 10.1.0-3ubuntu1 [9280 B] Get:30 http://ftpmaster.internal/ubuntu groovy/main amd64 libubsan1 amd64 10.1.0-3ubuntu1 [136 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main amd64 libtsan0 amd64 10.1.0-3ubuntu1 [320 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main amd64 libquadmath0 amd64 10.1.0-3ubuntu1 [146 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main amd64 liblsan0 amd64 10.1.0-3ubuntu1 [144 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main amd64 libitm1 amd64 10.1.0-3ubuntu1 [26.3 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main amd64 libgomp1 amd64 10.1.0-3ubuntu1 [101 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main amd64 gcc-10-base amd64 10.1.0-3ubuntu1 [20.0 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main amd64 libgcc-s1 amd64 10.1.0-3ubuntu1 [41.5 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main amd64 libcc1-0 amd64 10.1.0-3ubuntu1 [41.2 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main amd64 libstdc++6 amd64 10.1.0-3ubuntu1 [502 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main amd64 systemd-sysv amd64 245.5-3ubuntu1 [10.3 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main amd64 systemd-timesyncd amd64 245.5-3ubuntu1 [27.9 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main amd64 libacl1 amd64 2.2.53-8 [18.9 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main amd64 libapparmor1 amd64 2.13.3-7ubuntu6 [34.3 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main amd64 libcap2 amd64 1:2.34-2 [17.9 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main amd64 libudev1 amd64 245.5-3ubuntu1 [74.6 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main amd64 libdevmapper1.02.1 amd64 2:1.02.167-1ubuntu3 [127 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main amd64 libcryptsetup12 amd64 2:2.3.1-1ubuntu1 [192 kB] Get:48 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libunistring2 amd64 0.9.10-3 [369 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main amd64 libidn2-0 amd64 2.3.0-1 [52.6 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main amd64 libkmod2 amd64 27+20200310-2ubuntu1 [44.1 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Get:61 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 passwd amd64 1:4.8.1-1ubuntu6 [797 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main amd64 libcom-err2 amd64 1.45.6-1ubuntu1 [9664 B] Get:63 http://ftpmaster.internal/ubuntu groovy/main amd64 libprocps8 amd64 2:3.3.16-4ubuntu1 [32.9 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main amd64 libss2 amd64 1.45.6-1ubuntu1 [11.3 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main amd64 procps amd64 2:3.3.16-4ubuntu1 [232 kB] Get:66 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 ca-certificates all 20190110ubuntu2 [145 kB] Get:67 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libsqlite3-0 amd64 3.32.1-2 [550 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main amd64 tzdata all 2020a-0ubuntu1 [293 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main amd64 libctf0 amd64 2.34-7ubuntu1 [46.6 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main amd64 binutils-x86-64-linux-gnu amd64 2.34-7ubuntu1 [1613 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main amd64 libbinutils amd64 2.34-7ubuntu1 [474 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main amd64 binutils amd64 2.34-7ubuntu1 [3376 B] Get:73 http://ftpmaster.internal/ubuntu groovy/main amd64 binutils-common amd64 2.34-7ubuntu1 [207 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main amd64 libctf-nobfd0 amd64 2.34-7ubuntu1 [47.2 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main amd64 libasan5 amd64 9.3.0-13ubuntu1 [395 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/main amd64 g++-9 amd64 9.3.0-13ubuntu1 [8403 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/main amd64 gcc-9 amd64 9.3.0-13ubuntu1 [8239 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main amd64 libstdc++-9-dev amd64 9.3.0-13ubuntu1 [1714 kB] Get:79 http://ftpmaster.internal/ubuntu groovy/main amd64 libgcc-9-dev amd64 9.3.0-13ubuntu1 [2360 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main amd64 cpp-9 amd64 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19392522 amd64 groovy-proposed -c chroot:build-PACKAGEBUILD-19392522 --arch=amd64 --dist=groovy-proposed --nolog -A cnvkit_0.9.7-1.dsc Initiating build PACKAGEBUILD-19392522 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-179-generic #209-Ubuntu SMP Fri Apr 24 17:48:44 UTC 2020 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-018.buildd +==============================================================================+ | cnvkit 0.9.7-1 (amd64) 01 Jun 2020 23:11 | +==============================================================================+ Package: cnvkit Version: 0.9.7-1 Source Version: 0.9.7-1 Distribution: groovy-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/cnvkit-3Vggpc/cnvkit-0.9.7' with '<>' I: NOTICE: Log filtering will replace 'build/cnvkit-3Vggpc' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19392522/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cnvkit_0.9.7-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-lfPAQn/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-lfPAQn/apt_archive ./ InRelease Get:2 copy:/<>/resolver-lfPAQn/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-lfPAQn/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-lfPAQn/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-lfPAQn/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (269 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-lfPAQn/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12823 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12), 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 Filtered Build-Depends: debhelper-compat (= 12), 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 'sbuild-build-depends-cnvkit-dummy' in '/<>/resolver-MvFFos/apt_archive/sbuild-build-depends-cnvkit-dummy.deb'. Ign:1 copy:/<>/resolver-MvFFos/apt_archive ./ InRelease Get:2 copy:/<>/resolver-MvFFos/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-MvFFos/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-MvFFos/apt_archive ./ Sources [312 B] Get:5 copy:/<>/resolver-MvFFos/apt_archive ./ Packages [638 B] Fetched 3069 B in 0s (280 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install cnvkit build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-lyx gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasn1-8-heimdal libblas3 libbrotli1 libbsd0 libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libice6 libicu66 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnspr4 libnss3 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpoppler97 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db mime-support node-jquery po-debconf poppler-utils python-matplotlib-data python3 python3-all python3-biopython python3-cycler python3-dateutil python3-decorator python3-distutils python3-future python3-joblib python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-networkx python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-tz python3-vcf python3-yaml python3.8 python3.8-minimal r-base-core r-bioc-biocgenerics r-bioc-dnacopy ttf-bitstream-vera ucf unzip x11-common xdg-utils zip Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python3-mysqldb python3-rdflib python3-renderpm python3-psycopg2 raxml samtools t-coffee wise w3-dtd-mathml python-cycler-doc python-future-doc dvipng ffmpeg gir1.2-gtk-3.0 ghostscript inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra ttf-staypuft python-networkx-doc python3-gdal python3-pygraphviz | python3-pydot gfortran python-numpy-doc python3-dev python3-pytest python3-numpy-dbg python-pandas-doc python3-statsmodels python-pil-doc python3-pil-dbg python-pomegranate-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python-setuptools-doc python3.8-venv python3.8-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-biobase r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales poppler-data publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson python3-psutil python3-tk python3-numexpr python3-tables python3-xlrd python3-openpyxl python3-xlwt python3-bs4 python3-html5lib python3-lxml python3-olefile python3-renderpm r-recommended r-base-dev r-doc-html r-cran-runit libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-lyx gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasn1-8-heimdal libblas3 libbrotli1 libbsd0 libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libice6 libicu66 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnspr4 libnss3 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpoppler97 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db mime-support node-jquery po-debconf poppler-utils python-matplotlib-data python3 python3-all python3-biopython python3-cycler python3-dateutil python3-decorator python3-distutils python3-future python3-joblib python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-networkx python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-tz python3-vcf python3-yaml python3.8 python3.8-minimal r-base-core r-bioc-biocgenerics r-bioc-dnacopy sbuild-build-depends-cnvkit-dummy ttf-bitstream-vera ucf unzip x11-common xdg-utils zip 0 upgraded, 169 newly installed, 0 to remove and 0 not upgraded. Need to get 103 MB of archives. After this operation, 376 MB of additional disk space will be used. Get:1 copy:/<>/resolver-MvFFos/apt_archive ./ sbuild-build-depends-cnvkit-dummy 0.invalid.0 [968 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main amd64 liblocale-gettext-perl amd64 1.07-4 [17.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main amd64 libpython3.8-minimal amd64 3.8.3-1 [714 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main amd64 libexpat1 amd64 2.2.9-1build1 [73.3 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main amd64 python3.8-minimal amd64 3.8.3-1 [1897 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-minimal amd64 3.8.2-0ubuntu2 [23.6 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main amd64 mime-support all 3.64ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main amd64 libmpdec2 amd64 2.4.2-3 [81.1 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main amd64 libpython3.8-stdlib amd64 3.8.3-1 [1668 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main amd64 python3.8 amd64 3.8.3-1 [369 kB] Get:11 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gettext-base amd64 0.19.8.1-10build1 [50.2 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main amd64 libkrb5support0 amd64 1.17-6ubuntu4 [30.9 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main amd64 libk5crypto3 amd64 1.17-6ubuntu4 [80.2 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main amd64 libkeyutils1 amd64 1.6.1-2ubuntu1 [10.1 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main amd64 libkrb5-3 amd64 1.17-6ubuntu4 [330 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main amd64 libgssapi-krb5-2 amd64 1.17-6ubuntu4 [121 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main amd64 libpsl5 amd64 0.21.0-1ubuntu1 [51.5 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main amd64 libxau6 amd64 1:1.0.9-0ubuntu1 [7488 B] Get:39 http://ftpmaster.internal/ubuntu groovy/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu1 [10.6 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main amd64 libxcb1 amd64 1.14-2 [44.7 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main amd64 libx11-data all 2:1.6.9-2ubuntu1 [113 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main amd64 libx11-6 amd64 2:1.6.9-2ubuntu1 [573 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main amd64 libxext6 amd64 2:1.3.4-0ubuntu1 [29.1 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main amd64 m4 amd64 1.4.18-4 [199 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main amd64 autoconf all 2.69-11.1 [321 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main amd64 automake all 1:1.16.2-1ubuntu1 [521 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main amd64 autopoint all 0.19.8.1-10build1 [412 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main amd64 libtool all 2.4.6-14 [161 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main amd64 dh-autoreconf all 19 [16.1 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main amd64 libdebhelper-perl all 13.1ubuntu1 [64.0 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:55 http://ftpmaster.internal/ubuntu groovy/main amd64 libfile-stripnondeterminism-perl all 1.8.1-1 [17.1 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main amd64 dh-strip-nondeterminism all 1.8.1-1 [5232 B] Get:57 http://ftpmaster.internal/ubuntu groovy/main amd64 dwz amd64 0.13-5 [151 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main amd64 libcroco3 amd64 0.6.13-1 [82.5 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main amd64 gettext amd64 0.19.8.1-10build1 [895 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main amd64 po-debconf all 1.0.21 [233 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main amd64 debhelper all 13.1ubuntu1 [885 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-lib2to3 all 3.8.3-2 [74.1 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-distutils all 3.8.3-2 [140 kB] Get:65 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 dh-python all 4.20200315 [85.8 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main amd64 libfreetype6 amd64 2.10.1-2 [341 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/universe amd64 ttf-bitstream-vera all 1.10-8 [352 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main amd64 fontconfig-config all 2.13.1-2ubuntu3 [28.8 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main amd64 libfontconfig1 amd64 2.13.1-2ubuntu3 [114 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main amd64 fontconfig amd64 2.13.1-2ubuntu3 [171 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/universe amd64 fonts-lyx all 2.3.4.2-2 [154 kB] Get:72 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http://ftpmaster.internal/ubuntu groovy/main amd64 libheimbase1-heimdal amd64 7.7.0+dfsg-2 [29.7 kB] Get:83 http://ftpmaster.internal/ubuntu groovy/main amd64 libhcrypto4-heimdal amd64 7.7.0+dfsg-2 [88.0 kB] Get:84 http://ftpmaster.internal/ubuntu groovy/main amd64 libwind0-heimdal amd64 7.7.0+dfsg-2 [47.6 kB] Get:85 http://ftpmaster.internal/ubuntu groovy/main amd64 libhx509-5-heimdal amd64 7.7.0+dfsg-2 [107 kB] Get:86 http://ftpmaster.internal/ubuntu groovy/main amd64 libkrb5-26-heimdal amd64 7.7.0+dfsg-2 [207 kB] Get:87 http://ftpmaster.internal/ubuntu groovy/main amd64 libheimntlm0-heimdal amd64 7.7.0+dfsg-2 [15.1 kB] Get:88 http://ftpmaster.internal/ubuntu groovy/main amd64 libgssapi3-heimdal amd64 7.7.0+dfsg-2 [96.5 kB] Get:89 http://ftpmaster.internal/ubuntu groovy/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [14.9 kB] Get:90 http://ftpmaster.internal/ubuntu groovy/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [49.3 kB] Get:91 http://ftpmaster.internal/ubuntu groovy/main amd64 libldap-common all 2.4.49+dfsg-2ubuntu2 [17.4 kB] Get:92 http://ftpmaster.internal/ubuntu groovy/main amd64 libldap-2.4-2 amd64 2.4.49+dfsg-2ubuntu2 [156 kB] Get:93 http://ftpmaster.internal/ubuntu groovy/main amd64 libnghttp2-14 amd64 1.40.0-1build1 [78.7 kB] Get:94 http://ftpmaster.internal/ubuntu groovy/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build1 [54.9 kB] Get:95 http://ftpmaster.internal/ubuntu groovy/main amd64 libssh-4 amd64 0.9.4-1ubuntu1 [170 kB] Get:96 http://ftpmaster.internal/ubuntu groovy/main amd64 libcurl3-gnutls amd64 7.68.0-1ubuntu2 [231 kB] Get:97 http://ftpmaster.internal/ubuntu groovy/main amd64 libcurl4 amd64 7.68.0-1ubuntu2 [233 kB] Get:98 http://ftpmaster.internal/ubuntu groovy/main amd64 libdatrie1 amd64 0.2.12-3 [18.7 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/universe amd64 libdeflate0 amd64 1.6-1 [54.8 kB] Get:100 http://ftpmaster.internal/ubuntu groovy/main amd64 libgfortran5 amd64 10.1.0-3ubuntu1 [734 kB] Get:101 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[2308 B] Get:111 http://ftpmaster.internal/ubuntu groovy/universe amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get:112 http://ftpmaster.internal/ubuntu groovy/main amd64 liblapack3 amd64 3.9.0-2 [2156 kB] Get:113 http://ftpmaster.internal/ubuntu groovy/universe amd64 liblbfgsb0 amd64 3.0+dfsg.3-8 [29.5 kB] Get:114 http://ftpmaster.internal/ubuntu groovy/main amd64 liblcms2-2 amd64 2.9-4 [140 kB] Get:115 http://ftpmaster.internal/ubuntu groovy/main amd64 libnspr4 amd64 2:4.25-1 [107 kB] Get:116 http://ftpmaster.internal/ubuntu groovy/main amd64 libnss3 amd64 2:3.49.1-1ubuntu1 [1171 kB] Get:117 http://ftpmaster.internal/ubuntu groovy/main amd64 libthai-data all 0.1.28-3 [134 kB] Get:118 http://ftpmaster.internal/ubuntu groovy/main amd64 libthai0 amd64 0.1.28-3 [18.1 kB] Get:119 http://ftpmaster.internal/ubuntu groovy/main amd64 libpango-1.0-0 amd64 1.44.7-2ubuntu4 [162 kB] Get:120 http://ftpmaster.internal/ubuntu groovy/main amd64 libpangoft2-1.0-0 amd64 1.44.7-2ubuntu4 [34.9 kB] Get:121 http://ftpmaster.internal/ubuntu groovy/main amd64 libpangocairo-1.0-0 amd64 1.44.7-2ubuntu4 [24.8 kB] Get:122 http://ftpmaster.internal/ubuntu groovy/main amd64 libpaper1 amd64 1.1.28 [13.0 kB] Get:123 http://ftpmaster.internal/ubuntu groovy/main amd64 libpaper-utils amd64 1.1.28 [8400 B] Get:124 http://ftpmaster.internal/ubuntu groovy/main amd64 libopenjp2-7 amd64 2.3.1-1ubuntu4 [141 kB] Get:125 http://ftpmaster.internal/ubuntu groovy/main amd64 libjbig0 amd64 2.1-3.1build1 [26.7 kB] Get:126 http://ftpmaster.internal/ubuntu groovy/main amd64 libwebp6 amd64 0.6.1-2 [185 kB] Get:127 http://ftpmaster.internal/ubuntu groovy/main amd64 libtiff5 amd64 4.1.0+git191117-2build1 [161 kB] Get:128 http://ftpmaster.internal/ubuntu groovy/main amd64 libpoppler97 amd64 0.86.1-0ubuntu1 [915 kB] Get:129 http://ftpmaster.internal/ubuntu groovy/main amd64 libsm6 amd64 2:1.2.3-1 [16.1 kB] Get:130 http://ftpmaster.internal/ubuntu groovy/main amd64 libtcl8.6 amd64 8.6.10+dfsg-1 [902 kB] Get:131 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groovy-proposed/universe amd64 r-bioc-dnacopy amd64 1.62.0-1build1 [419 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 103 MB in 2s (44.1 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Setting up x11-common (1:7.7+19ubuntu14) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.40.0-1build1) ... Setting up libmagic1:amd64 (1:5.38-5) ... Setting up libdeflate0:amd64 (1.6-1) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-5) ... Setting up libldap-common (2.4.49+dfsg-2ubuntu2) ... Setting up libjbig0:amd64 (2.1-3.1build1) ... Setting up libkrb5support0:amd64 (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2) ... Setting up zip (3.0-11build1) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:amd64 (3.9.0-2) ... 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 libfreetype6:amd64 (2.10.1-2) ... 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Setting up liblapack3:amd64 (3.9.0-2) ... 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 (1.14-2) ... Setting up libtool (2.4.6-14) ... Setting up libxcb-render0:amd64 (1.14-2) ... Setting up fontconfig-config (2.13.1-2ubuntu3) ... Setting up libwebpdemux2:amd64 (0.6.1-2) ... Setting up libasn1-8-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.2-0ubuntu2) ... Setting up libnss3:amd64 (2:3.49.1-1ubuntu1) ... Setting up libxcb-shm0:amd64 (1.14-2) ... Setting up libpaper-utils (1.1.28) ... Setting up libhcrypto4-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up python3-tz (2020.1-1) ... Setting up help2man (1.47.15) ... Setting up python3-six (1.15.0-1) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up libwind0-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-reportlab-accel:amd64 (3.5.34-1ubuntu1) ... Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-6ubuntu4) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up libssh-4:amd64 (0.9.4-1ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.1-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up libx11-6:amd64 (2:1.6.9-2ubuntu1) ... Setting up python3-dateutil (2.8.1-4) ... Setting up libtiff5:amd64 (4.1.0+git191117-2build1) ... Setting up libfontconfig1:amd64 (2.13.1-2ubuntu3) ... Setting up libjs-jquery (3.5.1+dfsg-4) ... Setting up python3-lib2to3 (3.8.3-2) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-8) ... Setting up python3-pkg-resources (46.1.3-1) ... Setting up automake (1:1.16.2-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.8.3-2) ... Setting up dh-python (4.20200315) ... Setting up python3-pyfaidx (0.5.8-2) ... Setting up fontconfig (2.13.1-2ubuntu3) ... Regenerating fonts cache... done. Setting up gettext (0.19.8.1-10build1) ... Setting up python3-setuptools (46.1.3-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up python3-joblib (0.14.0-3) ... Setting up libhx509-5-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libpango-1.0-0:amd64 (1.44.7-2ubuntu4) ... Setting up libxext6:amd64 (2:1.3.4-0ubuntu1) ... Setting up python3-all (3.8.2-0ubuntu2) ... Setting up python3-yaml (5.3.1-2) ... Setting up libpoppler97:amd64 (0.86.1-0ubuntu1) ... Setting up python3-networkx (2.4-3ubuntu1) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.nodes['n1']['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.edges['n0','n1',1]['special'] is 0 Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libcairo2:amd64 (1.16.0-4ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-pil:amd64 (7.0.0-4build1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up python3-kiwisolver (1.0.1-3build1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up python3-numpy (1:1.18.4-1ubuntu1) ... Setting up python3-reportlab (3.5.34-1ubuntu1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up poppler-utils (0.86.1-0ubuntu1) ... Setting up libpangoft2-1.0-0:amd64 (1.44.7-2ubuntu4) ... Setting up python3-future (0.18.2-2) ... 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 (1.76+dfsg-2) ... Setting up libpangocairo-1.0-0:amd64 (1.44.7-2ubuntu4) ... Setting up libkrb5-26-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up python3-matplotlib (3.1.2-1ubuntu4) ... Setting up libxft2:amd64 (2.3.3-0ubuntu1) ... Setting up python3-scipy (1.4.1-2) ... Setting up po-debconf (1.0.21) ... Setting up python3-pomegranate (0.12.2-1) ... Setting up libtk8.6:amd64 (8.6.10-1) ... Setting up python3-pandas-lib (0.25.3+dfsg2-2) ... Setting up libheimntlm0-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up python3-pandas (0.25.3+dfsg2-2) ... Setting up libgssapi3-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:amd64 (2.4.49+dfsg-2ubuntu2) ... Setting up libcurl3-gnutls:amd64 (7.68.0-1ubuntu2) ... Setting up libcurl4:amd64 (7.68.0-1ubuntu2) ... Setting up libhts3:amd64 (1.10.2-3) ... Setting up python3-pysam (0.15.4+ds-3) ... Setting up python3-vcf (0.6.8+git20170215.476169c-7) ... Setting up r-base-core (4.0.0.20200530-1) ... Creating config file /etc/R/Renviron with new version Setting up r-bioc-biocgenerics (0.34.0-1build1) ... Setting up r-bioc-dnacopy (1.62.0-1build1) ... Setting up debhelper (13.1ubuntu1) ... Setting up sbuild-build-depends-cnvkit-dummy (0.invalid.0) ... Setting up dh-autoreconf (19) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... Processing triggers for systemd (245.5-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-179-generic amd64 (x86_64) Toolchain package versions: binutils_2.34-7ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-13ubuntu1 gcc-9_9.3.0-13ubuntu1 libc6-dev_2.31-0ubuntu9 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-3ubuntu1 linux-libc-dev_5.4.0-33.37 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.5 autoconf_2.69-11.1 automake_1:1.16.2-1ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu7 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-7ubuntu1 binutils-common_2.34-7ubuntu1 binutils-x86-64-linux-gnu_2.34-7ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.35.1-5ubuntu2 build-essential_12.8ubuntu1 bzip2_1.0.8-3 ca-certificates_20190110ubuntu2 coreutils_8.30-3ubuntu2 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mount_2.35.1-5ubuntu2 ncurses-base_6.2-1 ncurses-bin_6.2-1 node-jquery_3.5.1+dfsg-4 openssl_1.1.1f-1ubuntu2 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.2-1 perl-base_5.30.2-1 perl-modules-5.30_5.30.2-1 pinentry-curses_1.1.0-3build1 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 poppler-utils_0.86.1-0ubuntu1 procps_2:3.3.16-4ubuntu1 python-matplotlib-data_3.1.2-1ubuntu4 python3_3.8.2-0ubuntu2 python3-all_3.8.2-0ubuntu2 python3-biopython_1.76+dfsg-2 python3-cycler_0.10.0-3 python3-dateutil_2.8.1-4 python3-decorator_4.4.2-0ubuntu1 python3-distutils_3.8.3-2 python3-future_0.18.2-2 python3-joblib_0.14.0-3 python3-kiwisolver_1.0.1-3build1 python3-lib2to3_3.8.3-2 python3-matplotlib_3.1.2-1ubuntu4 python3-minimal_3.8.2-0ubuntu2 python3-networkx_2.4-3ubuntu1 python3-numpy_1:1.18.4-1ubuntu1 python3-pandas_0.25.3+dfsg2-2 python3-pandas-lib_0.25.3+dfsg2-2 python3-pil_7.0.0-4build1 python3-pkg-resources_46.1.3-1 python3-pomegranate_0.12.2-1 python3-pyfaidx_0.5.8-2 python3-pyparsing_2.4.7-1 python3-pysam_0.15.4+ds-3 python3-reportlab_3.5.34-1ubuntu1 python3-reportlab-accel_3.5.34-1ubuntu1 python3-scipy_1.4.1-2 python3-setuptools_46.1.3-1 python3-six_1.15.0-1 python3-tz_2020.1-1 python3-vcf_0.6.8+git20170215.476169c-7 python3-yaml_5.3.1-2 python3.8_3.8.3-1 python3.8-minimal_3.8.3-1 r-base-core_4.0.0.20200530-1 r-bioc-biocgenerics_0.34.0-1build1 r-bioc-dnacopy_1.62.0-1build1 readline-common_8.0-4 sbuild-build-depends-cnvkit-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_245.5-3ubuntu1 systemd-sysv_245.5-3ubuntu1 systemd-timesyncd_245.5-3ubuntu1 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 ttf-bitstream-vera_1.10-8 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.02.11.2 ucf_3.0042 unzip_6.0-25ubuntu1 util-linux_2.35.1-5ubuntu2 x11-common_1:7.7+19ubuntu14 xdg-utils_1.1.3-2ubuntu1 xz-utils_5.2.4-1 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Jun 1 14:20:10 2020 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cnvkit_0.9.7-1.dsc dpkg-source: info: extracting cnvkit in cnvkit-0.9.7 dpkg-source: info: unpacking cnvkit_0.9.7.orig.tar.gz dpkg-source: info: unpacking cnvkit_0.9.7-1.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 Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19392522 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19392522 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19392522 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.7-1 dpkg-buildpackage: info: source distribution unstable 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 '/<>' cd test && /usr/bin/make clean || /bin/true make[2]: Entering directory '/<>/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 '/<>/test' if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi dh_auto_clean I: pybuild base:217: python3.8 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.8_cnvkit/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.8' 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 '/<>' 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:217: python3.8 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>' [ -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:217: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/samutil.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/commands.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/export.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/cmdutil.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/plots.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/__init__.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/descriptives.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/batch.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/heatmap.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/reports.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/cnary.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/smoothing.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/importers.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/metrics.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/cluster.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/reference.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/parallel.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/diagram.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/access.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/target.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/import_rna.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/antitarget.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/autobin.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/rna.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/_version.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/segfilters.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/scatter.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/bintest.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/fix.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/segmetrics.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/core.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/vary.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/coverage.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/params.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/call.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib creating /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/none.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation creating /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/merge.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/combiners.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/__init__.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/subtract.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/gary.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/rangelabel.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/subdivide.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/intersect.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/chromsort.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome creating /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/tab.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/bedio.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/__init__.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/seqdict.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/seg.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/picard.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/textcoord.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/gff.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/genepred.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfio.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/util.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio running build_scripts creating build creating build/scripts-3.8 copying and adjusting ./cnvkit -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-skg_convert -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-cnv_updater -> build/scripts-3.8 copying ./scripts/snpfilter.sh -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-cnv_annotate -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-guess_baits -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-reference2targets -> build/scripts-3.8 changing mode of build/scripts-3.8/cnvkit from 644 to 755 changing mode of build/scripts-3.8/cnvkit-skg_convert from 644 to 755 changing mode of build/scripts-3.8/cnvkit-cnv_expression_correlate from 644 to 755 changing mode of build/scripts-3.8/cnvkit-cnv_updater from 644 to 755 changing mode of build/scripts-3.8/cnvkit-cnv_annotate from 644 to 755 changing mode of build/scripts-3.8/cnvkit-guess_baits from 644 to 755 changing mode of build/scripts-3.8/cnvkit-reference2targets 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 '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' cd test && /usr/bin/make -j4 make[2]: Entering directory '/<>/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/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Created directory build/ Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 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/ Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.targetcoverage.cnn with 6646 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 WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions 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/ 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 WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Correcting for GC bias... Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions Correcting for density bias... WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Loading build/p2-20_5.antitargetcoverage.cnn Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ Correcting for GC bias... Loading build/p2-5_5.antitargetcoverage.cnn 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/ Correcting for GC bias... Loading build/p2-9_5.antitargetcoverage.cnn Correcting for GC bias... Calculating average bin coverages WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 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 Processing target: p2-5_5 Processing target: p2-20_1 Processing target: p2-9_2 Keeping 6308 of 6646 bins Processing target: p2-20_2 Keeping 6308 of 6646 bins 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... Correcting for density bias... Keeping 6308 of 6646 bins Processing antitarget: p2-5_5 Processing antitarget: p2-20_1 Processing antitarget: p2-9_2 Correcting for GC bias... Correcting for density bias... Keeping 12455 of 12563 bins Processing antitarget: p2-20_2 Keeping 12455 of 12563 bins Correcting for GC bias... Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias WARNING: Skipping correction for RepeatMasker bias Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.14 x more variable than antitargets Targets are 1.14 x more variable than antitargets Targets are 1.75 x more variable than antitargets Targets are 1.09 x more variable than antitargets Wrote build/p2-5_5.cnr with 18763 regions Wrote build/p2-20_1.cnr with 18763 regions Wrote build/p2-9_2.cnr with 18763 regions Wrote build/p2-20_2.cnr with 18763 regions 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 python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns Processing target: p2-20_3 Processing target: p2-20_4 Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Processing target: p2-20_5 Keeping 6308 of 6646 bins Correcting for GC bias... Keeping 6308 of 6646 bins Correcting for density bias... Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Correcting for GC bias... Processing antitarget: p2-20_3 Correcting for density bias... Processing antitarget: p2-20_4 Processing antitarget: p2-20_5 Keeping 12455 of 12563 bins Keeping 12455 of 12563 bins Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias WARNING: Skipping correction for RepeatMasker bias Targets are 2.60 x more variable than antitargets Antitargets are 1.08 x more variable than targets Targets are 1.43 x more variable than antitargets Wrote build/p2-20_5.cnr with 18763 regions Wrote build/p2-20_3.cnr with 18763 regions Wrote build/p2-20_4.cnr with 18763 regions 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 segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns 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 Dropped 1 / 949 bins on chromosome chr6 Dropped 8 / 49 bins on chromosome chrY Wrote build/p2-5_5.cns with 71 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns Dropped 7 / 49 bins on chromosome chrY Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 27 / 49 bins on chromosome chrY Wrote build/p2-20_2.cns with 125 regions Dropped 6 / 49 bins on chromosome chrY 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.cns with 107 regions Wrote build/p2-20_1.cns with 117 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns 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 Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Wrote p2-5_5-scatter.pdf 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 Smoothing overshot at 3 / 97 indices: (-19.887157566382854, -3.337830278732133) vs. original (-19.2826, -0.27873000000000003) Dropped 11 / 49 bins on chromosome chrY Wrote build/p2-20_3.cns with 74 regions 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 Wrote p2-9_2-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 Dropped 6 / 49 bins on chromosome chrY Showing 1480 probes and 0 selected genes in region chr1 Wrote build/p2-20_5.cns with 129 regions Dropped 8 / 49 bins on chromosome chrY 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 Wrote p2-9_2-chr1-scatter.pdf Wrote build/p2-20_4.cns with 137 regions Showing 201 probes and 0 selected genes in region chr21 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 Wrote p2-9_2-chr21-scatter.pdf python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf Showing 330 probes and 24 selected genes in region chr9:149999-45000000 Showing 179 probes and 2 selected genes in region chr9:0-14504268 Wrote p2-9_2-chr9p-scatter.pdf Detected file format: bed Showing 41 probes and 3 selected genes in region chr9:2000000-4000000 python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf Showing 53 probes and 4 selected genes in region chr9:8000000-12000000 Treating sample p2-5_5 as female python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf Treating sample p2-9_2 as female Treating sample p2-20_1 as female Treating sample p2-20_2 as female Wrote p2-5_5-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf Wrote p2-9_2-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf Wrote p2-20_1-diagram.pdf Treating sample p2-5_5 as female python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf Wrote p2-5_5-cbs-diagram.pdf Wrote p2-20_2-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf 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 Treating sample p2-9_2 as female Wrote p2-9_2-cbs-diagram.pdf Treating sample p2-20_1 as female 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 Wrote p2-20_1-cbs-diagram.pdf Treating sample p2-20_2 as female 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 Treating sample p2-5_5 as female Wrote p2-20_2-cbs-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 Treating sample p2-9_2 as female Treating sample p2-20_1 as female Treating sample p2-20_2 as female Wrote p2-5_5-both-diagram.pdf 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 p2-20_1-both-diagram.pdf Treating sample p2-5_5 as female Treating sample p2-9_2 as female Treating sample p2-20_1 as female Wrote p2-20_2-both-diagram.pdf Treating sample p2-20_2 as female Wrote p2-9_2-both-diagram.pdf Treating sample p2-20_3 as female Treating sample p2-20_4 as female python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt Treating sample p2-20_5 as female python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt 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 Found 15 gene breakpoints Wrote p2-9_2-breaks.txt Treating sample p2-9_2 as female 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 Wrote heatmap-picard.pdf Wrote gender-picard.txt 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 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 Found 53 gene-level gains and losses Wrote p2-9_2-genemetrics.txt python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus Wrote p2-all.seg python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt Selected test sample NA12882 and control sample NA12878 Loaded 3654 records; skipped: 514 somatic, 394 depth Kept 2631 heterozygous of 3654 VCF records Wrote p2-9_2.nexus python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns Treating sample p2-5_5 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-5_5.call.cns with 71 regions python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns 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_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns 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 python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns Wrote p2-all.cdt python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns 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 Wrote p2-all-jtv.txt Treating sample p2-20_3 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_3.call.cns with 74 regions python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns 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_4 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_4.call.cns with 137 regions 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 python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input Treating sample p2-9_2.call as female 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 Wrote p2-9_2.vcf Placed 705 variants into 18763 bins 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 Wrote p2-9_2.nexus-ogt python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv Wrote p2-9_2.theta2.input python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv Wrote p2-5_5-segmetrics.cns with 71 regions Wrote p2-5_5-metrics.tsv 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 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 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 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-segmetrics.cns with 107 regions Wrote p2-9_2-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 Wrote p2-20-metrics.tsv make[2]: Leaving directory '/<>/test' cd test && /usr/bin/make -j4 clean || /bin/true make[2]: Entering directory '/<>/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 '/<>/test' rm -Rf test/build test/*.tsv make[1]: Leaving directory '/<>' 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 '/<>' [ -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:217: /usr/bin/python3 setup.py install --root /<>/debian/cnvkit running install running build running build_py running build_scripts running install_lib creating /<>/debian/cnvkit/usr creating /<>/debian/cnvkit/usr/lib creating /<>/debian/cnvkit/usr/lib/python3.8 creating /<>/debian/cnvkit/usr/lib/python3.8/dist-packages creating /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/samutil.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/commands.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/export.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/cmdutil.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/plots.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/descriptives.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/batch.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/heatmap.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/reports.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/cnary.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/smoothing.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/importers.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/metrics.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/cluster.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/reference.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/parallel.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/diagram.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/access.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/target.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/import_rna.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib creating /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/none.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/flasso.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/cbs.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/haar.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/hmm.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/antitarget.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/autobin.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/rna.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/_version.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segfilters.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/scatter.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/bintest.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/fix.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmetrics.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/core.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/vary.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/coverage.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/params.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/call.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib creating /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/merge.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/combiners.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/subtract.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/gary.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/rangelabel.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/subdivide.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome creating /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/tab.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/bedio.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/seqdict.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/seg.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/picard.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/textcoord.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/gff.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/genepred.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/vcfio.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/util.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/vcfsimple.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/intersect.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/chromsort.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/samutil.py to samutil.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/commands.py to commands.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/export.py to export.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/cmdutil.py to cmdutil.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/plots.py to plots.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/descriptives.py to descriptives.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/batch.py to batch.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/heatmap.py to heatmap.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/reports.py to reports.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/cnary.py to cnary.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/smoothing.py to smoothing.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/importers.py to importers.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/metrics.py to metrics.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/cluster.py to cluster.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/reference.py to reference.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/parallel.py to parallel.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/diagram.py to diagram.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/access.py to access.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/target.py to target.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/import_rna.py to import_rna.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/none.py to none.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/flasso.py to flasso.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/cbs.py to cbs.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/haar.py to haar.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/hmm.py to hmm.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/antitarget.py to antitarget.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/autobin.py to autobin.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/rna.py to rna.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/_version.py to _version.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segfilters.py to segfilters.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/scatter.py to scatter.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/bintest.py to bintest.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/fix.py to fix.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmetrics.py to segmetrics.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/core.py to core.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/vary.py to vary.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/coverage.py to coverage.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/params.py to params.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/call.py to call.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/merge.py to merge.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/combiners.py to combiners.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/subtract.py to subtract.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/gary.py to gary.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/rangelabel.py to rangelabel.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/subdivide.py to subdivide.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/tab.py to tab.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/bedio.py to bedio.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/seqdict.py to seqdict.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/seg.py to seg.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/picard.py to picard.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/textcoord.py to textcoord.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/gff.py to gff.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/genepred.py to genepred.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/vcfio.py to vcfio.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/util.py to util.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/vcfsimple.py to vcfsimple.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/intersect.py to intersect.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/chromsort.py to chromsort.cpython-38.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 /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/CNVkit-0.9.7.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-skg_convert -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-cnv_expression_correlate -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-cnv_updater -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/snpfilter.sh -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-cnv_annotate -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-guess_baits -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-reference2targets -> /<>/debian/cnvkit/usr/bin changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-skg_convert to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 755 changing mode of /<>/debian/cnvkit/usr/bin/snpfilter.sh to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-guess_baits to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-reference2targets 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 0.9.7 cd scripts && PYTHONPATH=../ help2man --no-info \ --version-string=0.9.7 --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 '/<>' 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_installinit -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 -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 144 pkgstriptranslations: processing cnvkit (in debian/cnvkit); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/cnvkit/DEBIAN/control, package cnvkit, directory debian/cnvkit pkgstripfiles: Running PNG optimization (using 4 cpus) for package cnvkit ... pkgstripfiles: No PNG files. dpkg-deb: building package 'cnvkit' in '../cnvkit_0.9.7-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../cnvkit_0.9.7-1_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) -------------------------------------------------------------------------------- Build finished at 20200601-2315 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ cnvkit_0.9.7-1_amd64.changes: ----------------------------- Format: 1.8 Date: Mon, 01 Jun 2020 16:19:46 +0200 Source: cnvkit Binary: cnvkit Architecture: amd64 Version: 0.9.7-1 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Michael R. Crusoe Description: cnvkit - Copy number variant detection from targeted DNA sequencing Changes: cnvkit (0.9.7-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.5.0 (routine-update) * Refreshed the patches * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. Checksums-Sha1: d7c22c59fec6a8f089a09cbede43d789ef92b382 9691 cnvkit_0.9.7-1_amd64.buildinfo 1c37cbfcc95f35a95bbfb4d29a6936e83c527c29 15424880 cnvkit_0.9.7-1_amd64.deb Checksums-Sha256: 86873da75b370e18b6266d121321f888eb79d9389b4e1a4d6e4bfe7ad79c21dd 9691 cnvkit_0.9.7-1_amd64.buildinfo 25a85d088d1f83dd88fa071e765aaef0d56377a60d4a467721bf7662410eb06a 15424880 cnvkit_0.9.7-1_amd64.deb Files: 92e8f7adf8b4358b2018999adbcad7b9 9691 science optional cnvkit_0.9.7-1_amd64.buildinfo d2cf07322a0fb352cf3ed220992071aa 15424880 science optional cnvkit_0.9.7-1_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ cnvkit_0.9.7-1_amd64.deb ------------------------ new debian package, version 2.0. size 15424880 bytes: control archive=5984 bytes. 904 bytes, 15 lines control 16464 bytes, 188 lines md5sums 237 bytes, 12 lines * postinst #!/bin/sh 386 bytes, 12 lines * prerm #!/bin/sh Package: cnvkit Version: 0.9.7-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 69054 Depends: python3-biopython, python3-matplotlib, python3-numpy, python3-pandas, python3-pomegranate, python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3-sklearn, python3:any, r-bioc-dnacopy Section: science Priority: optional Homepage: http://cnvkit.readthedocs.org Description: Copy number variant detection from targeted DNA sequencing A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from targeted DNA sequencing. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. drwxr-xr-x root/root 0 2020-06-01 14:19 ./ drwxr-xr-x root/root 0 2020-06-01 14:19 ./usr/ drwxr-xr-x root/root 0 2020-06-01 14:19 ./usr/bin/ -rwxr-xr-x root/root 285 2020-06-01 14:19 ./usr/bin/cnvkit -rwxr-xr-x root/root 959 2020-06-01 14:19 ./usr/bin/cnvkit-cnv_annotate -rwxr-xr-x root/root 4315 2020-06-01 14:19 ./usr/bin/cnvkit-cnv_expression_correlate -rwxr-xr-x root/root 2311 2020-06-01 14:19 ./usr/bin/cnvkit-cnv_updater -rwxr-xr-x root/root 10212 2020-06-01 14:19 ./usr/bin/cnvkit-guess_baits -rwxr-xr-x root/root 1136 2020-06-01 14:19 ./usr/bin/cnvkit-reference2targets -rwxr-xr-x root/root 3375 2020-06-01 14:19 ./usr/bin/cnvkit-skg_convert -rwxr-xr-x root/root 1064 2020-05-29 06:04 ./usr/bin/snpfilter.sh drwxr-xr-x root/root 0 2020-06-01 14:19 ./usr/lib/ drwxr-xr-x root/root 0 2020-06-01 14:19 ./usr/lib/python3/ 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2020-06-01 14:19 ./usr/share/man/man1/cnvkit-reference.1.gz -rw-r--r-- root/root 563 2020-06-01 14:19 ./usr/share/man/man1/cnvkit-reference2targets.1.gz -rw-r--r-- root/root 1652 2020-06-01 14:19 ./usr/share/man/man1/cnvkit-scatter.1.gz -rw-r--r-- root/root 1546 2020-06-01 14:19 ./usr/share/man/man1/cnvkit-segment.1.gz -rw-r--r-- root/root 964 2020-06-01 14:19 ./usr/share/man/man1/cnvkit-segmetrics.1.gz -rw-r--r-- root/root 490 2020-06-01 14:19 ./usr/share/man/man1/cnvkit-sex.1.gz -rw-r--r-- root/root 642 2020-06-01 14:19 ./usr/share/man/man1/cnvkit-target.1.gz -rw-r--r-- root/root 1489 2020-06-01 14:19 ./usr/share/man/man1/cnvkit.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 156708 Build-Time: 160 Distribution: groovy-proposed Host Architecture: amd64 Install-Time: 33 Job: cnvkit_0.9.7-1.dsc Machine Architecture: amd64 Package: cnvkit Package-Time: 195 Source-Version: 0.9.7-1 Space: 156708 Status: successful Version: 0.9.7-1 -------------------------------------------------------------------------------- Finished at 20200601-2315 Build needed 00:03:15, 156708k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19392522 Scanning for processes to kill in build PACKAGEBUILD-19392522