Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/c/cnvkit/cnvkit_0.9.8-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/cnvkit-0.9.8-18nu_4iwu/cnvkit_0.9.8-1_amd64.buildinfo Get source package info: cnvkit=0.9.8-1 Source URL: http://snapshot.notset.fr/mr/package/cnvkit/0.9.8-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-14 automake=1:1.16.3-1 autopoint=0.21-3 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-1 binutils=2.35.1-6 binutils-common=2.35.1-6 binutils-x86-64-linux-gnu=2.35.1-6 bsdextrautils=2.36.1-4 bsdutils=1:2.36.1-4 build-essential=12.8 bzip2=1.0.8-4 ca-certificates=20200601 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.1-3 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.1 debianutils=4.11.2 dh-autoreconf=19 dh-python=4.20201102 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13+20201015-2 file=1:5.39-3 findutils=4.7.0+git20201010-2 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-lyx=2.3.6-1 g++=4:10.2.0-1 g++-10=10.2.1-3 gcc=4:10.2.0-1 gcc-10=10.2.1-3 gcc-10-base=10.2.1-3 gettext=0.21-3 gettext-base=0.21-3 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 help2man=1.47.16 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-9 libarchive-zip-perl=1.68-1 libasan6=10.2.1-3 libatomic1=10.2.1-3 libattr1=1:2.4.48-6 libaudit-common=1:3.0-1 libaudit1=1:3.0-1 libbinutils=2.35.1-6 libblas3=3.9.0-3 libblkid1=2.36.1-4 libbrotli1=1.0.9-2+b2 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-6 libc-dev-bin=2.31-6 libc6=2.31-6 libc6-dev=2.31-6 libcairo2=1.16.0-4 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-3 libcom-err2=1.45.6-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-6 libctf0=2.35.1-6 libcurl3-gnutls=7.74.0-1 libcurl4=7.74.0-1 libdatrie1=0.2.12-3 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.3.1 libdeflate0=1.6-1 libdpkg-perl=1.20.5 libelf1=0.182-2 libexpat1=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgcc-10-dev=10.2.1-3 libgcc-s1=10.2.1-3 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran5=10.2.1-3 libglib2.0-0=2.66.4-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-3 libgomp1=10.2.1-3 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-4 libharfbuzz0b=2.6.7-1 libhogweed6=3.6-2 libhts3=1.11-3 libice6=2:1.0.10-1 libicu67=67.1-5 libidn2-0=2.3.0-4 libimagequant0=2.12.2-1.1 libisl23=0.23-1 libitm1=10.2.1-3 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.0.5-1.1 libjs-jquery=3.5.1+dfsg+~3.5.5-4 libjs-jquery-ui=1.12.1+dfsg-7 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack3=3.9.0-3 liblbfgsb0=3.0+dfsg.3-9 liblcms2-2=2.9-4+b1 libldap-2.4-2=2.4.56+dfsg-1 liblocale-gettext-perl=1.07-4+b1 liblsan0=10.2.1-3 liblz4-1=1.9.3-1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-4 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnettle8=3.6-2 libnghttp2-14=1.42.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnspr4=2:4.29-1 libnss3=2:3.60-1 libopenjp2-7=2.3.1-1 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-2 libpam-modules-bin=1.4.0-2 libpam-runtime=1.4.0-2 libpam0g=1.4.0-2 libpango-1.0-0=1.46.2-3 libpangocairo-1.0-0=1.46.2-3 libpangoft2-1.0-0=1.46.2-3 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpng16-16=1.6.37-3 libpoppler102=20.09.0-3 libprocps8=2:3.3.16-5 libpsl5=0.21.0-1.1 libpython3-stdlib=3.9.1-1 libpython3.9-minimal=3.9.1-1 libpython3.9-stdlib=3.9.1-1 libquadmath0=10.2.1-3 libreadline8=8.1-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libsigsegv2=2.12-3 libsm6=2:1.2.3-1 libsmartcols1=2.36.1-4 libsqlite3-0=3.34.0-1 libssh2-1=1.9.0-2 libssl1.1=1.1.1i-1 libstdc++-10-dev=10.2.1-3 libstdc++6=10.2.1-3 libsub-override-perl=0.09-2 libsystemd0=247.2-3 libtasn1-6=4.16.0-2 libtcl8.6=8.6.10+dfsg-1 libthai-data=0.1.28-3 libthai0=0.1.28-3 libtiff5=4.2.0-1 libtinfo6=6.2+20201114-2 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtk8.6=8.6.10-1 libtool=2.4.6-14 libtsan0=10.2.1-3 libubsan1=10.2.1-3 libuchardet0=0.0.7-1 libudev1=247.2-3 libunistring2=0.9.10-4 libuuid1=2.36.1-4 libwebp6=0.6.1-2+b1 libwebpdemux2=0.6.1-2+b1 libwebpmux3=0.6.1-2+b1 libx11-6=2:1.6.12-1 libx11-data=2:1.6.12-1 libxau6=1:1.0.8-1+b2 libxcb-render0=1.14-2.1 libxcb-shm0=1.14-2.1 libxcb1=1.14-2.1 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1.1 libxft2=2.3.2-2 libxml2=2.9.10+dfsg-6.3+b1 libxrender1=1:0.9.10-1 libxss1=1:1.2.3-1 libxt6=1:1.2.0-1 libyaml-0-2=0.2.2-1 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.9.15-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 mailcap=3.68 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=1.0.1 mime-support=3.66 ncurses-base=6.2+20201114-1 ncurses-bin=6.2+20201114-1 openssl=1.1.1i-1 patch=2.7.6-6 perl=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 po-debconf=1.0.21+nmu1 poppler-utils=20.09.0-3 procps=2:3.3.16-5 python-matplotlib-data=3.3.2-2 python3=3.9.1-1 python3-all=3.9.1-1 python3-biopython=1.78+dfsg-4 python3-certifi=2020.6.20-1 python3-cycler=0.10.0-3 python3-dateutil=2.8.1-4 python3-decorator=4.4.2-2 python3-distutils=3.9.1-1 python3-future=0.18.2-5 python3-joblib=0.17.0-2 python3-kiwisolver=1.3.1-1+b1 python3-lib2to3=3.9.1-1 python3-matplotlib=3.3.2-2+b1 python3-minimal=3.9.1-1 python3-networkx=2.5+ds-2 python3-numpy=1:1.19.4-1+b1 python3-pandas=1.1.5+dfsg-1 python3-pandas-lib=1.1.5+dfsg-1 python3-pil=8.0.1-1+b1 python3-pkg-resources=51.1.0-1 python3-pomegranate=0.13.4-1+b2 python3-pyfaidx=0.5.9.2-1 python3-pyparsing=2.4.7-1 python3-pysam=0.15.4+ds-3+b2 python3-reportlab=3.5.57-1 python3-reportlab-accel=3.5.57-1 python3-scipy=1.5.4-1+b1 python3-setuptools=51.1.0-1 python3-six=1.15.0-2 python3-tz=2020.5-1 python3-vcf=0.6.8+git20170215.476169c-7+b3 python3-yaml=5.3.1-3+b1 python3.9=3.9.1-1 python3.9-minimal=3.9.1-1 r-base-core=4.0.3-1 r-bioc-biocgenerics=0.36.0-1 r-bioc-dnacopy=1.64.0-1 readline-common=8.1-1 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 ttf-bitstream-vera=1.10-8.1 tzdata=2020e-1 ucf=3.0043 unzip=6.0-25 util-linux=2.36.1-4 x11-common=1:7.7+21 xdg-utils=1.1.3-2 xz-utils=5.2.4-1+b1 zip=3.0-11+b1 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210106T142920Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201230T203527Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d cnvkit=0.9.8-1 && mkdir -p /build/cnvkit-73S0w1 && dpkg-source --no-check -x /*.dsc /build/cnvkit-73S0w1/cnvkit-0.9.8 && chown -R builduser:builduser /build/cnvkit-73S0w1" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/cnvkit-73S0w1/cnvkit-0.9.8 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1609514230" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/cnvkit-73S0w1 /tmp/cnvkit-0.9.8-18nu_4iwu bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201230T203527Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.KYnJohBBC8 as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.KYnJohBBC8 Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201230T203527Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201230T203527Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (923 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4648 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-6) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210106T142920Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201230T203527Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.KYnJohBBC8 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210106T142920Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201230T203527Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20210106T142920Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210106T142920Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210106T142920Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20210106T142920Z unstable/main amd64 Packages [11.6 MB] Fetched 34.3 MB in 29s (1188 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.KYnJohBBC8 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d cnvkit=0.9.8-1 && mkdir -p /build/cnvkit-73S0w1 && dpkg-source --no-check -x /*.dsc /build/cnvkit-73S0w1/cnvkit-0.9.8 && chown -R builduser:builduser /build/cnvkit-73S0w1"' exec /tmp/mmdebstrap.KYnJohBBC8 Reading package lists... NOTICE: 'cnvkit' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/cnvkit.git Please use: git clone https://salsa.debian.org/med-team/cnvkit.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 23.7 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main cnvkit 0.9.8-1 (dsc) [2324 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main cnvkit 0.9.8-1 (tar) [23.7 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main cnvkit 0.9.8-1 (diff) [6184 B] Fetched 23.7 MB in 19s (1243 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'cnvkit_0.9.8-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting cnvkit in /build/cnvkit-73S0w1/cnvkit-0.9.8 dpkg-source: info: unpacking cnvkit_0.9.8.orig.tar.gz dpkg-source: info: unpacking cnvkit_0.9.8-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-py-ext dpkg-source: info: applying python3compat.patch dpkg-source: info: applying spelling dpkg-source: info: applying controldir I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/cnvkit-73S0w1/cnvkit-0.9.8 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1609514230" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.KYnJohBBC8 dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.8-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/cnvkit-73S0w1/cnvkit-0.9.8' cd test && /usr/bin/make clean || /bin/true make[2]: Entering directory '/build/cnvkit-73S0w1/cnvkit-0.9.8/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/build/cnvkit-73S0w1/cnvkit-0.9.8/test' if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi dh_auto_clean I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it rm -rf test/p2-20-metrics.tsv test/p2-5_5-metrics.tsv test/p2-9_2-metrics.tsv rm -rf test/build CNVkit.egg-info make[1]: Leaving directory '/build/cnvkit-73S0w1/cnvkit-0.9.8' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/cnvkit-73S0w1/cnvkit-0.9.8' [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted build if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ mv ${script} cnvkit-${script%%.py}; \ done; \ fi dh_auto_build I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/reference.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/heatmap.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/import_rna.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cnary.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/batch.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/smoothing.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/samutil.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/diagram.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/__init__.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/rna.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/descriptives.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/core.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/autobin.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/access.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/fix.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/metrics.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/vary.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/export.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/params.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/target.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/coverage.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cluster.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/commands.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/plots.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/scatter.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/_version.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/segmetrics.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/antitarget.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/segfilters.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/bintest.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cmdutil.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/importers.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/parallel.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/reports.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/call.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib creating /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/none.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation creating /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/chromsort.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/intersect.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/subtract.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/__init__.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/combiners.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/merge.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/gary.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/subdivide.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/rangelabel.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome creating /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/textcoord.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfio.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/__init__.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/seg.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/util.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/bedio.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/gff.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/picard.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/genepred.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/seqdict.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/tab.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio running build_scripts creating build creating build/scripts-3.9 copying and adjusting /build/cnvkit-73S0w1/cnvkit-0.9.8/cnvkit -> build/scripts-3.9 copying and adjusting /build/cnvkit-73S0w1/cnvkit-0.9.8/scripts/cnvkit-cnv_annotate -> build/scripts-3.9 copying and adjusting /build/cnvkit-73S0w1/cnvkit-0.9.8/scripts/cnvkit-reference2targets -> build/scripts-3.9 copying and adjusting /build/cnvkit-73S0w1/cnvkit-0.9.8/scripts/cnvkit-guess_baits -> build/scripts-3.9 copying and adjusting /build/cnvkit-73S0w1/cnvkit-0.9.8/scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.9 copying /build/cnvkit-73S0w1/cnvkit-0.9.8/scripts/snpfilter.sh -> build/scripts-3.9 copying and adjusting /build/cnvkit-73S0w1/cnvkit-0.9.8/scripts/cnvkit-cnv_updater -> build/scripts-3.9 copying and adjusting /build/cnvkit-73S0w1/cnvkit-0.9.8/scripts/cnvkit-skg_convert -> build/scripts-3.9 changing mode of build/scripts-3.9/cnvkit from 644 to 755 changing mode of build/scripts-3.9/cnvkit-cnv_annotate from 644 to 755 changing mode of build/scripts-3.9/cnvkit-reference2targets from 644 to 755 changing mode of build/scripts-3.9/cnvkit-guess_baits from 644 to 755 changing mode of build/scripts-3.9/cnvkit-cnv_expression_correlate from 644 to 755 changing mode of build/scripts-3.9/cnvkit-cnv_updater from 644 to 755 changing mode of build/scripts-3.9/cnvkit-skg_convert from 644 to 755 cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py make[1]: Leaving directory '/build/cnvkit-73S0w1/cnvkit-0.9.8' debian/rules override_dh_auto_test make[1]: Entering directory '/build/cnvkit-73S0w1/cnvkit-0.9.8' cd test && /usr/bin/make -j32 make[2]: Entering directory '/build/cnvkit-73S0w1/cnvkit-0.9.8/test' python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ecn1kjv8 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-l0wqvtru because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-klmnlymz because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7wn30dsl because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-y19jdnol because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-eqfdlzsw because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-a4efu1sc because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-22oz6iza because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xvrr9r28 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-e634ppk2 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-48fdumrx because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-r6krsxsa because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-idql34xo because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-bs2l8q8s because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-cvi3qeu8 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Created directory build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions 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 WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-k93gcxs0 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Number of target and antitarget files: 3, 3 No FASTA reference genome provided; skipping GC, RM calculations Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female Loading build/p2-20_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-5_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-9_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-20_5.antitargetcoverage.cnn Correcting for GC bias... Loading build/p2-5_5.antitargetcoverage.cnn Correcting for GC bias... Loading build/p2-9_5.antitargetcoverage.cnn Correcting for GC bias... Calculating average bin coverages Calculating bin spreads Targets: 338 (5.0858%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 " chr1:2435319-2436685 log2=-0.709 spread=0.503 ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 " chr1:120611883-120612051 log2=0.070 spread=0.050 NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 " chr1:156842391-156842479 log2=-0.398 spread=0.290 MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 " chr1:183481886-183481951 log2=-0.040 spread=0.119 CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 " chr1:243800859-243801066 log2=0.023 spread=0.063 MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 " chr2:25536716-25536891 log2=0.702 spread=0.033 MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 REL chr2:61108881-61109061 log2=1.026 spread=0.559 " chr2:61128072-61128256 log2=0.115 spread=0.173 " chr2:61145275-61145462 log2=0.014 spread=0.099 CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 " chr2:128095237-128095425 log2=0.215 spread=0.212 METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 " chr3:97160189-97160367 log2=-0.050 spread=0.191 ATR chr3:142254935-142255077 log2=0.024 spread=0.027 " chr3:142286854-142287031 log2=-0.076 spread=0.116 GAK chr4:896278-896357 log2=-1.505 spread=1.261 FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 " chr4:1803044-1803507 log2=-0.073 spread=0.117 " chr4:1808792-1809022 log2=0.252 spread=0.108 CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 " chr4:178514600-178514725 log2=-0.098 spread=0.096 TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 " chr5:1295312-1295381 log2=-0.690 spread=0.462 CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 " chr5:25519857-25520034 log2=-0.015 spread=0.095 RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 " chr5:38962338-38962525 log2=0.005 spread=0.019 " chr5:38966685-38966862 log2=0.006 spread=0.165 " chr5:38978620-38978763 log2=0.040 spread=0.030 " chr5:39074133-39074327 log2=-0.158 spread=0.139 CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 " chr5:51030131-51030313 log2=-0.034 spread=0.192 MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 " chr5:56168412-56168590 log2=0.479 spread=0.038 CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 " chr5:86637023-86637168 log2=0.054 spread=0.111 " chr5:86642414-86642592 log2=0.254 spread=0.162 " chr5:86648912-86649096 log2=0.092 spread=0.062 " chr5:86670598-86670778 log2=0.222 spread=0.198 MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 APC chr5:112101965-112102138 log2=0.104 spread=0.217 NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 " chr5:170837567-170837631 log2=0.085 spread=0.349 FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 " chr5:180046203-180046404 log2=-1.531 spread=0.722 " chr5:180076418-180076603 log2=-2.224 spread=1.416 TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 " chr6:31939599-31940313 log2=-19.582 spread=0.181 STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 " chr6:31946632-31946824 log2=-20.052 spread=0.088 " chr6:31947142-31947366 log2=-20.114 spread=0.066 " chr6:31948176-31948360 log2=-19.982 spread=0.149 " chr6:31948382-31948612 log2=-19.757 spread=0.165 " chr6:31948730-31949253 log2=-20.048 spread=0.014 NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 " chr6:32164046-32164227 log2=-19.755 spread=0.189 " chr6:32164652-32164888 log2=-19.984 spread=0.154 " chr6:32165021-32165403 log2=-19.625 spread=0.196 " chr6:32166163-32166545 log2=-20.043 spread=0.072 " chr6:32166648-32166962 log2=-3.514 spread=5.742 " chr6:32168554-32168821 log2=-19.601 spread=0.197 " chr6:32168844-32169306 log2=-19.683 spread=0.166 " chr6:32169801-32170391 log2=-19.405 spread=0.205 " chr6:32171492-32171691 log2=-20.095 spread=0.101 " chr6:32171861-32172198 log2=-3.141 spread=7.288 " chr6:32178478-32178749 log2=-19.927 spread=0.164 " chr6:32180197-32180441 log2=-10.902 spread=9.532 " chr6:32180544-32180722 log2=-19.675 spread=0.186 " chr6:32180857-32181062 log2=-19.562 spread=0.227 " chr6:32181411-32181646 log2=-19.966 spread=0.171 " chr6:32181832-32182066 log2=-19.961 spread=0.172 " chr6:32182948-32183194 log2=-19.935 spread=0.168 " chr6:32184667-32185079 log2=-19.923 spread=0.165 " chr6:32185720-32185919 log2=-19.707 spread=0.197 " chr6:32187317-32187601 log2=-19.765 spread=0.173 " chr6:32187871-32188094 log2=-19.660 spread=0.188 " chr6:32188127-32188451 log2=-19.622 spread=0.169 " chr6:32188481-32188693 log2=-19.902 spread=0.132 " chr6:32188704-32189133 log2=-19.501 spread=0.193 " chr6:32190258-32190616 log2=-19.570 spread=0.209 " chr6:32190724-32190908 log2=-19.540 spread=0.232 " chr6:32191570-32191668 log2=-19.773 spread=0.178 " chr6:32191676-32191753 log2=-19.374 spread=0.201 FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 " chr6:128316545-128316699 log2=-0.070 spread=0.050 MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 " chr6:157099442-157099991 log2=-0.846 spread=0.504 " chr6:157100042-157100634 log2=-1.570 spread=0.825 IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 " chr7:98491365-98491541 log2=0.209 spread=0.153 " chr7:98493314-98493496 log2=0.389 spread=0.207 SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 " chr7:128829048-128829358 log2=-0.474 spread=0.315 BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 " chr7:140484736-140484912 log2=0.081 spread=0.150 " chr7:140487956-140488430 log2=-0.089 spread=0.142 " chr7:140493336-140493442 log2=-0.340 spread=0.283 " chr7:140624315-140624540 log2=-0.497 spread=0.342 TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 WRN chr8:30925752-30925890 log2=0.120 spread=0.158 " chr8:30941153-30941335 log2=0.079 spread=0.294 " chr8:30942625-30942802 log2=0.044 spread=0.247 " chr8:30947918-30948092 log2=0.151 spread=0.124 " chr8:31000128-31000252 log2=-0.099 spread=0.098 " chr8:31001006-31001182 log2=-0.002 spread=0.062 GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 " chr8:37698557-37699898 log2=-0.612 spread=0.029 ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 " chr8:48845528-48845758 log2=0.056 spread=0.196 " chr8:48866846-48867043 log2=-0.067 spread=0.097 " chr8:48868369-48868526 log2=-0.239 spread=0.174 " chr8:48872485-48872722 log2=-0.636 spread=0.464 CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 " chr9:2101491-2101640 log2=0.244 spread=0.104 JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 " chr9:5067014-5067883 log2=0.146 spread=0.089 " chr9:5068184-5070306 log2=0.133 spread=0.092 " chr9:5076944-5077152 log2=0.046 spread=0.137 PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 " chr9:21986759-21986899 log2=0.058 spread=0.175 LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 " chr9:87425375-87425452 log2=0.494 spread=0.066 PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 " chr9:139250747-139251032 log2=-0.223 spread=0.273 " chr9:139252418-139252703 log2=-0.512 spread=0.264 NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 " chr9:139417262-139417677 log2=-0.173 spread=0.191 " chr9:139440110-139440287 log2=-1.257 spread=0.500 MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 CGH chr10:22505654-22505837 log2=0.072 spread=0.107 RET chr10:43572644-43572830 log2=-1.376 spread=1.092 " chr10:43600360-43600677 log2=-0.341 spread=0.222 PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 " chr10:89685254-89685374 log2=0.244 spread=0.259 TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 " chr10:93579008-93579121 log2=0.166 spread=0.220 SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 " chr10:112679716-112679934 log2=-0.008 spread=0.028 CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 " chr11:94170270-94170454 log2=0.095 spread=0.285 YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 ATM chr11:108153392-108153639 log2=0.113 spread=0.136 " chr11:108164020-108164234 log2=-0.056 spread=0.040 " chr11:108217986-108218135 log2=0.359 spread=0.277 MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 " chr12:25391004-25391186 log2=0.368 spread=0.128 DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 " chr12:51206782-51207287 log2=-0.012 spread=0.101 PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 " chr13:26970356-26970536 log2=0.137 spread=0.121 FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 " chr13:32903506-32903689 log2=0.019 spread=0.232 " chr13:32918645-32918823 log2=0.158 spread=0.114 " chr13:32920899-32921077 log2=0.014 spread=0.247 RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 " chr13:48919164-48919369 log2=0.025 spread=0.094 " chr13:48921877-48922044 log2=0.106 spread=0.147 " chr13:48923026-48923204 log2=0.360 spread=0.016 " chr13:48938965-48939147 log2=0.084 spread=0.356 " chr13:48941578-48941767 log2=0.238 spread=0.212 " chr13:48947486-48947665 log2=0.025 spread=0.126 " chr13:48954166-48954251 log2=0.061 spread=0.273 " chr13:49037815-49038005 log2=0.063 spread=0.062 " chr13:49047410-49047589 log2=0.053 spread=0.170 CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 " chr13:85527771-85527948 log2=0.007 spread=0.222 GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 " chr13:110438332-110438432 log2=-3.643 spread=2.325 CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 " chr14:20291466-20291612 log2=0.697 spread=0.248 NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 " chr14:36989195-36989373 log2=0.023 spread=0.162 SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 " chr14:50619741-50619923 log2=0.003 spread=0.272 " chr14:50697856-50698044 log2=0.277 spread=0.334 MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 " chr14:71275790-71275923 log2=-2.815 spread=1.938 TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 CGH chr15:20870700-20870881 log2=1.102 spread=0.611 " chr15:38544477-38545455 log2=-0.348 spread=0.179 SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 " chr15:41803968-41804185 log2=-2.202 spread=0.188 " chr15:41804261-41804494 log2=-0.402 spread=0.392 NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 " chr16:2611404-2611585 log2=-5.171 spread=1.963 " chr16:2611721-2611943 log2=-11.810 spread=9.172 " chr16:2615504-2615725 log2=-20.113 spread=0.007 " chr16:2616307-2616486 log2=-20.054 spread=0.072 " chr16:2631267-2631414 log2=-20.009 spread=0.061 " chr16:2631583-2631734 log2=-20.089 spread=0.090 " chr16:2633363-2633616 log2=-20.101 spread=0.089 CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 CGH chr16:31526705-31526886 log2=0.057 spread=0.074 CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 " chr16:50826460-50826650 log2=0.239 spread=0.204 CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 " chr16:60005694-60005857 log2=-0.366 spread=0.298 CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 " chr17:12011053-12011253 log2=0.028 spread=0.232 NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 " chr17:29496854-29497046 log2=0.226 spread=0.193 RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 " chr17:30519172-30519355 log2=0.163 spread=0.289 " chr17:30525911-30526093 log2=-0.157 spread=0.046 ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 " chr19:2210351-2210545 log2=-0.860 spread=0.261 " chr19:2226130-2227152 log2=-0.113 spread=0.120 GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 " chr19:15311544-15311749 log2=-1.887 spread=1.202 JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 " chr19:33792774-33793010 log2=-1.781 spread=0.127 " chr19:33793014-33793356 log2=-0.541 spread=0.385 CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 " chr19:45873698-45873881 log2=-0.522 spread=0.327 BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 " chr21:36265140-36265318 log2=0.042 spread=0.039 CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 " chr22:29115325-29115465 log2=0.055 spread=0.390 SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 " chrX:1317372-1317594 log2=-21.121 spread=0.049 " chrX:1321225-1321435 log2=-20.851 spread=0.196 " chrX:1325274-1325530 log2=-21.121 spread=0.011 " chrX:1327651-1327830 log2=-21.000 spread=0.029 " chrX:1331391-1331576 log2=-21.018 spread=0.052 KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 " chrX:123185143-123185290 log2=-1.018 spread=0.062 " chrX:123202378-123202544 log2=-0.959 spread=0.103 FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 " chrY:9008607-9008759 log2=-1.012 spread=0.097 " chrY:13131970-13132039 log2=-1.004 spread=0.074 " chrY:19506485-19506650 log2=-1.018 spread=0.034 " chrY:21033918-21034071 log2=-1.013 spread=0.057 " chrY:28463435-28463622 log2=-0.952 spread=0.039 " chrY:28514033-28514208 log2=-0.992 spread=0.026 Antitargets: 108 (0.8597%) bins failed filters Wrote build/reference-picard.cnn with 19209 regions python3 ../cnvkit.py fix build/p2-5_5.targetcoverage.cnn build/p2-5_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-5_5.cnr python3 ../cnvkit.py fix build/p2-9_2.targetcoverage.cnn build/p2-9_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-9_2.cnr python3 ../cnvkit.py fix build/p2-20_1.targetcoverage.cnn build/p2-20_1.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_1.cnr python3 ../cnvkit.py fix build/p2-20_2.targetcoverage.cnn build/p2-20_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_2.cnr python3 ../cnvkit.py fix build/p2-20_3.targetcoverage.cnn build/p2-20_3.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_3.cnr python3 ../cnvkit.py fix build/p2-20_4.targetcoverage.cnn build/p2-20_4.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_4.cnr python3 ../cnvkit.py fix build/p2-20_5.targetcoverage.cnn build/p2-20_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_5.cnr Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7mdoeu9w because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2j2dslgf because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-eb1ymuh5 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-akxqobcm because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_v2x0s63 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-6qmz4cud because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-jbt7l8_w because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Processing target: p2-20_5 Processing target: p2-20_2 Processing target: p2-5_5 Processing target: p2-20_4 Keeping 6308 of 6646 bins Keeping 6308 of 6646 bins Processing target: p2-20_1 Processing target: p2-20_3 Correcting for GC bias... Processing target: p2-9_2 Correcting for density bias... Correcting for GC bias... Keeping 6308 of 6646 bins Keeping 6308 of 6646 bins Correcting for density bias... Keeping 6308 of 6646 bins Processing antitarget: p2-20_5 Correcting for GC bias... Keeping 6308 of 6646 bins Correcting for GC bias... Processing antitarget: p2-20_2 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Correcting for density bias... Correcting for density bias... Correcting for GC bias... Correcting for GC bias... Correcting for density bias... Correcting for density bias... Processing antitarget: p2-20_4 Processing antitarget: p2-5_5 Processing antitarget: p2-20_1 Keeping 12455 of 12563 bins Keeping 12455 of 12563 bins Processing antitarget: p2-20_3 Processing antitarget: p2-9_2 Correcting for GC bias... Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Keeping 12455 of 12563 bins WARNING: Skipping correction for RepeatMasker bias Keeping 12455 of 12563 bins Keeping 12455 of 12563 bins Keeping 12455 of 12563 bins Correcting for GC bias... Keeping 12455 of 12563 bins Correcting for GC bias... Correcting for GC bias... 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 WARNING: Skipping correction for RepeatMasker bias WARNING: Skipping correction for RepeatMasker bias Targets are 1.09 x more variable than antitargets Targets are 2.60 x more variable than antitargets Targets are 1.43 x more variable than antitargets Targets are 1.75 x more variable than antitargets Targets are 1.14 x more variable than antitargets Targets are 1.14 x more variable than antitargets Wrote build/p2-20_2.cnr with 18763 regions Antitargets are 1.08 x more variable than targets Wrote build/p2-20_5.cnr with 18763 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf Wrote build/p2-20_1.cnr with 18763 regions Wrote build/p2-5_5.cnr with 18763 regions Wrote build/p2-20_4.cnr with 18763 regions Wrote build/p2-9_2.cnr with 18763 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns Wrote build/p2-20_3.cnr with 18763 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf python3 ../cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt python3 ../cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt Matplotlib created a temporary config/cache directory at /tmp/matplotlib-i72km4f5 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_4wt9v7o because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-quk8739m because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-5j6ljkki because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1okmbzje because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_k4l0yqi because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3nuq3vsn because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-hvj6wmbp because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-uqic2c1l because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-t4jli7q2 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3q0015_n because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-a19c26cs because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-u9xs1s1g because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rh091hq8 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0hiipd83 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Treating sample p2-20_2 as female 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 Treating sample p2-5_5 as female Treating sample p2-20_1 as female Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Selected test sample NA12882 and control sample NA12878 Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Treating sample p2-9_2 as female Loaded 3654 records; skipped: 514 somatic, 394 depth Kept 2631 heterozygous of 3654 VCF records Wrote p2-9_2.nexus Dropped 1 / 949 bins on chromosome chr6 Placed 705 variants into 18763 bins Wrote p2-9_2.nexus-ogt Wrote p2-all.cdt Wrote p2-all-jtv.txt Dropped 11 / 49 bins on chromosome chrY Dropped 7 / 49 bins on chromosome chrY Dropped 8 / 49 bins on chromosome chrY Wrote build/p2-20_3.cns with 74 regions Wrote build/p2-20_2.cns with 125 regions python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns Dropped 27 / 49 bins on chromosome chrY Wrote build/p2-5_5.cns with 71 regions 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/p2-20_2.cns build/p2-20_2.cnr -t 0.3 -o p2-20_2-both-diagram.pdf python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns Dropped 6 / 49 bins on chromosome chrY 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 python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-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 python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns python3 ../cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ --ci -b 50 -a 0.5 python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv Dropped 6 / 49 bins on chromosome chrY Wrote build/p2-9_2.cns with 107 regions Dropped 8 / 49 bins on chromosome chrY Wrote build/p2-20_5.cns with 129 regions python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -t --y-min=-2.5 -o p2-9_2-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c 'chr9:150000-45000000' -o p2-9_2-chr9p-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -g SMARCA2,PTPRD -w 4e6 -o p2-9_2-SMARCA2-PTPRD-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -l regions.bed -o p2-9_2-bed_regions-scatter.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf 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 python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt 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 call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input python3 ../cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ --mean --median --mode --t-test \ --stdev --mad --mse --iqr --bivar \ --ci --pi --sem --smooth-bootstrap python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vrrmy9_t because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2gtv4pxu because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-yk_y5z83 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fxs1imh6 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-h6_0pws7 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote build/p2-20_1.cns with 117 regions Matplotlib created a temporary config/cache directory at /tmp/matplotlib-130lo6eb because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-a1e23lgp because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-bxdrt144 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qyms2ret because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wiwmx1iv because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote build/p2-20_4.cns with 137 regions python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vje9347n because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns build/p2-20_1.cnr -t 0.3 -o p2-20_1-both-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-b9tu3229 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-nkp0nf5q because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-chouidii because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-a3gvo4h5 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-45vbesgl because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-cdnr0zk2 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-p8pjvrcn because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-f6joi162 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_4508r51 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-m4qfk9zr because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-skikoeh_ because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-jhxdh52t because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rdnepikk because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-kdmgzsik because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-uhr41cb5 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_2 as female Rescaling sample with purity 0.65, ploidy 2 Wrote p2-20_2-diagram.pdf Wrote build/p2-20_2.call.cns with 125 regions 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 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 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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-d8j69qo0 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Wrote p2-5_5-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-90_5k68x because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-5_5.call.cns with 71 regions Treating sample p2-5_5 as female Treating sample p2-20_2 as female 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_2 as female Treating sample p2-5_5 as female 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 metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv Wrote p2-5_5-metrics.tsv Wrote p2-5_5-cbs-diagram.pdf Wrote p2-20_1-diagram.pdf Wrote p2-20_2-cbs-diagram.pdf Showing 179 probes and 2 selected genes in region chr9:0-14504268 Detected file format: bed Treating sample p2-9_2 as female Rescaling sample with purity 0.65, ploidy 2 Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 Wrote build/p2-9_2.call.cns with 107 regions Treating sample p2-9_2 as female Showing 201 probes and 0 selected genes in region chr21 Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 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 Wrote p2-5_5-segmetrics.cns with 71 regions Matplotlib created a temporary config/cache directory at /tmp/matplotlib-b1syrzml because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Showing 1480 probes and 0 selected genes in region chr1 Treating sample p2-9_2 as female Wrote p2-9_2-cbs-diagram.pdf Treating sample p2-20_5 as female Rescaling sample with purity 0.65, ploidy 2 Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf Wrote build/p2-20_5.call.cns with 129 regions Matplotlib created a temporary config/cache directory at /tmp/matplotlib-m7gkpv7w because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Showing 330 probes and 13 selected genes in region chr9:149999-45000000 Treating sample p2-9_2 as female Wrote p2-9_2-metrics.tsv Wrote p2-9_2.theta2.input Found 15 gene breakpoints Wrote p2-9_2-breaks.txt Treating sample p2-20_1 as female Wrote p2-9_2-chr21-scatter.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-78dvyzi4 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-68rjgaqv because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3k92p8ru because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-20_1-cbs-diagram.pdf Wrote gender-picard.txt Wrote p2-9_2-chr9p-scatter.pdf Wrote p2-9_2-diagram.pdf Treating sample p2-20_1 as female Matplotlib created a temporary config/cache directory at /tmp/matplotlib-j6q4twgs because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Smoothing overshot at 3 / 97 indices: (-19.887157566382854, -3.337830278732133) vs. original (-19.2826, -0.27873000000000003) Wrote p2-9_2-chr1-scatter.pdf Wrote p2-all.seg Treating sample p2-5_5 as female Treating sample p2-9_2 as female Treating sample p2-20_1 as female Treating sample p2-20_2 as female Treating sample p2-20_3 as female Treating sample p2-20_4 as female Treating sample p2-20_5 as female Treating sample p2-20_4 as female Rescaling sample with purity 0.65, ploidy 2 Treating sample p2-20_1 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_4.call.cns with 137 regions Wrote build/p2-20_1.call.cns with 117 regions 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 Treating sample p2-9_2.call as female Found 53 gene-level gains and losses Wrote p2-9_2-genemetrics.txt Wrote p2-20-metrics.tsv Matplotlib created a temporary config/cache directory at /tmp/matplotlib-h989j882 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-9_2.vcf Wrote p2-5_5-scatter.pdf 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 heatmap-picard.pdf Wrote p2-9_2-scatter.pdf which pdfunite && pdfunite p2-5_5-scatter.pdf p2-9_2-scatter.pdf p2-9_2-chr1-scatter.pdf p2-9_2-chr21-scatter.pdf p2-9_2-chr9p-scatter.pdf p2-9_2-SMARCA2-PTPRD-scatter.pdf p2-9_2-bed_regions-scatter.pdf all-scatters.pdf || touch all-scatters.pdf /usr/bin/pdfunite Wrote p2-5_5-both-diagram.pdf Wrote p2-20_2-both-diagram.pdf Wrote p2-9_2-both-diagram.pdf Wrote p2-20_1-both-diagram.pdf which pdfunite && pdfunite p2-5_5-diagram.pdf p2-9_2-diagram.pdf p2-20_1-diagram.pdf p2-20_2-diagram.pdf p2-5_5-cbs-diagram.pdf p2-9_2-cbs-diagram.pdf p2-20_1-cbs-diagram.pdf p2-20_2-cbs-diagram.pdf p2-5_5-both-diagram.pdf p2-9_2-both-diagram.pdf p2-20_1-both-diagram.pdf p2-20_2-both-diagram.pdf all-diagrams.pdf || touch all-diagrams.pdf /usr/bin/pdfunite make[2]: Leaving directory '/build/cnvkit-73S0w1/cnvkit-0.9.8/test' cd test && /usr/bin/make -j32 clean || /bin/true make[2]: Entering directory '/build/cnvkit-73S0w1/cnvkit-0.9.8/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/build/cnvkit-73S0w1/cnvkit-0.9.8/test' rm -Rf test/build test/*.tsv make[1]: Leaving directory '/build/cnvkit-73S0w1/cnvkit-0.9.8' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/cnvkit-73S0w1/cnvkit-0.9.8' [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted install if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ mv ${script} cnvkit-${script%%.py}; \ done; \ fi dh_auto_install I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit running install running build running build_py running build_scripts running install_lib creating /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr creating /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib creating /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9 creating /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages creating /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/chromsort.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/intersect.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/subtract.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/__init__.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/combiners.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/merge.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/gary.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/subdivide.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/rangelabel.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome creating /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/textcoord.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/vcfio.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/__init__.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/seg.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/util.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/bedio.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/vcfsimple.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/gff.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/picard.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/genepred.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/seqdict.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/tab.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio creating /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/reference.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/heatmap.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/import_rna.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cnary.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/batch.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/smoothing.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/samutil.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/diagram.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/__init__.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/rna.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/descriptives.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/core.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/autobin.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/access.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/fix.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/metrics.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/vary.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/export.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/params.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/target.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/coverage.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cluster.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/commands.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/plots.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/scatter.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/_version.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmetrics.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/antitarget.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segfilters.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/bintest.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cmdutil.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/importers.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib creating /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/__init__.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/haar.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/none.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/flasso.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/hmm.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/cbs.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/parallel.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/reports.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /build/cnvkit-73S0w1/cnvkit-0.9.8/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/call.py -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/chromsort.py to chromsort.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/intersect.py to intersect.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/subtract.py to subtract.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/combiners.py to combiners.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/merge.py to merge.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/gary.py to gary.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/subdivide.py to subdivide.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/rangelabel.py to rangelabel.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/textcoord.py to textcoord.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/vcfio.py to vcfio.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/seg.py to seg.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/util.py to util.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/bedio.py to bedio.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/vcfsimple.py to vcfsimple.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/gff.py to gff.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/picard.py to picard.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/genepred.py to genepred.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/seqdict.py to seqdict.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/tab.py to tab.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/reference.py to reference.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/heatmap.py to heatmap.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/import_rna.py to import_rna.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cnary.py to cnary.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/batch.py to batch.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/smoothing.py to smoothing.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/samutil.py to samutil.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/diagram.py to diagram.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/rna.py to rna.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/descriptives.py to descriptives.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/core.py to core.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/autobin.py to autobin.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/access.py to access.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/fix.py to fix.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/metrics.py to metrics.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/vary.py to vary.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/export.py to export.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/params.py to params.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/target.py to target.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/coverage.py to coverage.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cluster.py to cluster.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/commands.py to commands.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/plots.py to plots.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/scatter.py to scatter.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/_version.py to _version.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmetrics.py to segmetrics.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/antitarget.py to antitarget.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segfilters.py to segfilters.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/bintest.py to bintest.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cmdutil.py to cmdutil.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/importers.py to importers.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/__init__.py to __init__.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/haar.py to haar.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/none.py to none.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/flasso.py to flasso.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/hmm.py to hmm.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/cbs.py to cbs.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/parallel.py to parallel.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/reports.py to reports.cpython-39.pyc byte-compiling /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/call.py to call.cpython-39.pyc running install_egg_info running egg_info creating CNVkit.egg-info writing CNVkit.egg-info/PKG-INFO writing dependency_links to CNVkit.egg-info/dependency_links.txt writing requirements to CNVkit.egg-info/requires.txt writing top-level names to CNVkit.egg-info/top_level.txt writing manifest file 'CNVkit.egg-info/SOURCES.txt' reading manifest file 'CNVkit.egg-info/SOURCES.txt' writing manifest file 'CNVkit.egg-info/SOURCES.txt' Copying CNVkit.egg-info to /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/lib/python3.9/dist-packages/CNVkit-0.9.8.egg-info Skipping SOURCES.txt running install_scripts creating /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_annotate -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-reference2targets -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-guess_baits -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_expression_correlate -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/snpfilter.sh -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_updater -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-skg_convert -> /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin changing mode of /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 755 changing mode of /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit to 755 changing mode of /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-reference2targets to 755 changing mode of /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-guess_baits to 755 changing mode of /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 755 changing mode of /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin/snpfilter.sh to 755 changing mode of /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 755 changing mode of /build/cnvkit-73S0w1/cnvkit-0.9.8/debian/cnvkit/usr/bin/cnvkit-skg_convert to 755 help2man --no-info --version-option=version \ --name="a command-line toolkit for copy number analysis." \ ./cnvkit > debian/cnvkit.1 PYTHONPATH=$PYTHONPATH:. debian/genmanpages.py 0.9.8 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xf5c2or7 because the default path (/nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. cd scripts && PYTHONPATH=../ help2man --no-info \ --version-string=0.9.8 --help-option='-h' \ ./cnvkit-reference2targets --name='Extract target and antitarget BED files from a CNVkit reference file.' \ > ../debian/cnvkit-reference2targets.1; cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py make[1]: Leaving directory '/build/cnvkit-73S0w1/cnvkit-0.9.8' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_installexamples -a -O--buildsystem=pybuild dh_installman -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -a -O--buildsystem=pybuild dh_strip -a -a -O--buildsystem=pybuild dh_makeshlibs -a -a -O--buildsystem=pybuild dh_shlibdeps -a -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'cnvkit' in '../cnvkit_0.9.8-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../cnvkit_0.9.8-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/cnvkit-73S0w1 /tmp/cnvkit-0.9.8-18nu_4iwu I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.KYnJohBBC8... I: success in 753.3497 seconds md5: cnvkit_0.9.8-1_amd64.deb: OK sha1: cnvkit_0.9.8-1_amd64.deb: OK sha256: cnvkit_0.9.8-1_amd64.deb: OK Checksums: OK