I: pbuilder: network access will be disabled during build I: Current time: Sun May 21 19:20:29 +14 2023 I: pbuilder-time-stamp: 1684646429 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [cnvkit_0.9.9-2.dsc] I: copying [./cnvkit_0.9.9.orig.tar.gz] I: copying [./cnvkit_0.9.9-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Oct 15 20:51:53 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.9-2.dsc: no acceptable signature found dpkg-source: info: extracting cnvkit in cnvkit-0.9.9 dpkg-source: info: unpacking cnvkit_0.9.9.orig.tar.gz dpkg-source: info: unpacking cnvkit_0.9.9-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-py-ext dpkg-source: info: applying python3compat.patch dpkg-source: info: applying spelling dpkg-source: info: applying controldir I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1491079/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 21 19:20 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1491079/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1491079/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=882c3ef5c74f496fb42a72b686766d15 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1491079 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Qf497ie2/pbuilderrc_ckGR --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Qf497ie2/b2 --logfile b2/build.log --extrapackages usrmerge cnvkit_0.9.9-2.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 May 21 19:20 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/1491079/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-pyfaidx, help2man, python3-biopython, python3-pandas, python3-numpy, python3-pysam, python3-scipy, python3-matplotlib, python3-pyvcf, python3-future, python3-pomegranate, r-bioc-dnacopy, poppler-utils dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pyvcf; however: Package python3-pyvcf is not installed. pbuilder-satisfydepends-dummy depends on python3-future; however: Package python3-future is not installed. pbuilder-satisfydepends-dummy depends on python3-pomegranate; however: Package python3-pomegranate is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-dnacopy; however: Package r-bioc-dnacopy is not installed. pbuilder-satisfydepends-dummy depends on poppler-utils; however: Package poppler-utils is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lyx{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcurl3-gnutls{a} libcurl4{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhts3{a} libhtscodecs2{a} libice6{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpoppler126{a} libproc2-0{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsm6{a} libssh2-1{a} libsub-override-perl{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libxt6{a} libyaml-0-2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} openssl{a} po-debconf{a} poppler-utils{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-beniget{a} python3-biopython{a} python3-brotli{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-fonttools{a} python3-fs{a} python3-future{a} python3-gast{a} python3-joblib{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-ply{a} python3-pomegranate{a} python3-pyfaidx{a} python3-pyparsing{a} python3-pysam{a} python3-pythran{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-vcf{a} python3-yaml{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} r-base-core{a} r-bioc-biocgenerics{a} r-bioc-dnacopy{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} ucf{a} unicode-data{a} unzip{a} w3c-sgml-lib{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl isympy-common javascript-common libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx ncbi-blast+ poppler-data psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-gdal python3-html5lib python3-jinja2 python3-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-psutil python3-pydot python3-pygraphviz python3-pytest python3-simplejson python3-tables r-base-dev r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 210 newly installed, 0 to remove and 0 not upgraded. Need to get 184 MB of archives. After unpacking 853 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 14 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-9 [386 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-1+b1 [189 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libpoppler126 amd64 22.12.0-2+b1 [1852 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.1 [99.2 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.1 [109 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 poppler-utils amd64 22.12.0-2+b1 [192 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 154 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get: 157 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get: 160 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get: 161 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-3 [98.3 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+b1 [74.4 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B] Get: 175 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-3 [30.1 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 python3-future all 0.18.2-6 [348 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 python3-joblib all 1.2.0-4 [211 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 python3-networkx all 2.8.8-1 [1425 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 python3-yaml amd64 6.0-3+b2 [119 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 python3-pomegranate amd64 0.14.8-3+b1 [2509 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 python3-pyfaidx all 0.7.1-2 [28.0 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 python3-vcf amd64 0.6.8+git20170215.476169c-9+b1 [43.1 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get: 206 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocgenerics all 0.44.0-2 [600 kB] Get: 210 http://deb.debian.org/debian bookworm/main amd64 r-bioc-dnacopy amd64 1.72.3-1 [377 kB] Fetched 184 MB in 6s (32.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19596 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19926 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.70+nmu1_all.deb ... Unpacking mailcap (3.70+nmu1) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../5-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20384 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.0.8-1_amd64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../008-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../011-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../014-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package ucf. Preparing to unpack .../016-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../017-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../018-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../019-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../020-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../021-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../022-libtcl8.6_8.6.13+dfsg-2_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.13+dfsg-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../023-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../024-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../025-libfreetype6_2.12.1+dfsg-5_amd64.deb ... Unpacking libfreetype6:amd64 (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../026-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package libfontenc1:amd64. Preparing to unpack .../027-libfontenc1_1%3a1.1.4-1_amd64.deb ... Unpacking libfontenc1:amd64 (1:1.1.4-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../028-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../029-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../030-xfonts-utils_1%3a7.7+6_amd64.deb ... Unpacking xfonts-utils (1:7.7+6) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../031-fonts-urw-base35_20200910-7_all.deb ... Unpacking fonts-urw-base35 (20200910-7) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../032-fontconfig-config_2.14.1-4_amd64.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../033-libfontconfig1_2.14.1-4_amd64.deb ... Unpacking libfontconfig1:amd64 (2.14.1-4) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../034-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../035-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../036-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../037-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../038-libx11-data_2%3a1.8.4-2_all.deb ... Unpacking libx11-data (2:1.8.4-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../039-libx11-6_2%3a1.8.4-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.4-2) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../040-libxrender1_1%3a0.9.10-1.1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../041-libxft2_2.3.6-1_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../042-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../043-libxss1_1%3a1.2.3-1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../044-libtk8.6_8.6.13-2_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.13-2) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../045-tk8.6-blt2.5_2.5.3+dfsg-4.1_amd64.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Selecting previously unselected package blt. Preparing to unpack .../046-blt_2.5.3+dfsg-4.1_amd64.deb ... Unpacking blt (2.5.3+dfsg-4.1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../047-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../048-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../049-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../050-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../051-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../052-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../053-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../054-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../055-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../056-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../057-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../058-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../059-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../060-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../061-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../062-python3-lib2to3_3.11.2-3_all.deb ... Unpacking python3-lib2to3 (3.11.2-3) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../063-python3-distutils_3.11.2-3_all.deb ... Unpacking python3-distutils (3.11.2-3) ... Selecting previously unselected package dh-python. Preparing to unpack .../064-dh-python_5.20230130_all.deb ... Unpacking dh-python (5.20230130) ... Selecting previously unselected package fontconfig. Preparing to unpack .../065-fontconfig_2.14.1-4_amd64.deb ... Unpacking fontconfig (2.14.1-4) ... Selecting previously unselected package fonts-lyx. Preparing to unpack .../066-fonts-lyx_2.3.7-1_all.deb ... Unpacking fonts-lyx (2.3.7-1) ... Selecting previously unselected package help2man. Preparing to unpack .../067-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../068-libblas3_3.11.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2) ... Selecting previously unselected package libboost1.74-dev:amd64. Preparing to unpack .../069-libboost1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../070-libboost-dev_1.74.0.3_amd64.deb ... Unpacking libboost-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../071-libpixman-1-0_0.42.2-1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.42.2-1) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../072-libxcb-render0_1.15-1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.15-1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../073-libxcb-shm0_1.15-1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.15-1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../074-libcairo2_1.16.0-7_amd64.deb ... Unpacking libcairo2:amd64 (1.16.0-7) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../075-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../076-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../077-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../078-libnghttp2-14_1.52.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../079-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../080-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../081-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../082-libcurl3-gnutls_7.88.1-9_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.88.1-9) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../083-libcurl4_7.88.1-9_amd64.deb ... Unpacking libcurl4:amd64 (7.88.1-9) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../084-libdatrie1_0.2.13-2+b1_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.13-2+b1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../085-libdeflate0_1.14-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../086-libexpat1-dev_2.5.0-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.5.0-1) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../087-libfribidi0_1.0.8-2.1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.8-2.1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../088-libgfortran5_12.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (12.2.0-14) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../089-libglib2.0-0_2.74.6-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.74.6-2) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../090-libgraphite2-3_1.3.14-1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../091-libharfbuzz0b_6.0.0+dfsg-3_amd64.deb ... Unpacking libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../092-libhtscodecs2_1.3.0-4_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.3.0-4) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../093-libhts3_1.16+ds-3_amd64.deb ... Unpacking libhts3:amd64 (1.16+ds-3) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../094-libice6_2%3a1.0.10-1_amd64.deb ... Unpacking libice6:amd64 (2:1.0.10-1) ... Selecting previously unselected package libimagequant0:amd64. Preparing to unpack .../095-libimagequant0_2.17.0-1_amd64.deb ... Unpacking libimagequant0:amd64 (2.17.0-1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../096-libjbig0_2.1-6.1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../097-libjpeg62-turbo_1%3a2.1.5-2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-2) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../098-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../099-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../100-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../101-libjs-sphinxdoc_5.3.0-4_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-4) ... Selecting previously unselected package libopenblas0-pthread:amd64. Preparing to unpack .../102-libopenblas0-pthread_0.3.21+ds-4_amd64.deb ... Unpacking libopenblas0-pthread:amd64 (0.3.21+ds-4) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../103-liblapack3_3.11.0-2_amd64.deb ... Unpacking liblapack3:amd64 (3.11.0-2) ... Selecting previously unselected package liblbfgsb0:amd64. Preparing to unpack .../104-liblbfgsb0_3.0+dfsg.4-1_amd64.deb ... Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../105-liblcms2-2_2.14-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.14-2) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../106-liblerc4_4.0.0+ds-2_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-2) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../107-libnspr4_2%3a4.35-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.35-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../108-libnss3_2%3a3.87.1-1_amd64.deb ... Unpacking libnss3:amd64 (2:3.87.1-1) ... Selecting previously unselected package libopenblas0:amd64. Preparing to unpack .../109-libopenblas0_0.3.21+ds-4_amd64.deb ... Unpacking libopenblas0:amd64 (0.3.21+ds-4) ... Selecting previously unselected package libopenblas-pthread-dev:amd64. Preparing to unpack .../110-libopenblas-pthread-dev_0.3.21+ds-4_amd64.deb ... Unpacking libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... Selecting previously unselected package libopenblas-dev:amd64. Preparing to unpack .../111-libopenblas-dev_0.3.21+ds-4_amd64.deb ... Unpacking libopenblas-dev:amd64 (0.3.21+ds-4) ... Selecting previously unselected package libopenjp2-7:amd64. Preparing to unpack .../112-libopenjp2-7_2.5.0-1+b1_amd64.deb ... Unpacking libopenjp2-7:amd64 (2.5.0-1+b1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../113-libthai-data_0.1.29-1_all.deb ... Unpacking libthai-data (0.1.29-1) ... Selecting previously unselected package libthai0:amd64. Preparing to unpack .../114-libthai0_0.1.29-1_amd64.deb ... Unpacking libthai0:amd64 (0.1.29-1) ... Selecting previously unselected package libpango-1.0-0:amd64. Preparing to unpack .../115-libpango-1.0-0_1.50.12+ds-1_amd64.deb ... Unpacking libpango-1.0-0:amd64 (1.50.12+ds-1) ... Selecting previously unselected package libpangoft2-1.0-0:amd64. Preparing to unpack .../116-libpangoft2-1.0-0_1.50.12+ds-1_amd64.deb ... Unpacking libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Selecting previously unselected package libpangocairo-1.0-0:amd64. Preparing to unpack .../117-libpangocairo-1.0-0_1.50.12+ds-1_amd64.deb ... Unpacking libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Selecting previously unselected package libpaper1:amd64. Preparing to unpack .../118-libpaper1_1.1.29_amd64.deb ... Unpacking libpaper1:amd64 (1.1.29) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../119-libpaper-utils_1.1.29_amd64.deb ... Unpacking libpaper-utils (1.1.29) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../120-libwebp7_1.2.4-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.2.4-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../121-libtiff6_4.5.0-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.0-5) ... Selecting previously unselected package libpoppler126:amd64. Preparing to unpack .../122-libpoppler126_22.12.0-2+b1_amd64.deb ... Unpacking libpoppler126:amd64 (22.12.0-2+b1) ... Selecting previously unselected package libpython3.11:amd64. Preparing to unpack .../123-libpython3.11_3.11.2-6_amd64.deb ... Unpacking libpython3.11:amd64 (3.11.2-6) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../124-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libpython3.11-dev:amd64. Preparing to unpack .../125-libpython3.11-dev_3.11.2-6_amd64.deb ... Unpacking libpython3.11-dev:amd64 (3.11.2-6) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../126-libpython3-dev_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.11.2-1+b1) ... Selecting previously unselected package libpython3-all-dev:amd64. Preparing to unpack .../127-libpython3-all-dev_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-all-dev:amd64 (3.11.2-1+b1) ... Selecting previously unselected package libqhull-r8.0:amd64. Preparing to unpack .../128-libqhull-r8.0_2020.2-5_amd64.deb ... Unpacking libqhull-r8.0:amd64 (2020.2-5) ... Selecting previously unselected package libraqm0:amd64. Preparing to unpack .../129-libraqm0_0.7.0-4.1_amd64.deb ... Unpacking libraqm0:amd64 (0.7.0-4.1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../130-libsm6_2%3a1.2.3-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.3-1) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../131-libwebpdemux2_1.2.4-0.1_amd64.deb ... Unpacking libwebpdemux2:amd64 (1.2.4-0.1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../132-libwebpmux3_1.2.4-0.1_amd64.deb ... Unpacking libwebpmux3:amd64 (1.2.4-0.1) ... Selecting previously unselected package libxsimd-dev:amd64. Preparing to unpack .../133-libxsimd-dev_8.1.0-7_amd64.deb ... Unpacking libxsimd-dev:amd64 (8.1.0-7) ... Selecting previously unselected package libxslt1.1:amd64. Preparing to unpack .../134-libxslt1.1_1.1.35-1_amd64.deb ... Unpacking libxslt1.1:amd64 (1.1.35-1) ... Selecting previously unselected package libxt6:amd64. Preparing to unpack .../135-libxt6_1%3a1.2.1-1.1_amd64.deb ... Unpacking libxt6:amd64 (1:1.2.1-1.1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../136-libyaml-0-2_0.2.5-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1) ... Selecting previously unselected package poppler-utils. Preparing to unpack .../137-poppler-utils_22.12.0-2+b1_amd64.deb ... Unpacking poppler-utils (22.12.0-2+b1) ... Selecting previously unselected package python-matplotlib-data. Preparing to unpack .../138-python-matplotlib-data_3.6.3-1_all.deb ... Unpacking python-matplotlib-data (3.6.3-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../139-python3-all_3.11.2-1+b1_amd64.deb ... Unpacking python3-all (3.11.2-1+b1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../140-python3.11-dev_3.11.2-6_amd64.deb ... Unpacking python3.11-dev (3.11.2-6) ... Selecting previously unselected package python3-dev. Preparing to unpack .../141-python3-dev_3.11.2-1+b1_amd64.deb ... Unpacking python3-dev (3.11.2-1+b1) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../142-python3-all-dev_3.11.2-1+b1_amd64.deb ... Unpacking python3-all-dev (3.11.2-1+b1) ... Selecting previously unselected package python3-appdirs. Preparing to unpack .../143-python3-appdirs_1.4.4-3_all.deb ... Unpacking python3-appdirs (1.4.4-3) ... Selecting previously unselected package python3-attr. Preparing to unpack .../144-python3-attr_22.2.0-1_all.deb ... Unpacking python3-attr (22.2.0-1) ... Selecting previously unselected package python3-gast. Preparing to unpack .../145-python3-gast_0.5.2-2_all.deb ... Unpacking python3-gast (0.5.2-2) ... Selecting previously unselected package python3-beniget. Preparing to unpack .../146-python3-beniget_0.4.1-3_all.deb ... Unpacking python3-beniget (0.4.1-3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../147-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../148-python3-numpy_1%3a1.24.2-1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1) ... Selecting previously unselected package python3-renderpm:amd64. Preparing to unpack .../149-python3-renderpm_3.6.12-1+b1_amd64.deb ... Unpacking python3-renderpm:amd64 (3.6.12-1+b1) ... Selecting previously unselected package python3-reportlab-accel:amd64. Preparing to unpack .../150-python3-reportlab-accel_3.6.12-1+b1_amd64.deb ... Unpacking python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Selecting previously unselected package python3-tk:amd64. Preparing to unpack .../151-python3-tk_3.11.2-3_amd64.deb ... Unpacking python3-tk:amd64 (3.11.2-3) ... Selecting previously unselected package python3-pil.imagetk:amd64. Preparing to unpack .../152-python3-pil.imagetk_9.4.0-1.1+b1_amd64.deb ... Unpacking python3-pil.imagetk:amd64 (9.4.0-1.1+b1) ... Selecting previously unselected package python3-pil:amd64. Preparing to unpack .../153-python3-pil_9.4.0-1.1+b1_amd64.deb ... Unpacking python3-pil:amd64 (9.4.0-1.1+b1) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../154-python3-reportlab_3.6.12-1_all.deb ... Unpacking python3-reportlab (3.6.12-1) ... Selecting previously unselected package xml-core. Preparing to unpack .../155-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../156-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../157-python3-biopython_1.80+dfsg-4+b1_amd64.deb ... Unpacking python3-biopython (1.80+dfsg-4+b1) ... Selecting previously unselected package python3-brotli. Preparing to unpack .../158-python3-brotli_1.0.9-2+b6_amd64.deb ... Unpacking python3-brotli (1.0.9-2+b6) ... Selecting previously unselected package python3-contourpy. Preparing to unpack .../159-python3-contourpy_1.0.7-1+b1_amd64.deb ... Unpacking python3-contourpy (1.0.7-1+b1) ... Selecting previously unselected package python3-cycler. Preparing to unpack .../160-python3-cycler_0.11.0-1_all.deb ... Unpacking python3-cycler (0.11.0-1) ... Selecting previously unselected package python3-six. Preparing to unpack .../161-python3-six_1.16.0-4_all.deb ... Unpacking python3-six (1.16.0-4) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../162-python3-dateutil_2.8.2-2_all.deb ... Unpacking python3-dateutil (2.8.2-2) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../163-python3-decorator_5.1.1-3_all.deb ... Unpacking python3-decorator (5.1.1-3) ... Selecting previously unselected package python3-ply. Preparing to unpack .../164-python3-ply_3.11-5_all.deb ... Unpacking python3-ply (3.11-5) ... Selecting previously unselected package python3-pythran. Preparing to unpack .../165-python3-pythran_0.11.0+ds-7_amd64.deb ... Unpacking python3-pythran (0.11.0+ds-7) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../166-python3-scipy_1.10.1-2_amd64.deb ... Unpacking python3-scipy (1.10.1-2) ... Selecting previously unselected package python3-ufolib2. Preparing to unpack .../167-python3-ufolib2_0.14.0+dfsg1-1_all.deb ... Unpacking python3-ufolib2 (0.14.0+dfsg1-1) ... Selecting previously unselected package python3-mpmath. Preparing to unpack .../168-python3-mpmath_1.2.1-2_all.deb ... Unpacking python3-mpmath (1.2.1-2) ... Selecting previously unselected package python3-sympy. Preparing to unpack .../169-python3-sympy_1.11.1-1_all.deb ... Unpacking python3-sympy (1.11.1-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../170-python3-tz_2022.7.1-3_all.deb ... Unpacking python3-tz (2022.7.1-3) ... Selecting previously unselected package python3-fs. Preparing to unpack .../171-python3-fs_2.4.16-2_all.deb ... Unpacking python3-fs (2.4.16-2) ... Selecting previously unselected package python3-lxml:amd64. Preparing to unpack .../172-python3-lxml_4.9.2-1+b1_amd64.deb ... Unpacking python3-lxml:amd64 (4.9.2-1+b1) ... Selecting previously unselected package python3-lz4. Preparing to unpack .../173-python3-lz4_4.0.2+dfsg-1+b2_amd64.deb ... Unpacking python3-lz4 (4.0.2+dfsg-1+b2) ... Selecting previously unselected package unicode-data. Preparing to unpack .../174-unicode-data_15.0.0-1_all.deb ... Unpacking unicode-data (15.0.0-1) ... Selecting previously unselected package python3-fonttools. Preparing to unpack .../175-python3-fonttools_4.38.0-1+b1_amd64.deb ... Unpacking python3-fonttools (4.38.0-1+b1) ... Selecting previously unselected package python3-future. Preparing to unpack .../176-python3-future_0.18.2-6_all.deb ... Unpacking python3-future (0.18.2-6) ... Selecting previously unselected package python3-joblib. Preparing to unpack .../177-python3-joblib_1.2.0-4_all.deb ... Unpacking python3-joblib (1.2.0-4) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../178-python3-kiwisolver_1.4.4-1+b1_amd64.deb ... Unpacking python3-kiwisolver (1.4.4-1+b1) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../179-python3-pyparsing_3.0.9-1_all.deb ... Unpacking python3-pyparsing (3.0.9-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../180-python3-packaging_23.0-1_all.deb ... Unpacking python3-packaging (23.0-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../181-python3-matplotlib_3.6.3-1+b1_amd64.deb ... Unpacking python3-matplotlib (3.6.3-1+b1) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../182-python3-networkx_2.8.8-1_all.deb ... Unpacking python3-networkx (2.8.8-1) ... Selecting previously unselected package python3-pandas-lib:amd64. Preparing to unpack .../183-python3-pandas-lib_1.5.3+dfsg-2_amd64.deb ... Unpacking python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../184-python3-pandas_1.5.3+dfsg-2_all.deb ... Unpacking python3-pandas (1.5.3+dfsg-2) ... Selecting previously unselected package python3-yaml. Preparing to unpack .../185-python3-yaml_6.0-3+b2_amd64.deb ... Unpacking python3-yaml (6.0-3+b2) ... Selecting previously unselected package python3-pomegranate. Preparing to unpack .../186-python3-pomegranate_0.14.8-3+b1_amd64.deb ... Unpacking python3-pomegranate (0.14.8-3+b1) ... Selecting previously unselected package python3-pyfaidx. Preparing to unpack .../187-python3-pyfaidx_0.7.1-2_all.deb ... Unpacking python3-pyfaidx (0.7.1-2) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../188-python3-pysam_0.20.0+ds-3+b1_amd64.deb ... Unpacking python3-pysam (0.20.0+ds-3+b1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../189-python3-setuptools_66.1.1-1_all.deb ... Unpacking python3-setuptools (66.1.1-1) ... Selecting previously unselected package python3-vcf. Preparing to unpack .../190-python3-vcf_0.6.8+git20170215.476169c-9+b1_amd64.deb ... Unpacking python3-vcf (0.6.8+git20170215.476169c-9+b1) ... Selecting previously unselected package zip. Preparing to unpack .../191-zip_3.0-13_amd64.deb ... Unpacking zip (3.0-13) ... Selecting previously unselected package unzip. Preparing to unpack .../192-unzip_6.0-28_amd64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../193-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../194-r-base-core_4.2.2.20221110-2_amd64.deb ... Unpacking r-base-core (4.2.2.20221110-2) ... Selecting previously unselected package r-bioc-biocgenerics. Preparing to unpack .../195-r-bioc-biocgenerics_0.44.0-2_all.deb ... Unpacking r-bioc-biocgenerics (0.44.0-2) ... Selecting previously unselected package r-bioc-dnacopy. Preparing to unpack .../196-r-bioc-dnacopy_1.72.3-1_amd64.deb ... Unpacking r-bioc-dnacopy (1.72.3-1) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.14-2) ... Setting up libpixman-1-0:amd64 (0.42.2-1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libdatrie1:amd64 (0.2.13-2+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libglib2.0-0:amd64 (2.74.6-2) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.7-1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libqhull-r8.0:amd64 (2020.2-5) ... Setting up file (1:5.44-3) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:amd64 (8.1.0-7) ... Setting up zip (3.0-13) ... Setting up libfontenc1:amd64 (1:1.1.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libnspr4:amd64 (2:4.35-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.2.4-0.1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:amd64 (4.5.0-5) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libopenjp2-7:amd64 (2.5.0-1+b1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libthai-data (0.1.29-1) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up sgml-base (1.31) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.0.8-1) ... Setting up libwebpmux3:amd64 (1.2.4-0.1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up mailcap (3.70+nmu1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up liblocale-gettext-perl (1.07-5) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up mime-support (3.66) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libwebpdemux2:amd64 (1.2.4-0.1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libcurl4:amd64 (7.88.1-9) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-9) ... Setting up libpaper-utils (1.1.29) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libpoppler126:amd64 (22.12.0-2+b1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up poppler-utils (22.12.0-2+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up python3-tz (2022.7.1-3) ... Setting up python3-six (1.16.0-4) ... Setting up python3-pil:amd64 (9.4.0-1.1+b1) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Setting up r-base-core (4.2.2.20221110-2) ... Creating config file /etc/R/Renviron with new version Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-lxml:amd64 (4.9.2-1+b1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130) ... Setting up python3-pyfaidx (0.7.1-2) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up r-bioc-biocgenerics (0.44.0-2) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3-renderpm:amd64 (3.6.12-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-joblib (1.2.0-4) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3.11-dev (3.11.2-6) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3-ply (3.11-5) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-yaml (6.0-3+b2) ... Setting up python3-tk:amd64 (3.11.2-3) ... Setting up python3-networkx (2.8.8-1) ... Setting up python3-vcf (0.6.8+git20170215.476169c-9+b1) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up python3-pil.imagetk:amd64 (9.4.0-1.1+b1) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up r-bioc-dnacopy (1.72.3-1) ... Setting up python3-contourpy (1.0.7-1+b1) ... Setting up python3-future (0.18.2-6) ... update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode Setting up python3-all-dev (3.11.2-1+b1) ... Setting up python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up python3-scipy (1.10.1-2) ... Setting up python3-pomegranate (0.14.8-3+b1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/1491079/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/1491079/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/cnvkit-0.9.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../cnvkit_0.9.9-2_source.changes dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.9-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/cnvkit-0.9.9' cd test && /usr/bin/make clean || /bin/true make[2]: Entering directory '/build/cnvkit-0.9.9/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/build/cnvkit-0.9.9/test' if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi dh_auto_clean I: pybuild base:240: python3.11 setup.py clean running clean removing '/build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -rf test/p2-20-metrics.tsv test/p2-5_5-metrics.tsv test/p2-9_2-metrics.tsv rm -rf test/build CNVkit.egg-info make[1]: Leaving directory '/build/cnvkit-0.9.9' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/cnvkit-0.9.9' [ -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:240: /usr/bin/python3 setup.py build running build running build_py creating /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/commands.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/vary.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/target.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/smoothing.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/segmetrics.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/segfilters.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/scatter.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/samutil.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/rna.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/reports.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/reference.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/plots.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/params.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/parallel.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/metrics.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/importers.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/import_rna.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/heatmap.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/fix.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/export.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/diagram.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/descriptives.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/coverage.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/core.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/cnary.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/cmdutil.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/cluster.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/call.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/bintest.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/batch.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/autobin.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/antitarget.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/access.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/_version.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib copying cnvlib/__init__.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib creating /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/none.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation creating /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome copying skgenome/subtract.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome copying skgenome/subdivide.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome copying skgenome/rangelabel.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome copying skgenome/merge.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome copying skgenome/intersect.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome copying skgenome/gary.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome copying skgenome/combiners.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome copying skgenome/chromsort.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome copying skgenome/__init__.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome creating /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfio.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/util.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/textcoord.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/tab.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/seqdict.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/seg.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/picard.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/gff.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/genepred.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/bedio.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio copying skgenome/tabio/__init__.py -> /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio running build_scripts creating build creating build/scripts-3.11 copying and adjusting /build/cnvkit-0.9.9/cnvkit -> build/scripts-3.11 copying and adjusting /build/cnvkit-0.9.9/scripts/cnvkit-skg_convert -> build/scripts-3.11 copying and adjusting /build/cnvkit-0.9.9/scripts/cnvkit-reference2targets -> build/scripts-3.11 copying and adjusting /build/cnvkit-0.9.9/scripts/cnvkit-guess_baits -> build/scripts-3.11 copying and adjusting /build/cnvkit-0.9.9/scripts/cnvkit-genome_instability_index -> build/scripts-3.11 copying and adjusting /build/cnvkit-0.9.9/scripts/cnvkit-cnv_updater -> build/scripts-3.11 copying and adjusting /build/cnvkit-0.9.9/scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.11 copying and adjusting /build/cnvkit-0.9.9/scripts/cnvkit-cnv_annotate -> build/scripts-3.11 copying /build/cnvkit-0.9.9/scripts/snpfilter.sh -> build/scripts-3.11 changing mode of build/scripts-3.11/cnvkit from 644 to 755 changing mode of build/scripts-3.11/cnvkit-skg_convert from 644 to 755 changing mode of build/scripts-3.11/cnvkit-reference2targets from 644 to 755 changing mode of build/scripts-3.11/cnvkit-guess_baits from 644 to 755 changing mode of build/scripts-3.11/cnvkit-genome_instability_index from 644 to 755 changing mode of build/scripts-3.11/cnvkit-cnv_updater from 644 to 755 changing mode of build/scripts-3.11/cnvkit-cnv_expression_correlate from 644 to 755 changing mode of build/scripts-3.11/cnvkit-cnv_annotate from 644 to 755 cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py make[1]: Leaving directory '/build/cnvkit-0.9.9' debian/rules override_dh_auto_test make[1]: Entering directory '/build/cnvkit-0.9.9' cd test && /usr/bin/make make[2]: Entering directory '/build/cnvkit-0.9.9/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/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0i14cdk9 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Created directory build/ Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-gwx0yg_o because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories 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... /build/cnvkit-0.9.9/cnvlib/reference.py:149: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. ref_df = ref_df.append(anti_ref_df, ignore_index=True, sort=False) 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-csve24gj because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-5_5 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-5_5 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) Targets are 1.14 x more variable than antitargets Wrote build/p2-5_5.cnr with 18763 regions python3 ../cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-y7ozoxmq because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zycuyp99 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-jzsf8uv2 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-9_2 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-9_2 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) Targets are 1.75 x more variable than antitargets Wrote build/p2-9_2.cnr with 18763 regions python3 ../cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-dnlnj88g because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-984b18po because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_ousdsy8 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-20_1 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_1 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) Targets are 1.14 x more variable than antitargets Wrote build/p2-20_1.cnr with 18763 regions python3 ../cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ar4nw_fh because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-law1qox7 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-m6347o19 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-20_2 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_2 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) Targets are 1.09 x more variable than antitargets Wrote build/p2-20_2.cnr with 18763 regions python3 ../cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-x5njw0w1 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-eai_qoxw because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py fix build/p2-20_3.targetcoverage.cnn build/p2-20_3.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_3.cnr /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1jupgjp3 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-20_3 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_3 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) Antitargets are 1.08 x more variable than targets Wrote build/p2-20_3.cnr with 18763 regions python3 ../cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-sa3fxek3 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-siseeeg6 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-26cznrr2 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-20_4 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_4 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) Targets are 1.43 x more variable than antitargets Wrote build/p2-20_4.cnr with 18763 regions 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-m0dfnzr9 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Processing target: p2-20_5 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_5 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) /build/cnvkit-0.9.9/skgenome/gary.py:484: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. self.data = self.data.append(other.data, ignore_index=True) Targets are 2.60 x more variable than antitargets Wrote build/p2-20_5.cnr with 18763 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fp9mtc5w because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 8 / 49 bins on chromosome chrY Wrote build/p2-5_5.cns with 71 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-261cvj09 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 1 / 949 bins on chromosome chr6 Dropped 27 / 49 bins on chromosome chrY Wrote build/p2-9_2.cns with 107 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-cap79u30 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 6 / 49 bins on chromosome chrY Wrote build/p2-20_1.cns with 117 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_o4qqkzs because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 7 / 49 bins on chromosome chrY Wrote build/p2-20_2.cns with 125 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-a3wre7o1 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 11 / 49 bins on chromosome chrY Wrote build/p2-20_3.cns with 74 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-hbnb5kew because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 8 / 49 bins on chromosome chrY Wrote build/p2-20_4.cns with 137 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-zxk9pjx5 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 6 / 49 bins on chromosome chrY Wrote build/p2-20_5.cns with 129 regions 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-03czubzk because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote p2-5_5-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -t --y-min=-2.5 -o p2-9_2-scatter.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-55a_z3r0 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Smoothing overshot at 3 / 97 indices: (-19.88715756638286, -3.337830278732127) vs. original (-19.2826, -0.27873) Wrote 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-unu9pzay because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Showing 1480 probes and 0 selected genes in region chr1 Wrote 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-h588peqx because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Showing 201 probes and 0 selected genes in region chr21 Wrote 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-v7op0elf because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Showing 330 probes and 13 selected genes in region chr9:149999-45000000 Wrote 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-812u3u0s because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Showing 179 probes and 2 selected genes in region chr9:0-14504268 Wrote 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ojqd7yjt because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Detected file format: bed Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 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 python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-k6rtbrh9 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-5_5 as female /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): Wrote p2-5_5-diagram.pdf python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2g8vx1oy because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2 as female /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): Wrote p2-9_2-diagram.pdf python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-qq2li07l because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_1 as female /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): Wrote p2-20_1-diagram.pdf python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wbi8_tmx because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_2 as female /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): Wrote p2-20_2-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-4k_zfc2u because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-5_5 as female Wrote p2-5_5-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-4tzp_adv because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2 as female Wrote p2-9_2-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7yeyrgp4 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_1 as female Wrote p2-20_1-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-4vtuiv_u because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_2 as female Wrote p2-20_2-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3nuvqxrn because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-5_5 as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): Wrote p2-5_5-both-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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-b98t1c3d because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2 as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): Wrote p2-9_2-both-diagram.pdf 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xrcg5vnh because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_1 as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): Wrote p2-20_1-both-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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-74uryuxl because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_2 as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): Wrote p2-20_2-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 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-n4i0ovws because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories 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 Wrote heatmap-picard.pdf python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-67_gru0l because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Found 15 gene breakpoints Wrote 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-g0if41_3 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2 as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): /build/cnvkit-0.9.9/skgenome/gary.py:692: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead. for idx, genestr in self.data['gene'].iteritems(): Found 345 gene-level gains and losses Wrote p2-9_2-genemetrics.txt python3 ../cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-51elnjdt because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote gender-picard.txt 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-czly4hns because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-csw877am because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote p2-all-jtv.txt python3 ../cnvkit.py export seg build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-all.seg /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-us4eg2hz because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote p2-all.seg python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-c9ymzrcw because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Wrote 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-cfniikne because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Selected test sample NA12882 and control sample NA12878 Loaded 3654 records; skipped: 514 somatic, 394 depth Kept 2631 heterozygous of 3654 VCF records /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): Placed 705 variants into 18763 bins Wrote p2-9_2.nexus-ogt python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1tlqpqhk because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-5_5 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-5_5.call.cns with 71 regions python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-m6grcpj6 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-9_2.call.cns with 107 regions python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-7k5sbsra because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_1 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_1.call.cns with 117 regions python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-j6i_uo4k because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_2 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_2.call.cns with 125 regions python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-nc0o_iuk because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_3 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_3.call.cns with 74 regions python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0e3xc6ah because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_4 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_4.call.cns with 137 regions python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-bcgsbeog because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-20_5 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_5.call.cns with 129 regions python3 ../cnvkit.py export 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-cvgrggx2 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories 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 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-z13baj4t because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories Treating sample p2-9_2.call as female /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): Wrote p2-9_2.vcf python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3vehayd7 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): Wrote 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-aasrh3p8 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): Wrote p2-9_2-segmetrics.cns with 107 regions 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 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-h4krb7r5 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): Wrote p2-5_5-segmetrics.cns with 71 regions python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ua_k0z1b because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): Wrote p2-5_5-metrics.tsv python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-_2ztwzyh because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): Wrote p2-9_2-metrics.tsv python3 ../cnvkit.py metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-iacrd7ww because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): /build/cnvkit-0.9.9/skgenome/intersect.py:39: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. other_chroms = {c: o for c, o in other.groupby(['chromosome'], sort=False)} /build/cnvkit-0.9.9/skgenome/intersect.py:40: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning. for chrom, ctable in table.groupby(['chromosome'], sort=False): Wrote p2-20-metrics.tsv make[2]: Leaving directory '/build/cnvkit-0.9.9/test' cd test && /usr/bin/make clean || /bin/true make[2]: Entering directory '/build/cnvkit-0.9.9/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/build/cnvkit-0.9.9/test' rm -Rf test/build test/*.tsv make[1]: Leaving directory '/build/cnvkit-0.9.9' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/cnvkit-0.9.9' [ -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:240: /usr/bin/python3 setup.py install --root /build/cnvkit-0.9.9/debian/cnvkit running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_scripts running install_lib creating /build/cnvkit-0.9.9/debian/cnvkit/usr creating /build/cnvkit-0.9.9/debian/cnvkit/usr/lib creating /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11 creating /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages creating /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome creating /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/__init__.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/bedio.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/genepred.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/gff.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/picard.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/seg.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/seqdict.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/tab.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/textcoord.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/util.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/vcfio.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/tabio/vcfsimple.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/__init__.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/chromsort.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/combiners.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/gary.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/intersect.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/merge.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/rangelabel.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/subdivide.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/skgenome/subtract.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome creating /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib creating /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation/__init__.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation/cbs.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation/flasso.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation/haar.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation/hmm.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmentation/none.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/__init__.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/_version.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/access.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/antitarget.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/autobin.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/batch.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/bintest.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/call.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/cluster.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/cmdutil.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/cnary.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/core.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/coverage.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/descriptives.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/diagram.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/export.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/fix.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/heatmap.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/import_rna.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/importers.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/metrics.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/parallel.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/params.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/plots.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/reference.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/reports.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/rna.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/samutil.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/scatter.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segfilters.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/segmetrics.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/smoothing.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/target.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/vary.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib copying /build/cnvkit-0.9.9/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/commands.py -> /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/__init__.py to __init__.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/bedio.py to bedio.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/genepred.py to genepred.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/gff.py to gff.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/picard.py to picard.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/seg.py to seg.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/seqdict.py to seqdict.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/tab.py to tab.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/textcoord.py to textcoord.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/util.py to util.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/vcfio.py to vcfio.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/tabio/vcfsimple.py to vcfsimple.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/__init__.py to __init__.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/chromsort.py to chromsort.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/combiners.py to combiners.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/gary.py to gary.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/intersect.py to intersect.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/merge.py to merge.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/rangelabel.py to rangelabel.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/subdivide.py to subdivide.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/skgenome/subtract.py to subtract.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation/__init__.py to __init__.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation/cbs.py to cbs.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation/flasso.py to flasso.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation/haar.py to haar.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation/hmm.py to hmm.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmentation/none.py to none.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/__init__.py to __init__.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/_version.py to _version.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/access.py to access.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/antitarget.py to antitarget.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/autobin.py to autobin.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/batch.py to batch.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/bintest.py to bintest.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/call.py to call.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/cluster.py to cluster.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/cmdutil.py to cmdutil.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/cnary.py to cnary.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/core.py to core.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/coverage.py to coverage.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/descriptives.py to descriptives.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/diagram.py to diagram.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/export.py to export.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/fix.py to fix.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/heatmap.py to heatmap.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/import_rna.py to import_rna.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/importers.py to importers.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/metrics.py to metrics.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/parallel.py to parallel.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/params.py to params.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/plots.py to plots.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/reference.py to reference.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/reports.py to reports.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/rna.py to rna.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/samutil.py to samutil.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/scatter.py to scatter.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segfilters.py to segfilters.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/segmetrics.py to segmetrics.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/smoothing.py to smoothing.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/target.py to target.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/vary.py to vary.cpython-311.pyc byte-compiling /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/cnvlib/commands.py to commands.cpython-311.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' adding license file 'LICENSE' writing manifest file 'CNVkit.egg-info/SOURCES.txt' Copying CNVkit.egg-info to /build/cnvkit-0.9.9/debian/cnvkit/usr/lib/python3.11/dist-packages/CNVkit-0.9.9.egg-info Skipping SOURCES.txt running install_scripts creating /build/cnvkit-0.9.9/debian/cnvkit/usr/bin copying build/scripts-3.11/snpfilter.sh -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin copying build/scripts-3.11/cnvkit-cnv_annotate -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin copying build/scripts-3.11/cnvkit-cnv_expression_correlate -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin copying build/scripts-3.11/cnvkit-cnv_updater -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin copying build/scripts-3.11/cnvkit-genome_instability_index -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin copying build/scripts-3.11/cnvkit-guess_baits -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin copying build/scripts-3.11/cnvkit-reference2targets -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin copying build/scripts-3.11/cnvkit-skg_convert -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin copying build/scripts-3.11/cnvkit -> /build/cnvkit-0.9.9/debian/cnvkit/usr/bin changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/snpfilter.sh to 775 changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 755 changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 755 changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 755 changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/cnvkit-genome_instability_index to 755 changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/cnvkit-guess_baits to 755 changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/cnvkit-reference2targets to 755 changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/cnvkit-skg_convert to 755 changing mode of /build/cnvkit-0.9.9/debian/cnvkit/usr/bin/cnvkit to 755 help2man --no-info --version-option=version \ --name="a command-line toolkit for copy number analysis." \ ./cnvkit > debian/cnvkit.1 PYTHONPATH=$PYTHONPATH:. debian/genmanpages.py 0.9.9 /build/cnvkit-0.9.9/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. from pandas import Int64Index Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fz3g2bv4 because the default path (/nonexistent/second-build/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Fontconfig error: No writable cache directories cd scripts && PYTHONPATH=../ help2man --no-info \ --version-string=0.9.9 --help-option='-h' \ ./cnvkit-reference2targets --name='Extract target and antitarget BED files from a CNVkit reference file.' \ > ../debian/cnvkit-reference2targets.1; cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py make[1]: Leaving directory '/build/cnvkit-0.9.9' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'cnvkit' in '../cnvkit_0.9.9-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../cnvkit_0.9.9-2_amd64.buildinfo dpkg-genchanges --build=binary -O../cnvkit_0.9.9-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1491079/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1491079/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1491079 and its subdirectories I: Current time: Sun May 21 19:45:46 +14 2023 I: pbuilder-time-stamp: 1684647946