I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 1 08:42:20 +14 2021 I: pbuilder-time-stamp: 1638297740 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [cnvkit_0.9.5-3.dsc] I: copying [./cnvkit_0.9.5.orig.tar.gz] I: copying [./cnvkit_0.9.5-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Mar 29 00:43:40 2019 +14 gpgv: using RSA key 5FB46F83D3B952046335D26D78DC68DB326D8438 gpgv: issuer "osallou@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cnvkit_0.9.5-3.dsc dpkg-source: info: extracting cnvkit in cnvkit-0.9.5 dpkg-source: info: unpacking cnvkit_0.9.5.orig.tar.gz dpkg-source: info: unpacking cnvkit_0.9.5-3.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: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3397097/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/3397097/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3397097/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(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= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=22dc9bd75ffe4406b58a581fe9163d19 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=3397097 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/tmp.RcEykp4YkN/pbuilderrc_rfDO --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RcEykp4YkN/b2 --logfile b2/build.log cnvkit_0.9.5-3.dsc' SUDO_GID=110 SUDO_UID=105 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 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Dec 1 08:42 sh -> bash lrwxrwxrwx 1 root root 4 Nov 8 11:58 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/3397097/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 (>= 11~), 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, 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 ... 19195 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 (>= 11~); however: Package debhelper 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 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} bsdmainutils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbsd0{a} libcairo2{a} libcroco3{a} libcurl3-gnutls{a} libcurl4{a} libdatrie1{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts2{a} libice6{a} libicu63{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpoppler82{a} libpsl5{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libssh2-1{a} libssl1.1{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff5{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libxt6{a} lsb-base{a} m4{a} man-db{a} mime-support{a} openssl{a} po-debconf{a} poppler-utils{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-biopython{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-distutils{a} python3-future{a} python3-kiwisolver{a} python3-lib2to3{a} python3-matplotlib{a} python3-minimal{a} python3-numpy{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-pyfaidx{a} python3-pyparsing{a} python3-pysam{a} python3-pyvcf{a} python3-reportlab{a} python3-reportlab-accel{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-tz{a} python3.7{a} python3.7-minimal{a} r-base-core{a} r-bioc-dnacopy{a} readline-common{a} sensible-utils{a} ttf-bitstream-vera{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx ncbi-blast+ poppler-data publicsuffix python-biopython-doc python3-bs4 python3-html5lib python3-lxml python3-numexpr python3-olefile python3-renderpm python3-tables python3-tk r-base-dev r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 156 newly installed, 0 to remove and 0 not upgraded. Need to get 103 MB of archives. After unpacking 329 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u7 [845 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 ttf-bitstream-vera all 1.10-8 [352 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 fonts-lyx all 2.3.2-1 [199 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libcairo2 amd64 1.16.0-4+deb10u1 [688 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libdatrie1 amd64 0.2.12-2 [39.3 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libfribidi0 amd64 1.0.5-3.1+deb10u1 [63.7 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libjs-jquery all 3.3.1~dfsg-3+deb10u1 [332 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u3 [1159 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libopenjp2-7 amd64 2.3.0-2+deb10u2 [158 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libthai-data all 0.1.28-2 [170 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libthai0 amd64 0.1.28-2 [54.1 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libpango-1.0-0 amd64 1.42.4-8~deb10u1 [186 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libpangoft2-1.0-0 amd64 1.42.4-8~deb10u1 [68.3 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libpangocairo-1.0-0 amd64 1.42.4-8~deb10u1 [55.7 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libpaper1 amd64 1.1.28 [21.3 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libpaper-utils amd64 1.1.28 [18.0 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u2 [271 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 libpoppler82 amd64 0.71.0-5 [1507 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 libtcl8.6 amd64 8.6.9+dfsg-2 [1005 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libtk8.6 amd64 8.6.9-2 [768 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u1 [87.6 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u1 [97.8 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 poppler-utils amd64 0.71.0-5 [184 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 python-matplotlib-data all 3.0.2-2 [4138 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 python3-all amd64 3.7.3-1 [1068 B] Get: 130 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 131 http://deb.debian.org/debian buster/main amd64 python3-numpy amd64 1:1.16.2-1 [2119 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 python3-reportlab-accel amd64 3.5.13-1+deb10u1 [35.3 kB] Get: 133 http://deb.debian.org/debian buster/main amd64 python3-pil amd64 5.4.1-2+deb10u2 [395 kB] Get: 134 http://deb.debian.org/debian buster/main amd64 python3-reportlab all 3.5.13-1+deb10u1 [541 kB] Get: 135 http://deb.debian.org/debian buster/main amd64 python3-biopython amd64 1.73+dfsg-1 [1287 kB] Get: 136 http://deb.debian.org/debian buster/main amd64 python3-six all 1.12.0-1 [15.7 kB] Get: 137 http://deb.debian.org/debian buster/main amd64 python3-cycler all 0.10.0-1 [7556 B] Get: 138 http://deb.debian.org/debian buster/main amd64 python3-dateutil all 2.7.3-3 [64.5 kB] Get: 139 http://deb.debian.org/debian buster/main amd64 python3-decorator all 4.3.0-1.1 [14.5 kB] Get: 140 http://deb.debian.org/debian buster/main amd64 python3-future all 0.16.0-1 [346 kB] Get: 141 http://deb.debian.org/debian buster/main amd64 python3-kiwisolver amd64 1.0.1-2+b1 [65.4 kB] Get: 142 http://deb.debian.org/debian buster/main amd64 python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB] Get: 143 http://deb.debian.org/debian buster/main amd64 python3-matplotlib amd64 3.0.2-2 [5353 kB] Get: 144 http://deb.debian.org/debian buster/main amd64 python3-tz all 2019.1-1 [27.1 kB] Get: 145 http://deb.debian.org/debian buster/main amd64 python3-pandas-lib amd64 0.23.3+dfsg-3 [3475 kB] Get: 146 http://deb.debian.org/debian buster/main amd64 python3-pandas all 0.23.3+dfsg-3 [1750 kB] Get: 147 http://deb.debian.org/debian buster/main amd64 python3-pyfaidx all 0.5.5.2-1 [25.3 kB] Get: 148 http://deb.debian.org/debian buster/main amd64 python3-pysam amd64 0.15.2+ds-2 [1661 kB] Get: 149 http://deb.debian.org/debian buster/main amd64 python3-pyvcf amd64 0.6.8+git20170215.476169c-1 [54.8 kB] Get: 150 http://deb.debian.org/debian buster/main amd64 python3-scipy amd64 1.1.0-7 [10.0 MB] Get: 151 http://deb.debian.org/debian buster/main amd64 python3-setuptools all 40.8.0-1 [306 kB] Get: 152 http://deb.debian.org/debian buster/main amd64 zip amd64 3.0-11+b1 [234 kB] Get: 153 http://deb.debian.org/debian buster/main amd64 unzip amd64 6.0-23+deb10u2 [172 kB] Get: 154 http://deb.debian.org/debian buster/main amd64 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get: 155 http://deb.debian.org/debian buster/main amd64 r-base-core amd64 3.5.2-1 [23.9 MB] Get: 156 http://deb.debian.org/debian buster/main amd64 r-bioc-dnacopy amd64 1.56.0-1 [419 kB] Fetched 103 MB in 2s (65.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../06-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../07-libssl1.1_1.1.1d-0+deb10u7_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Selecting previously unselected package libpython3.7-minimal:amd64. Preparing to unpack .../08-libpython3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../09-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../10-python3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u3) ... Setting up libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u3) ... 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 ... 20105 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.3-1_amd64.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../2-libmpdec2_2.4.2-2_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../4-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libpython3.7-stdlib:amd64. Preparing to unpack .../5-libpython3.7-stdlib_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package python3.7. Preparing to unpack .../6-python3.7_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7 (3.7.3-2+deb10u3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../7-libpython3-stdlib_3.7.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... 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 ... 20566 files and directories currently installed.) Preparing to unpack .../000-python3_3.7.3-1_amd64.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../003-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../006-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../007-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../008-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... 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Unpacking r-bioc-dnacopy (1.56.0-1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libgraphite2-3:amd64 (1.3.13-7) ... Setting up liblcms2-2:amd64 (2.9-3) ... Setting up libpixman-1-0:amd64 (0.36.0-1) ... Setting up lsb-base (10.2019051400) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up mime-support (3.62) ... Setting up libdatrie1:amd64 (0.2.12-2) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.2-1) ... Setting up unzip (6.0-23+deb10u2) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up zip (3.0-11+b1) ... Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up libx11-data (2:1.6.7-1+deb10u2) ... Setting up libnspr4:amd64 (2:4.20-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libfribidi0:amd64 (1.0.5-3.1+deb10u1) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up libtcl8.6:amd64 (8.6.9+dfsg-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libwebp6:amd64 (0.6.1-2+deb10u1) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libopenjp2-7:amd64 (2.3.0-2+deb10u2) ... Setting up libthai-data (0.1.28-2) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u2) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Setting up python-matplotlib-data (3.0.2-2) ... Setting up openssl (1.1.1d-0+deb10u7) ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up xdg-utils (1.1.3-1+deb10u1) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libtool (2.4.6-9) ... Setting up libxcb-render0:amd64 (1.13.1-2) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:amd64 (2:3.42.1-1+deb10u3) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up help2man (1.47.8) ... Setting up libthai0:amd64 (0.1.28-2) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libblas3:amd64 (3.8.0-2) ... 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 libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up libfreetype6:amd64 (2.9.1-3+deb10u2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libcurl4:amd64 (7.64.0-4+deb10u2) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Setting up libharfbuzz0b:amd64 (2.3.1-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpaper1:amd64 (1.1.28) ... Creating config file /etc/papersize with new version Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up liblapack3:amd64 (3.8.0-2) ... 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 gettext (0.19.8.1-9) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up libpaper-utils (1.1.28) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-tz (2019.1-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-1) ... Setting up python3-pil:amd64 (5.4.1-2+deb10u2) ... Setting up python3-decorator (4.3.0-1.1) ... Setting up python3-pyparsing (2.2.0+dfsg1-2) ... Setting up python3-cycler (0.10.0-1) ... Setting up python3-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Setting up libxt6:amd64 (1:1.1.5-1+b3) ... Setting up python3-reportlab (3.5.13-1+deb10u1) ... Setting up python3-dateutil (2.7.3-3) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up python3-pyfaidx (0.5.5.2-1) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up python3-setuptools (40.8.0-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up po-debconf (1.0.21) ... Setting up libtk8.6:amd64 (8.6.9-2) ... Setting up libpango-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up libpoppler82:amd64 (0.71.0-5) ... Setting up python3-all (3.7.3-1) ... Setting up libcairo2:amd64 (1.16.0-4+deb10u1) ... Setting up python3-pyvcf (0.6.8+git20170215.476169c-1) ... Setting up python3-kiwisolver (1.0.1-2+b1) ... Setting up python3-numpy (1:1.16.2-1) ... Setting up poppler-utils (0.71.0-5) ... Setting up libpangoft2-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up python3-future (0.16.0-1) ... update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode Setting up python3-biopython (1.73+dfsg-1) ... Setting up libpangocairo-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up python3-matplotlib (3.0.2-2) ... Setting up python3-pysam (0.15.2+ds-2) ... Setting up python3-scipy (1.1.0-7) ... Setting up python3-pandas-lib (0.23.3+dfsg-3) ... Setting up python3-pandas (0.23.3+dfsg-3) ... Setting up r-base-core (3.5.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-bioc-dnacopy (1.56.0-1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20200601~deb10u2) ... 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... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package hostname: Name or service not known I: Running cd /build/cnvkit-0.9.5/ && 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_0.9.5-3_source.changes dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.5-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Olivier Sallou dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/cnvkit-0.9.5' cd test && /usr/bin/make clean || /bin/true make[2]: Entering directory '/build/cnvkit-0.9.5/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-0.9.5/test' if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi dh_auto_clean I: pybuild base:217: python3.7 setup.py clean running clean removing '/build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.7' 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-0.9.5' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python3.7 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/cnvkit-0.9.5' [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted build if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ mv ${script} cnvkit-${script%%.py}; \ done; \ fi dh_auto_build I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/commands.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/ztest.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/vary.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/target.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/smoothing.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/segmetrics.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/segfilters.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/scatter.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/samutil.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/rna.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/reports.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/reference.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/plots.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/params.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/parallel.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/metrics.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/importers.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/import_rna.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/heatmap.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/fix.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/export.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/diagram.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/descriptives.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/coverage.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/core.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/cnary.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/cmdutil.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/call.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/batch.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/autobin.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/antitarget.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/access.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/_version.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/__init__.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib creating /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/none.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation creating /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/subtract.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/subdivide.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/rangelabel.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/merge.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/intersect.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/gary.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/combiners.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/chromsort.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/__init__.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome creating /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfio.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/util.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/textcoord.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/tab.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/seqdict.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/seg.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/picard.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/gff.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/genepred.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/bedio.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/__init__.py -> /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio running build_scripts creating build creating build/scripts-3.7 copying and adjusting ./cnvkit -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-skg_convert -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-reference2targets -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-guess_baits -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_ztest -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_updater -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_annotate -> build/scripts-3.7 copying ./scripts/snpfilter.sh -> build/scripts-3.7 changing mode of build/scripts-3.7/cnvkit from 664 to 775 changing mode of build/scripts-3.7/cnvkit-skg_convert from 664 to 775 changing mode of build/scripts-3.7/cnvkit-reference2targets from 664 to 775 changing mode of build/scripts-3.7/cnvkit-guess_baits from 664 to 775 changing mode of build/scripts-3.7/cnvkit-cnv_ztest from 664 to 775 changing mode of build/scripts-3.7/cnvkit-cnv_updater from 664 to 775 changing mode of build/scripts-3.7/cnvkit-cnv_expression_correlate from 664 to 775 changing mode of build/scripts-3.7/cnvkit-cnv_annotate from 664 to 775 cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py make[1]: Leaving directory '/build/cnvkit-0.9.5' debian/rules override_dh_auto_test make[1]: Entering directory '/build/cnvkit-0.9.5' cd test && /usr/bin/make -j15 make[2]: Entering directory '/build/cnvkit-0.9.5/test' python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-20_5.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv -d build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Created directory build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_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/p2-20_5.targetcoverage.cnn with 6646 regions Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn 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=67.2 x 0.532 = 35.7) --> assuming male Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=38.7 x 0.532 = 20.6) --> assuming male Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=94.8 x 0.532 = 50.4) --> assuming male Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=6.53 x 0.809 = 5.28) --> assuming male Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=9.76 x 0.895 = 8.74) --> assuming male Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=18.1 x 0.895 = 16.2) --> assuming male Loading build/p2-20_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading target build/p2-5_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading target build/p2-9_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Calculating average bin coverages Calculating bin spreads Loading build/p2-20_5.antitargetcoverage.cnn Correcting for GC bias... Loading target build/p2-5_5.antitargetcoverage.cnn Correcting for GC bias... Loading target build/p2-9_5.antitargetcoverage.cnn Correcting for GC bias... Calculating average bin coverages Calculating bin spreads Targets: 89 (1.3392%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) NOTCH2 chr1:120572470-120572622 log2=-2.599 spread=1.522 GAK chr4:896278-896357 log2=-1.523 spread=1.267 MAP3K1 chr5:56111354-56111894 log2=-1.492 spread=1.060 FLT4 chr5:180076418-180076603 log2=-2.232 spread=1.421 DOM3Z chr6:31938905-31939081 log2=-20.033 spread=0.045 " chr6:31939599-31940313 log2=-19.608 spread=0.181 STK19 chr6:31940351-31940562 log2=-19.003 spread=0.189 " chr6:31946632-31946824 log2=-20.060 spread=0.088 " chr6:31947142-31947366 log2=-20.128 spread=0.065 " chr6:31948176-31948360 log2=-19.992 spread=0.148 " chr6:31948382-31948612 log2=-19.780 spread=0.162 " chr6:31948730-31949253 log2=-20.063 spread=0.020 NOTCH4 chr6:32163159-32163956 log2=-19.331 spread=0.202 " chr6:32164046-32164227 log2=-19.777 spread=0.180 " chr6:32164652-32164888 log2=-19.995 spread=0.151 " chr6:32165021-32165403 log2=-19.643 spread=0.195 " chr6:32166163-32166545 log2=-20.057 spread=0.076 " chr6:32166648-32166962 log2=-3.526 spread=5.774 " chr6:32168554-32168821 log2=-19.621 spread=0.193 " chr6:32168844-32169306 log2=-19.700 spread=0.164 " chr6:32169801-32170391 log2=-19.433 spread=0.206 " chr6:32171492-32171691 log2=-20.108 spread=0.103 " chr6:32171861-32172198 log2=-3.146 spread=7.284 " chr6:32178478-32178749 log2=-19.934 spread=0.167 " chr6:32180197-32180441 log2=-10.912 spread=9.531 " chr6:32180544-32180722 log2=-19.700 spread=0.182 " chr6:32180857-32181062 log2=-19.591 spread=0.214 " chr6:32181411-32181646 log2=-19.979 spread=0.168 " chr6:32181832-32182066 log2=-19.971 spread=0.174 " chr6:32182948-32183194 log2=-19.947 spread=0.171 " chr6:32184667-32185079 log2=-19.931 spread=0.162 " chr6:32185720-32185919 log2=-19.724 spread=0.192 " chr6:32187317-32187601 log2=-19.783 spread=0.171 " chr6:32187871-32188094 log2=-19.686 spread=0.190 " chr6:32188127-32188451 log2=-19.636 spread=0.165 " chr6:32188481-32188693 log2=-19.906 spread=0.130 " chr6:32188704-32189133 log2=-19.522 spread=0.199 " chr6:32190258-32190616 log2=-19.586 spread=0.207 " chr6:32190724-32190908 log2=-19.562 spread=0.218 " chr6:32191570-32191668 log2=-19.792 spread=0.174 " chr6:32191676-32191753 log2=-19.393 spread=0.201 CGH chr7:52520101-52520286 log2=-1.534 spread=1.178 SMO chr7:128828938-128829041 log2=-2.070 spread=1.324 GPR124 chr8:37654740-37655077 log2=-1.623 spread=1.026 GPSM1 chr9:139222089-139222248 log2=-4.896 spread=2.116 MRC1 chr10:18136438-18136613 log2=-1.967 spread=3.254 RET chr10:43572644-43572830 log2=-1.394 spread=1.097 FLT3 chr13:28674525-28674708 log2=-2.268 spread=1.749 IRS2 chr13:110438332-110438432 log2=-3.655 spread=2.330 CGH chr14:19220933-19221047 log2=-1.234 spread=1.211 MAP3K9 chr14:71275790-71275923 log2=-2.828 spread=1.943 LTK chr15:41803310-41803809 log2=-1.970 spread=1.452 PDPK1 chr16:2588022-2588201 log2=-1.783 spread=1.088 " chr16:2611404-2611585 log2=-5.189 spread=1.939 " chr16:2611721-2611943 log2=-11.822 spread=9.176 " chr16:2615504-2615725 log2=-20.129 spread=0.003 " chr16:2616307-2616486 log2=-20.077 spread=0.072 " chr16:2631267-2631414 log2=-20.027 spread=0.061 " chr16:2631583-2631734 log2=-20.122 spread=0.087 " chr16:2633363-2633616 log2=-20.108 spread=0.092 BOLA2B chr16:29466011-29466278 log2=-19.007 spread=0.177 MAP2K4 chr17:11924151-11924355 log2=-2.111 spread=1.902 GIPC3 chr19:3585549-3585853 log2=-1.530 spread=1.093 INSR chr19:7293751-7294042 log2=-2.032 spread=1.542 NOTCH3 chr19:15311544-15311749 log2=-1.901 spread=1.207 CD79A chr19:42384673-42384848 log2=-1.888 spread=1.229 CRLF2 chrX:1314835-1315039 log2=-20.125 spread=0.029 " chrX:1317372-1317594 log2=-20.136 spread=0.045 " chrX:1321225-1321435 log2=-19.869 spread=0.196 " chrX:1325274-1325530 log2=-20.131 spread=0.012 " chrX:1327651-1327830 log2=-20.012 spread=0.030 " chrX:1331391-1331576 log2=-20.024 spread=0.051 CGH chrY:2654543-2654722 log2=-4.357 spread=4.442 " chrY:3023482-3023672 log2=-4.960 spread=6.784 " chrY:4564417-4564597 log2=-11.686 spread=9.039 " chrY:7540620-7540741 log2=-5.016 spread=6.755 " chrY:9008607-9008759 log2=-12.124 spread=8.796 " chrY:13131970-13132039 log2=-20.071 spread=0.102 " chrY:13199435-13199623 log2=-4.281 spread=6.165 " chrY:15007107-15007258 log2=-6.946 spread=7.403 " chrY:16504318-16504496 log2=-5.090 spread=6.641 " chrY:18022729-18022918 log2=-5.529 spread=6.991 " chrY:19506485-19506650 log2=-11.896 spread=8.895 " chrY:21033918-21034071 log2=-20.101 spread=0.087 " chrY:22554204-22554385 log2=-6.070 spread=7.225 " chrY:24000593-24000773 log2=-4.446 spread=4.603 " chrY:28462977-28463157 log2=-5.435 spread=7.074 " chrY:28463435-28463622 log2=-11.305 spread=9.238 " chrY:28514033-28514208 log2=-12.104 spread=8.739 Antitargets: 111 (0.8835%) bins failed filters Wrote build/reference-picard.cnn with 19209 regions python3 ../cnvkit.py fix build/p2-5_5.targetcoverage.cnn build/p2-5_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-5_5.cnr python3 ../cnvkit.py fix build/p2-9_2.targetcoverage.cnn build/p2-9_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-9_2.cnr python3 ../cnvkit.py fix build/p2-20_1.targetcoverage.cnn build/p2-20_1.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_1.cnr python3 ../cnvkit.py fix build/p2-20_2.targetcoverage.cnn build/p2-20_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_2.cnr python3 ../cnvkit.py fix build/p2-20_3.targetcoverage.cnn build/p2-20_3.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_3.cnr python3 ../cnvkit.py fix build/p2-20_4.targetcoverage.cnn build/p2-20_4.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_4.cnr python3 ../cnvkit.py fix build/p2-20_5.targetcoverage.cnn build/p2-20_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_5.cnr Processing target: p2-20_3 Processing target: p2-20_4 Keeping 6557 of 6646 bins Processing target: p2-5_5 Correcting for GC bias... Keeping 6557 of 6646 bins Correcting for density bias... Correcting for GC bias... Processing target: p2-20_1 Keeping 6557 of 6646 bins Correcting for density bias... Processing target: p2-20_5 Correcting for GC bias... Correcting for density bias... Processing target: p2-9_2 Keeping 6557 of 6646 bins Processing antitarget: p2-20_3 Correcting for GC bias... Processing antitarget: p2-20_4 Correcting for density bias... Keeping 6557 of 6646 bins Keeping 6557 of 6646 bins Processing antitarget: p2-5_5 Keeping 12452 of 12563 bins Correcting for GC bias... Correcting for GC bias... Correcting for GC bias... Keeping 12452 of 12563 bins Correcting for density bias... Processing antitarget: p2-20_1 Keeping 12452 of 12563 bins Correcting for density bias... Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Processing target: p2-20_2 Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Keeping 12452 of 12563 bins Processing antitarget: p2-20_5 WARNING: Skipping correction for RepeatMasker bias Processing antitarget: p2-9_2 Correcting for GC bias... Keeping 6557 of 6646 bins Antitargets are 1.01 x more variable than targets Correcting for GC bias... Targets are 1.18 x more variable than antitargets WARNING: Skipping correction for RepeatMasker bias Targets are 1.09 x more variable than antitargets Correcting for density bias... Keeping 12452 of 12563 bins Keeping 12452 of 12563 bins Correcting for GC bias... Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias WARNING: Skipping correction for RepeatMasker bias Processing antitarget: p2-20_2 Wrote build/p2-20_4.cnr with 19009 regions Targets are 1.60 x more variable than antitargets Wrote build/p2-20_3.cnr with 19009 regions Targets are 1.08 x more variable than antitargets Wrote build/p2-5_5.cnr with 19009 regions Targets are 1.34 x more variable than antitargets Keeping 12452 of 12563 bins python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns Correcting for GC bias... python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf WARNING: Skipping correction for RepeatMasker bias Wrote build/p2-20_5.cnr with 19009 regions Wrote build/p2-20_1.cnr with 19009 regions Wrote build/p2-9_2.cnr with 19009 regions Targets are 1.04 x more variable than antitargets python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt Wrote build/p2-20_2.cnr with 19009 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf python3 ../cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt python3 ../cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt Treating sample p2-5_5 as male Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Selected test sample NA12882 and control sample NA12878 Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Loaded 3654 records; skipped: 514 somatic, 394 depth Treating sample p2-20_1 as male Kept 2631 heterozygous of 3654 VCF records Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Treating sample p2-9_2 as male Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Treating sample p2-20_2 as male Wrote p2-9_2.nexus /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Dropped 1 / 966 bins on chromosome chr6 /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Wrote build/p2-20_3.cns with 48 regions Wrote build/p2-5_5.cns with 49 regions /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Dropped 1 / 5 bins on chromosome chrY Wrote build/p2-20_1.cns with 78 regions /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Wrote build/p2-20_4.cns with 65 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 python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns Wrote build/p2-20_5.cns with 64 regions /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] Wrote build/p2-9_2.cns with 57 regions python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns Wrote p2-20_1-diagram.pdf python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input Treating sample p2-5_5 as male Treating sample p2-20_3 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_3.call.cns with 48 regions Treating sample p2-5_5 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-5_5.call.cns with 49 regions /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] /usr/lib/python3/dist-packages/scipy/signal/_arraytools.py:45: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. b = a[a_slice] python3 ../cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ --mean --median --mode \ --stdev --mad --mse --iqr --bivar \ --ci --pi --sem python3 ../cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ --ci -b 50 -a 0.5 Wrote build/p2-20_2.cns with 77 regions Treating sample p2-5_5 as male Wrote p2-5_5-cbs-diagram.pdf python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv Treating sample p2-20_4 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_4.call.cns with 65 regions python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o 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 Wrote p2-9_2-diagram.pdf Treating sample p2-20_5 as male Rescaling sample with purity 0.65, ploidy 2 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 Wrote build/p2-20_5.call.cns with 64 regions Placed 727 variants into 19009 bins Wrote p2-9_2.nexus-ogt Wrote p2-20_2-diagram.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 Wrote p2-5_5-diagram.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c 'chr9:150000-45000000' -o p2-9_2-chr9p-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -g SMARCA2,PTPRD -w 4e6 -o p2-9_2-SMARCA2-PTPRD-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -l regions.bed -o p2-9_2-bed_regions-scatter.pdf Wrote p2-9_2.theta2.input python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf Wrote p2-5_5-segmetrics.cns with 49 regions Wrote p2-9_2-metrics.tsv python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf Showing 186 probes and 2 selected genes in region chr9:0-14504268 python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf Showing 1498 probes and 0 selected genes in region chr1 Detected file format: bed Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf Showing 43 probes and 1 selected genes in region chr9:2000000-4000000 Wrote p2-5_5-metrics.tsv Wrote p2-20-metrics.tsv Showing 54 probes and 1 selected genes in region chr9:8000000-12000000 Showing 341 probes and 14 selected genes in region chr9:149999-45000000 python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns build/p2-9_2.cnr -t 0.3 -o p2-9_2-both-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns build/p2-20_1.cnr -t 0.3 -o 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 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 Treating sample p2-9_2 as male Wrote p2-9_2-segmetrics.cns with 57 regions Wrote p2-9_2-cbs-diagram.pdf Treating sample p2-20_1 as male Wrote p2-20_1-cbs-diagram.pdf Wrote p2-9_2-chr9p-scatter.pdf python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt /build/cnvkit-0.9.5/cnvlib/export.py:70: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order. ("GWEIGHT", 1), Wrote p2-all.cdt python3 ../cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt python3 ../cnvkit.py export seg build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-all.seg Treating sample p2-20_2 as male python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns Wrote p2-20_2-cbs-diagram.pdf python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns Wrote p2-9_2-chr1-scatter.pdf Treating sample p2-5_5 as male Treating sample p2-9_2 as male Treating sample p2-20_1 as male python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns Treating sample p2-20_2 as male Treating sample p2-20_3 as male Treating sample p2-20_4 as male Treating sample p2-20_5 as male Wrote p2-all-jtv.txt Wrote p2-5_5-scatter.pdf Treating sample p2-20_2 as male Treating sample p2-9_2 as male Treating sample p2-20_1 as male Treating sample p2-20_1 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_1.call.cns with 78 regions Found 1 gene breakpoints Wrote p2-9_2-breaks.txt Treating sample p2-9_2 as male Wrote p2-all.seg Treating sample p2-20_2 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_2.call.cns with 77 regions Treating sample p2-9_2 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-9_2.call.cns with 57 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 python3 ../cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf Wrote gender-picard.txt Wrote heatmap-picard.pdf Wrote p2-5_5-both-diagram.pdf Treating sample p2-5_5.call as male Treating sample p2-9_2.call as male Treating sample p2-20_1.call as male Treating sample p2-20_2.call as male Treating sample p2-20_3.call as male Treating sample p2-20_4.call as male Treating sample p2-20_5.call as male Found 322 gene-level gains and losses Wrote p2-9_2-genemetrics.txt Wrote p2-all.bed Treating sample p2-9_2.call as male Wrote p2-9_2.vcf Wrote p2-9_2-scatter.pdf which pdfunite && pdfunite p2-5_5-scatter.pdf p2-9_2-scatter.pdf p2-9_2-chr1-scatter.pdf p2-9_2-chr9p-scatter.pdf p2-9_2-SMARCA2-PTPRD-scatter.pdf p2-9_2-bed_regions-scatter.pdf all-scatters.pdf || touch all-scatters.pdf /usr/bin/pdfunite Wrote p2-9_2-both-diagram.pdf Wrote p2-20_2-both-diagram.pdf Wrote p2-20_1-both-diagram.pdf which pdfunite && pdfunite p2-5_5-diagram.pdf p2-9_2-diagram.pdf p2-20_1-diagram.pdf p2-20_2-diagram.pdf p2-5_5-cbs-diagram.pdf p2-9_2-cbs-diagram.pdf p2-20_1-cbs-diagram.pdf p2-20_2-cbs-diagram.pdf p2-5_5-both-diagram.pdf p2-9_2-both-diagram.pdf p2-20_1-both-diagram.pdf p2-20_2-both-diagram.pdf all-diagrams.pdf || touch all-diagrams.pdf /usr/bin/pdfunite make[2]: Leaving directory '/build/cnvkit-0.9.5/test' cd test && /usr/bin/make -j15 clean || /bin/true make[2]: Entering directory '/build/cnvkit-0.9.5/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-0.9.5/test' rm -Rf test/build test/*.tsv make[1]: Leaving directory '/build/cnvkit-0.9.5' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/cnvkit-0.9.5' [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted install if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ mv ${script} cnvkit-${script%%.py}; \ done; \ fi dh_auto_install I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/cnvkit-0.9.5/debian/cnvkit running install running build running build_py running build_scripts running install_lib creating /build/cnvkit-0.9.5/debian/cnvkit/usr creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7 creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/__init__.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/bedio.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/genepred.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/gff.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/picard.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/seg.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/seqdict.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/tab.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/textcoord.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/util.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/vcfio.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/vcfsimple.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/__init__.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/chromsort.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/combiners.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/gary.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/intersect.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/merge.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/rangelabel.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/subdivide.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/skgenome/subtract.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib creating /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/__init__.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/cbs.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/flasso.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/haar.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/hmm.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/none.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/__init__.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/_version.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/access.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/antitarget.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/autobin.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/batch.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/call.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/cmdutil.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/cnary.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/core.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/coverage.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/descriptives.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/diagram.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/export.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/fix.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/heatmap.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/import_rna.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/importers.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/metrics.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/parallel.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/params.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/plots.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/reference.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/reports.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/rna.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/samutil.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/scatter.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segfilters.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmetrics.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/smoothing.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/target.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/vary.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/ztest.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /build/cnvkit-0.9.5/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/commands.py -> /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/__init__.py to __init__.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/bedio.py to bedio.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/genepred.py to genepred.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/gff.py to gff.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/picard.py to picard.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/seg.py to seg.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/seqdict.py to seqdict.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/tab.py to tab.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/textcoord.py to textcoord.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/util.py to util.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/vcfio.py to vcfio.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/vcfsimple.py to vcfsimple.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/__init__.py to __init__.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/chromsort.py to chromsort.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/combiners.py to combiners.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/gary.py to gary.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/intersect.py to intersect.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/merge.py to merge.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/rangelabel.py to rangelabel.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/subdivide.py to subdivide.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/subtract.py to subtract.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/__init__.py to __init__.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/cbs.py to cbs.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/flasso.py to flasso.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/haar.py to haar.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/hmm.py to hmm.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/none.py to none.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/__init__.py to __init__.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/_version.py to _version.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/access.py to access.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/antitarget.py to antitarget.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/autobin.py to autobin.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/batch.py to batch.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/call.py to call.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/cmdutil.py to cmdutil.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/cnary.py to cnary.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/core.py to core.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/coverage.py to coverage.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/descriptives.py to descriptives.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/diagram.py to diagram.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/export.py to export.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/fix.py to fix.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/heatmap.py to heatmap.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/import_rna.py to import_rna.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/importers.py to importers.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/metrics.py to metrics.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/parallel.py to parallel.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/params.py to params.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/plots.py to plots.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/reference.py to reference.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/reports.py to reports.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/rna.py to rna.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/samutil.py to samutil.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/scatter.py to scatter.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segfilters.py to segfilters.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmetrics.py to segmetrics.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/smoothing.py to smoothing.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/target.py to target.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/vary.py to vary.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/ztest.py to ztest.cpython-37.pyc byte-compiling /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/commands.py to commands.cpython-37.pyc running install_egg_info running egg_info creating CNVkit.egg-info writing CNVkit.egg-info/PKG-INFO writing dependency_links to CNVkit.egg-info/dependency_links.txt writing requirements to CNVkit.egg-info/requires.txt writing top-level names to CNVkit.egg-info/top_level.txt writing manifest file 'CNVkit.egg-info/SOURCES.txt' reading manifest file 'CNVkit.egg-info/SOURCES.txt' writing manifest file 'CNVkit.egg-info/SOURCES.txt' Copying CNVkit.egg-info to /build/cnvkit-0.9.5/debian/cnvkit/usr/lib/python3.7/dist-packages/CNVkit-0.9.5.egg-info Skipping SOURCES.txt running install_scripts creating /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/snpfilter.sh -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-cnv_annotate -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-cnv_expression_correlate -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-cnv_updater -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-cnv_ztest -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-guess_baits -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-reference2targets -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-skg_convert -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit -> /build/cnvkit-0.9.5/debian/cnvkit/usr/bin changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/snpfilter.sh to 775 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 775 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 775 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 775 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-cnv_ztest to 775 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-guess_baits to 775 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-reference2targets to 775 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit-skg_convert to 775 changing mode of /build/cnvkit-0.9.5/debian/cnvkit/usr/bin/cnvkit to 775 help2man --no-info --version-option=version \ --name="a command-line toolkit for copy number analysis." \ ./cnvkit > debian/cnvkit.1 PYTHONPATH=$PYTHONPATH:. debian/genmanpages.py 0.9.5 cd scripts && PYTHONPATH=../ help2man --no-info \ --version-string=0.9.5 --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-0.9.5' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installinit -O--buildsystem=pybuild dh_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_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'cnvkit' in '../cnvkit_0.9.5-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../cnvkit_0.9.5-3_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/3397097/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3397097/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/3397097 and its subdirectories I: Current time: Wed Dec 1 08:48:24 +14 2021 I: pbuilder-time-stamp: 1638298104