I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 31 15:37:57 +14 2020 I: pbuilder-time-stamp: 1598837877 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 [python-pysam_0.15.2+ds-2.dsc] I: copying [./python-pysam_0.15.2+ds.orig.tar.xz] I: copying [./python-pysam_0.15.2+ds-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Feb 21 00:46:46 2019 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pysam_0.15.2+ds-2.dsc dpkg-source: info: extracting python-pysam in python-pysam-0.15.2+ds dpkg-source: info: unpacking python-pysam_0.15.2+ds.orig.tar.xz dpkg-source: info: unpacking python-pysam_0.15.2+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_remote.patch dpkg-source: info: applying skip_test_needing_missing_data.patch dpkg-source: info: applying spelling dpkg-source: info: applying test_index_not_compression I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/20239/tmp/hooks/D01_modify_environment starting debug: Running on codethink-sled10-arm64. 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/20239/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/20239/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=20239 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.iDqmm7u6pq/pbuilderrc_t32x --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.iDqmm7u6pq/b2 --logfile b2/build.log python-pysam_0.15.2+ds-2.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.4.0-187-generic #217-Ubuntu SMP Tue Jul 21 04:16:35 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14264 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 35576 Mar 1 2019 cat -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash -rwxr-xr-x 1 root root 97136 Mar 1 2019 date -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd -rwxr-xr-x 1 root root 93752 Mar 1 2019 df -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir -rwxr-xr-x 1 root root 75984 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 31368 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 27256 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 23 09:38 fusermount -rwxr-xr-x 1 root root 174304 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 89656 Jan 6 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln -rwxr-xr-x 1 root root 52544 Jul 27 2018 login -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 10 2019 more -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138736 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 35560 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 31 15:38 sh -> bash lrwxrwxrwx 1 root root 4 Aug 24 22:27 sh.distrib -> dash -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty -rwsr-xr-x 1 root root 59424 Jan 10 2019 su -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch -rwxr-xr-x 1 root root 27256 Mar 1 2019 true -rwxr-xr-x 1 root root 14264 Apr 23 09:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34824 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/20239/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: arm64 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-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 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-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.9); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on python-all-dev; however: Package python-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python-setuptools; however: Package python-setuptools is not installed. pbuilder-satisfydepends-dummy depends on cython (>= 0.23); however: Package cython is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on cython3 (>= 0.23); however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on samtools (>= 1.9); however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on bcftools (>= 1.9); however: Package bcftools is not installed. pbuilder-satisfydepends-dummy depends on python-pytest; however: Package python-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest 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} bcftools{a} bsdmainutils{a} cython{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython-all-dev{a} libpython-dev{a} libpython-stdlib{a} libpython2-dev{a} libpython2-stdlib{a} libpython2.7{a} libpython2.7-dev{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.7{a} libpython3.7-dev{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-all{a} python-all-dev{a} python-atomicwrites{a} python-attr{a} python-dev{a} python-funcsigs{a} python-minimal{a} python-more-itertools{a} python-pathlib2{a} python-pkg-resources{a} python-pluggy{a} python-py{a} python-pytest{a} python-scandir{a} python-setuptools{a} python-six{a} python2{a} python2-dev{a} python2-minimal{a} python2.7{a} python2.7-dev{a} python2.7-minimal{a} python3{a} python3-all{a} python3-all-dev{a} python3-atomicwrites{a} python3-attr{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pytest{a} python3-setuptools{a} python3-six{a} python3.7{a} python3.7-dev{a} python3.7-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl cwltool krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 124 newly installed, 0 to remove and 0 not upgraded. Need to get 78.6 MB of archives. After unpacking 232 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 libpython3.7-minimal arm64 3.7.3-2+deb10u2 [588 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 python3.7-minimal arm64 3.7.3-2+deb10u2 [1404 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 python3-minimal arm64 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libmpdec2 arm64 2.4.2-2 [77.7 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libpython3.7-stdlib arm64 3.7.3-2+deb10u2 [1641 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 python3.7 arm64 3.7.3-2+deb10u2 [330 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libpython3-stdlib arm64 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 python3 arm64 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libkeyutils1 arm64 1.6-6 [14.9 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libkrb5support0 arm64 1.17-3 [64.7 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libk5crypto3 arm64 1.17-3 [122 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libkrb5-3 arm64 1.17-3 [353 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libgssapi-krb5-2 arm64 1.17-3 [150 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-1+deb10u1 [69.3 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libsasl2-2 arm64 2.1.27+dfsg-1+deb10u1 [105 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 libldap-2.4-2 arm64 2.4.47+dfsg-3+deb10u2 [216 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 libnghttp2-14 arm64 1.36.0-2+deb10u1 [81.9 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libpsl5 arm64 0.20.2-2 [53.6 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2 [55.7 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 libssh2-1 arm64 1.8.0-2.1 [135 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 libcurl3-gnutls arm64 7.64.0-4+deb10u1 [310 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 libdeflate0 arm64 1.2-1 [51.4 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 libhts2 arm64 1.9-11 [277 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 bcftools arm64 1.9-1 [478 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 cython arm64 0.29.2-2 [1244 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 cython3 arm64 0.29.2-2 [1259 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 65 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 66 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 67 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 68 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 69 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 70 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 71 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 72 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 73 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 74 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 75 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 76 http://deb.debian.org/debian buster/main arm64 dh-exec arm64 0.23.1 [25.9 kB] Get: 77 http://deb.debian.org/debian buster/main arm64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 78 http://deb.debian.org/debian buster/main arm64 python3-distutils all 3.7.3-1 [142 kB] Get: 79 http://deb.debian.org/debian buster/main arm64 dh-python all 3.20190308 [99.3 kB] Get: 80 http://deb.debian.org/debian buster/main arm64 libexpat1-dev arm64 2.2.6-2+deb10u1 [128 kB] Get: 81 http://deb.debian.org/debian buster/main arm64 liblzma-dev arm64 5.2.4-1 [209 kB] Get: 82 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Get: 83 http://deb.debian.org/debian buster/main arm64 libhts-dev arm64 1.9-11 [4338 kB] Get: 84 http://deb.debian.org/debian buster/main arm64 libpython2.7 arm64 2.7.16-2+deb10u1 [958 kB] Get: 85 http://deb.debian.org/debian buster/main arm64 libpython2.7-dev arm64 2.7.16-2+deb10u1 [31.5 MB] Get: 86 http://deb.debian.org/debian buster/main arm64 libpython2-dev arm64 2.7.16-1 [20.9 kB] Get: 87 http://deb.debian.org/debian buster/main arm64 libpython-dev arm64 2.7.16-1 [20.9 kB] Get: 88 http://deb.debian.org/debian buster/main arm64 libpython-all-dev arm64 2.7.16-1 [1064 B] Get: 89 http://deb.debian.org/debian buster/main arm64 libpython3.7 arm64 3.7.3-2+deb10u2 [1371 kB] Get: 90 http://deb.debian.org/debian buster/main arm64 libpython3.7-dev arm64 3.7.3-2+deb10u2 [2380 kB] Get: 91 http://deb.debian.org/debian buster/main arm64 libpython3-dev arm64 3.7.3-1 [20.1 kB] Get: 92 http://deb.debian.org/debian buster/main arm64 libpython3-all-dev arm64 3.7.3-1 [1068 B] Get: 93 http://deb.debian.org/debian buster/main arm64 python-all arm64 2.7.16-1 [1044 B] Get: 94 http://deb.debian.org/debian buster/main arm64 python2.7-dev arm64 2.7.16-2+deb10u1 [296 kB] Get: 95 http://deb.debian.org/debian buster/main arm64 python2-dev arm64 2.7.16-1 [1216 B] Get: 96 http://deb.debian.org/debian buster/main arm64 python-dev arm64 2.7.16-1 [1192 B] Get: 97 http://deb.debian.org/debian buster/main arm64 python-all-dev arm64 2.7.16-1 [1068 B] Get: 98 http://deb.debian.org/debian buster/main arm64 python-atomicwrites all 1.1.5-2 [6808 B] Get: 99 http://deb.debian.org/debian buster/main arm64 python-attr all 18.2.0-1 [37.2 kB] Get: 100 http://deb.debian.org/debian buster/main arm64 python-funcsigs all 1.0.2-4 [13.7 kB] Get: 101 http://deb.debian.org/debian buster/main arm64 python-six all 1.12.0-1 [15.7 kB] Get: 102 http://deb.debian.org/debian buster/main arm64 python-more-itertools all 4.2.0-1 [42.3 kB] Get: 103 http://deb.debian.org/debian buster/main arm64 python-scandir arm64 1.9.0-2 [18.0 kB] Get: 104 http://deb.debian.org/debian buster/main arm64 python-pathlib2 all 2.3.3-1 [18.3 kB] Get: 105 http://deb.debian.org/debian buster/main arm64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 106 http://deb.debian.org/debian buster/main arm64 python-pluggy all 0.8.0-1 [20.5 kB] Get: 107 http://deb.debian.org/debian buster/main arm64 python-py all 1.7.0-2 [86.5 kB] Get: 108 http://deb.debian.org/debian buster/main arm64 python-pytest all 3.10.1-2 [243 kB] Get: 109 http://deb.debian.org/debian buster/main arm64 python-setuptools all 40.8.0-1 [382 kB] Get: 110 http://deb.debian.org/debian buster/main arm64 python3-all arm64 3.7.3-1 [1068 B] Get: 111 http://deb.debian.org/debian buster/main arm64 python3.7-dev arm64 3.7.3-2+deb10u2 [509 kB] Get: 112 http://deb.debian.org/debian buster/main arm64 python3-dev arm64 3.7.3-1 [1264 B] Get: 113 http://deb.debian.org/debian buster/main arm64 python3-all-dev arm64 3.7.3-1 [1064 B] Get: 114 http://deb.debian.org/debian buster/main arm64 python3-atomicwrites all 1.1.5-2 [6892 B] Get: 115 http://deb.debian.org/debian buster/main arm64 python3-attr all 18.2.0-1 [37.3 kB] Get: 116 http://deb.debian.org/debian buster/main arm64 python3-six all 1.12.0-1 [15.7 kB] Get: 117 http://deb.debian.org/debian buster/main arm64 python3-more-itertools all 4.2.0-1 [42.2 kB] Get: 118 http://deb.debian.org/debian buster/main arm64 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 119 http://deb.debian.org/debian buster/main arm64 python3-pluggy all 0.8.0-1 [20.6 kB] Get: 120 http://deb.debian.org/debian buster/main arm64 python3-py all 1.7.0-2 [86.6 kB] Get: 121 http://deb.debian.org/debian buster/main arm64 python3-pytest all 3.10.1-2 [243 kB] Get: 122 http://deb.debian.org/debian buster/main arm64 python3-setuptools all 40.8.0-1 [306 kB] Get: 123 http://deb.debian.org/debian buster/main arm64 samtools arm64 1.9-4 [424 kB] Get: 124 http://deb.debian.org/debian buster/main arm64 tabix arm64 1.9-11 [272 kB] Fetched 78.6 MB in 4s (19.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:arm64. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_arm64.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_arm64.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:arm64. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_arm64.deb ... Unpacking libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_arm64.deb ... Unpacking libexpat1:arm64 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:arm64. Preparing to unpack .../14-libreadline7_7.0-5_arm64.deb ... Unpacking libreadline7:arm64 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:arm64. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:arm64. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_arm64.deb ... Unpacking libpython2-stdlib:arm64 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:arm64. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_arm64.deb ... Unpacking libpython-stdlib:arm64 (2.7.16-1) ... Setting up libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20631 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_arm64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (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 ... 20664 files and directories currently installed.) Preparing to unpack .../python_2.7.16-1_arm64.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package libpython3.7-minimal:arm64. Preparing to unpack .../libpython3.7-minimal_3.7.3-2+deb10u2_arm64.deb ... Unpacking libpython3.7-minimal:arm64 (3.7.3-2+deb10u2) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.3-2+deb10u2_arm64.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u2) ... Setting up libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Setting up libpython3.7-minimal:arm64 (3.7.3-2+deb10u2) ... Setting up libexpat1:arm64 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u2) ... 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 ... 20918 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.3-1_arm64.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package libmpdec2:arm64. Preparing to unpack .../libmpdec2_2.4.2-2_arm64.deb ... Unpacking libmpdec2:arm64 (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:arm64. Preparing to unpack .../libpython3.7-stdlib_3.7.3-2+deb10u2_arm64.deb ... Unpacking libpython3.7-stdlib:arm64 (3.7.3-2+deb10u2) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2+deb10u2_arm64.deb ... Unpacking python3.7 (3.7.3-2+deb10u2) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../libpython3-stdlib_3.7.3-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (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 ... 21330 files and directories currently installed.) Preparing to unpack .../00-python3_3.7.3-1_arm64.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../03-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../06-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../07-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../08-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../09-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../10-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../11-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../12-libkeyutils1_1.6-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6-6) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../13-libkrb5support0_1.17-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.17-3) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../14-libk5crypto3_1.17-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.17-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../15-libkrb5-3_1.17-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.17-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../16-libgssapi-krb5-2_1.17-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.17-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../17-libsasl2-modules-db_2.1.27+dfsg-1+deb10u1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../18-libsasl2-2_2.1.27+dfsg-1+deb10u1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../19-libldap-common_2.4.47+dfsg-3+deb10u2_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libldap-2.4-2:arm64. Preparing to unpack .../20-libldap-2.4-2_2.4.47+dfsg-3+deb10u2_arm64.deb ... Unpacking libldap-2.4-2:arm64 (2.4.47+dfsg-3+deb10u2) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../21-libnghttp2-14_1.36.0-2+deb10u1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.36.0-2+deb10u1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../22-libpsl5_0.20.2-2_arm64.deb ... Unpacking libpsl5:arm64 (0.20.2-2) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../23-librtmp1_2.4+20151223.gitfa8646d.1-2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../24-libssh2-1_1.8.0-2.1_arm64.deb ... Unpacking libssh2-1:arm64 (1.8.0-2.1) ... Selecting previously unselected package libcurl3-gnutls:arm64. Preparing to unpack .../25-libcurl3-gnutls_7.64.0-4+deb10u1_arm64.deb ... Unpacking libcurl3-gnutls:arm64 (7.64.0-4+deb10u1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../26-libdeflate0_1.2-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.2-1) ... Selecting previously unselected package libhts2:arm64. Preparing to unpack .../27-libhts2_1.9-11_arm64.deb ... Unpacking libhts2:arm64 (1.9-11) ... Selecting previously unselected package bcftools. Preparing to unpack .../28-bcftools_1.9-1_arm64.deb ... Unpacking bcftools (1.9-1) ... Selecting previously unselected package cython. Preparing to unpack .../29-cython_0.29.2-2_arm64.deb ... Unpacking cython (0.29.2-2) ... Selecting previously unselected package cython3. Preparing to unpack .../30-cython3_0.29.2-2_arm64.deb ... Unpacking cython3 (0.29.2-2) ... Selecting previously unselected package libtool. Preparing to unpack .../31-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. 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Setting up libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libnghttp2-14:arm64 (1.36.0-2+deb10u1) ... Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up libdeflate0:arm64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up libkrb5support0:arm64 (1.17-3) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libexpat1-dev:arm64 (2.2.6-2+deb10u1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:arm64 (1.17-3) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-1+deb10u1) ... Setting up liblzma-dev:arm64 (5.2.4-1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libssh2-1:arm64 (1.8.0-2.1) ... Setting up libkrb5-3:arm64 (1.17-3) ... Setting up libmpdec2:arm64 (2.4.2-2) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up libreadline7:arm64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libpython3.7-stdlib:arm64 (3.7.3-2+deb10u2) ... Setting up libpython3.7:arm64 (3.7.3-2+deb10u2) ... Setting up libtool (2.4.6-9) ... Setting up libpython3.7-dev:arm64 (3.7.3-2+deb10u2) ... Setting up libldap-2.4-2:arm64 (2.4.47+dfsg-3+deb10u2) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... 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:arm64 (1.17-3) ... Setting up libcroco3:arm64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libpython3-stdlib:arm64 (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 python3.7 (3.7.3-2+deb10u2) ... Setting up libpython2.7:arm64 (2.7.16-2+deb10u1) ... Setting up libpython2.7-dev:arm64 (2.7.16-2+deb10u1) ... Setting up gettext (0.19.8.1-9) ... Setting up libpython3-dev:arm64 (3.7.3-1) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:arm64 (2.7.16-1) ... Setting up libcurl3-gnutls:arm64 (7.64.0-4+deb10u1) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up python3.7-dev (3.7.3-2+deb10u2) ... Setting up python3-atomicwrites (1.1.5-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-1) ... Setting up libpython-stdlib:arm64 (2.7.16-1) ... Setting up libpython3-all-dev:arm64 (3.7.3-1) ... Setting up cython3 (0.29.2-2) ... Setting up python3-pluggy (0.8.0-1) ... Setting up libpython2-dev:arm64 (2.7.16-1) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up tabix (1.9-11) ... Setting up python (2.7.16-1) ... Setting up python2.7-dev (2.7.16-2+deb10u1) ... 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-more-itertools (4.2.0-1) ... Setting up python3-attr (18.2.0-1) ... Setting up cython (0.29.2-2) ... Setting up python2-dev (2.7.16-1) ... Setting up python3-setuptools (40.8.0-1) ... Setting up libhts2:arm64 (1.9-11) ... Setting up python3-py (1.7.0-2) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up python3-pytest (3.10.1-2) ... Setting up po-debconf (1.0.21) ... Setting up bcftools (1.9-1) ... Setting up libhts-dev:arm64 (1.9-11) ... Setting up python3-all (3.7.3-1) ... Setting up python-all (2.7.16-1) ... Setting up python-attr (18.2.0-1) ... Setting up samtools (1.9-4) ... Setting up python-atomicwrites (1.1.5-2) ... Setting up libpython-dev:arm64 (2.7.16-1) ... Setting up python-six (1.12.0-1) ... Setting up python-more-itertools (4.2.0-1) ... Setting up python-pluggy (0.8.0-1) ... Setting up python3-dev (3.7.3-1) ... Setting up python-setuptools (40.8.0-1) ... Setting up python-funcsigs (1.0.2-4) ... Setting up python-scandir (1.9.0-2) ... Setting up python-py (1.7.0-2) ... Setting up python-dev (2.7.16-1) ... Setting up python3-all-dev (3.7.3-1) ... Setting up libpython-all-dev:arm64 (2.7.16-1) ... Setting up python-pathlib2 (2.3.3-1) ... Setting up python-pytest (3.10.1-2) ... Setting up python-all-dev (2.7.16-1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.1.1) ... Setting up dh-exec (0.23.1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 I: Running cd /build/python-pysam-0.15.2+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.15.2+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Map '/build/python-pysam-0.15.2+ds/tests/pysam_data' wordt binnengegaan rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ with_md.sam.gz \ *.fq.gz make[1]: Map '/build/python-pysam-0.15.2+ds/tests/pysam_data' wordt verlaten cd tests/cbcf_data && /usr/bin/make clean make[1]: Map '/build/python-pysam-0.15.2+ds/tests/cbcf_data' wordt binnengegaan rm -f *.gz *.tbi *.csi *.bcf make[1]: Map '/build/python-pysam-0.15.2+ds/tests/cbcf_data' wordt verlaten find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete #find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully find . -name "*.bai*" -delete find . -name "*.cram*" -delete #find . -name "*.bam" -delete # which deletes files tested rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh clean --with python2,python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Map '/build/python-pysam-0.15.2+ds' wordt binnengegaan dh_auto_clean I: pybuild base:217: python2.7 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info make[1]: Map '/build/python-pysam-0.15.2+ds' wordt verlaten dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python2,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: python2.7 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:217: python3.7 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/config.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/version.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/utils.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/samtools.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/bcftools.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/__init__.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/Pileup.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam creating /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include copying pysam/include/__init__.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libchtslib.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcvcf.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcutils.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libctabix.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcsamtools.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcsamfile.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcfaidx.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcbcftools.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcbcf.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/pysam_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/pysam_stream.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/htslib_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/csamtools_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/cbcftools_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam creating /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/config.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/version.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sample.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam_header.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools creating /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools creating /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32 running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libchtslib.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libchtslib' extension creating build creating build/temp.linux-arm64-2.7 creating build/temp.linux-arm64-2.7/pysam aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-arm64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-arm64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libchtslib.o build/temp.linux-arm64-2.7/pysam/htslib_util.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcsamtools.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcsamtools' extension creating build/temp.linux-arm64-2.7/samtools creating build/temp.linux-arm64-2.7/samtools/lz4 aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-arm64-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.linux-arm64-2.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-arm64-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c samtools/lz4/lz4.c -o build/temp.linux-arm64-2.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcsamtools.o build/temp.linux-arm64-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-arm64-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-arm64-2.7/samtools/stats.c.pysam.o build/temp.linux-arm64-2.7/samtools/samtools.pysam.o build/temp.linux-arm64-2.7/samtools/sample.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_view.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam_header.c.pysam.o build/temp.linux-arm64-2.7/samtools/sam.c.pysam.o build/temp.linux-arm64-2.7/samtools/phase.c.pysam.o build/temp.linux-arm64-2.7/samtools/padding.c.pysam.o build/temp.linux-arm64-2.7/samtools/faidx.c.pysam.o build/temp.linux-arm64-2.7/samtools/dict.c.pysam.o build/temp.linux-arm64-2.7/samtools/cut_target.c.pysam.o build/temp.linux-arm64-2.7/samtools/bedidx.c.pysam.o build/temp.linux-arm64-2.7/samtools/bedcov.c.pysam.o build/temp.linux-arm64-2.7/samtools/bamtk.c.pysam.o build/temp.linux-arm64-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_split.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_md.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_markdup.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_index.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_import.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_color.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-arm64-2.7/samtools/bam.c.pysam.o build/temp.linux-arm64-2.7/samtools/lz4/lz4.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcbcftools.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcbcftools' extension creating build/temp.linux-arm64-2.7/bcftools aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-arm64-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In function ‘init_data’, inlined from ‘main_vcfcall’ at bcftools/vcfcall.c.pysam.c:810:5: bcftools/vcfcall.c.pysam.c:423:39: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] args->aux.ploidy = (uint8_t*) malloc(args->nsamples); ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:29, from /usr/include/htslib/vcf.h:40, from bcftools/vcfcall.c.pysam.c:34: bcftools/vcfcall.c.pysam.c: In function ‘main_vcfcall’: /usr/include/stdlib.h:539:14: note: in a call to allocation function ‘malloc’ declared here extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur; ^~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/reheader.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bcftools.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-arm64-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcbcftools.o build/temp.linux-arm64-2.7/bcftools/filter.c.pysam.o build/temp.linux-arm64-2.7/bcftools/version.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfsort.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-arm64-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/tabix.c.pysam.o build/temp.linux-arm64-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-arm64-2.7/bcftools/reheader.c.pysam.o build/temp.linux-arm64-2.7/bcftools/regidx.c.pysam.o build/temp.linux-arm64-2.7/bcftools/prob1.c.pysam.o build/temp.linux-arm64-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-arm64-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-arm64-2.7/bcftools/mcall.c.pysam.o build/temp.linux-arm64-2.7/bcftools/main.c.pysam.o build/temp.linux-arm64-2.7/bcftools/kmin.c.pysam.o build/temp.linux-arm64-2.7/bcftools/hclust.c.pysam.o build/temp.linux-arm64-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/em.c.pysam.o build/temp.linux-arm64-2.7/bcftools/csq.c.pysam.o build/temp.linux-arm64-2.7/bcftools/convert.c.pysam.o build/temp.linux-arm64-2.7/bcftools/consensus.c.pysam.o build/temp.linux-arm64-2.7/bcftools/ccall.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bin.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bcftools.pysam.o build/temp.linux-arm64-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-arm64-2.7/bcftools/HMM.c.pysam.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN cythoning pysam/libcutils.pyx to pysam/libcutils.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcutils' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-arm64-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6089:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration] bcftools_set_stderr(__pyx_t_9); ^~~~~~~~~~~~~~~~~~~ samtools_set_stderr pysam/libcutils.c:6233:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration] bcftools_set_stdout_fn(__pyx_t_12); ^~~~~~~~~~~~~~~~~~~~~~ samtools_set_stdout_fn pysam/libcutils.c:6244:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration] bcftools_set_stdout(__pyx_t_9); ^~~~~~~~~~~~~~~~~~~ samtools_set_stdout pysam/libcutils.c:6999:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration] bcftools_set_optind(1); ^~~~~~~~~~~~~~~~~~~ samtools_set_optind pysam/libcutils.c:7078:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ samtools_main pysam/libcutils.c:7147:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration] bcftools_unset_stderr(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stderr pysam/libcutils.c:7183:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration] bcftools_unset_stdout(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stdout pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:11401:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcutils.c:5821:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-arm64-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcutils.o build/temp.linux-arm64-2.7/pysam/pysam_util.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcalignmentfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcalignmentfile' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-arm64-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:29332:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); ~^~~~~~~~~~~~~~~~~~~ In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:619: /usr/include/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); ~~~~~~~~~~~~~~~~~~~~~~^~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:27585:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:13687:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcalignmentfile.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcsamfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcsamfile' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-arm64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcsamfile.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcalignedsegment.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcalignedsegment' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-arm64-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c:14226:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcalignedsegment.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN cythoning pysam/libctabix.pyx to pysam/libctabix.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libctabix.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libctabix' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-arm64-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:8631:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: pysam/libctabix.c:13697:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:13729:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:14099:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) ^~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libctabix.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcfaidx.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcfaidx' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-arm64-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcfaidx.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbcf.pyx to pysam/libcbcf.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcbcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcbcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-arm64-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:32813:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen)); ^~~~~~~~~~~~ In file included from pysam/htslib_util.h:5, from pysam/libcbcf.c:618: /usr/include/htslib/vcf.h:439:11: note: declared here char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcbcf.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcbgzf.pyx tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libcbgzf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-arm64-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcbgzf.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libctabixproxies.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'pysam.libctabixproxies' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-arm64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libctabixproxies.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN cythoning pysam/libcvcf.pyx to pysam/libcvcf.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/pysam/libcvcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libcvcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-arm64-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.74’: pysam/libcvcf.c:24828:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-QCkEc0/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-2.7/pysam/libcvcf.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN I: pybuild base:217: /usr/bin/python3 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/config.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/version.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/utils.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/samtools.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/bcftools.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/__init__.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/Pileup.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam creating /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include copying pysam/include/__init__.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) copying pysam/libchtslib.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcvcf.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcutils.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libctabix.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcsamtools.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcsamfile.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcfaidx.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcbcftools.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcbcf.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/pysam_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/pysam_stream.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/htslib_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/csamtools_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam copying pysam/cbcftools_util.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam creating /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/config.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/version.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sample.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam_header.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/sam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools copying samtools/bam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools creating /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools creating /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 copying samtools/win32/xcurses.h -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32 Fixing /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.linux-arm64-3.7 creating build/temp.linux-arm64-3.7/pysam aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libchtslib.c -o build/temp.linux-arm64-3.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/htslib_util.c -o build/temp.linux-arm64-3.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libchtslib.o build/temp.linux-arm64-3.7/pysam/htslib_util.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) building 'pysam.libcsamtools' extension creating build/temp.linux-arm64-3.7/samtools creating build/temp.linux-arm64-3.7/samtools/lz4 aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcsamtools.c -o build/temp.linux-arm64-3.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/tmp_file.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/stats.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/samtools.pysam.c -o build/temp.linux-arm64-3.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sample.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_view.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam_header.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/sam.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/phase.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/padding.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/faidx.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/dict.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/cut_target.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bedidx.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bedcov.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bamtk.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_split.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_md.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_index.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_import.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_color.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/bam.c.pysam.c -o build/temp.linux-arm64-3.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c samtools/lz4/lz4.c -o build/temp.linux-arm64-3.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcsamtools.o build/temp.linux-arm64-3.7/samtools/tmp_file.c.pysam.o build/temp.linux-arm64-3.7/samtools/stats_isize.c.pysam.o build/temp.linux-arm64-3.7/samtools/stats.c.pysam.o build/temp.linux-arm64-3.7/samtools/samtools.pysam.o build/temp.linux-arm64-3.7/samtools/sample.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam_view.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam_utils.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam_opts.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam_header.c.pysam.o build/temp.linux-arm64-3.7/samtools/sam.c.pysam.o build/temp.linux-arm64-3.7/samtools/phase.c.pysam.o build/temp.linux-arm64-3.7/samtools/padding.c.pysam.o build/temp.linux-arm64-3.7/samtools/faidx.c.pysam.o build/temp.linux-arm64-3.7/samtools/dict.c.pysam.o build/temp.linux-arm64-3.7/samtools/cut_target.c.pysam.o build/temp.linux-arm64-3.7/samtools/bedidx.c.pysam.o build/temp.linux-arm64-3.7/samtools/bedcov.c.pysam.o build/temp.linux-arm64-3.7/samtools/bamtk.c.pysam.o build/temp.linux-arm64-3.7/samtools/bamshuf.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_stat.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_split.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_sort.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_reheader.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_md.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_mate.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_markdup.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_index.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_import.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_flags.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_color.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_cat.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_aux.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam2depth.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam2bcf.c.pysam.o build/temp.linux-arm64-3.7/samtools/bam.c.pysam.o build/temp.linux-arm64-3.7/samtools/lz4/lz4.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) building 'pysam.libcbcftools' extension creating build/temp.linux-arm64-3.7/bcftools aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcbcftools.c -o build/temp.linux-arm64-3.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/filter.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/version.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/tabix.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/reheader.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/regidx.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/prob1.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/mcall.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/main.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/kmin.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/hclust.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/em.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/csq.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/convert.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/consensus.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/ccall.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bin.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bcftools.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c bcftools/HMM.c.pysam.c -o build/temp.linux-arm64-3.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcbcftools.o build/temp.linux-arm64-3.7/bcftools/filter.c.pysam.o build/temp.linux-arm64-3.7/bcftools/version.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcmp.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfview.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfstats.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfsort.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfsom.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfroh.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfquery.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfisec.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfindex.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcffilter.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfcall.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-arm64-3.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/tabix.c.pysam.o build/temp.linux-arm64-3.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-arm64-3.7/bcftools/reheader.c.pysam.o build/temp.linux-arm64-3.7/bcftools/regidx.c.pysam.o build/temp.linux-arm64-3.7/bcftools/prob1.c.pysam.o build/temp.linux-arm64-3.7/bcftools/ploidy.c.pysam.o build/temp.linux-arm64-3.7/bcftools/mpileup.c.pysam.o build/temp.linux-arm64-3.7/bcftools/mcall.c.pysam.o build/temp.linux-arm64-3.7/bcftools/main.c.pysam.o build/temp.linux-arm64-3.7/bcftools/kmin.c.pysam.o build/temp.linux-arm64-3.7/bcftools/hclust.c.pysam.o build/temp.linux-arm64-3.7/bcftools/gvcf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/em.c.pysam.o build/temp.linux-arm64-3.7/bcftools/csq.c.pysam.o build/temp.linux-arm64-3.7/bcftools/convert.c.pysam.o build/temp.linux-arm64-3.7/bcftools/consensus.c.pysam.o build/temp.linux-arm64-3.7/bcftools/ccall.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bin.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bcftools.pysam.o build/temp.linux-arm64-3.7/bcftools/bam_sample.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-arm64-3.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-arm64-3.7/bcftools/HMM.c.pysam.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcutils.c' Cython extension (up-to-date) building 'pysam.libcutils' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcutils.c -o build/temp.linux-arm64-3.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’: pysam/libcutils.c:6089:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration] bcftools_set_stderr(__pyx_t_9); ^~~~~~~~~~~~~~~~~~~ samtools_set_stderr pysam/libcutils.c:6233:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration] bcftools_set_stdout_fn(__pyx_t_12); ^~~~~~~~~~~~~~~~~~~~~~ samtools_set_stdout_fn pysam/libcutils.c:6244:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration] bcftools_set_stdout(__pyx_t_9); ^~~~~~~~~~~~~~~~~~~ samtools_set_stdout pysam/libcutils.c:6999:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration] bcftools_set_optind(1); ^~~~~~~~~~~~~~~~~~~ samtools_set_optind pysam/libcutils.c:7078:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration] __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs); ^~~~~~~~~~~~~ samtools_main pysam/libcutils.c:7147:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration] bcftools_unset_stderr(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stderr pysam/libcutils.c:7183:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration] bcftools_unset_stdout(); ^~~~~~~~~~~~~~~~~~~~~ samtools_unset_stdout pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:526:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^~~~~~~~~~~~~~~ pysam/libcutils.c:5821:7: note: ‘__pyx_v_retval’ was declared here int __pyx_v_retval; ^~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/pysam_util.c -o build/temp.linux-arm64-3.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcutils.o build/temp.linux-arm64-3.7/pysam/pysam_util.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcsamtools.cpython-37m-aarch64-linux-gnu -lcbcftools.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) building 'pysam.libcalignmentfile' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcalignmentfile.c -o build/temp.linux-arm64-3.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:29332:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); ~^~~~~~~~~~~~~~~~~~~ In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:619: /usr/include/htslib/sam.h:686:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); ~~~~~~~~~~~~~~~~~~~~~~^~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:27585:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:13687:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcalignmentfile.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) building 'pysam.libcsamfile' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcsamfile.c -o build/temp.linux-arm64-3.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcsamfile.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) building 'pysam.libcalignedsegment' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcalignedsegment.c -o build/temp.linux-arm64-3.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c:14226:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result] (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcalignedsegment.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabix.c' Cython extension (up-to-date) building 'pysam.libctabix' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libctabix.c -o build/temp.linux-arm64-3.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:8631:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); ^ pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: pysam/libctabix.c:13697:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:13729:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) ^~~~~~~~ pysam/libctabix.c:14099:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) ^~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libctabix.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) building 'pysam.libcfaidx' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcfaidx.c -o build/temp.linux-arm64-3.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcfaidx.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbcf.c' Cython extension (up-to-date) building 'pysam.libcbcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcbcf.c -o build/temp.linux-arm64-3.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’: pysam/libcbcf.c:32813:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen)); ^~~~~~~~~~~~ In file included from pysam/htslib_util.h:5, from pysam/libcbcf.c:618: /usr/include/htslib/vcf.h:439:11: note: declared here char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcbcf.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) building 'pysam.libcbgzf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcbgzf.c -o build/temp.linux-arm64-3.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcbgzf.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) building 'pysam.libctabixproxies' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libctabixproxies.c -o build/temp.linux-arm64-3.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libctabixproxies.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libcvcf' extension aarch64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcvcf.c -o build/temp.linux-arm64-3.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.79’: pysam/libcvcf.c:24828:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.7/pysam/libcvcf.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-aarch64-linux-gnu -lcutils.cpython-37m-aarch64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Map '/build/python-pysam-0.15.2+ds' wordt binnengegaan cd tests/pysam_data && /usr/bin/make all make[2]: Map '/build/python-pysam-0.15.2+ds/tests/pysam_data' wordt binnengegaan samtools faidx ex1.fa samtools import ex1.fa.fai ex1.sam.gz ex1.bam samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz [mpileup] 1 samples in 1 input files gunzip < ex1.sam.gz > ex1.sam samtools index ex1.bam samtools view -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view -bS ex2.sam > ex2.bam samtools index ex2.bam samtools calmd --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 gunzip < with_md.sam.gz > with_md.sam samtools view -bS with_md.sam > with_md.bam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated samtools index with_md.bam samtools view -buS ex2.sam > uncompressed.bam samtools view -bS example_dash_in_chr.sam > example_dash_in_chr.bam samtools view -bS tag_bug.sam > tag_bug.bam samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam samtools view -bS softclip.sam > softclip.bam samtools view -bS example_empty_with_header.sam > example_empty_with_header.bam samtools view -bS test_unaligned.sam > test_unaligned.bam samtools view -bS ex9_fail.sam > ex9_fail.bam samtools view -bS ex10.sam > ex10.bam samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam samtools view -bS example_empty_header.sam > example_empty_header.bam samtools view -bS ex6.sam > ex6.bam samtools view -bS ex9_nofail.sam > ex9_nofail.bam samtools view -bS issue100.sam > issue100.bam samtools view -bS ex5.sam > ex5.bam samtools view -bS example_reverse_complement.sam > example_reverse_complement.bam samtools view -bS ex8.sam > ex8.bam samtools view -bS rg_with_tab.sam > rg_with_tab.bam samtools view -bS ex_spliced.sam > ex_spliced.bam samtools view -bS example_btag.sam > example_btag.bam samtools view -bS ex4.sam > ex4.bam samtools view -bS test_query_position.sam > test_query_position.bam touch tmp.list samtools import tmp.list example_unmapped_reads_no_sq.sam example_unmapped_reads_no_sq.bam rm -f tmp.list samtools view -bS example_user_header.sam > example_user_header.bam samtools view -bS ex3.sam > ex3.bam samtools index example_dash_in_chr.bam samtools index tag_bug.bam samtools index test_mapped_unmapped.bam samtools index softclip.bam samtools index example_empty_with_header.bam samtools index test_unaligned.bam samtools index ex9_fail.bam samtools index ex10.bam samtools index example_aligned_pairs.bam samtools index example_empty_header.bam samtools index ex6.bam samtools index ex9_nofail.bam samtools index issue100.bam samtools index ex5.bam samtools index example_reverse_complement.bam samtools index ex8.bam samtools index rg_with_tab.bam samtools index ex_spliced.bam samtools index example_btag.bam samtools index ex4.bam samtools index test_query_position.bam samtools index example_unmapped_reads_no_sq.bam samtools index example_user_header.bam samtools index ex3.bam samtools view -bC -T ex1.fa ex1.sam > ex1.cram samtools view -bC -T ex1.fa ex2.sam > ex2.cram samtools view -bC -T ex1.fa ex3.sam > ex3.cram samtools index ex1.cram samtools index ex2.cram samtools index ex3.cram cp ex1.bam example_bai.bam samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai head -c 124000 ex2.bam > ex2_truncated.bam grep "^@" ex2.sam | samtools view -Sb - > empty.bam samtools index empty.bam cp ex1.bam explicit_index.bam cp ex1.cram explicit_index.cram gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz bgzip < ex1.fa > ex1.fa.gz samtools faidx ex1.fa.gz cp ex1.bam ex1_csi.bam samtools index -c ex1_csi.bam rm with_md.sam make[2]: Map '/build/python-pysam-0.15.2+ds/tests/pysam_data' wordt verlaten cd tests/cbcf_data && /usr/bin/make all make[2]: Map '/build/python-pysam-0.15.2+ds/tests/cbcf_data' wordt binnengegaan bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index bcftools index example_vcf42_withcontigs.vcf.gz # create csi index bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz tabix -p vcf gnomad_fixed.vcf.gz # create tbi index bcftools index gnomad_fixed.vcf.gz # create csi index bgzip < gnomad.vcf > gnomad.vcf.gz tabix -p vcf gnomad.vcf.gz # create tbi index bcftools index gnomad.vcf.gz # create csi index bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz tabix -p vcf missing_genotypes.vcf.gz # create tbi index bcftools index missing_genotypes.vcf.gz # create csi index bgzip < example_vcf42.vcf > example_vcf42.vcf.gz tabix -p vcf example_vcf42.vcf.gz # create tbi index bcftools index example_vcf42.vcf.gz # create csi index bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index bcftools index example_vcf42_only_header.vcf.gz # create csi index bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf bcftools index example_vcf42_withcontigs.bcf bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf bcftools index example_vcf40.bcf bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools index gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools view -O b gnomad.vcf.gz -o gnomad.bcf bcftools index gnomad.bcf bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf bcftools index example_vcf42.bcf bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf bcftools index example_vcf42_only_header.bcf make[2]: Map '/build/python-pysam-0.15.2+ds/tests/cbcf_data' wordt verlaten dh_auto_test I: pybuild base:217: cd /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests ============================= test session starts ============================== platform linux2 -- Python 2.7.16, pytest-3.10.1, py-1.7.0, pluggy-0.8.0 -- /usr/bin/python2.7 cachedir: .pytest_cache rootdir: /build/python-pysam-0.15.2+ds, inifile: setup.cfg collecting ... collected 926 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testLongTags PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_AgdhVC PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_XVKCcx PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_SR3ect PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_cXdN2k PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_RAbdXR PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_epj9Pb PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal SKIPPED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal SKIPPED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file missing_directory/new_file.bam PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing SKIPPED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =============================== warnings summary =============================== /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367 /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/_compile_test.pyx tree = Parsing.p_module(s, pxd, full_module_name) .pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1459: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) -- Docs: https://docs.pytest.org/en/latest/warnings.html ============= 909 passed, 17 skipped, 2 warnings in 110.86 seconds ============= I: pybuild base:217: cd /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build; python3.7 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.7.3, pytest-3.10.1, py-1.7.0, pluggy-0.8.0 -- /usr/bin/python3.7 cachedir: .pytest_cache rootdir: /build/python-pysam-0.15.2+ds, inifile: setup.cfg collecting ... collected 930 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testLongTags PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1fxavrk6 PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_pw81ewps PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_p1kdaqny PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_fmighc_0 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_rl1khlba PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_3aou2d38 PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file missing_directory/new_file.bam PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam [E::hts_open_format] Failed to open file exdoesntexist.bam [E::hts_open_format] Failed to open file exdoesntexist.sam PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/pysam_data/ex1.bam.bai PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/compile_test.py::BAMTest::testCount PASSED tests/compile_test.py::GTFTest::testCount PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestUnicode::testFromTabix PASSED tests/tabix_test.py::TestUnicode::testFromVCF PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =============================== warnings summary =============================== pysam/__init__.py:16 /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working import pysam.libcsamfile as libcsamfile /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working import pysam.libcsamfile as libcsamfile /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367 /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/_compile_test.pyx tree = Parsing.p_module(s, pxd, full_module_name) tests/samtools_test.py:48 /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/samtools_test.py:48: DeprecationWarning: invalid escape sequence \s x = re.search("Version:\s+(\S+)", lines).groups()[0] tests/samtools_test.py:192 /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/samtools_test.py:192: DeprecationWarning: invalid escape sequence \( full_statement = re.sub("%\(out\)s", self.executable, statement) tests/samtools_test.py:202 /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/samtools_test.py:202: DeprecationWarning: invalid escape sequence \( pysam_parts = [re.sub("%\(out\)s", "pysam", x) for x in parts[1:]] tests/samtools_test.py:275 /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/samtools_test.py:275: DeprecationWarning: invalid escape sequence \s expected = "Usage:\s+{} {}".format(self.executable, command) tests/tabixproxies_test.py:131 /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/tabixproxies_test.py:131: DeprecationWarning: invalid escape sequence \d s = re.sub("\"(\d+)\"", r"\1", s) .pybuild/cpython3_3.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/tests/AlignmentFile_test.py:1459: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) -- Docs: https://docs.pytest.org/en/latest/warnings.html ============= 920 passed, 10 skipped, 9 warnings in 112.82 seconds ============= make[1]: Map '/build/python-pysam-0.15.2+ds' wordt verlaten create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python2,python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py install --root /build/python-pysam-0.15.2+ds/debian/python-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) running install_lib creating /build/python-pysam-0.15.2+ds/debian/python-pysam creating /build/python-pysam-0.15.2+ds/debian/python-pysam/usr creating /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib creating /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7 creating /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/log.txt -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages creating /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/config.py -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/bcftools.pyc -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/version.pyc -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/config.pyc -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/samtools.pyc -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/Pileup.pyc -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/utils.pyc -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/__init__.pyc -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/cbcftools_util.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/csamtools_util.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/htslib_util.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_stream.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_util.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.pxd -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam creating /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include creating /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/HMM.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam_sample.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bin.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/call.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/convert.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/filter.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/gvcf.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/hclust.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/khash_str2str.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kheap.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kmin.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/mw.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/ploidy.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/prob1.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/rbuf.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/regidx.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcfbuf.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcmp.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/version.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/config.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools creating /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools creating /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/xcurses.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/zconf.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/zlib.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32 copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_endian.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_lpileup.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_plbuf.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bedidx.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam_header.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam_opts.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sample.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.pysam.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/stats_isize.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/tmp_file.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/version.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/config.h -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/__init__.py -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/Pileup.py -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/__init__.py -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/bcftools.py -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/samtools.py -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/utils.py -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/version.py -> /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam byte-compiling /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/config.py to config.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/__init__.py to __init__.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/Pileup.py to Pileup.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/__init__.py to __init__.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/bcftools.py to bcftools.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/samtools.py to samtools.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/utils.py to utils.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/version.py to version.pyc running install_egg_info running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/INSTALL' warning: no files found matching 'htslib/NEWS' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib.pc.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'htslib/os/*.c' warning: no files found matching 'htslib/os/*.h' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /build/python-pysam-0.15.2+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.15.2.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/python-pysam-0.15.2+ds/debian/python3-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'samtools/win32/__init__.py' not found (or not a regular file) Fixing /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) running install_lib creating /build/python-pysam-0.15.2+ds/debian/python3-pysam creating /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr creating /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib creating /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7 creating /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/log.txt -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages creating /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam creating /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/bcftools.cpython-37.pyc -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/version.cpython-37.pyc -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/config.cpython-37.pyc -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/samtools.cpython-37.pyc -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/Pileup.cpython-37.pyc -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/utils.cpython-37.pyc -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__pycache__/__init__.cpython-37.pyc -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__pycache__ copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-aarch64-linux-gnu.so -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/cbcftools_util.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/csamtools_util.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/htslib_util.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/pysam_stream.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/pysam_util.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.pxd -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam creating /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include creating /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/HMM.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bam_sample.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bcftools.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bin.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/call.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/convert.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/filter.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/gvcf.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/hclust.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/khash_str2str.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/kheap.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/kmin.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/mw.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/ploidy.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/prob1.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/rbuf.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/regidx.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/vcfbuf.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/vcmp.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/version.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/config.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools creating /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools creating /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/xcurses.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/zconf.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/zlib.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32 copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam2bcf.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_endian.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_lpileup.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_plbuf.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bedidx.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam_header.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam_opts.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sample.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/samtools.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/samtools.pysam.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/stats_isize.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/tmp_file.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/version.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/config.h -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam copying /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py -> /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam byte-compiling /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/config.py to config.cpython-37.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/__init__.py to __init__.cpython-37.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/Pileup.py to Pileup.cpython-37.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__init__.py to __init__.cpython-37.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/bcftools.py to bcftools.cpython-37.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/samtools.py to samtools.cpython-37.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/utils.py to utils.cpython-37.pyc byte-compiling /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/version.py to version.cpython-37.pyc running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/INSTALL' warning: no files found matching 'htslib/NEWS' warning: no previously-included files found matching 'htslib/config.h' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/htslib_vars.mk' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/config.mk.in' warning: no files found matching 'htslib/config.h.in' warning: no files found matching 'htslib/htslib.pc.in' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' warning: no files found matching 'htslib/os/*.c' warning: no files found matching 'htslib/os/*.h' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /build/python-pysam-0.15.2+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam-0.15.2.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Map '/build/python-pysam-0.15.2+ds' wordt binnengegaan cd tests/pysam_data && /usr/bin/make clean make[2]: Map '/build/python-pysam-0.15.2+ds/tests/pysam_data' wordt binnengegaan rm -fr *.bam *.bai *.fai *.pileup* *.cram \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam \ with_md.sam.gz \ *.fq.gz make[2]: Map '/build/python-pysam-0.15.2+ds/tests/pysam_data' wordt verlaten cd tests/cbcf_data && /usr/bin/make clean make[2]: Map '/build/python-pysam-0.15.2+ds/tests/cbcf_data' wordt binnengegaan rm -f *.gz *.tbi *.csi *.bcf make[2]: Map '/build/python-pysam-0.15.2+ds/tests/cbcf_data' wordt verlaten find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete #find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully find . -name "*.bai*" -delete find . -name "*.cram*" -delete #find . -name "*.bam" -delete # which deletes files tested rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh_install -Xtest.gtf.gz find debian -name log.txt -delete make[1]: Map '/build/python-pysam-0.15.2+ds' wordt verlaten dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python2 -O--buildsystem=pybuild I: dh_python2 fs:343: renaming libcalignedsegment.so to libcalignedsegment.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcalignmentfile.so to libcalignmentfile.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcbcf.so to libcbcf.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcbcftools.so to libcbcftools.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcbgzf.so to libcbgzf.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcfaidx.so to libcfaidx.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libchtslib.so to libchtslib.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcsamfile.so to libcsamfile.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcsamtools.so to libcsamtools.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libctabix.so to libctabix.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libctabixproxies.so to libctabixproxies.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcutils.so to libcutils.aarch64-linux-gnu.so I: dh_python2 fs:343: renaming libcvcf.so to libcvcf.aarch64-linux-gnu.so dh_python3 -O--buildsystem=pybuild dh_installinit -O--buildsystem=pybuild dh_lintian -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 dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python-pysam: substitution variable ${python:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python-pysam: substitution variable ${python:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: pakket 'python-pysam-dbgsym' wordt gebouwd in '../python-pysam-dbgsym_0.15.2+ds-2_arm64.deb'. dpkg-deb: pakket 'python3-pysam' wordt gebouwd in '../python3-pysam_0.15.2+ds-2_arm64.deb'. dpkg-deb: pakket 'python-pysam' wordt gebouwd in '../python-pysam_0.15.2+ds-2_arm64.deb'. dpkg-deb: pakket 'python-pysam-tests' wordt gebouwd in '../python-pysam-tests_0.15.2+ds-2_all.deb'. dpkg-deb: pakket 'python3-pysam-dbgsym' wordt gebouwd in '../python3-pysam-dbgsym_0.15.2+ds-2_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../python-pysam_0.15.2+ds-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/20239/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/20239/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/20239 and its subdirectories I: Current time: Mon Aug 31 16:02:34 +14 2020 I: pbuilder-time-stamp: 1598839354