Diff of the two buildlogs: -- --- b1/build.log 2022-08-26 12:19:27.543563472 +0000 +++ b2/build.log 2022-08-26 12:20:09.717986297 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Aug 26 00:05:22 -12 2022 -I: pbuilder-time-stamp: 1661515522 +I: Current time: Fri Sep 29 08:42:34 +14 2023 +I: pbuilder-time-stamp: 1695926554 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Feb 19 22:46:46 2019 -12 +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 @@ -31,136 +31,171 @@ dpkg-source: info: applying test_index_not_compression I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3467907/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3074934/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +lrwxrwxrwx 1 root root 4 Sep 29 08:42 /bin/sh -> 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/3074934/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3074934/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='310c0c27a5504ea58e34655180da7c7a' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3467907' - PS1='# ' - PS2='> ' + INVOCATION_ID=6c2f4d8ca76d496ca55f3da1fc906e9e + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3074934 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.dy8GHCjWPC/pbuilderrc_KZip --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.dy8GHCjWPC/b1 --logfile b1/build.log python-pysam_0.15.2+ds-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.dy8GHCjWPC/pbuilderrc_xWAu --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.dy8GHCjWPC/b2 --logfile b2/build.log python-pysam_0.15.2+ds-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-17-amd64 #1 SMP Debian 5.10.136-1 (2022-08-13) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.18.0-0.deb11.3-amd64 #1 SMP PREEMPT_DYNAMIC Debian 5.18.14-1~bpo11+1 (2022-07-28) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 6 20:23 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/3467907/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 29 08:42 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 10 04:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/3074934/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -226,639 +261,256 @@ 0 packages upgraded, 124 newly installed, 0 to remove and 0 not upgraded. Need to get 127 MB of archives. After unpacking 303 MB will be used. Writing extended state information... -Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] -Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] -Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] -Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] -Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] -Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] -Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] -Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] -Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] -Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] -Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u1 [1551 kB] -Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] -Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] -Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] -Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] -Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] -Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] -Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] -Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] -Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] -Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] -Get: 22 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] -Get: 23 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] -Get: 24 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] -Get: 25 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] -Get: 26 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] -Get: 27 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] -Get: 28 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] -Get: 29 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] -Get: 30 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] -Get: 31 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] -Get: 32 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] -Get: 33 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] -Get: 34 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] -Get: 35 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] -Get: 36 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] -Get: 37 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] -Get: 38 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] -Get: 39 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] -Get: 40 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] -Get: 41 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] -Get: 42 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] -Get: 43 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] -Get: 44 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] -Get: 45 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] -Get: 46 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] -Get: 47 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] -Get: 48 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] -Get: 49 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] -Get: 50 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] -Get: 51 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] -Get: 52 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] -Get: 53 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] -Get: 54 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] -Get: 55 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] -Get: 56 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] -Get: 57 http://deb.debian.org/debian buster/main amd64 bcftools amd64 1.9-1 [527 kB] -Get: 58 http://deb.debian.org/debian buster/main amd64 cython amd64 0.29.2-2 [1365 kB] -Get: 59 http://deb.debian.org/debian buster/main amd64 cython3 amd64 0.29.2-2 [1392 kB] -Get: 60 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] -Get: 61 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] -Get: 62 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] -Get: 63 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] -Get: 64 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] -Get: 65 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] -Get: 66 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] -Get: 67 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] -Get: 68 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u3 [8293 kB] -Get: 69 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u3 [689 kB] -Get: 70 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] -Get: 71 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] -Get: 72 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] -Get: 73 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] -Get: 74 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] -Get: 75 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] -Get: 76 http://deb.debian.org/debian buster/main amd64 dh-exec amd64 0.23.1 [26.3 kB] -Get: 77 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] -Get: 78 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] -Get: 79 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] -Get: 80 http://deb.debian.org/debian buster/main amd64 libexpat1-dev amd64 2.2.6-2+deb10u4 [155 kB] -Get: 81 http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1 [210 kB] -Get: 82 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] -Get: 83 http://deb.debian.org/debian buster/main amd64 libhts-dev amd64 1.9-12~deb10u1 [4347 kB] -Get: 84 http://deb.debian.org/debian buster/main amd64 libpython2.7 amd64 2.7.16-2+deb10u1 [1036 kB] -Get: 85 http://deb.debian.org/debian buster/main amd64 libpython2.7-dev amd64 2.7.16-2+deb10u1 [31.6 MB] -Get: 86 http://deb.debian.org/debian buster/main amd64 libpython2-dev amd64 2.7.16-1 [20.9 kB] -Get: 87 http://deb.debian.org/debian buster/main amd64 libpython-dev amd64 2.7.16-1 [20.9 kB] -Get: 88 http://deb.debian.org/debian buster/main amd64 libpython-all-dev amd64 2.7.16-1 [1064 B] -Get: 89 http://deb.debian.org/debian buster/main amd64 libpython3.7 amd64 3.7.3-2+deb10u3 [1498 kB] -Get: 90 http://deb.debian.org/debian buster/main amd64 libpython3.7-dev amd64 3.7.3-2+deb10u3 [48.4 MB] -Get: 91 http://deb.debian.org/debian buster/main amd64 libpython3-dev amd64 3.7.3-1 [20.1 kB] -Get: 92 http://deb.debian.org/debian buster/main amd64 libpython3-all-dev amd64 3.7.3-1 [1068 B] -Get: 93 http://deb.debian.org/debian buster/main amd64 python-all amd64 2.7.16-1 [1044 B] -Get: 94 http://deb.debian.org/debian buster/main amd64 python2.7-dev amd64 2.7.16-2+deb10u1 [294 kB] -Get: 95 http://deb.debian.org/debian buster/main amd64 python2-dev amd64 2.7.16-1 [1212 B] -Get: 96 http://deb.debian.org/debian buster/main amd64 python-dev amd64 2.7.16-1 [1192 B] -Get: 97 http://deb.debian.org/debian buster/main amd64 python-all-dev amd64 2.7.16-1 [1068 B] -Get: 98 http://deb.debian.org/debian buster/main amd64 python-atomicwrites all 1.1.5-2 [6808 B] -Get: 99 http://deb.debian.org/debian buster/main amd64 python-attr all 18.2.0-1 [37.2 kB] -Get: 100 http://deb.debian.org/debian buster/main amd64 python-funcsigs all 1.0.2-4 [13.7 kB] -Get: 101 http://deb.debian.org/debian buster/main amd64 python-six all 1.12.0-1 [15.7 kB] -Get: 102 http://deb.debian.org/debian buster/main amd64 python-more-itertools all 4.2.0-1 [42.3 kB] -Get: 103 http://deb.debian.org/debian buster/main amd64 python-scandir amd64 1.9.0-2 [18.3 kB] -Get: 104 http://deb.debian.org/debian buster/main amd64 python-pathlib2 all 2.3.3-1 [18.3 kB] -Get: 105 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] -Get: 106 http://deb.debian.org/debian buster/main amd64 python-pluggy all 0.8.0-1 [20.5 kB] -Get: 107 http://deb.debian.org/debian buster/main amd64 python-py all 1.7.0-2 [86.5 kB] -Get: 108 http://deb.debian.org/debian buster/main amd64 python-pytest all 3.10.1-2 [243 kB] -Get: 109 http://deb.debian.org/debian buster/main amd64 python-setuptools all 40.8.0-1 [382 kB] -Get: 110 http://deb.debian.org/debian buster/main amd64 python3-all amd64 3.7.3-1 [1068 B] -Get: 111 http://deb.debian.org/debian buster/main amd64 python3.7-dev amd64 3.7.3-2+deb10u3 [510 kB] -Get: 112 http://deb.debian.org/debian buster/main amd64 python3-dev amd64 3.7.3-1 [1264 B] -Get: 113 http://deb.debian.org/debian buster/main amd64 python3-all-dev amd64 3.7.3-1 [1064 B] -Get: 114 http://deb.debian.org/debian buster/main amd64 python3-atomicwrites all 1.1.5-2 [6892 B] -Get: 115 http://deb.debian.org/debian buster/main amd64 python3-attr all 18.2.0-1 [37.3 kB] -Get: 116 http://deb.debian.org/debian buster/main amd64 python3-six all 1.12.0-1 [15.7 kB] -Get: 117 http://deb.debian.org/debian buster/main amd64 python3-more-itertools all 4.2.0-1 [42.2 kB] -Get: 118 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] -Get: 119 http://deb.debian.org/debian buster/main amd64 python3-pluggy all 0.8.0-1 [20.6 kB] -Get: 120 http://deb.debian.org/debian buster/main amd64 python3-py all 1.7.0-2 [86.6 kB] -Get: 121 http://deb.debian.org/debian buster/main amd64 python3-pytest all 3.10.1-2 [243 kB] -Get: 122 http://deb.debian.org/debian buster/main amd64 python3-setuptools all 40.8.0-1 [306 kB] -Get: 123 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] -Get: 124 http://deb.debian.org/debian buster/main amd64 tabix amd64 1.9-12~deb10u1 [292 kB] -Fetched 127 MB in 2s (51.8 MB/s) -debconf: delaying package configuration, since apt-utils is not installed -Selecting previously unselected package libbsd0:amd64. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) -Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... -Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... -Selecting previously unselected package bsdmainutils. -Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... -Unpacking bsdmainutils (11.1.2+b1) ... -Selecting previously unselected package libuchardet0:amd64. -Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... -Unpacking libuchardet0:amd64 (0.0.6-3) ... -Selecting previously unselected package groff-base. -Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... -Unpacking groff-base (1.22.4-3+deb10u1) ... -Selecting previously unselected package libpipeline1:amd64. -Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... -Unpacking libpipeline1:amd64 (1.5.1-2) ... -Selecting previously unselected package man-db. -Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... -Unpacking man-db (2.8.5-2) ... -Selecting previously unselected package libpython2.7-minimal:amd64. -Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... -Unpacking libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... -Selecting previously unselected package python2.7-minimal. -Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_amd64.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_amd64.deb ... -Unpacking python2-minimal (2.7.16-1) ... -Selecting previously unselected package python-minimal. -Preparing to unpack .../09-python-minimal_2.7.16-1_amd64.deb ... -Unpacking python-minimal (2.7.16-1) ... -Selecting previously unselected package libssl1.1:amd64. -Preparing to unpack .../10-libssl1.1_1.1.1n-0+deb10u1_amd64.deb ... -Unpacking libssl1.1:amd64 (1.1.1n-0+deb10u1) ... -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:amd64. -Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u4_amd64.deb ... -Unpacking libexpat1:amd64 (2.2.6-2+deb10u4) ... -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:amd64. -Preparing to unpack .../14-libreadline7_7.0-5_amd64.deb ... -Unpacking libreadline7:amd64 (7.0-5) ... -Selecting previously unselected package libpython2.7-stdlib:amd64. -Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_amd64.deb ... -Unpacking libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... -Selecting previously unselected package python2.7. -Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_amd64.deb ... -Unpacking python2.7 (2.7.16-2+deb10u1) ... -Selecting previously unselected package libpython2-stdlib:amd64. -Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_amd64.deb ... -Unpacking libpython2-stdlib:amd64 (2.7.16-1) ... -Selecting previously unselected package libpython-stdlib:amd64. -Preparing to unpack .../18-libpython-stdlib_2.7.16-1_amd64.deb ... -Unpacking libpython-stdlib:amd64 (2.7.16-1) ... -Setting up libpython2.7-minimal:amd64 (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 ... 20658 files and directories currently installed.) -Preparing to unpack .../python2_2.7.16-1_amd64.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 ... 20691 files and directories currently installed.) -Preparing to unpack .../python_2.7.16-1_amd64.deb ... -Unpacking python (2.7.16-1) ... -Selecting previously unselected package libpython3.7-minimal:amd64. -Preparing to unpack .../libpython3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... -Unpacking libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... -Selecting previously unselected package python3.7-minimal. -Preparing to unpack .../python3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... -Unpacking python3.7-minimal (3.7.3-2+deb10u3) ... -Setting up libssl1.1:amd64 (1.1.1n-0+deb10u1) ... -Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... -Setting up libexpat1:amd64 (2.2.6-2+deb10u4) ... -Setting up python3.7-minimal (3.7.3-2+deb10u3) ... -Selecting previously unselected package python3-minimal. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20945 files and directories currently installed.) -Preparing to unpack .../python3-minimal_3.7.3-1_amd64.deb ... -Unpacking python3-minimal (3.7.3-1) ... -Selecting previously unselected package libmpdec2:amd64. -Preparing to unpack .../libmpdec2_2.4.2-2_amd64.deb ... -Unpacking libmpdec2:amd64 (2.4.2-2) ... -Selecting previously unselected package libpython3.7-stdlib:amd64. -Preparing to unpack .../libpython3.7-stdlib_3.7.3-2+deb10u3_amd64.deb ... -Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... -Selecting previously unselected package python3.7. -Preparing to unpack .../python3.7_3.7.3-2+deb10u3_amd64.deb ... -Unpacking python3.7 (3.7.3-2+deb10u3) ... -Selecting previously unselected package libpython3-stdlib:amd64. -Preparing to unpack .../libpython3-stdlib_3.7.3-1_amd64.deb ... -Unpacking libpython3-stdlib:amd64 (3.7.3-1) ... -Setting up python3-minimal (3.7.3-1) ... -Selecting previously unselected package python3. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21357 files and directories currently installed.) -Preparing to unpack .../00-python3_3.7.3-1_amd64.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+deb10u2_amd64.deb ... -Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... -Selecting previously unselected package libmagic1:amd64. -Preparing to unpack .../03-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... -Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... -Selecting previously unselected package file. -Preparing to unpack .../04-file_1%3a5.35-4+deb10u2_amd64.deb ... -Unpacking file (1:5.35-4+deb10u2) ... -Selecting previously unselected package gettext-base. -Preparing to unpack .../05-gettext-base_0.19.8.1-9_amd64.deb ... -Unpacking gettext-base (0.19.8.1-9) ... -Selecting previously unselected package libsigsegv2:amd64. -Preparing to unpack .../06-libsigsegv2_2.12-2_amd64.deb ... -Unpacking libsigsegv2:amd64 (2.12-2) ... -Selecting previously unselected package m4. -Preparing to unpack .../07-m4_1.4.18-2_amd64.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:amd64. -Preparing to unpack .../12-libkeyutils1_1.6-6_amd64.deb ... -Unpacking libkeyutils1:amd64 (1.6-6) ... -Selecting previously unselected package libkrb5support0:amd64. -Preparing to unpack .../13-libkrb5support0_1.17-3+deb10u3_amd64.deb ... -Unpacking libkrb5support0:amd64 (1.17-3+deb10u3) ... -Selecting previously unselected package libk5crypto3:amd64. -Preparing to unpack .../14-libk5crypto3_1.17-3+deb10u3_amd64.deb ... -Unpacking libk5crypto3:amd64 (1.17-3+deb10u3) ... -Selecting previously unselected package libkrb5-3:amd64. -Preparing to unpack .../15-libkrb5-3_1.17-3+deb10u3_amd64.deb ... -Unpacking libkrb5-3:amd64 (1.17-3+deb10u3) ... -Selecting previously unselected package libgssapi-krb5-2:amd64. -Preparing to unpack .../16-libgssapi-krb5-2_1.17-3+deb10u3_amd64.deb ... -Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... -Selecting previously unselected package libsasl2-modules-db:amd64. -Preparing to unpack .../17-libsasl2-modules-db_2.1.27+dfsg-1+deb10u2_amd64.deb ... -Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... -Selecting previously unselected package libsasl2-2:amd64. -Preparing to unpack .../18-libsasl2-2_2.1.27+dfsg-1+deb10u2_amd64.deb ... -Unpacking libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... -Selecting previously unselected package libldap-common. -Preparing to unpack .../19-libldap-common_2.4.47+dfsg-3+deb10u6_all.deb ... -Unpacking libldap-common (2.4.47+dfsg-3+deb10u6) ... -Selecting previously unselected package libldap-2.4-2:amd64. -Preparing to unpack .../20-libldap-2.4-2_2.4.47+dfsg-3+deb10u6_amd64.deb ... -Unpacking libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... -Selecting previously unselected package libnghttp2-14:amd64. -Preparing to unpack .../21-libnghttp2-14_1.36.0-2+deb10u1_amd64.deb ... -Unpacking libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... -Selecting previously unselected package libpsl5:amd64. -Preparing to unpack .../22-libpsl5_0.20.2-2_amd64.deb ... -Unpacking libpsl5:amd64 (0.20.2-2) ... -Selecting previously unselected package librtmp1:amd64. -Preparing to unpack .../23-librtmp1_2.4+20151223.gitfa8646d.1-2_amd64.deb ... -Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... -Selecting previously unselected package libssh2-1:amd64. -Preparing to unpack .../24-libssh2-1_1.8.0-2.1_amd64.deb ... -Unpacking libssh2-1:amd64 (1.8.0-2.1) ... -Selecting previously unselected package libcurl3-gnutls:amd64. -Preparing to unpack .../25-libcurl3-gnutls_7.64.0-4+deb10u2_amd64.deb ... -Unpacking libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... -Selecting previously unselected package libdeflate0:amd64. -Preparing to unpack .../26-libdeflate0_1.2-1_amd64.deb ... -Unpacking libdeflate0:amd64 (1.2-1) ... -Selecting previously unselected package libhts2:amd64. -Preparing to unpack .../27-libhts2_1.9-12~deb10u1_amd64.deb ... -Unpacking libhts2:amd64 (1.9-12~deb10u1) ... -Selecting previously unselected package bcftools. -Preparing to unpack .../28-bcftools_1.9-1_amd64.deb ... -Unpacking bcftools (1.9-1) ... -Selecting previously unselected package cython. -Preparing to unpack .../29-cython_0.29.2-2_amd64.deb ... -Unpacking cython (0.29.2-2) ... -Selecting previously unselected package cython3. -Preparing to unpack .../30-cython3_0.29.2-2_amd64.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. -Preparing to unpack .../32-dh-autoreconf_19_all.deb ... -Unpacking dh-autoreconf (19) ... -Selecting previously unselected package libarchive-zip-perl. -Preparing to unpack .../33-libarchive-zip-perl_1.64-1_all.deb ... -Unpacking libarchive-zip-perl (1.64-1) ... -Selecting previously unselected package libfile-stripnondeterminism-perl. -Preparing to unpack .../34-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... -Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... -Selecting previously unselected package dh-strip-nondeterminism. -Preparing to unpack .../35-dh-strip-nondeterminism_1.1.2-1_all.deb ... -Unpacking dh-strip-nondeterminism (1.1.2-1) ... -Selecting previously unselected package libelf1:amd64. -Preparing to unpack .../36-libelf1_0.176-1.1_amd64.deb ... -Unpacking libelf1:amd64 (0.176-1.1) ... -Selecting previously unselected package dwz. -Preparing to unpack .../37-dwz_0.12-3_amd64.deb ... -Unpacking dwz (0.12-3) ... -Selecting previously unselected package libglib2.0-0:amd64. -Preparing to unpack .../38-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... -Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... -Selecting previously unselected package libicu63:amd64. -Preparing to unpack .../39-libicu63_63.1-6+deb10u3_amd64.deb ... -Unpacking libicu63:amd64 (63.1-6+deb10u3) ... -Selecting previously unselected package libxml2:amd64. -Preparing to unpack .../40-libxml2_2.9.4+dfsg1-7+deb10u3_amd64.deb ... -Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u3) ... -Selecting previously unselected package libcroco3:amd64. -Preparing to unpack .../41-libcroco3_0.6.12-3_amd64.deb ... -Unpacking libcroco3:amd64 (0.6.12-3) ... -Selecting previously unselected package libncurses6:amd64. -Preparing to unpack .../42-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... -Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... -Selecting previously unselected package gettext. -Preparing to unpack .../43-gettext_0.19.8.1-9_amd64.deb ... -Unpacking gettext (0.19.8.1-9) ... -Selecting previously unselected package intltool-debian. -Preparing to unpack .../44-intltool-debian_0.35.0+20060710.5_all.deb ... -Unpacking intltool-debian (0.35.0+20060710.5) ... -Selecting previously unselected package po-debconf. -Preparing to unpack .../45-po-debconf_1.0.21_all.deb ... -Unpacking po-debconf (1.0.21) ... -Selecting previously unselected package debhelper. -Preparing to unpack .../46-debhelper_12.1.1_all.deb ... -Unpacking debhelper (12.1.1) ... -Selecting previously unselected package dh-exec. -Preparing to unpack .../47-dh-exec_0.23.1_amd64.deb ... -Unpacking dh-exec (0.23.1) ... -Selecting previously unselected package python3-lib2to3. -Preparing to unpack .../48-python3-lib2to3_3.7.3-1_all.deb ... -Unpacking python3-lib2to3 (3.7.3-1) ... -Selecting previously unselected package python3-distutils. -Preparing to unpack .../49-python3-distutils_3.7.3-1_all.deb ... -Unpacking python3-distutils (3.7.3-1) ... -Selecting previously unselected package dh-python. -Preparing to unpack .../50-dh-python_3.20190308_all.deb ... -Unpacking dh-python (3.20190308) ... -Selecting previously unselected package libexpat1-dev:amd64. -Preparing to unpack .../51-libexpat1-dev_2.2.6-2+deb10u4_amd64.deb ... -Unpacking libexpat1-dev:amd64 (2.2.6-2+deb10u4) ... -Selecting previously unselected package liblzma-dev:amd64. -Preparing to unpack .../52-liblzma-dev_5.2.4-1_amd64.deb ... -Unpacking liblzma-dev:amd64 (5.2.4-1) ... -Selecting previously unselected package zlib1g-dev:amd64. -Preparing to unpack .../53-zlib1g-dev_1%3a1.2.11.dfsg-1_amd64.deb ... -Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... -Selecting previously unselected package libhts-dev:amd64. -Preparing to unpack .../54-libhts-dev_1.9-12~deb10u1_amd64.deb ... -Unpacking libhts-dev:amd64 (1.9-12~deb10u1) ... -Selecting previously unselected package libpython2.7:amd64. -Preparing to unpack .../55-libpython2.7_2.7.16-2+deb10u1_amd64.deb ... -Unpacking libpython2.7:amd64 (2.7.16-2+deb10u1) ... -Selecting previously unselected package libpython2.7-dev:amd64. -Preparing to unpack .../56-libpython2.7-dev_2.7.16-2+deb10u1_amd64.deb ... -Unpacking libpython2.7-dev:amd64 (2.7.16-2+deb10u1) ... -Selecting previously unselected package libpython2-dev:amd64. -Preparing to unpack .../57-libpython2-dev_2.7.16-1_amd64.deb ... -Unpacking libpython2-dev:amd64 (2.7.16-1) ... -Selecting previously unselected package libpython-dev:amd64. -Preparing to unpack .../58-libpython-dev_2.7.16-1_amd64.deb ... -Unpacking libpython-dev:amd64 (2.7.16-1) ... -Selecting previously unselected package libpython-all-dev:amd64. -Preparing to unpack .../59-libpython-all-dev_2.7.16-1_amd64.deb ... -Unpacking libpython-all-dev:amd64 (2.7.16-1) ... -Selecting previously unselected package libpython3.7:amd64. -Preparing to unpack .../60-libpython3.7_3.7.3-2+deb10u3_amd64.deb ... -Unpacking libpython3.7:amd64 (3.7.3-2+deb10u3) ... -Selecting previously unselected package libpython3.7-dev:amd64. -Preparing to unpack .../61-libpython3.7-dev_3.7.3-2+deb10u3_amd64.deb ... -Unpacking libpython3.7-dev:amd64 (3.7.3-2+deb10u3) ... -Selecting previously unselected package libpython3-dev:amd64. -Preparing to unpack .../62-libpython3-dev_3.7.3-1_amd64.deb ... -Unpacking libpython3-dev:amd64 (3.7.3-1) ... -Selecting previously unselected package libpython3-all-dev:amd64. -Preparing to unpack .../63-libpython3-all-dev_3.7.3-1_amd64.deb ... -Unpacking libpython3-all-dev:amd64 (3.7.3-1) ... -Selecting previously unselected package python-all. -Preparing to unpack .../64-python-all_2.7.16-1_amd64.deb ... -Unpacking python-all (2.7.16-1) ... -Selecting previously unselected package python2.7-dev. -Preparing to unpack .../65-python2.7-dev_2.7.16-2+deb10u1_amd64.deb ... -Unpacking python2.7-dev (2.7.16-2+deb10u1) ... -Selecting previously unselected package python2-dev. -Preparing to unpack .../66-python2-dev_2.7.16-1_amd64.deb ... -Unpacking python2-dev (2.7.16-1) ... -Selecting previously unselected package python-dev. -Preparing to unpack .../67-python-dev_2.7.16-1_amd64.deb ... -Unpacking python-dev (2.7.16-1) ... -Selecting previously unselected package python-all-dev. -Preparing to unpack .../68-python-all-dev_2.7.16-1_amd64.deb ... -Unpacking python-all-dev (2.7.16-1) ... -Selecting previously unselected package python-atomicwrites. -Preparing to unpack .../69-python-atomicwrites_1.1.5-2_all.deb ... -Unpacking python-atomicwrites (1.1.5-2) ... -Selecting previously unselected package python-attr. -Preparing to unpack .../70-python-attr_18.2.0-1_all.deb ... -Unpacking python-attr (18.2.0-1) ... -Selecting previously unselected package python-funcsigs. -Preparing to unpack .../71-python-funcsigs_1.0.2-4_all.deb ... -Unpacking python-funcsigs (1.0.2-4) ... -Selecting previously unselected package python-six. -Preparing to unpack .../72-python-six_1.12.0-1_all.deb ... -Unpacking python-six (1.12.0-1) ... -Selecting previously unselected package python-more-itertools. -Preparing to unpack .../73-python-more-itertools_4.2.0-1_all.deb ... -Unpacking python-more-itertools (4.2.0-1) ... -Selecting previously unselected package python-scandir. -Preparing to unpack .../74-python-scandir_1.9.0-2_amd64.deb ... -Unpacking python-scandir (1.9.0-2) ... -Selecting previously unselected package python-pathlib2. -Preparing to unpack .../75-python-pathlib2_2.3.3-1_all.deb ... -Unpacking python-pathlib2 (2.3.3-1) ... -Selecting previously unselected package python-pkg-resources. -Preparing to unpack .../76-python-pkg-resources_40.8.0-1_all.deb ... -Unpacking python-pkg-resources (40.8.0-1) ... -Selecting previously unselected package python-pluggy. -Preparing to unpack .../77-python-pluggy_0.8.0-1_all.deb ... -Unpacking python-pluggy (0.8.0-1) ... -Selecting previously unselected package python-py. -Preparing to unpack .../78-python-py_1.7.0-2_all.deb ... -Unpacking python-py (1.7.0-2) ... -Selecting previously unselected package python-pytest. -Preparing to unpack .../79-python-pytest_3.10.1-2_all.deb ... -Unpacking python-pytest (3.10.1-2) ... -Selecting previously unselected package python-setuptools. -Preparing to unpack .../80-python-setuptools_40.8.0-1_all.deb ... -Unpacking python-setuptools (40.8.0-1) ... -Selecting previously unselected package python3-all. -Preparing to unpack .../81-python3-all_3.7.3-1_amd64.deb ... -Unpacking python3-all (3.7.3-1) ... -Selecting previously unselected package python3.7-dev. -Preparing to unpack .../82-python3.7-dev_3.7.3-2+deb10u3_amd64.deb ... -Unpacking python3.7-dev (3.7.3-2+deb10u3) ... -Selecting previously unselected package python3-dev. -Preparing to unpack .../83-python3-dev_3.7.3-1_amd64.deb ... -Unpacking python3-dev (3.7.3-1) ... -Selecting previously unselected package python3-all-dev. -Preparing to unpack .../84-python3-all-dev_3.7.3-1_amd64.deb ... -Unpacking python3-all-dev (3.7.3-1) ... -Selecting previously unselected package python3-atomicwrites. -Preparing to unpack .../85-python3-atomicwrites_1.1.5-2_all.deb ... -Unpacking python3-atomicwrites (1.1.5-2) ... -Selecting previously unselected package python3-attr. -Preparing to unpack .../86-python3-attr_18.2.0-1_all.deb ... -Unpacking python3-attr (18.2.0-1) ... -Selecting previously unselected package python3-six. -Preparing to unpack .../87-python3-six_1.12.0-1_all.deb ... -Unpacking python3-six (1.12.0-1) ... -Selecting previously unselected package python3-more-itertools. -Preparing to unpack .../88-python3-more-itertools_4.2.0-1_all.deb ... -Unpacking python3-more-itertools (4.2.0-1) ... -Selecting previously unselected package python3-pkg-resources. -Preparing to unpack .../89-python3-pkg-resources_40.8.0-1_all.deb ... -Unpacking python3-pkg-resources (40.8.0-1) ... -Selecting previously unselected package python3-pluggy. -Preparing to unpack .../90-python3-pluggy_0.8.0-1_all.deb ... -Unpacking python3-pluggy (0.8.0-1) ... -Selecting previously unselected package python3-py. -Preparing to unpack .../91-python3-py_1.7.0-2_all.deb ... -Unpacking python3-py (1.7.0-2) ... -Selecting previously unselected package python3-pytest. -Preparing to unpack .../92-python3-pytest_3.10.1-2_all.deb ... -Unpacking python3-pytest (3.10.1-2) ... -Selecting previously unselected package python3-setuptools. -Preparing to unpack .../93-python3-setuptools_40.8.0-1_all.deb ... -Unpacking python3-setuptools (40.8.0-1) ... -Selecting previously unselected package samtools. -Preparing to unpack .../94-samtools_1.9-4_amd64.deb ... -Unpacking samtools (1.9-4) ... -Selecting previously unselected package tabix. -Preparing to unpack .../95-tabix_1.9-12~deb10u1_amd64.deb ... -Unpacking tabix (1.9-12~deb10u1) ... -Setting up libpipeline1:amd64 (1.5.1-2) ... -Setting up libkeyutils1:amd64 (1.6-6) ... -Setting up libpsl5:amd64 (0.20.2-2) ... -Setting up mime-support (3.62) ... -Setting up libmagic-mgc (1:5.35-4+deb10u2) ... -Setting up libarchive-zip-perl (1.64-1) ... -Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... -No schema files found: doing nothing. -Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... -Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... -Setting up libdeflate0:amd64 (1.2-1) ... -Setting up gettext-base (0.19.8.1-9) ... -Setting up file (1:5.35-4+deb10u2) ... -Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... -Setting up libicu63:amd64 (63.1-6+deb10u3) ... -Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... -Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... -Setting up autotools-dev (20180224.1) ... -Setting up libexpat1-dev:amd64 (2.2.6-2+deb10u4) ... -Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... -Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... -Setting up libsigsegv2:amd64 (2.12-2) ... -Setting up autopoint (0.19.8.1-9) ... -Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... -Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... -Setting up liblzma-dev:amd64 (5.2.4-1) ... -Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... -Setting up sensible-utils (0.0.12) ... -Setting up libuchardet0:amd64 (0.0.6-3) ... -Setting up libssh2-1:amd64 (1.8.0-2.1) ... -Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... -Setting up libmpdec2:amd64 (2.4.2-2) ... -Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... -Setting up libelf1:amd64 (0.176-1.1) ... -Setting up readline-common (7.0-5) ... -Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u3) ... -Setting up libreadline7:amd64 (7.0-5) ... -Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... -Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... -Setting up libpython3.7:amd64 (3.7.3-2+deb10u3) ... -Setting up libtool (2.4.6-9) ... -Setting up libpython3.7-dev:amd64 (3.7.3-2+deb10u3) ... -Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... -Setting up m4 (1.4.18-2) ... -Setting up libpython2.7-stdlib:amd64 (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:amd64 (1.17-3+deb10u3) ... -Setting up libcroco3:amd64 (0.6.12-3) ... -Setting up autoconf (2.69-11) ... -Setting up dwz (0.12-3) ... -Setting up groff-base (1.22.4-3+deb10u1) ... -Setting up libpython3-stdlib:amd64 (3.7.3-1) ... -Setting up automake (1:1.16.1-4) ... -update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode -Setting up python3.7 (3.7.3-2+deb10u3) ... -Setting up libpython2.7:amd64 (2.7.16-2+deb10u1) ... -Setting up libpython2.7-dev:amd64 (2.7.16-2+deb10u1) ... -Setting up gettext (0.19.8.1-9) ... -Setting up libpython3-dev:amd64 (3.7.3-1) ... -Setting up python2.7 (2.7.16-2+deb10u1) ... -Setting up libpython2-stdlib:amd64 (2.7.16-1) ... -Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... -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+deb10u3) ... -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:amd64 (2.7.16-1) ... -Setting up libpython3-all-dev:amd64 (3.7.3-1) ... -Setting up cython3 (0.29.2-2) ... -Setting up python3-pluggy (0.8.0-1) ... -Setting up libpython2-dev:amd64 (2.7.16-1) ... -Setting up python3-lib2to3 (3.7.3-1) ... -Setting up tabix (1.9-12~deb10u1) ... -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:amd64 (1.9-12~deb10u1) ... -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:amd64 (1.9-12~deb10u1) ... -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:amd64 (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:amd64 (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+deb10u1) ... +Err http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 + Could not connect to 85.184.249.68:3128 (85.184.249.68). - connect (111: Connection refused) +Err http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 bcftools amd64 1.9-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 cython amd64 0.29.2-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 cython3 amd64 0.29.2-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 dh-exec amd64 0.23.1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libexpat1-dev amd64 2.2.6-2+deb10u4 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libhts-dev amd64 1.9-12~deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython2.7 amd64 2.7.16-2+deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython2.7-dev amd64 2.7.16-2+deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython2-dev amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython-dev amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython-all-dev amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython3.7 amd64 3.7.3-2+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython3.7-dev amd64 3.7.3-2+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython3-dev amd64 3.7.3-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 libpython3-all-dev amd64 3.7.3-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-all amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python2.7-dev amd64 2.7.16-2+deb10u1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python2-dev amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-dev amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-all-dev amd64 2.7.16-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-atomicwrites all 1.1.5-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-attr all 18.2.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-funcsigs all 1.0.2-4 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-six all 1.12.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-more-itertools all 4.2.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-scandir amd64 1.9.0-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-pathlib2 all 2.3.3-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-pluggy all 0.8.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-py all 1.7.0-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-pytest all 3.10.1-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python-setuptools all 40.8.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-all amd64 3.7.3-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3.7-dev amd64 3.7.3-2+deb10u3 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-dev amd64 3.7.3-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-all-dev amd64 3.7.3-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-atomicwrites all 1.1.5-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-attr all 18.2.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-six all 1.12.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-more-itertools all 4.2.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-pluggy all 0.8.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-py all 1.7.0-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-pytest all 3.10.1-2 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 python3-setuptools all 40.8.0-1 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 + Unable to connect to 85.184.249.68:3128: +Err http://deb.debian.org/debian buster/main amd64 tabix amd64 1.9-12~deb10u1 + Unable to connect to 85.184.249.68:3128: +E: Failed to fetch http://deb.debian.org/debian/pool/main/libb/libbsd/libbsd0_0.9.1-2+deb10u1_amd64.deb: Could not connect to 85.184.249.68:3128 (85.184.249.68). - connect (111: Connection refused) +E: Unable to fetch some packages; try '-o APT::Get::Fix-Missing=true' to continue with missing packages Reading package lists... Building dependency tree... Reading state information... @@ -866,4065 +518,11 @@ 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" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-pysam_0.15.2+ds-2_source.changes -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 amd64 - fakeroot debian/rules clean -cd tests/pysam_data && /usr/bin/make clean -make[1]: Entering directory '/build/python-pysam-0.15.2+ds/tests/pysam_data' -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]: Leaving directory '/build/python-pysam-0.15.2+ds/tests/pysam_data' -cd tests/cbcf_data && /usr/bin/make clean -make[1]: Entering directory '/build/python-pysam-0.15.2+ds/tests/cbcf_data' -rm -f *.gz *.tbi *.csi *.bcf -make[1]: Leaving directory '/build/python-pysam-0.15.2+ds/tests/cbcf_data' -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]: Entering directory '/build/python-pysam-0.15.2+ds' -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-amd64' 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-amd64' 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]: Leaving directory '/build/python-pysam-0.15.2+ds' - 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-amd64-2.7 -creating build/temp.linux-amd64-2.7/pysam -x86_64-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-amd64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libchtslib.o build/temp.linux-amd64-2.7/pysam/htslib_util.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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-amd64-2.7/samtools -creating build/temp.linux-amd64-2.7/samtools/lz4 -x86_64-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-amd64-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libcsamtools.o build/temp.linux-amd64-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-amd64-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-amd64-2.7/samtools/stats.c.pysam.o build/temp.linux-amd64-2.7/samtools/samtools.pysam.o build/temp.linux-amd64-2.7/samtools/sample.c.pysam.o build/temp.linux-amd64-2.7/samtools/sam_view.c.pysam.o build/temp.linux-amd64-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-amd64-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-amd64-2.7/samtools/sam_header.c.pysam.o build/temp.linux-amd64-2.7/samtools/sam.c.pysam.o build/temp.linux-amd64-2.7/samtools/phase.c.pysam.o build/temp.linux-amd64-2.7/samtools/padding.c.pysam.o build/temp.linux-amd64-2.7/samtools/faidx.c.pysam.o build/temp.linux-amd64-2.7/samtools/dict.c.pysam.o build/temp.linux-amd64-2.7/samtools/cut_target.c.pysam.o build/temp.linux-amd64-2.7/samtools/bedidx.c.pysam.o build/temp.linux-amd64-2.7/samtools/bedcov.c.pysam.o build/temp.linux-amd64-2.7/samtools/bamtk.c.pysam.o build/temp.linux-amd64-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_split.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_md.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_markdup.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_index.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_import.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_color.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-amd64-2.7/samtools/bam.c.pysam.o build/temp.linux-amd64-2.7/samtools/lz4/lz4.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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-amd64-2.7/bcftools -x86_64-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-amd64-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/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; - ^~~~~~ -x86_64-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-amd64-2.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libcbcftools.o build/temp.linux-amd64-2.7/bcftools/filter.c.pysam.o build/temp.linux-amd64-2.7/bcftools/version.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfsort.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-amd64-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-amd64-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-amd64-2.7/bcftools/tabix.c.pysam.o build/temp.linux-amd64-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-amd64-2.7/bcftools/reheader.c.pysam.o build/temp.linux-amd64-2.7/bcftools/regidx.c.pysam.o build/temp.linux-amd64-2.7/bcftools/prob1.c.pysam.o build/temp.linux-amd64-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-amd64-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-amd64-2.7/bcftools/mcall.c.pysam.o build/temp.linux-amd64-2.7/bcftools/main.c.pysam.o build/temp.linux-amd64-2.7/bcftools/kmin.c.pysam.o build/temp.linux-amd64-2.7/bcftools/hclust.c.pysam.o build/temp.linux-amd64-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-amd64-2.7/bcftools/em.c.pysam.o build/temp.linux-amd64-2.7/bcftools/csq.c.pysam.o build/temp.linux-amd64-2.7/bcftools/convert.c.pysam.o build/temp.linux-amd64-2.7/bcftools/consensus.c.pysam.o build/temp.linux-amd64-2.7/bcftools/ccall.c.pysam.o build/temp.linux-amd64-2.7/bcftools/bin.c.pysam.o build/temp.linux-amd64-2.7/bcftools/bcftools.pysam.o build/temp.linux-amd64-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-amd64-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-amd64-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-amd64-2.7/bcftools/HMM.c.pysam.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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 -x86_64-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-amd64-2.7/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; - ^~~~~~~~~~~~~~ -x86_64-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-amd64-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libcutils.o build/temp.linux-amd64-2.7/pysam/pysam_util.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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 -x86_64-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-amd64-2.7/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)); - ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libcalignmentfile.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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 -x86_64-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-amd64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libcsamfile.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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 -x86_64-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-amd64-2.7/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)); - ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libcalignedsegment.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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 -x86_64-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-amd64-2.7/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) - ^~~~~~~~ -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libctabix.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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 -x86_64-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-amd64-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libcfaidx.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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 -x86_64-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-amd64-2.7/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) - ^~~~~~~~~~~~~~~~ -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libcbcf.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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 -x86_64-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-amd64-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libcbgzf.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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 -x86_64-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-amd64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libctabixproxies.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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 -x86_64-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-amd64-2.7/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) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -x86_64-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/python2.7-2.7.16=. -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-amd64-2.7/pysam/libcvcf.o -L/build/python-pysam-0.15.2+ds/pysam -L/usr/lib/x86_64-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-amd64-3.7 -creating build/temp.linux-amd64-3.7/pysam -x86_64-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-amd64-3.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/pysam/libchtslib.o build/temp.linux-amd64-3.7/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-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) -building 'pysam.libcsamtools' extension -creating build/temp.linux-amd64-3.7/samtools -creating build/temp.linux-amd64-3.7/samtools/lz4 -x86_64-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-amd64-3.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/pysam/libcsamtools.o build/temp.linux-amd64-3.7/samtools/tmp_file.c.pysam.o build/temp.linux-amd64-3.7/samtools/stats_isize.c.pysam.o build/temp.linux-amd64-3.7/samtools/stats.c.pysam.o build/temp.linux-amd64-3.7/samtools/samtools.pysam.o build/temp.linux-amd64-3.7/samtools/sample.c.pysam.o build/temp.linux-amd64-3.7/samtools/sam_view.c.pysam.o build/temp.linux-amd64-3.7/samtools/sam_utils.c.pysam.o build/temp.linux-amd64-3.7/samtools/sam_opts.c.pysam.o build/temp.linux-amd64-3.7/samtools/sam_header.c.pysam.o build/temp.linux-amd64-3.7/samtools/sam.c.pysam.o build/temp.linux-amd64-3.7/samtools/phase.c.pysam.o build/temp.linux-amd64-3.7/samtools/padding.c.pysam.o build/temp.linux-amd64-3.7/samtools/faidx.c.pysam.o build/temp.linux-amd64-3.7/samtools/dict.c.pysam.o build/temp.linux-amd64-3.7/samtools/cut_target.c.pysam.o build/temp.linux-amd64-3.7/samtools/bedidx.c.pysam.o build/temp.linux-amd64-3.7/samtools/bedcov.c.pysam.o build/temp.linux-amd64-3.7/samtools/bamtk.c.pysam.o build/temp.linux-amd64-3.7/samtools/bamshuf.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_stat.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_split.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_sort.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_reheader.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_md.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_mate.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_markdup.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_index.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_import.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_flags.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_color.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_cat.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_aux.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam2depth.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam2bcf.c.pysam.o build/temp.linux-amd64-3.7/samtools/bam.c.pysam.o build/temp.linux-amd64-3.7/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-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) -building 'pysam.libcbcftools' extension -creating build/temp.linux-amd64-3.7/bcftools -x86_64-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-amd64-3.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/pysam/libcbcftools.o build/temp.linux-amd64-3.7/bcftools/filter.c.pysam.o build/temp.linux-amd64-3.7/bcftools/version.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcmp.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfview.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfstats.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfsort.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfsom.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfroh.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfquery.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfisec.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfindex.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcffilter.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfcall.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-amd64-3.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-amd64-3.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-amd64-3.7/bcftools/tabix.c.pysam.o build/temp.linux-amd64-3.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-amd64-3.7/bcftools/reheader.c.pysam.o build/temp.linux-amd64-3.7/bcftools/regidx.c.pysam.o build/temp.linux-amd64-3.7/bcftools/prob1.c.pysam.o build/temp.linux-amd64-3.7/bcftools/ploidy.c.pysam.o build/temp.linux-amd64-3.7/bcftools/mpileup.c.pysam.o build/temp.linux-amd64-3.7/bcftools/mcall.c.pysam.o build/temp.linux-amd64-3.7/bcftools/main.c.pysam.o build/temp.linux-amd64-3.7/bcftools/kmin.c.pysam.o build/temp.linux-amd64-3.7/bcftools/hclust.c.pysam.o build/temp.linux-amd64-3.7/bcftools/gvcf.c.pysam.o build/temp.linux-amd64-3.7/bcftools/em.c.pysam.o build/temp.linux-amd64-3.7/bcftools/csq.c.pysam.o build/temp.linux-amd64-3.7/bcftools/convert.c.pysam.o build/temp.linux-amd64-3.7/bcftools/consensus.c.pysam.o build/temp.linux-amd64-3.7/bcftools/ccall.c.pysam.o build/temp.linux-amd64-3.7/bcftools/bin.c.pysam.o build/temp.linux-amd64-3.7/bcftools/bcftools.pysam.o build/temp.linux-amd64-3.7/bcftools/bam_sample.c.pysam.o build/temp.linux-amd64-3.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-amd64-3.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-amd64-3.7/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-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libcutils.c' Cython extension (up-to-date) -building 'pysam.libcutils' extension -x86_64-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-amd64-3.7/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; - ^~~~~~~~~~~~~~ -x86_64-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-amd64-3.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/pysam/libcutils.o build/temp.linux-amd64-3.7/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-x86_64-linux-gnu -lcsamtools.cpython-37m-x86_64-linux-gnu -lcbcftools.cpython-37m-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) -building 'pysam.libcalignmentfile' extension -x86_64-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-amd64-3.7/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)); - ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -x86_64-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-amd64-3.7/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-x86_64-linux-gnu -lcutils.cpython-37m-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) -building 'pysam.libcsamfile' extension -x86_64-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-amd64-3.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/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-x86_64-linux-gnu -lcutils.cpython-37m-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) -building 'pysam.libcalignedsegment' extension -x86_64-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-amd64-3.7/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)); - ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -x86_64-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-amd64-3.7/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-x86_64-linux-gnu -lcutils.cpython-37m-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libctabix.c' Cython extension (up-to-date) -building 'pysam.libctabix' extension -x86_64-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-amd64-3.7/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) - ^~~~~~~~ -x86_64-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-amd64-3.7/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-x86_64-linux-gnu -lcutils.cpython-37m-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) -building 'pysam.libcfaidx' extension -x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-0.15.2+ds/samtools -I/build/python-pysam-0.15.2+ds/samtools/lz4 -I/build/python-pysam-0.15.2+ds/bcftools -I/build/python-pysam-0.15.2+ds/pysam -I/build/python-pysam-0.15.2+ds -I/usr/include/python3.7m -c pysam/libcfaidx.c -o build/temp.linux-amd64-3.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/pysam/libcfaidx.o -L/build/python-pysam-0.15.2+ds/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-x86_64-linux-gnu -lcutils.cpython-37m-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libcbcf.c' Cython extension (up-to-date) -building 'pysam.libcbcf' extension -x86_64-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-amd64-3.7/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) - ^~~~~~~~~~~~~~~~ -x86_64-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-amd64-3.7/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-x86_64-linux-gnu -lcutils.cpython-37m-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) -building 'pysam.libcbgzf' extension -x86_64-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-amd64-3.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/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-x86_64-linux-gnu -lcutils.cpython-37m-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) -building 'pysam.libctabixproxies' extension -x86_64-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-amd64-3.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -x86_64-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-amd64-3.7/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-x86_64-linux-gnu -lcutils.cpython-37m-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN -skipping 'pysam/libcvcf.c' Cython extension (up-to-date) -building 'pysam.libcvcf' extension -x86_64-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-amd64-3.7/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) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -x86_64-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-amd64-3.7/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-x86_64-linux-gnu -lcutils.cpython-37m-x86_64-linux-gnu -o /build/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN - debian/rules override_dh_auto_test -make[1]: Entering directory '/build/python-pysam-0.15.2+ds' -cd tests/pysam_data && /usr/bin/make all -make[2]: Entering directory '/build/python-pysam-0.15.2+ds/tests/pysam_data' -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]: Leaving directory '/build/python-pysam-0.15.2+ds/tests/pysam_data' -cd tests/cbcf_data && /usr/bin/make all -make[2]: Entering directory '/build/python-pysam-0.15.2+ds/tests/cbcf_data' -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]: Leaving directory '/build/python-pysam-0.15.2+ds/tests/cbcf_data' -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_yjj7Ff -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_jxjeFt -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_OVE1_o -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_gd0fLc -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_qfC7Ey -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_9gThi9 -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 82.66 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_2nx7vafg -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_zz0u25dc -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_flkgsun2 -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_x85n1p97 -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_3mfr9y5b -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_e597tuzm -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 75.41 seconds ============== -make[1]: Leaving directory '/build/python-pysam-0.15.2+ds' - 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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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]: Entering directory '/build/python-pysam-0.15.2+ds' -cd tests/pysam_data && /usr/bin/make clean -make[2]: Entering directory '/build/python-pysam-0.15.2+ds/tests/pysam_data' -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]: Leaving directory '/build/python-pysam-0.15.2+ds/tests/pysam_data' -cd tests/cbcf_data && /usr/bin/make clean -make[2]: Entering directory '/build/python-pysam-0.15.2+ds/tests/cbcf_data' -rm -f *.gz *.tbi *.csi *.bcf -make[2]: Leaving directory '/build/python-pysam-0.15.2+ds/tests/cbcf_data' -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]: Leaving directory '/build/python-pysam-0.15.2+ds' - 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.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libcalignmentfile.so to libcalignmentfile.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libcbcf.so to libcbcf.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libcbcftools.so to libcbcftools.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libcbgzf.so to libcbgzf.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libcfaidx.so to libcfaidx.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libchtslib.so to libchtslib.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libcsamfile.so to libcsamfile.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libcsamtools.so to libcsamtools.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libctabix.so to libctabix.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libctabixproxies.so to libctabixproxies.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libcutils.so to libcutils.x86_64-linux-gnu.so -I: dh_python2 fs:343: renaming libcvcf.so to libcvcf.x86_64-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: building package 'python-pysam' in '../python-pysam_0.15.2+ds-2_amd64.deb'. -dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.15.2+ds-2_amd64.deb'. -dpkg-deb: building package 'python-pysam-tests' in '../python-pysam-tests_0.15.2+ds-2_all.deb'. -dpkg-deb: building package 'python-pysam-dbgsym' in '../python-pysam-dbgsym_0.15.2+ds-2_amd64.deb'. -dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.15.2+ds-2_amd64.deb'. - dpkg-genbuildinfo --build=binary - dpkg-genchanges --build=binary >../python-pysam_0.15.2+ds-2_amd64.changes -dpkg-genchanges: info: binary-only upload (no source code included) - dpkg-source --after-build . -dpkg-buildpackage: info: binary-only upload (no source included) -dpkg-genchanges: info: not including original source code in upload -I: copying local configuration +E: pbuilder-satisfydepends failed. 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/3467907 and its subdirectories -I: Current time: Fri Aug 26 00:19:27 -12 2022 -I: pbuilder-time-stamp: 1661516367 +I: removing directory /srv/workspace/pbuilder/3074934 and its subdirectories