https://launchpad.net/ubuntu/+source/python-pysam/0.15.4+ds-1build1/+build/19109737 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-112 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 python-debian_0.1.36build1. Syncing the system clock with the buildd NTP service... 6 Apr 15:09:20 ntpdate[25725]: adjust time server 10.211.37.1 offset 0.000457 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19109737 --image-type chroot /home/buildd/filecache-default/88ad86cb2b525f1abddded96eadf8014548f7845 Creating target for build PACKAGEBUILD-19109737 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19109737 Starting target for build PACKAGEBUILD-19109737 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19109737 'deb http://ftpmaster.internal/ubuntu focal main universe' Overriding sources.list in build-PACKAGEBUILD-19109737 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19109737 Updating target for build PACKAGEBUILD-19109737 Ign:1 http://archive-team.internal/bootstrap/riscv64 focal InRelease Get:2 http://ftpmaster.internal/ubuntu focal InRelease [265 kB] Get:3 http://archive-team.internal/bootstrap/riscv64 focal Release [757 B] Ign:4 http://archive-team.internal/bootstrap/riscv64 focal Release.gpg Get:5 http://ftpmaster.internal/ubuntu focal-proposed InRelease [265 kB] Get:6 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 Packages [174 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 Packages [821 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main Translation-en [502 kB] Get:9 http://ftpmaster.internal/ubuntu focal/universe riscv64 Packages [6775 kB] Get:10 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5128 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 Packages [42.5 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [35.8 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/restricted Translation-en [860 B] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 Packages [132 kB] Get:15 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [114 kB] Get:16 http://ftpmaster.internal/ubuntu focal-proposed/multiverse riscv64 Packages [1140 B] Fetched 14.3 MB in 29s (494 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt coreutils cpp-9 g++-9 gcc-8-base gcc-9 gcc-9-base libapt-pkg6.0 libc-bin libc-dev-bin libc6 libc6-dev libgcc-9-dev libgnutls30 liblocale-gettext-perl libperl5.30 libstdc++-9-dev libsystemd0 libtext-charwidth-perl libtext-iconv-perl libudev1 login passwd perl-base 24 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 40.4 MB of archives. After this operation, 329 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu focal/main riscv64 coreutils riscv64 8.30-3ubuntu2 [1158 kB] Get:2 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 login riscv64 1:4.8.1-1ubuntu4 [216 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main riscv64 perl-base riscv64 5.30.0-9build1 [1419 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 libc6-dev riscv64 2.31-0ubuntu7 [3659 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 libc-dev-bin riscv64 2.31-0ubuntu7 [62.5 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 libc6 riscv64 2.31-0ubuntu7 [2272 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 libc-bin riscv64 2.31-0ubuntu7 [505 kB] Get:8 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libsystemd0 riscv64 245.2-1ubuntu3 [242 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libudev1 riscv64 245.2-1ubuntu3 [69.0 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libapt-pkg6.0 riscv64 2.0.1ubuntu1 [797 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main riscv64 libgnutls30 riscv64 3.6.13-2ubuntu1 [720 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 apt riscv64 2.0.1ubuntu1 [1231 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main riscv64 liblocale-gettext-perl riscv64 1.07-4 [16.5 kB] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 passwd riscv64 1:4.8.1-1ubuntu4 [752 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-charwidth-perl riscv64 0.04-10 [9460 B] Get:16 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-iconv-perl riscv64 1.7-7 [13.2 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main riscv64 g++-9 riscv64 9.3.0-10ubuntu1 [6926 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main riscv64 gcc-9 riscv64 9.3.0-10ubuntu1 [6788 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main riscv64 libstdc++-9-dev riscv64 9.3.0-10ubuntu1 [3649 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main riscv64 libgcc-9-dev riscv64 9.3.0-10ubuntu1 [404 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main riscv64 cpp-9 riscv64 9.3.0-10ubuntu1 [6046 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main riscv64 gcc-9-base riscv64 9.3.0-10ubuntu1 [19.2 kB] Get:23 http://ftpmaster.internal/ubuntu focal/universe riscv64 gcc-8-base riscv64 8.4.0-3ubuntu2 [18.4 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main riscv64 libperl5.30 riscv64 5.30.0-9build1 [3422 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.4 MB in 8s (5368 kB/s) (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3ubuntu2_riscv64.deb ... Unpacking coreutils (8.30-3ubuntu2) over (8.30-3ubuntu2) ... Setting up coreutils (8.30-3ubuntu2) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../login_1%3a4.8.1-1ubuntu4_riscv64.deb ... Unpacking login (1:4.8.1-1ubuntu4) over (1:4.8.1-1ubuntu3) ... Setting up login (1:4.8.1-1ubuntu4) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../perl-base_5.30.0-9build1_riscv64.deb ... Unpacking perl-base (5.30.0-9build1) over (5.30.0-9build1) ... Setting up perl-base (5.30.0-9build1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.31-0ubuntu7_riscv64.deb ... Unpacking libc6-dev:riscv64 (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Preparing to unpack .../libc-dev-bin_2.31-0ubuntu7_riscv64.deb ... 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Setting up libudev1:riscv64 (245.2-1ubuntu3) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.0.1ubuntu1_riscv64.deb ... Unpacking libapt-pkg6.0:riscv64 (2.0.1ubuntu1) over (2.0.1) ... Setting up libapt-pkg6.0:riscv64 (2.0.1ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.13-2ubuntu1_riscv64.deb ... Unpacking libgnutls30:riscv64 (3.6.13-2ubuntu1) over (3.6.11.1-2ubuntu2) ... Setting up libgnutls30:riscv64 (3.6.13-2ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../apt_2.0.1ubuntu1_riscv64.deb ... Unpacking apt (2.0.1ubuntu1) over (2.0.1) ... Setting up apt (2.0.1ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_riscv64.deb ... Unpacking liblocale-gettext-perl (1.07-4) over (1.07-4) ... 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Unpacking libgcc-9-dev:riscv64 (9.3.0-10ubuntu1) over (9.3.0-8ubuntu1) ... Preparing to unpack .../6-cpp-9_9.3.0-10ubuntu1_riscv64.deb ... Unpacking cpp-9 (9.3.0-10ubuntu1) over (9.3.0-8ubuntu1) ... Preparing to unpack .../7-gcc-9-base_9.3.0-10ubuntu1_riscv64.deb ... Unpacking gcc-9-base:riscv64 (9.3.0-10ubuntu1) over (9.3.0-8ubuntu1) ... Preparing to unpack .../8-gcc-8-base_8.4.0-3ubuntu2_riscv64.deb ... Unpacking gcc-8-base:riscv64 (8.4.0-3ubuntu2) over (8.4.0-3ubuntu1) ... Preparing to unpack .../9-libperl5.30_5.30.0-9build1_riscv64.deb ... Unpacking libperl5.30:riscv64 (5.30.0-9build1) over (5.30.0-9build1) ... Setting up libtext-iconv-perl (1.7-7) ... Setting up libtext-charwidth-perl (0.04-10) ... Setting up gcc-8-base:riscv64 (8.4.0-3ubuntu2) ... Setting up libperl5.30:riscv64 (5.30.0-9build1) ... Setting up libc-dev-bin (2.31-0ubuntu7) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:riscv64 (9.3.0-10ubuntu1) ... Setting up libgcc-9-dev:riscv64 (9.3.0-10ubuntu1) ... Setting up cpp-9 (9.3.0-10ubuntu1) ... Setting up libc6-dev:riscv64 (2.31-0ubuntu7) ... Setting up gcc-9 (9.3.0-10ubuntu1) ... Setting up libstdc++-9-dev:riscv64 (9.3.0-10ubuntu1) ... Setting up g++-9 (9.3.0-10ubuntu1) ... Processing triggers for libc-bin (2.31-0ubuntu7) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19109737 riscv64 focal -c chroot:build-PACKAGEBUILD-19109737 --arch=riscv64 --dist=focal --nolog python-pysam_0.15.4+ds-1build1.dsc Initiating build PACKAGEBUILD-19109737 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-112 +==============================================================================+ | python-pysam 0.15.4+ds-1build1 (riscv64) Mon, 06 Apr 2020 15:13:29 +0000 | +==============================================================================+ Package: python-pysam Version: 0.15.4+ds-1build1 Source Version: 0.15.4+ds-1build1 Distribution: focal Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19109737/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-FlLA5j/resolver-oQbrcp' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.15.4+ds-1build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-pysam-FlLA5j/python-pysam-0.15.4+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-FlLA5j' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [470 B] Get:5 copy:/<>/apt_archive ./ Packages [548 B] Fetched 1975 B in 1s (3818 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libgpm2 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python-all python-all-dev python-atomicwrites python-attr python-configparser python-contextlib2 python-funcsigs python-importlib-metadata python-more-itertools python-packaging python-pathlib2 python-pkg-resources python-pluggy python-py python-pyparsing python-pytest python-scandir python-setuptools python-six python-wcwidth python-zipp python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev python3-distutils python3-importlib-metadata python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pyparsing python3-pytest python3-setuptools python3-six python3-wcwidth python3-zipp python3.8 python3.8-dev python3.8-minimal samtools tabix tzdata zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python python-numpy python-matplotlib texlive-latex-recommended wamerican | wordlist whois vacation cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-attr-doc python-funcsigs-doc subversion python-pyparsing-doc python-mock python-setuptools-doc python2-doc python-tk python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.8-venv python3.8-doc Recommended packages: python-dev curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdmainutils cython cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python-all python-all-dev python-atomicwrites python-attr python-configparser python-contextlib2 python-funcsigs python-importlib-metadata python-more-itertools python-packaging python-pathlib2 python-pkg-resources python-pluggy python-py python-pyparsing python-pytest python-scandir python-setuptools python-six python-wcwidth python-zipp python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-atomicwrites python3-attr python3-dev python3-distutils python3-importlib-metadata python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pyparsing python3-pytest python3-setuptools python3-six python3-wcwidth python3-zipp python3.8 python3.8-dev python3.8-minimal samtools sbuild-build-depends-main-dummy tabix tzdata zlib1g-dev 0 upgraded, 144 newly installed, 0 to remove and 0 not upgraded. Need to get 51.7 MB of archives. After this operation, 284 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [972 B] Get:2 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libldap-2.4-2 riscv64 2.4.49+dfsg-2ubuntu1 [137 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main riscv64 libpython3.8-minimal riscv64 3.8.2-1ubuntu1 [698 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 libexpat1 riscv64 2.2.9-1build1 [68.8 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 python3.8-minimal riscv64 3.8.2-1ubuntu1 [1447 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-minimal riscv64 3.8.2-0ubuntu2 [23.6 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 mime-support all 3.64ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main riscv64 libmpdec2 riscv64 2.4.2-3 [79.2 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main riscv64 libpython3.8-stdlib riscv64 3.8.2-1ubuntu1 [1557 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main riscv64 python3.8 riscv64 3.8.2-1ubuntu1 [364 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main riscv64 libpython3-stdlib riscv64 3.8.2-0ubuntu2 [7072 B] Get:12 http://ftpmaster.internal/ubuntu focal/main riscv64 python3 riscv64 3.8.2-0ubuntu2 [47.6 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main riscv64 libbsd0 riscv64 0.10.0-1 [42.0 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main riscv64 bsdmainutils riscv64 11.1.2ubuntu3 [176 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main riscv64 libuchardet0 riscv64 0.0.6-3build1 [64.9 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main riscv64 groff-base riscv64 1.22.4-4build1 [816 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main riscv64 libpipeline1 riscv64 1.5.2-2build1 [23.9 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main riscv64 man-db riscv64 2.9.1-1 [1075 kB] Get:19 http://ftpmaster.internal/ubuntu focal/universe riscv64 libpython2.7-minimal riscv64 2.7.17-1ubuntu6 [335 kB] Get:20 http://ftpmaster.internal/ubuntu focal/universe riscv64 python2.7-minimal riscv64 2.7.17-1ubuntu6 [948 kB] Get:21 http://ftpmaster.internal/ubuntu focal/universe riscv64 python2-minimal riscv64 2.7.17-2ubuntu4 [27.5 kB] Get:22 http://ftpmaster.internal/ubuntu focal/universe riscv64 libpython2.7-stdlib riscv64 2.7.17-1ubuntu6 [1774 kB] Get:23 http://ftpmaster.internal/ubuntu focal/universe riscv64 python2.7 riscv64 2.7.17-1ubuntu6 [248 kB] Get:24 http://ftpmaster.internal/ubuntu focal/universe riscv64 libpython2-stdlib riscv64 2.7.17-2ubuntu4 [7072 B] Get:25 http://ftpmaster.internal/ubuntu focal/universe riscv64 python2 riscv64 2.7.17-2ubuntu4 [26.5 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main riscv64 libncurses6 riscv64 6.2-0ubuntu2 [86.2 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic-mgc riscv64 1:5.38-4 [218 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic1 riscv64 1:5.38-4 [70.5 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main riscv64 file riscv64 1:5.38-4 [22.5 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main riscv64 libelf1 riscv64 0.176-1.1build1 [41.8 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main riscv64 libglib2.0-0 riscv64 2.64.1-1 [1122 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main riscv64 tzdata all 2019c-3ubuntu1 [294 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main riscv64 libicu66 riscv64 66.1-2ubuntu2 [8406 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main riscv64 libxml2 riscv64 2.9.10+dfsg-4build1 [558 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-pkg-resources all 45.2.0-1 [130 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-six all 1.14.0-2 [12.1 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext-base riscv64 0.19.8.1-10build1 [47.4 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main riscv64 libkrb5support0 riscv64 1.17-6ubuntu4 [28.3 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main riscv64 libk5crypto3 riscv64 1.17-6ubuntu4 [91.8 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main riscv64 libkeyutils1 riscv64 1.6-6ubuntu1 [9316 B] Get:41 http://ftpmaster.internal/ubuntu focal/main riscv64 libkrb5-3 riscv64 1.17-6ubuntu4 [295 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main riscv64 libgssapi-krb5-2 riscv64 1.17-6ubuntu4 [107 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main riscv64 libpsl5 riscv64 0.21.0-1ubuntu1 [50.5 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main riscv64 libsigsegv2 riscv64 2.12-2 [13.0 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main riscv64 m4 riscv64 1.4.18-4 [188 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main riscv64 autoconf all 2.69-11.1 [321 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main riscv64 autotools-dev all 20180224.1 [39.6 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main riscv64 automake all 1:1.16.1-4ubuntu6 [522 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main riscv64 autopoint all 0.19.8.1-10build1 [412 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main riscv64 libbrotli1 riscv64 1.0.7-6build1 [279 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main riscv64 libroken18-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [36.5 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main riscv64 libasn1-8-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [145 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main riscv64 libheimbase1-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [24.7 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main riscv64 libhcrypto4-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [86.5 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main riscv64 libwind0-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [47.0 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main riscv64 libhx509-5-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [90.1 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main riscv64 libkrb5-26-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [175 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main riscv64 libheimntlm0-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [13.4 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main riscv64 libgssapi3-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [83.3 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main riscv64 libsasl2-modules-db riscv64 2.1.27+dfsg-2 [13.7 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main riscv64 libsasl2-2 riscv64 2.1.27+dfsg-2 [45.2 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main riscv64 libldap-common all 2.4.49+dfsg-2ubuntu1 [17.3 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main riscv64 libnghttp2-14 riscv64 1.40.0-1build1 [70.9 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2build1 [50.8 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main riscv64 libssh-4 riscv64 0.9.3-2ubuntu1 [147 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main riscv64 libcurl3-gnutls riscv64 7.68.0-1ubuntu1 [205 kB] Get:67 http://ftpmaster.internal/ubuntu focal/universe riscv64 libdeflate0 riscv64 1.5-3 [52.1 kB] Get:68 http://ftpmaster.internal/ubuntu focal/universe riscv64 libhts3 riscv64 1.10.2-3 [328 kB] Get:69 http://ftpmaster.internal/ubuntu focal/universe riscv64 bcftools riscv64 1.10.2-2 [570 kB] Get:70 http://ftpmaster.internal/ubuntu focal/universe riscv64 cython riscv64 0.29.14-0.1ubuntu3 [1292 kB] Get:71 http://ftpmaster.internal/ubuntu focal/universe riscv64 cython3 riscv64 0.29.14-0.1ubuntu3 [1361 kB] Get:72 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libtool all 2.4.6-14 [161 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-autoreconf all 19 [16.1 kB] Get:74 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libdebhelper-perl all 12.10ubuntu1 [62.1 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main riscv64 libarchive-zip-perl all 1.67-2 [90.5 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main riscv64 libsub-override-perl all 0.09-2 [9532 B] Get:77 http://ftpmaster.internal/ubuntu focal/main riscv64 libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:79 http://ftpmaster.internal/ubuntu focal/main riscv64 dwz riscv64 0.13-5 [147 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main riscv64 libcroco3 riscv64 0.6.13-1 [71.1 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext riscv64 0.19.8.1-10build1 [844 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main riscv64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main riscv64 po-debconf all 1.0.21 [233 kB] Get:84 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 debhelper all 12.10ubuntu1 [877 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-lib2to3 all 3.8.2-1ubuntu1 [74.1 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-distutils all 3.8.2-1ubuntu1 [140 kB] Get:87 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 dh-python all 4.20200315 [85.8 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main riscv64 libexpat1-dev riscv64 2.2.9-1build1 [224 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main riscv64 liblzma-dev riscv64 5.2.4-1 [226 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main riscv64 zlib1g-dev riscv64 1:1.2.11.dfsg-2ubuntu1 [207 kB] Get:91 http://ftpmaster.internal/ubuntu focal/universe riscv64 libhts-dev riscv64 1.10.2-3 [92.0 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main riscv64 libjs-jquery all 3.3.1~dfsg-3 [329 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main riscv64 libjs-underscore all 1.9.1~dfsg-1 [98.6 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main riscv64 libjs-sphinxdoc all 1.8.5-7ubuntu1 [97.0 kB] Get:95 http://ftpmaster.internal/ubuntu focal/universe riscv64 libpython2.7 riscv64 2.7.17-1ubuntu6 [910 kB] Get:96 http://ftpmaster.internal/ubuntu focal/universe riscv64 libpython2.7-dev riscv64 2.7.17-1ubuntu6 [5028 kB] Get:97 http://ftpmaster.internal/ubuntu focal/universe riscv64 libpython2-dev riscv64 2.7.17-2ubuntu4 [7144 B] Get:98 http://ftpmaster.internal/ubuntu focal/universe riscv64 libpython-all-dev riscv64 2.7.17-2ubuntu4 [1112 B] Get:99 http://ftpmaster.internal/ubuntu focal/main riscv64 libpython3.8 riscv64 3.8.2-1ubuntu1 [1450 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main riscv64 libpython3.8-dev riscv64 3.8.2-1ubuntu1 [8375 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main riscv64 libpython3-dev riscv64 3.8.2-0ubuntu2 [7236 B] Get:102 http://ftpmaster.internal/ubuntu focal/main riscv64 libpython3-all-dev riscv64 3.8.2-0ubuntu2 [1112 B] Get:103 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-all riscv64 2.7.17-2ubuntu4 [1104 B] Get:104 http://ftpmaster.internal/ubuntu focal/universe riscv64 python2.7-dev riscv64 2.7.17-1ubuntu6 [292 kB] Get:105 http://ftpmaster.internal/ubuntu focal/universe riscv64 python2-dev riscv64 2.7.17-2ubuntu4 [1268 B] Get:106 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-all-dev riscv64 2.7.17-2ubuntu4 [1120 B] Get:107 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-atomicwrites all 1.1.5-2build1 [6936 B] Get:108 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-attr all 19.3.0-2 [33.8 kB] Get:109 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-configparser all 3.5.0b2-3build1 [59.0 kB] Get:110 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-contextlib2 all 0.6.0-2 [11.3 kB] Get:111 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-funcsigs all 1.0.2-4build1 [13.5 kB] Get:112 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-six all 1.14.0-2 [12.0 kB] Get:113 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-scandir riscv64 1.10.0-2ubuntu3 [17.5 kB] Get:114 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-pathlib2 all 2.3.5-1ubuntu1 [17.6 kB] Get:115 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-more-itertools all 4.2.0-1build1 [39.5 kB] Get:116 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-zipp all 1.0.0-1 [5224 B] Get:117 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-importlib-metadata all 1.5.0-1 [9928 B] Get:118 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-pyparsing all 2.4.6-1 [61.2 kB] Get:119 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-packaging all 20.3-1 [26.7 kB] Get:120 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-pkg-resources all 44.0.0-2 [129 kB] Get:121 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-pluggy all 0.13.0-2 [18.3 kB] Get:122 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-py all 1.8.1-1 [65.3 kB] Get:123 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-wcwidth all 0.1.8+dfsg1-3 [17.3 kB] Get:124 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-pytest all 4.6.9-1 [178 kB] Get:125 http://ftpmaster.internal/ubuntu focal/universe riscv64 python-setuptools all 44.0.0-2 [330 kB] Get:126 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-all riscv64 3.8.2-0ubuntu2 [1104 B] Get:127 http://ftpmaster.internal/ubuntu focal/main riscv64 python3.8-dev riscv64 3.8.2-1ubuntu1 [519 kB] Get:128 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-dev riscv64 3.8.2-0ubuntu2 [1216 B] Get:129 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-all-dev riscv64 3.8.2-0ubuntu2 [1116 B] Get:130 http://ftpmaster.internal/ubuntu focal/universe riscv64 python3-atomicwrites all 1.1.5-2build1 [7016 B] Get:131 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-attr all 19.3.0-2 [33.9 kB] Get:132 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-more-itertools all 4.2.0-1build1 [39.4 kB] Get:133 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-zipp all 1.0.0-1 [5312 B] Get:134 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-importlib-metadata all 1.5.0-1 [9992 B] Get:135 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-pyparsing all 2.4.6-1 [61.3 kB] Get:136 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-packaging all 20.3-1 [26.8 kB] Get:137 http://ftpmaster.internal/ubuntu focal/universe riscv64 python3-pluggy all 0.13.0-2 [18.4 kB] Get:138 http://ftpmaster.internal/ubuntu focal/universe riscv64 python3-py all 1.8.1-1 [65.4 kB] Get:139 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-wcwidth all 0.1.8+dfsg1-3 [17.4 kB] Get:140 http://ftpmaster.internal/ubuntu focal/universe riscv64 python3-pytest all 4.6.9-1 [178 kB] Get:141 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-setuptools all 45.2.0-1 [330 kB] Get:142 http://ftpmaster.internal/ubuntu focal/universe riscv64 samtools riscv64 1.10-3 [486 kB] Get:143 http://ftpmaster.internal/ubuntu focal/universe riscv64 tabix riscv64 1.10.2-3 [337 kB] Get:144 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-exec riscv64 0.23.2 [23.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 51.7 MB in 13s (4127 kB/s) Selecting previously unselected package libpython3.8-minimal:riscv64. (Reading database ... 9816 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.2-1ubuntu1_riscv64.deb ... Unpacking libpython3.8-minimal:riscv64 (3.8.2-1ubuntu1) ... Selecting previously unselected package libexpat1:riscv64. Preparing to unpack .../libexpat1_2.2.9-1build1_riscv64.deb ... Unpacking libexpat1:riscv64 (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.2-1ubuntu1_riscv64.deb ... Unpacking python3.8-minimal (3.8.2-1ubuntu1) ... Setting up libpython3.8-minimal:riscv64 (3.8.2-1ubuntu1) ... Setting up libexpat1:riscv64 (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.2-1ubuntu1) ... Selecting previously unselected package python3-minimal. (Reading database ... 10107 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.2-0ubuntu2_riscv64.deb ... Unpacking python3-minimal (3.8.2-0ubuntu2) ... 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Setting up libmagic1:riscv64 (1:5.38-4) ... Setting up libdeflate0 (1.5-3) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.49+dfsg-2ubuntu1) ... Setting up libkrb5support0:riscv64 (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:riscv64 (2.1.27+dfsg-2) ... Setting up libpython2.7-stdlib:riscv64 (2.7.17-1ubuntu6) ... Setting up tzdata (2019c-3ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Apr 6 15:18:47 UTC 2020. Universal Time is now: Mon Apr 6 15:18:47 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1) ... Setting up libexpat1-dev:riscv64 (2.2.9-1build1) ... Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libncurses6:riscv64 (6.2-0ubuntu2) ... Setting up libsigsegv2:riscv64 (2.12-2) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libk5crypto3:riscv64 (1.17-6ubuntu4) ... 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Setting up bsdmainutils (11.1.2ubuntu3) ... 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:riscv64 (1.17-6ubuntu4) ... Setting up cython3 (0.29.14-0.1ubuntu3) ... Setting up libjs-sphinxdoc (1.8.5-7ubuntu1) ... Setting up libssh-4:riscv64 (0.9.3-2ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up python-funcsigs (1.0.2-4build1) ... Setting up dwz (0.13-5) ... Setting up python-scandir (1.10.0-2ubuntu3) ... Setting up python-wcwidth (0.1.8+dfsg1-3) ... Setting up groff-base (1.22.4-4build1) ... Setting up libpython2-dev:riscv64 (2.7.17-2ubuntu4) ... Setting up python-contextlib2 (0.6.0-2) ... Setting up python3-lib2to3 (3.8.2-1ubuntu1) ... Setting up libxml2:riscv64 (2.9.10+dfsg-4build1) ... Setting up python-packaging (20.3-1) ... Setting up python2.7-dev (2.7.17-1ubuntu6) ... Setting up python3-pkg-resources (45.2.0-1) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.8.2-1ubuntu1) ... Setting up dh-python (4.20200315) ... Setting up python3-more-itertools (4.2.0-1build1) ... Setting up python3-attr (19.3.0-2) ... Setting up cython (0.29.14-0.1ubuntu3) ... Setting up python2-dev (2.7.17-2ubuntu4) ... Setting up python3-setuptools (45.2.0-1) ... Setting up libpython-all-dev:riscv64 (2.7.17-2ubuntu4) ... Setting up python3-py (1.8.1-1) ... Setting up python-pkg-resources (44.0.0-2) ... Setting up libhx509-5-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up python-pathlib2 (2.3.5-1ubuntu1) ... Setting up python-zipp (1.0.0-1) ... Setting up python3-all (3.8.2-0ubuntu2) ... Setting up python-all (2.7.17-2ubuntu4) ... Setting up python3-zipp (1.0.0-1) ... Setting up python-attr (19.3.0-2) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-packaging (20.3-1) ... Setting up python-configparser (3.5.0b2-3build1) ... Setting up libpython3.8-dev:riscv64 (3.8.2-1ubuntu1) ... Setting up libcroco3:riscv64 (0.6.13-1) ... Setting up python-setuptools (44.0.0-2) ... Setting up python3.8-dev (3.8.2-1ubuntu1) ... Setting up python-all-dev (2.7.17-2ubuntu4) ... Setting up python-py (1.8.1-1) ... Setting up libkrb5-26-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up python-importlib-metadata (1.5.0-1) ... Setting up gettext (0.19.8.1-10build1) ... Setting up libpython3-dev:riscv64 (3.8.2-0ubuntu2) ... Setting up python3-importlib-metadata (1.5.0-1) ... Setting up libheimntlm0-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libgssapi3-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up python-pluggy (0.13.0-2) ... 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Processing triggers for libc-bin (2.31-0ubuntu7) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 (riscv64) Toolchain package versions: binutils_2.34-5ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-10ubuntu1 gcc-9_9.3.0-10ubuntu1 libc6-dev_2.31-0ubuntu7 libstdc++-9-dev_9.3.0-10ubuntu1 libstdc++6_10-20200324-1ubuntu1 linux-libc-dev_5.4.0-21.25 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1build1 apt_2.0.1ubuntu1 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu4 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libudev1_245.2-1ubuntu3 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu8 libwind0-heimdal_7.7.0+dfsg-1ubuntu1 libxml2_2.9.10+dfsg-4build1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.0-21.25 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu4 logsave_1.45.5-2ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu8 ncurses-base_6.2-0ubuntu2 ncurses-bin_6.2-0ubuntu2 openssl_1.1.1d-2ubuntu6 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu4 patch_2.7.6-6 perl_5.30.0-9build1 perl-base_5.30.0-9build1 perl-modules-5.30_5.30.0-9build1 pinentry-curses_1.1.0-3build1 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 python-all_2.7.17-2ubuntu4 python-all-dev_2.7.17-2ubuntu4 python-atomicwrites_1.1.5-2build1 python-attr_19.3.0-2 python-configparser_3.5.0b2-3build1 python-contextlib2_0.6.0-2 python-funcsigs_1.0.2-4build1 python-importlib-metadata_1.5.0-1 python-more-itertools_4.2.0-1build1 python-packaging_20.3-1 python-pathlib2_2.3.5-1ubuntu1 python-pkg-resources_44.0.0-2 python-pluggy_0.13.0-2 python-py_1.8.1-1 python-pyparsing_2.4.6-1 python-pytest_4.6.9-1 python-scandir_1.10.0-2ubuntu3 python-setuptools_44.0.0-2 python-six_1.14.0-2 python-wcwidth_0.1.8+dfsg1-3 python-zipp_1.0.0-1 python2_2.7.17-2ubuntu4 python2-dev_2.7.17-2ubuntu4 python2-minimal_2.7.17-2ubuntu4 python2.7_2.7.17-1ubuntu6 python2.7-dev_2.7.17-1ubuntu6 python2.7-minimal_2.7.17-1ubuntu6 python3_3.8.2-0ubuntu2 python3-all_3.8.2-0ubuntu2 python3-all-dev_3.8.2-0ubuntu2 python3-atomicwrites_1.1.5-2build1 python3-attr_19.3.0-2 python3-dev_3.8.2-0ubuntu2 python3-distutils_3.8.2-1ubuntu1 python3-importlib-metadata_1.5.0-1 python3-lib2to3_3.8.2-1ubuntu1 python3-minimal_3.8.2-0ubuntu2 python3-more-itertools_4.2.0-1build1 python3-packaging_20.3-1 python3-pkg-resources_45.2.0-1 python3-pluggy_0.13.0-2 python3-py_1.8.1-1 python3-pyparsing_2.4.6-1 python3-pytest_4.6.9-1 python3-setuptools_45.2.0-1 python3-six_1.14.0-2 python3-wcwidth_0.1.8+dfsg1-3 python3-zipp_1.0.0-1 python3.8_3.8.2-1ubuntu1 python3.8-dev_3.8.2-1ubuntu1 python3.8-minimal_3.8.2-1ubuntu1 readline-common_8.0-4 samtools_1.10-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1ubuntu1 tabix_1.10.2-3 tar_1.30+dfsg-7 tzdata_2019c-3ubuntu1 ubuntu-keyring_2020.02.11.1 util-linux_2.34-0.1ubuntu8 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: python-pysam Binary: python-pysam, python3-pysam, python-pysam-tests Architecture: any all Version: 0.15.4+ds-1build1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://pysam.readthedocs.org/en/latest Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/python-pysam Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git Testsuite: autopkgtest, autopkgtest-pkg-python Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 12), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix , samtools (>= 1.9) , bcftools (>= 1.9) , python-pytest , python3-pytest Package-List: python-pysam deb python optional arch=any python-pysam-tests deb python optional arch=all python3-pysam deb python optional arch=any Checksums-Sha1: 87966f23329c1c2aaa2bd724a6317cb9ebd4c7aa 1361548 python-pysam_0.15.4+ds.orig.tar.xz b8004b3170caaba4a81192ab5ea39931a9613884 373756 python-pysam_0.15.4+ds-1build1.debian.tar.xz Checksums-Sha256: b139f1f4e9a3aaa5771072da42bfad6ea313456ffe3ff91d2f8fafa98f669b68 1361548 python-pysam_0.15.4+ds.orig.tar.xz 92f1d0692883eb5f86ada0b4137e61b12df57ab278925d876e9598030443a502 373756 python-pysam_0.15.4+ds-1build1.debian.tar.xz Files: 00f152314fe13c9f43a8ebb7308c2714 1361548 python-pysam_0.15.4+ds.orig.tar.xz 3d6a3a90f13af1a3ec1c59cfcd508b73 373756 python-pysam_0.15.4+ds-1build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJEBAEBCAAuFiEE1WVxuIqLuvFAv2PWvX6qYHePpvUFAl5LruYQHGRva29AdWJ1 bnR1LmNvbQAKCRC9fqpgd4+m9VytD/4mU9nC7hjeRl+CZimprtPJ5wy+32nQ+f46 gakcFqSscG0In4NQSv7DJel8LSLxODxrOK2/3Bh3LxTSzaR/HxzB50xreP9PBhZu 1lTiguUBK4KyjaUaW7YBdIS0oa8GePjbN1pIH7mrRYaiOSYO4bkJQYNgnzGdsmid wegU2eMgrlaoiU5ftWOjmqMqcDCywmhUMvgvl1oqHtCMqILXUIpt5Tx92VYipIKF nEdtg6epNTbKCQwKwcu37hOy+AVow8ZTRFK1H4SzX48pe3fAyROiHELXyb4DX207 nSenCo4gANnnZdhhRq1amw56UrdNg1oN8QBgMEuL/J3IZb7SHPbgtVqPT2+7EIrW c7jdBBLr0pXZbkWU5P898I8vbGsOe918clbMz68u8Of8Oe/4Ff0uPHXuX4uNQxtt D4lHvO4YIsZTq60M/F3sivSid6K4MkQR01nBaqqF0vxNMa5XpBBDIZo05WL6ydPR 0l3igl5e9w/Nw/+lqbrKhDo9CvBUSMtl83e1jKNLcXFJXGa7cCmwyVmMmp0Bx9b6 dcEj4L6z/miba6SxwF9eMUzbnVaIhxnfiN0D/cSGbM55fCGJ3YbWLedmY4jWbj8f t+EzjFco53+GLOgVTt0SRW89uBl+W93MRihCA8OoLz4Omfziuchh1ET5Lq3CbB0i 8CQR/amWZg== =OX8K -----END PGP SIGNATURE----- gpgv: Signature made Tue Feb 18 09:31:18 2020 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-pysam_0.15.4+ds-1build1.dsc dpkg-source: info: extracting python-pysam in /<> dpkg-source: info: unpacking python-pysam_0.15.4+ds.orig.tar.xz dpkg-source: info: unpacking python-pysam_0.15.4+ds-1build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_remote.patch dpkg-source: info: applying spelling dpkg-source: info: applying hts1.10 dpkg-source: info: applying samtools_v1.10_full dpkg-source: info: applying bcftools_v1.10_full dpkg-source: info: applying clean_less Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19109737 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19109737 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19109737 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.15.4+ds-1build1 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 fakeroot debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/<>/tests/pysam_data' rm -fr *.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 '/<>/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete 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 '/<>' 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 '/<>/.pybuild/cpython2_2.7_pysam/build' (and everything under it) 'build/bdist.linux-riscv64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:217: python3.8 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/.pybuild/cpython3_3.8_pysam/build' (and everything under it) 'build/bdist.linux-riscv64' does not exist -- can't clean it 'build/scripts-3.8' 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 '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python2,python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base: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: python3.8 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 -a -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python2 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 /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/version.py -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/__init__.py -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/Pileup.py -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/samtools.py -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/config.py -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/utils.py -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/bcftools.py -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam creating /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/.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) copying pysam/libchtslib.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcsamtools.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcbcf.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/cbcftools_util.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/pysam_util.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam copying pysam/htslib_util.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam creating /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/version.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/config.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sam.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools creating /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/variantkey.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/hex.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/cols.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libchtslib.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcsamtools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcbcftools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcutils.pyx to pysam/libcutils.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcalignmentfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcalignmentfile.pyx:2528:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2533:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2538:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcsamfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcalignedsegment.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabix.pyx to pysam/libctabix.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libctabix.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcfaidx.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcf.pyx to pysam/libcbcf.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcbcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcbgzf.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libctabixproxies.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcvcf.pyx to pysam/libcvcf.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcvcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libchtslib' extension creating build creating build/temp.linux-riscv64-2.7 creating build/temp.linux-riscv64-2.7/pysam riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-riscv64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-riscv64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libchtslib.o build/temp.linux-riscv64-2.7/pysam/htslib_util.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamtools' extension creating build/temp.linux-riscv64-2.7/samtools creating build/temp.linux-riscv64-2.7/samtools/lz4 riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-riscv64-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/coverage.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.linux-riscv64-2.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-riscv64-2.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c samtools/lz4/lz4.c -o build/temp.linux-riscv64-2.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libcsamtools.o build/temp.linux-riscv64-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_color.c.pysam.o build/temp.linux-riscv64-2.7/samtools/faidx.c.pysam.o build/temp.linux-riscv64-2.7/samtools/stats.c.pysam.o build/temp.linux-riscv64-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-riscv64-2.7/samtools/cut_target.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-riscv64-2.7/samtools/dict.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bedcov.c.pysam.o build/temp.linux-riscv64-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bamtk.c.pysam.o build/temp.linux-riscv64-2.7/samtools/phase.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_split.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-riscv64-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-riscv64-2.7/samtools/padding.c.pysam.o build/temp.linux-riscv64-2.7/samtools/coverage.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_fastq.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam.c.pysam.o build/temp.linux-riscv64-2.7/samtools/sam.c.pysam.o build/temp.linux-riscv64-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_index.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_md.c.pysam.o build/temp.linux-riscv64-2.7/samtools/samtools.pysam.o build/temp.linux-riscv64-2.7/samtools/sample.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-riscv64-2.7/samtools/sam_view.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bedidx.c.pysam.o build/temp.linux-riscv64-2.7/samtools/bam_markdup.c.pysam.o build/temp.linux-riscv64-2.7/samtools/lz4/lz4.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-riscv64-2.7/bcftools riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-riscv64-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/bcftools.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/reheader.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/cols.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-riscv64-2.7/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:1062:5: bcftools/vcfcall.c.pysam.c:655:39: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 655 | args->aux.ploidy = (uint8_t*) malloc(args->nsamples); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:30, from /usr/include/htslib/vcf.h:41, 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 539 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-riscv64-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libcbcftools.o build/temp.linux-riscv64-2.7/bcftools/HMM.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/ccall.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/kmin.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/convert.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/main.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/csq.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/consensus.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/hclust.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/prob1.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfsort.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/bcftools.pysam.o build/temp.linux-riscv64-2.7/bcftools/reheader.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/version.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/cols.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/regidx.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/em.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/filter.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/tabix.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/bin.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/mcall.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-riscv64-2.7/bcftools/tsv2vcf.c.pysam.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-riscv64-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-riscv64-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libcutils.o build/temp.linux-riscv64-2.7/pysam/pysam_util.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-riscv64-2.7/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:29326:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] 29326 | __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)); | ~^~~~~~~~~~~~~~~~~~~ | | | bam_pileup1_t ** {aka struct **} In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:604: /usr/include/htslib/sam.h:1709:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} 1709 | 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:27579:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] 27579 | (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:13704:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] 13704 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libcalignmentfile.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-riscv64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libcsamfile.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-riscv64-2.7/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:14243:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result] 14243 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libcalignedsegment.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-riscv64-2.7/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:8643:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 8643 | __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:13709:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13709 | __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:13741:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13741 | __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:14111:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 14111 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) | ^~~~~~~~ riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libctabix.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-riscv64-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libcfaidx.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-riscv64-2.7/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_11VariantFile_6close’: pysam/libcbcf.c:65254:18: warning: ignoring return value of ‘bcf_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] 65254 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’: pysam/libcbcf.c:64982:18: warning: ignoring return value of ‘bcf_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] 64982 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: pysam/libcbcf.c:70057:18: warning: ignoring return value of ‘bcf_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] 70057 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_22add_sample’: pysam/libcbcf.c:34796:12: warning: ignoring return value of ‘bcf_hdr_sync’, declared with attribute warn_unused_result [-Wunused-result] 34796 | (void)(bcf_hdr_sync(__pyx_v_self->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’: pysam/libcbcf.c:34499:11: warning: ignoring return value of ‘bcf_hrec_add_key’, declared with attribute warn_unused_result [-Wunused-result] 34499 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_16, ((int)__pyx_t_17)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:34525:11: warning: ignoring return value of ‘bcf_hrec_set_val’, declared with attribute warn_unused_result [-Wunused-result] 34525 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_18, ((int)__pyx_t_17), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:34638:12: warning: ignoring return value of ‘bcf_hdr_sync’, declared with attribute warn_unused_result [-Wunused-result] 34638 | (void)(bcf_hdr_sync(__pyx_v_self->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_18add_line’: pysam/libcbcf.c:34067:12: warning: ignoring return value of ‘bcf_hdr_sync’, declared with attribute warn_unused_result [-Wunused-result] 34067 | (void)(bcf_hdr_sync(__pyx_v_self->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_16add_record’: pysam/libcbcf.c:33935:12: warning: ignoring return value of ‘bcf_hdr_sync’, declared with attribute warn_unused_result [-Wunused-result] 33935 | (void)(bcf_hdr_sync(__pyx_v_self->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libcbcf.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-riscv64-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libcbgzf.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-riscv64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libctabixproxies.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension riscv64-linux-gnu-gcc -pthread -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-riscv64-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-lWhUiq/python2.7-2.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC build/temp.linux-riscv64-2.7/pysam/libcvcf.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -L/<>/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<>/.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 /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/version.py -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/__init__.py -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/Pileup.py -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/samtools.py -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/config.py -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/utils.py -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/bcftools.py -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam creating /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/.pybuild/cpython3_3.8_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) copying pysam/libchtslib.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcsamtools.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcbcf.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/cbcftools_util.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/pysam_util.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam copying pysam/htslib_util.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam creating /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/version.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/config.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/sam.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools creating /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/variantkey.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/version.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/hex.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/cols.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools Fixing /<>/.pybuild/cpython3_3.8_pysam/build/pysam/version.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/config.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py /<>/.pybuild/cpython3_3.8_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 /<>/.pybuild/cpython3_3.8_pysam/build/pysam/version.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/config.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py /<>/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py /<>/.pybuild/cpython3_3.8_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) 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) building 'pysam.libchtslib' extension creating build/temp.linux-riscv64-3.8 creating build/temp.linux-riscv64-3.8/pysam riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libchtslib.c -o build/temp.linux-riscv64-3.8/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/htslib_util.c -o build/temp.linux-riscv64-3.8/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libchtslib.o build/temp.linux-riscv64-3.8/pysam/htslib_util.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamtools' extension creating build/temp.linux-riscv64-3.8/samtools creating build/temp.linux-riscv64-3.8/samtools/lz4 riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libcsamtools.c -o build/temp.linux-riscv64-3.8/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_color.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/faidx.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/stats.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/cut_target.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/dict.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bedcov.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bamtk.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/phase.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_split.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/padding.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/coverage.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/sam.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_index.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_md.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/samtools.pysam.c -o build/temp.linux-riscv64-3.8/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/sample.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/sam_view.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bedidx.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-riscv64-3.8/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c samtools/lz4/lz4.c -o build/temp.linux-riscv64-3.8/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libcsamtools.o build/temp.linux-riscv64-3.8/samtools/bam_plbuf.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_mate.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam2depth.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_color.c.pysam.o build/temp.linux-riscv64-3.8/samtools/faidx.c.pysam.o build/temp.linux-riscv64-3.8/samtools/stats.c.pysam.o build/temp.linux-riscv64-3.8/samtools/sam_opts.c.pysam.o build/temp.linux-riscv64-3.8/samtools/cut_target.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_addrprg.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_lpileup.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_reheader.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_aux.c.pysam.o build/temp.linux-riscv64-3.8/samtools/dict.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_plcmd.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bedcov.c.pysam.o build/temp.linux-riscv64-3.8/samtools/sam_utils.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_rmdup.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bamtk.c.pysam.o build/temp.linux-riscv64-3.8/samtools/phase.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_split.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bamshuf.c.pysam.o build/temp.linux-riscv64-3.8/samtools/tmp_file.c.pysam.o build/temp.linux-riscv64-3.8/samtools/padding.c.pysam.o build/temp.linux-riscv64-3.8/samtools/coverage.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_stat.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_fastq.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_flags.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam.c.pysam.o build/temp.linux-riscv64-3.8/samtools/sam.c.pysam.o build/temp.linux-riscv64-3.8/samtools/stats_isize.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_index.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_quickcheck.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_md.c.pysam.o build/temp.linux-riscv64-3.8/samtools/samtools.pysam.o build/temp.linux-riscv64-3.8/samtools/sample.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam2bcf.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_rmdupse.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_cat.c.pysam.o build/temp.linux-riscv64-3.8/samtools/sam_view.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_sort.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bedidx.c.pysam.o build/temp.linux-riscv64-3.8/samtools/bam_markdup.c.pysam.o build/temp.linux-riscv64-3.8/samtools/lz4/lz4.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-riscv64-3.8/bcftools riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libcbcftools.c -o build/temp.linux-riscv64-3.8/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/HMM.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/ccall.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/kmin.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/convert.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/main.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/csq.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/consensus.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/hclust.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/prob1.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/bcftools.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/reheader.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/version.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:694:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 694 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:30, from /usr/include/htslib/vcf.h:41, from bcftools/vcfmerge.c.pysam.c:34: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/cols.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/regidx.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/em.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/filter.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/tabix.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/bin.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/mcall.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-riscv64-3.8/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libcbcftools.o build/temp.linux-riscv64-3.8/bcftools/HMM.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfindex.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfisec.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/mpileup.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/ccall.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/kmin.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfconcat.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfsom.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/convert.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/bam_sample.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/main.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/csq.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/consensus.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/hclust.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/prob1.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfsort.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/bcftools.pysam.o build/temp.linux-riscv64-3.8/bcftools/reheader.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfstats.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/version.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfnorm.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfmerge.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/cols.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/regidx.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcffilter.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfroh.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfbuf.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfconvert.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/em.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfview.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfplugin.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/smpl_ilist.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcmp.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfquery.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/filter.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfannotate.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/tabix.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfcnv.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/ploidy.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/bam2bcf.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/bin.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/mcall.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/gvcf.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/vcfcall.c.pysam.o build/temp.linux-riscv64-3.8/bcftools/tsv2vcf.c.pysam.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libcutils.c -o build/temp.linux-riscv64-3.8/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:511:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] 511 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ pysam/libcutils.c:5890:7: note: ‘__pyx_v_retval’ was declared here 5890 | int __pyx_v_retval; | ^~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/pysam_util.c -o build/temp.linux-riscv64-3.8/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libcutils.o build/temp.linux-riscv64-3.8/pysam/pysam_util.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -lcsamtools.cpython-38-riscv64-linux-gnu -lcbcftools.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libcalignmentfile.c -o build/temp.linux-riscv64-3.8/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:29326:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] 29326 | __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)); | ~^~~~~~~~~~~~~~~~~~~ | | | bam_pileup1_t ** {aka struct **} In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:604: /usr/include/htslib/sam.h:1709:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct **’} 1709 | int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); | ~~~~~~~~~~~~~~~~~~~~~~^~~ riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libcalignmentfile.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -lcutils.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libcsamfile.c -o build/temp.linux-riscv64-3.8/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libcsamfile.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -lcutils.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libcalignedsegment.c -o build/temp.linux-riscv64-3.8/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libcalignedsegment.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -lcutils.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libctabix.c -o build/temp.linux-riscv64-3.8/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:8643:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 8643 | __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:13709:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13709 | __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:13741:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 13741 | __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:14111:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 14111 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) | ^~~~~~~~ riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libctabix.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -lcutils.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libcfaidx.c -o build/temp.linux-riscv64-3.8/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libcfaidx.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -lcutils.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libcbcf.c -o build/temp.linux-riscv64-3.8/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libcbcf.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -lcutils.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libcbgzf.c -o build/temp.linux-riscv64-3.8/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libcbgzf.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -lcutils.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcbgzf.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libctabixproxies.c -o build/temp.linux-riscv64-3.8/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libctabixproxies.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -lcutils.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension riscv64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<>/pysam -I/<> -I/usr/include/python3.8 -c pysam/libcvcf.c -o build/temp.linux-riscv64-3.8/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.0’: pysam/libcvcf.c:24840:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] 24840 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.8/pysam/libcvcf.o -L/<>/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -L/<>/.pybuild/cpython3_3.8_pysam/build/pysam -lz -lhts -lchtslib.cpython-38-riscv64-linux-gnu -lcutils.cpython-38-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.cpython-38-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Entering directory '/<>' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/<>/tests/pysam_data' samtools faidx ex1.fa samtools view -bt ex1.fa.fai -o ex1.bam ex1.sam.gz 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 test_mapped_unmapped.sam > test_mapped_unmapped.bam samtools view -bS softclip.sam > softclip.bam samtools view -bS tag_bug.sam > tag_bug.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 test_unaligned.sam > test_unaligned.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 example_reverse_complement.sam > example_reverse_complement.bam samtools view -bS ex5.sam > ex5.bam samtools view -bS ex_spliced.sam > ex_spliced.bam samtools view -bS example_btag.sam > example_btag.bam samtools view -bS test_query_position.sam > test_query_position.bam touch tmp.list samtools view -bt tmp.list -o example_unmapped_reads_no_sq.bam example_unmapped_reads_no_sq.sam rm -f tmp.list samtools view -bS ex4.sam > ex4.bam samtools view -bS ex8.sam > ex8.bam samtools view -bS ex3.sam > ex3.bam samtools index example_dash_in_chr.bam samtools index test_mapped_unmapped.bam samtools index softclip.bam samtools index tag_bug.bam samtools index ex9_fail.bam samtools index ex10.bam samtools index example_aligned_pairs.bam samtools index example_empty_header.bam samtools index test_unaligned.bam samtools index ex6.bam samtools index ex9_nofail.bam samtools index issue100.bam samtools index example_reverse_complement.bam samtools index ex5.bam samtools index ex_spliced.bam samtools index example_btag.bam samtools index test_query_position.bam samtools index example_unmapped_reads_no_sq.bam samtools index ex4.bam samtools index ex8.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 '/<>/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/<>/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 < example_vcf43.vcf > example_vcf43.vcf.gz tabix -p vcf example_vcf43.vcf.gz # create tbi index bcftools index example_vcf43.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_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index bcftools index example_vcf43_with_utf8.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 example_vcf43.vcf.gz -o example_vcf43.bcf bcftools index example_vcf43.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_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf bcftools index example_vcf43_with_utf8.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 '/<>/tests/cbcf_data' export PYBUILD_TEST_ARGS='|| true' ; dh_auto_test I: pybuild base:217: cd /<>/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest || true ============================= test session starts ============================== platform linux2 -- Python 2.7.17, pytest-4.6.9, py-1.8.1, pluggy-0.13.0 -- /usr/bin/python2.7 cachedir: .pytest_cache rootdir: /<>, inifile: setup.cfg collecting ... collected 933 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp___enter___Khxtcynegative_integers.bam' 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_s1hJwX' /<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_s1hJwX PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_Y5z2nN' /<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_Y5z2nN PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_DEWLdE PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_RDxRZm' /<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_RDxRZm PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 [E::cram_index_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_5c11q9' /<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_5c11q9 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_hmot5u 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 [E::hts_open_format] Failed to open file "/<>/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/example_empty_with_header.bam" : No such file or directory FAILED 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_m96ngPtmp_ex2.bam' PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM FAILED 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 FAILED 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" : No such file or directory 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread__22lHktmp_single.bam' [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_S6Knystmp_multi.bam' 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" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 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 FAILED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader FAILED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/example_no_seq_in_header.bam' PASSED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/example_no_seq_in_header_null_bytes.bam' PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader [E::hts_open_format] Failed to open file "/<>/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/rg_with_tab.bam" : No such file or directory FAILED 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::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/ex2_truncated.bam' [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" : No such file or directory PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /<>/.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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_0rHqMAtmp_largecigar.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" : No such file or directory PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_7LzI1v.bcf' PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [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.) [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::TestUnicode::test_record_with_unicode PASSED tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED tests/VariantRecord_test.py::test_unicode_annotation_can_be_added 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::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag 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_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::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::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_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_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::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::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::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::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_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::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_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::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 =================================== FAILURES =================================== __________________ TestHeaderBAM.test_dictionary_access_works __________________ self = def test_dictionary_access_works(self): for key in self.header.keys(): self.compare_headers({key: self.header[key]}, > {key: self.samfile.header[key]}) tests/AlignmentFileHeader_test.py:170: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:143: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID': 'P1', 'VN': '1.0'}, {'... != [{'ID': 'P1', 'VN': '1.0'}, {'... E E Second list contains 2 additional elements. E First extra element 2: E {'PP': 'P1', 'PN': 'samtools', 'ID': 'samtools', 'VN': '1.10', 'CL': 'samtools view -bS ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] _______________ TestHeaderBAM.test_header_content_is_as_expected _______________ self = def test_header_content_is_as_expected(self): > self.compare_headers(self.header, self.samfile.header.to_dict()) tests/AlignmentFileHeader_test.py:151: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:143: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID': 'P1', 'VN': '1.0'}, {'... != [{'ID': 'P1', 'VN': '1.0'}, {'... E E Second list contains 2 additional elements. E First extra element 2: E {'PP': 'P1', 'PN': 'samtools', 'ID': 'samtools', 'VN': '1.10', 'CL': 'samtools view -bS ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] _________________ TestHeaderCRAM.test_dictionary_access_works __________________ self = def test_dictionary_access_works(self): for key in self.header.keys(): self.compare_headers({key: self.header[key]}, > {key: self.samfile.header[key]}) tests/AlignmentFileHeader_test.py:170: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:229: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID': 'P1', 'VN': '1.0'}, {'... != [{'ID': 'P1', 'VN': '1.0'}, {'... E E Second list contains 2 additional elements. E First extra element 2: E {'PP': 'P1', 'PN': 'samtools', 'ID': 'samtools', 'VN': '1.10', 'CL': 'samtools view -bC -T ex1.fa ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] ______________ TestHeaderCRAM.test_header_content_is_as_expected _______________ self = def test_header_content_is_as_expected(self): > self.compare_headers(self.header, self.samfile.header.to_dict()) tests/AlignmentFileHeader_test.py:151: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:229: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID': 'P1', 'VN': '1.0'}, {'... != [{'ID': 'P1', 'VN': '1.0'}, {'... E E Second list contains 2 additional elements. E First extra element 2: E {'PP': 'P1', 'PN': 'samtools', 'ID': 'samtools', 'VN': '1.10', 'CL': 'samtools view -bC -T ex1.fa ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] _______________ BasicTestCRAMFromFetch.testPresentOptionalFields _______________ self = def testPresentOptionalFields(self): self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % > (self.reads[0].opt('NM'), 22)) E AssertionError: optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:259: AssertionError _______________________ BasicTestCRAMFromFetch.testTags ________________________ self = def testTags(self): self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), > ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD', '0C0T1G1C0C0A1G0^G0C1C... != [('MD', '0C0T1G1C0C0A1G0^G0C1C... E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:243: AssertionError _____________ BasicTestCRAMFromFilename.testPresentOptionalFields ______________ self = def testPresentOptionalFields(self): self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % > (self.reads[0].opt('NM'), 22)) E AssertionError: optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:259: AssertionError ______________________ BasicTestCRAMFromFilename.testTags ______________________ self = def testTags(self): self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), > ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD', '0C0T1G1C0C0A1G0^G0C1C... != [('MD', '0C0T1G1C0C0A1G0^G0C1C... E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:243: AssertionError _______________ BasicTestCRAMFromFile.testPresentOptionalFields ________________ self = def testPresentOptionalFields(self): self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % > (self.reads[0].opt('NM'), 22)) E AssertionError: optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:259: AssertionError ________________________ BasicTestCRAMFromFile.testTags ________________________ self = def testTags(self): self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), > ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD', '0C0T1G1C0C0A1G0^G0C1C... != [('MD', '0C0T1G1C0C0A1G0^G0C1C... E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:243: AssertionError ______________ BasicTestCRAMFromFileNo.testPresentOptionalFields _______________ self = def testPresentOptionalFields(self): self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % > (self.reads[0].opt('NM'), 22)) E AssertionError: optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:259: AssertionError _______________________ BasicTestCRAMFromFileNo.testTags _______________________ self = def testTags(self): self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), > ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD', '0C0T1G1C0C0A1G0^G0C1C... != [('MD', '0C0T1G1C0C0A1G0^G0C1C... E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:243: AssertionError ______________________________ TestIO.testBAM2SAM ______________________________ self = def testBAM2SAM(self): self.checkEcho("ex2.bam", "ex2.sam", "tmp_ex2.sam", > "rb", "wh") tests/AlignmentFile_test.py:500: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFile_test.py:452: in checkEcho output_filename)) E AssertionError: files ex2.sam and tmp_ex2.sam are not the same ________________________ TestIO.testEmptyWithHeaderBAM _________________________ self = def testEmptyWithHeaderBAM(self): self.assertRaises( ValueError, pysam.Samfile, os.path.join(BAM_DATADIR, "example_empty_with_header.bam"), > "rb") tests/AlignmentFile_test.py:802: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__ ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E IOError: [Errno 2] could not open alignment file `/<>/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/example_empty_with_header.bam`: No such file or directory pysam/libcalignmentfile.pyx:940: IOError ______________________________ TestIO.testSAM2BAM ______________________________ self = def testSAM2BAM(self): self.checkEcho("ex2.sam", "ex2.bam", "tmp_ex2.bam", "r", "wb", > checkf=checkGZBinaryEqual) tests/AlignmentFile_test.py:494: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFile_test.py:452: in checkEcho output_filename)) E AssertionError: files ex2.bam and tmp_ex2.bam are not the same _____________________ TestIO.testWriteUncompressedBAMFile ______________________ self = def testWriteUncompressedBAMFile(self): '''read from uncompressed BAM file, see issue #43''' input_filename = "ex2.sam" output_filename = "pysam_uncompressed.bam" reference_filename = "uncompressed.bam" self.checkEcho(input_filename, reference_filename, output_filename, > "r", "wb0") tests/AlignmentFile_test.py:783: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFile_test.py:452: in checkEcho output_filename)) E AssertionError: files uncompressed.bam and pysam_uncompressed.bam are not the same ___________________ TestDeNovoConstruction.testBAMWholeFile ____________________ self = def testBAMWholeFile(self): tmpfilename = "tmp_%i.bam" % id(self) outfile = pysam.AlignmentFile(tmpfilename, "wb", header=self.header) for x in self.reads: outfile.write(x) outfile.close() self.assertTrue( checkGZBinaryEqual(tmpfilename, self.bamfile), "mismatch when construction BAM file, see %s %s" % > (tmpfilename, self.bamfile)) E AssertionError: mismatch when construction BAM file, see tmp_274157514704.bam /<>/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/ex6.bam tests/AlignmentFile_test.py:1380: AssertionError _______________________ TestEmptyHeader.testEmptyHeader ________________________ self = def testEmptyHeader(self): s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'example_empty_header.bam')) > self.assertEqual(s.header.to_dict(), {'SQ': [{'LN': 1000, 'SN': 'chr1'}]}) E AssertionError: OrderedDict([('SQ', [{'LN': 1000, 'SN': 'chr1'}]), ('PG', [{'PN': 'samtools', 'ID': 'samtools', 'VN': '1.10', 'CL': 'samtools view -bS example_empty_header.sam'}])]) != {'SQ': [{'LN': 1000, 'SN': 'chr1'}]} tests/AlignmentFile_test.py:1406: AssertionError ___________________ TestHeaderWithProgramOptions.testHeader ____________________ self = def testHeader(self): s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, > 'rg_with_tab.bam')) tests/AlignmentFile_test.py:1448: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__ ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E IOError: [Errno 2] could not open alignment file `/<>/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/rg_with_tab.bam`: No such file or directory pysam/libcalignmentfile.pyx:940: IOError =============================== warnings summary =============================== /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369 /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/.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 /<>/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1472: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) .pybuild/cpython2_2.7_pysam/build/tests/samtools_test.py::SamtoolsTest::testStatements /<>/.pybuild/cpython2_2.7_pysam/build/tests/samtools_test.py:141: UserWarning: versions of pysam.samtools and samtools differ: 1.9 != 1.10 samtools_version)) -- Docs: https://docs.pytest.org/en/latest/warnings.html ======= 19 failed, 897 passed, 17 skipped, 3 warnings in 753.07 seconds ======== I: pybuild base:217: cd /<>/.pybuild/cpython3_3.8_pysam/build; python3.8 -m pytest || true ============================= test session starts ============================== platform linux -- Python 3.8.2, pytest-4.6.9, py-1.8.1, pluggy-0.13.0 -- /usr/bin/python3.8 cachedir: .pytest_cache rootdir: /<>, inifile: setup.cfg collecting ... collected 937 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp___enter___mexbyhg9negative_integers.bam' 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_a4e47phj' /<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_a4e47phj PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_v5w_68ik' /<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_v5w_68ik PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_0d5t8v3k PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_yyvnbg2y' /<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_yyvnbg2y PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 [E::cram_index_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_dqu5m1js' /<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_dqu5m1js PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_xafk_l4c 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 FAILED 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 [E::hts_open_format] Failed to open file "/<>/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_empty_with_header.bam" : No such file or directory FAILED 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_p3t2pdbbtmp_ex2.bam' PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM FAILED 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 FAILED 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" : No such file or directory 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_7w96hy3ftmp_single.bam' [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_vx4dqon2tmp_multi.bam' 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" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory 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 FAILED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader FAILED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_no_seq_in_header.bam' PASSED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_no_seq_in_header_null_bytes.bam' PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader [E::hts_open_format] Failed to open file "/<>/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/rg_with_tab.bam" : No such file or directory FAILED 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::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/ex2_truncated.bam' [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" : No such file or directory PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /<>/.pybuild/cpython3_3.8_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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_check_read_za3o9azltmp_largecigar.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 FAILED 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" : No such file or directory PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory 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 [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.8_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_4etq551c.bcf' PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [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.) [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::TestUnicode::test_record_with_unicode PASSED tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED tests/VariantRecord_test.py::test_unicode_annotation_can_be_added 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::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag 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_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_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_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_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_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_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_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_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_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_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_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_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::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_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_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_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_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_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_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_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_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::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_5::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G 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_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_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_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_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_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_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_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_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_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_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::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_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_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_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_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_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::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_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::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 =================================== FAILURES =================================== __________________ TestHeaderBAM.test_dictionary_access_works __________________ self = def test_dictionary_access_works(self): for key in self.header.keys(): > self.compare_headers({key: self.header[key]}, {key: self.samfile.header[key]}) tests/AlignmentFileHeader_test.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:143: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[155 chars]am'}] E E Second list contains 2 additional elements. E First extra element 2: E {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P1', 'VN': '1.10', 'CL': 'samtools view -bS ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] _______________ TestHeaderBAM.test_header_content_is_as_expected _______________ self = def test_header_content_is_as_expected(self): > self.compare_headers(self.header, self.samfile.header.to_dict()) tests/AlignmentFileHeader_test.py:151: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:143: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[155 chars]am'}] E E Second list contains 2 additional elements. E First extra element 2: E {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P1', 'VN': '1.10', 'CL': 'samtools view -bS ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bS ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] _________________ TestHeaderCRAM.test_dictionary_access_works __________________ self = def test_dictionary_access_works(self): for key in self.header.keys(): > self.compare_headers({key: self.header[key]}, {key: self.samfile.header[key]}) tests/AlignmentFileHeader_test.py:169: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:229: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[175 chars]am'}] E E Second list contains 2 additional elements. E First extra element 2: E {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P1', 'VN': '1.10', 'CL': 'samtools view -bC -T ex1.fa ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] ______________ TestHeaderCRAM.test_header_content_is_as_expected _______________ self = def test_header_content_is_as_expected(self): > self.compare_headers(self.header, self.samfile.header.to_dict()) tests/AlignmentFileHeader_test.py:151: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFileHeader_test.py:229: in compare_headers self.assertEqual(av, b[ak]) E AssertionError: Lists differ: [{'ID[43 chars]1.1'}] != [{'ID[43 chars]1.1'}, {'ID': 'samtools', 'PN': 'samtools', 'P[175 chars]am'}] E E Second list contains 2 additional elements. E First extra element 2: E {'ID': 'samtools', 'PN': 'samtools', 'PP': 'P1', 'VN': '1.10', 'CL': 'samtools view -bC -T ex1.fa ex3.sam'} E E - [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}] E + [{'ID': 'P1', 'VN': '1.0'}, E + {'ID': 'P2', 'VN': '1.1'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools', E + 'PN': 'samtools', E + 'PP': 'P1', E + 'VN': '1.10'}, E + {'CL': 'samtools view -bC -T ex1.fa ex3.sam', E + 'ID': 'samtools.1', E + 'PN': 'samtools', E + 'PP': 'P2', E + 'VN': '1.10'}] _______________ BasicTestCRAMFromFetch.testPresentOptionalFields _______________ self = def testPresentOptionalFields(self): > self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 22)) E AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:256: AssertionError _______________________ BasicTestCRAMFromFetch.testTags ________________________ self = def testTags(self): > self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:237: AssertionError _____________ BasicTestCRAMFromFilename.testPresentOptionalFields ______________ self = def testPresentOptionalFields(self): > self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 22)) E AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:256: AssertionError ______________________ BasicTestCRAMFromFilename.testTags ______________________ self = def testTags(self): > self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:237: AssertionError _______________ BasicTestCRAMFromFile.testPresentOptionalFields ________________ self = def testPresentOptionalFields(self): > self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 22)) E AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:256: AssertionError ________________________ BasicTestCRAMFromFile.testTags ________________________ self = def testTags(self): > self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:237: AssertionError ______________ BasicTestCRAMFromFileNo.testPresentOptionalFields _______________ self = def testPresentOptionalFields(self): > self.assertEqual( self.reads[0].opt('NM'), 22, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 22)) E AssertionError: 1 != 22 : optional field mismatch in read 1, NM: 1 != 22 tests/AlignmentFile_test.py:256: AssertionError _______________________ BasicTestCRAMFromFileNo.testTags _______________________ self = def testTags(self): > self.assertEqual( sorted(self.reads[0].tags), sorted([('RG', 'L1'), ('NM', 22), ('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), ('PG', 'P1'), ('XT', 'U'), ])) E AssertionError: Lists differ: [('MD[43 chars]1G1A2C0'), ('NM', 1), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] != [('MD[43 chars]1G1A2C0'), ('NM', 22), ('PG', 'P1'), ('RG', 'L1'), ('XT', 'U')] E E First differing element 1: E ('NM', 1) E ('NM', 22) E E [('MD', '0C0T1G1C0C0A1G0^G0C1C1G1A0T2G0G0G0A1C1G1G1A2C0'), E - ('NM', 1), E ? ^ E E + ('NM', 22), E ? ^^ E E ('PG', 'P1'), E ('RG', 'L1'), E ('XT', 'U')] tests/AlignmentFile_test.py:237: AssertionError ______________________________ TestIO.testBAM2SAM ______________________________ self = def testBAM2SAM(self): > self.checkEcho("ex2.bam", "ex2.sam", "tmp_ex2.sam", "rb", "wh") tests/AlignmentFile_test.py:497: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFile_test.py:447: in checkEcho self.assertTrue(checkf( E AssertionError: False is not true : files ex2.sam and tmp_ex2.sam are not the same ________________________ TestIO.testEmptyWithHeaderBAM _________________________ self = def testEmptyWithHeaderBAM(self): > self.assertRaises( ValueError, pysam.Samfile, os.path.join(BAM_DATADIR, "example_empty_with_header.bam"), "rb") tests/AlignmentFile_test.py:798: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__ ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E FileNotFoundError: [Errno 2] could not open alignment file `/<>/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/example_empty_with_header.bam`: No such file or directory pysam/libcalignmentfile.pyx:940: FileNotFoundError ______________________________ TestIO.testSAM2BAM ______________________________ self = def testSAM2BAM(self): > self.checkEcho("ex2.sam", "ex2.bam", "tmp_ex2.bam", "r", "wb", checkf=checkGZBinaryEqual) tests/AlignmentFile_test.py:490: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFile_test.py:447: in checkEcho self.assertTrue(checkf( E AssertionError: False is not true : files ex2.bam and tmp_ex2.bam are not the same _____________________ TestIO.testWriteUncompressedBAMFile ______________________ self = def testWriteUncompressedBAMFile(self): '''read from uncompressed BAM file, see issue #43''' input_filename = "ex2.sam" output_filename = "pysam_uncompressed.bam" reference_filename = "uncompressed.bam" > self.checkEcho(input_filename, reference_filename, output_filename, "r", "wb0") tests/AlignmentFile_test.py:780: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFile_test.py:447: in checkEcho self.assertTrue(checkf( E AssertionError: False is not true : files uncompressed.bam and pysam_uncompressed.bam are not the same ___________________ TestDeNovoConstruction.testBAMWholeFile ____________________ self = def testBAMWholeFile(self): tmpfilename = "tmp_%i.bam" % id(self) outfile = pysam.AlignmentFile(tmpfilename, "wb", header=self.header) for x in self.reads: outfile.write(x) outfile.close() > self.assertTrue( checkGZBinaryEqual(tmpfilename, self.bamfile), "mismatch when construction BAM file, see %s %s" % (tmpfilename, self.bamfile)) E AssertionError: False is not true : mismatch when construction BAM file, see tmp_274493881888.bam /<>/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/ex6.bam tests/AlignmentFile_test.py:1377: AssertionError _______________________ TestEmptyHeader.testEmptyHeader ________________________ self = def testEmptyHeader(self): s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'example_empty_header.bam')) > self.assertEqual(s.header.to_dict(), {'SQ': [{'LN': 1000, 'SN': 'chr1'}]}) E AssertionError: OrderedDict([('SQ', [{'SN': 'chr1', 'LN':[119 chars]}])]) != {'SQ': [{'LN': 1000, 'SN': 'chr1'}]} tests/AlignmentFile_test.py:1406: AssertionError ___________________ TestHeaderWithProgramOptions.testHeader ____________________ self = def testHeader(self): > s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'rg_with_tab.bam')) tests/AlignmentFile_test.py:1447: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pysam/libcalignmentfile.pyx:741: in pysam.libcalignmentfile.AlignmentFile.__cinit__ ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E FileNotFoundError: [Errno 2] could not open alignment file `/<>/.pybuild/cpython3_3.8_pysam/build/tests/pysam_data/rg_with_tab.bam`: No such file or directory pysam/libcalignmentfile.pyx:940: FileNotFoundError _______________________ StreamTest.test_text_processing ________________________ self = @unittest.skipIf(IS_PYTHON2, "no context manager in py2") def test_text_processing(self): with subprocess.Popen('head -n200', stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) as proc: in_stream = AlignmentFile(os.path.join(BAM_DATADIR, 'ex1.bam')) out_stream = AlignmentFile( proc.stdin, 'wh', header=in_stream.header) writer = alignmentfile_writer_thread(in_stream, out_stream) written, read = self.stream_process(proc, in_stream, out_stream, writer) > self.assertEqual(read, 198) E AssertionError: 197 != 198 tests/StreamFiledescriptors_test.py:61: AssertionError =============================== warnings summary =============================== /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369 /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/.pybuild/cpython3_3.8_pysam/build/tests/_compile_test.pyx tree = Parsing.p_module(s, pxd, full_module_name) .pybuild/cpython3_3.8_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator /<>/.pybuild/cpython3_3.8_pysam/build/tests/AlignmentFile_test.py:1471: UserWarning: no BGZF EOF marker; file may be truncated s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex2_truncated.bam'), .pybuild/cpython3_3.8_pysam/build/tests/samtools_test.py::SamtoolsTest::testStatements .pybuild/cpython3_3.8_pysam/build/tests/samtools_test.py::PysamTest::testStatements /<>/.pybuild/cpython3_3.8_pysam/build/tests/samtools_test.py:136: UserWarning: versions of pysam.samtools and samtools differ: 1.9 != 1.10 warnings.warn( -- Docs: https://docs.pytest.org/en/latest/warnings.html ======= 20 failed, 907 passed, 10 skipped, 4 warnings in 729.47 seconds ======== make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python2,python3 --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python2 setup.py install --root /<>/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 -> /<>/.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) 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 /<>/debian/python-pysam creating /<>/debian/python-pysam/usr creating /<>/debian/python-pysam/usr/lib creating /<>/debian/python-pysam/usr/lib/python2.7 creating /<>/debian/python-pysam/usr/lib/python2.7/dist-packages copying /<>/.pybuild/cpython2_2.7_pysam/build/tmp_274157514704.bam -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages creating /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/version.py -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/__init__.py -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/Pileup.py -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_stream.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/samtools.py -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/utils.pyc -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/config.py -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/Pileup.pyc -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/utils.py -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/bcftools.pyc -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/cbcftools_util.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_util.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/csamtools_util.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/htslib_util.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam creating /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/__init__.py -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include creating /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bedidx.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_endian.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam2bcf.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/version.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam_opts.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/tmp_file.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/config.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/stats_isize.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sample.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools creating /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/call.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bin.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/variantkey.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/convert.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/filter.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kheap.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kmin.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/gvcf.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/version.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/prob1.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcmp.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/config.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/ploidy.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/rbuf.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/regidx.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/hclust.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/hex.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/cols.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/mw.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam_sample.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/HMM.h -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/__init__.pyc -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.pxd -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/version.pyc -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/bcftools.py -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/samtools.pyc -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam/config.pyc -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam copying /<>/.pybuild/cpython2_2.7_pysam/build/tmp_ex2.bam -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages copying /<>/.pybuild/cpython2_2.7_pysam/build/log.txt -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages copying /<>/.pybuild/cpython2_2.7_pysam/build/pysam_uncompressed.bam -> /<>/debian/python-pysam/usr/lib/python2.7/dist-packages byte-compiling /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/version.py to version.pyc byte-compiling /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/__init__.py to __init__.pyc byte-compiling /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/Pileup.py to Pileup.pyc byte-compiling /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/samtools.py to samtools.pyc byte-compiling /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/config.py to config.pyc byte-compiling /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/utils.py to utils.pyc byte-compiling /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/__init__.py to __init__.pyc byte-compiling /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/bcftools.py to bcftools.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 /<>/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.15.4.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:217: /usr/bin/python3 setup.py install --root /<>/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 -> /<>/.pybuild/cpython3_3.8_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) Fixing /<>/.pybuild/cpython3_3.8_pysam/build/pysam/config.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /<>/.pybuild/cpython3_3.8_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 /<>/debian/python3-pysam creating /<>/debian/python3-pysam/usr creating /<>/debian/python3-pysam/usr/lib creating /<>/debian/python3-pysam/usr/lib/python3.8 creating /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages creating /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/version.py -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/__init__.py -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/Pileup.py -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/pysam_stream.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libchtslib.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/samtools.py -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/config.py -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcbgzf.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam creating /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/utils.cpython-38.pyc -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/Pileup.cpython-38.pyc -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/samtools.cpython-38.pyc -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/bcftools.cpython-38.pyc -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/config.cpython-38.pyc -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/version.cpython-38.pyc -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/__pycache__/__init__.cpython-38.pyc -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/utils.py -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/cbcftools_util.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/pysam_util.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcfaidx.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcutils.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/csamtools_util.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/htslib_util.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libctabixproxies.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam creating /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/__init__.py -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include creating /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/samtools.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bedidx.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_endian.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam2bcf.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/version.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sam_opts.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/tmp_file.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/config.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/stats_isize.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sam.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/samtools/sample.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/samtools creating /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/call.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bin.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/variantkey.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/convert.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/filter.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/kheap.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/kmin.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/gvcf.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bcftools.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/version.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/prob1.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/vcmp.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/config.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/ploidy.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/rbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/regidx.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/hclust.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/hex.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/cols.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/mw.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/bam_sample.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/include/bcftools/HMM.h -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignmentfile.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcalignedsegment.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libctabix.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcf.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcbcftools.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcvcf.pxd -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamtools.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/libcsamfile.cpython-38-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam/bcftools.py -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam copying /<>/.pybuild/cpython3_3.8_pysam/build/tmp_ex2.bam -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages copying /<>/.pybuild/cpython3_3.8_pysam/build/log.txt -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages copying /<>/.pybuild/cpython3_3.8_pysam/build/pysam_uncompressed.bam -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages copying /<>/.pybuild/cpython3_3.8_pysam/build/tmp_274493881888.bam -> /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages byte-compiling /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/version.py to version.cpython-38.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/Pileup.py to Pileup.cpython-38.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/samtools.py to samtools.cpython-38.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/config.py to config.cpython-38.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/utils.py to utils.cpython-38.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/include/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam/bcftools.py to bcftools.cpython-38.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 /<>/debian/python3-pysam/usr/lib/python3.8/dist-packages/pysam-0.15.4.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/<>' cd tests/pysam_data && /usr/bin/make clean make[2]: Entering directory '/<>/tests/pysam_data' rm -fr *.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 '/<>/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[2]: Entering directory '/<>/tests/cbcf_data' rm -f *.gz *.tbi *.csi *.bcf make[2]: Leaving directory '/<>/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete 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 '/<>' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_python2 -a -O--buildsystem=pybuild I: dh_python2 fs:343: renaming libcalignedsegment.so to libcalignedsegment.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libcalignmentfile.so to libcalignmentfile.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libcbcf.so to libcbcf.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libcbcftools.so to libcbcftools.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libcbgzf.so to libcbgzf.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libcfaidx.so to libcfaidx.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libchtslib.so to libchtslib.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libcsamfile.so to libcsamfile.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libcsamtools.so to libcsamtools.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libctabix.so to libctabix.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libctabixproxies.so to libctabixproxies.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libcutils.so to libcutils.riscv64-linux-gnu.so I: dh_python2 fs:343: renaming libcvcf.so to libcvcf.riscv64-linux-gnu.so dh_python3 -a -O--buildsystem=pybuild dh_installinit -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dwz: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcf.cpython-38-riscv64-linux-gnu.so: DWARF compression not beneficial - old size 1212562 new size 1220660 dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -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 -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing python3-pysam (in debian/python3-pysam); do_strip: , oemstrip: pkgstriptranslations: processing python-pysam (in debian/python-pysam); do_strip: , oemstrip: pkgstriptranslations: processing python3-pysam-dbgsym (in debian/.debhelper/python3-pysam/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python-pysam-dbgsym (in debian/.debhelper/python-pysam/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-pysam/DEBIAN/control, package python3-pysam, directory debian/python3-pysam pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " INFO: pkgstripfiles: waiting for lock (python3-pysam) ... pkgstripfiles: processing control file: debian/.debhelper/python3-pysam/dbgsym-root/DEBIAN/control, package python3-pysam-dbgsym, directory debian/.debhelper/python3-pysam/dbgsym-root dpkg-deb: building package 'python3-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-pysam/python3-pysam-dbgsym_0.15.4+ds-1build1_riscv64.deb'. INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... INFO: pkgstripfiles: waiting for lock (python3-pysam) ... pkgstripfiles: processing control file: debian/.debhelper/python-pysam/dbgsym-root/DEBIAN/control, package python-pysam-dbgsym, directory debian/.debhelper/python-pysam/dbgsym-root pkgstripfiles: processing control file: debian/python-pysam/DEBIAN/control, package python-pysam, directory debian/python-pysam dpkg-deb: building package 'python-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python-pysam/python-pysam-dbgsym_0.15.4+ds-1build1_riscv64.deb'. INFO: pkgstripfiles: waiting for lock (python3-pysam) ... pkgstripfiles: Truncating usr/share/doc/python-pysam/changelog.Debian.gz to topmost ten records INFO: pkgstripfiles: waiting for lock (python3-pysam) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-pysam' in '../python-pysam_0.15.4+ds-1build1_riscv64.deb'. pkgstripfiles: Truncating usr/share/doc/python3-pysam/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pysam ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.15.4+ds-1build1_riscv64.deb'. Renaming python-pysam-dbgsym_0.15.4+ds-1build1_riscv64.deb to python-pysam-dbgsym_0.15.4+ds-1build1_riscv64.ddeb Renaming python3-pysam-dbgsym_0.15.4+ds-1build1_riscv64.deb to python3-pysam-dbgsym_0.15.4+ds-1build1_riscv64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../python-pysam_0.15.4+ds-1build1_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-04-06T17:41:02Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pysam_0.15.4+ds-1build1_riscv64.changes: ----------------------------------------------- Format: 1.8 Date: Tue, 18 Feb 2020 10:23:54 +0100 Source: python-pysam Binary: python-pysam python3-pysam Architecture: riscv64 Version: 0.15.4+ds-1build1 Distribution: focal Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose Description: python-pysam - interface for the SAM/BAM sequence alignment and mapping format ( python3-pysam - interface for the SAM/BAM sequence alignment and mapping format ( Changes: python-pysam (0.15.4+ds-1build1) focal; urgency=medium . * No-change rebuild to drop python3.7. Checksums-Sha1: 616215facaca206bcc28753ec18dfea7d9985138 5826112 python-pysam-dbgsym_0.15.4+ds-1build1_riscv64.ddeb b1d081a90b7aefa42ce068ab3746d633b65d2136 9894 python-pysam_0.15.4+ds-1build1_riscv64.buildinfo 19e0df7e49b2081bf7b8c504d292de9098d4ee1a 1629480 python-pysam_0.15.4+ds-1build1_riscv64.deb 6cb269f0c1193b25fb2960d969311a6f0fc32345 7620592 python3-pysam-dbgsym_0.15.4+ds-1build1_riscv64.ddeb 61262eabb4e3ab3916937e9b8726f5503e5d89a6 1685768 python3-pysam_0.15.4+ds-1build1_riscv64.deb Checksums-Sha256: adf33c4e22618535f360b32a56d26e3652cfecb279b46dd23d8e1b0c777af52a 5826112 python-pysam-dbgsym_0.15.4+ds-1build1_riscv64.ddeb 7b0bc22a512f2c439635d6441b879f4a06978ba220d31cf9793b787f93e7dd54 9894 python-pysam_0.15.4+ds-1build1_riscv64.buildinfo 83f9c22d45a9b3ccd70ecb906b6d05fd646c12fe39422ada6ce775d343038b28 1629480 python-pysam_0.15.4+ds-1build1_riscv64.deb e6830d16faf9395f5d8463c7a4bb3574a90d9e9695fb710e810786eebd8fc9d1 7620592 python3-pysam-dbgsym_0.15.4+ds-1build1_riscv64.ddeb 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Format: 1.0 Source: python-pysam Binary: python-pysam python3-pysam python-pysam-tests Architecture: riscv64 Version: 0.15.4+ds-1build1 Checksums-Md5: e314aaccf1c792f3640cc98e31110bdf 5826112 python-pysam-dbgsym_0.15.4+ds-1build1_riscv64.ddeb fdc15fee3fd47f6047b09e66b65fe069 1629480 python-pysam_0.15.4+ds-1build1_riscv64.deb ca87a7bb1e7f68c47826550a8c3391dc 7620592 python3-pysam-dbgsym_0.15.4+ds-1build1_riscv64.ddeb 6b291e7fffcf39c08823d40fdcd90807 1685768 python3-pysam_0.15.4+ds-1build1_riscv64.deb Checksums-Sha1: 616215facaca206bcc28753ec18dfea7d9985138 5826112 python-pysam-dbgsym_0.15.4+ds-1build1_riscv64.ddeb 19e0df7e49b2081bf7b8c504d292de9098d4ee1a 1629480 python-pysam_0.15.4+ds-1build1_riscv64.deb 6cb269f0c1193b25fb2960d969311a6f0fc32345 7620592 python3-pysam-dbgsym_0.15.4+ds-1build1_riscv64.ddeb 61262eabb4e3ab3916937e9b8726f5503e5d89a6 1685768 python3-pysam_0.15.4+ds-1build1_riscv64.deb Checksums-Sha256: adf33c4e22618535f360b32a56d26e3652cfecb279b46dd23d8e1b0c777af52a 5826112 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7.7.0+dfsg-1ubuntu1), libatomic1 (= 10-20200324-1ubuntu1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2ubuntu6), libaudit1 (= 1:2.8.5-2ubuntu6), libbinutils (= 2.34-5ubuntu1), libblkid1 (= 2.34-0.1ubuntu8), libbrotli1 (= 1.0.7-6build1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.31-0ubuntu7), libc-dev-bin (= 2.31-0ubuntu7), libc6 (= 2.31-0ubuntu7), libc6-dev (= 2.31-0ubuntu7), libcap-ng0 (= 0.7.9-2.1build1), libcc1-0 (= 10-20200324-1ubuntu1), libcom-err2 (= 1.45.5-2ubuntu1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.10-10ubuntu4), libcrypt1 (= 1:4.4.10-10ubuntu4), libctf-nobfd0 (= 2.34-5ubuntu1), libctf0 (= 2.34-5ubuntu1), libcurl3-gnutls (= 7.68.0-1ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu2), libdebconfclient0 (= 0.251ubuntu1), libdebhelper-perl (= 12.10ubuntu1), libdeflate0 (= 1.5-3), libdpkg-perl (= 1.19.7ubuntu3), libelf1 (= 0.176-1.1build1), libexpat1 (= 2.2.9-1build1), libexpat1-dev (= 2.2.9-1build1), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.6.3-2), libgcc-9-dev (= 9.3.0-10ubuntu1), libgcc-s1 (= 10-20200324-1ubuntu1), libgcrypt20 (= 1.8.5-5ubuntu1), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.64.1-1), libgmp10 (= 2:6.2.0+dfsg-4), libgnutls30 (= 3.6.13-2ubuntu1), libgomp1 (= 10-20200324-1ubuntu1), libgpg-error0 (= 1.37-1), libgssapi-krb5-2 (= 1.17-6ubuntu4), libgssapi3-heimdal (= 7.7.0+dfsg-1ubuntu1), libhcrypto4-heimdal (= 7.7.0+dfsg-1ubuntu1), libheimbase1-heimdal (= 7.7.0+dfsg-1ubuntu1), libheimntlm0-heimdal (= 7.7.0+dfsg-1ubuntu1), libhogweed5 (= 3.5.1+really3.5.1-2), libhts-dev (= 1.10.2-3), libhts3 (= 1.10.2-3), libhx509-5-heimdal (= 7.7.0+dfsg-1ubuntu1), libicu66 (= 66.1-2ubuntu2), libidn2-0 (= 2.2.0-2), libisl22 (= 0.22.1-1), libjs-jquery (= 3.3.1~dfsg-3), libjs-sphinxdoc (= 1.8.5-7ubuntu1), libjs-underscore (= 1.9.1~dfsg-1), libk5crypto3 (= 1.17-6ubuntu4), libkeyutils1 (= 1.6-6ubuntu1), libkrb5-26-heimdal (= 7.7.0+dfsg-1ubuntu1), libkrb5-3 (= 1.17-6ubuntu4), libkrb5support0 (= 1.17-6ubuntu4), libldap-2.4-2 (= 2.4.49+dfsg-2ubuntu1), libldap-common (= 2.4.49+dfsg-2ubuntu1), liblz4-1 (= 1.9.2-2), liblzma-dev (= 5.2.4-1), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.38-4), libmagic1 (= 1:5.38-4), libmount1 (= 2.34-0.1ubuntu8), libmpc3 (= 1.1.0-1), libmpdec2 (= 2.4.2-3), libmpfr6 (= 4.0.2-1), libncurses6 (= 6.2-0ubuntu2), libncursesw6 (= 6.2-0ubuntu2), libnettle7 (= 3.5.1+really3.5.1-2), libnghttp2-14 (= 1.40.0-1build1), libp11-kit0 (= 0.23.20-1build1), libpam-modules (= 1.3.1-5ubuntu4), libpam-modules-bin (= 1.3.1-5ubuntu4), libpam-runtime (= 1.3.1-5ubuntu4), libpam0g (= 1.3.1-5ubuntu4), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-12build1), libperl5.30 (= 5.30.0-9build1), libpipeline1 (= 1.5.2-2build1), libpsl5 (= 0.21.0-1ubuntu1), libpython-all-dev (= 2.7.17-2ubuntu4), libpython2-dev (= 2.7.17-2ubuntu4), libpython2-stdlib (= 2.7.17-2ubuntu4), libpython2.7 (= 2.7.17-1ubuntu6), libpython2.7-dev (= 2.7.17-1ubuntu6), libpython2.7-minimal (= 2.7.17-1ubuntu6), libpython2.7-stdlib (= 2.7.17-1ubuntu6), libpython3-all-dev (= 3.8.2-0ubuntu2), libpython3-dev (= 3.8.2-0ubuntu2), libpython3-stdlib (= 3.8.2-0ubuntu2), libpython3.8 (= 3.8.2-1ubuntu1), libpython3.8-dev (= 3.8.2-1ubuntu1), libpython3.8-minimal (= 3.8.2-1ubuntu1), libpython3.8-stdlib (= 3.8.2-1ubuntu1), libreadline8 (= 8.0-4), libroken18-heimdal (= 7.7.0+dfsg-1ubuntu1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build1), libsasl2-2 (= 2.1.27+dfsg-2), libsasl2-modules-db (= 2.1.27+dfsg-2), libselinux1 (= 3.0-1build2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1ubuntu8), libsqlite3-0 (= 3.31.1-4), libssh-4 (= 0.9.3-2ubuntu1), libssl1.1 (= 1.1.1d-2ubuntu6), libstdc++-9-dev (= 9.3.0-10ubuntu1), libstdc++6 (= 10-20200324-1ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 245.2-1ubuntu3), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2-0ubuntu2), libtool (= 2.4.6-14), libuchardet0 (= 0.0.6-3build1), libudev1 (= 245.2-1ubuntu3), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1ubuntu8), libwind0-heimdal (= 7.7.0+dfsg-1ubuntu1), libxml2 (= 2.9.10+dfsg-4build1), libzstd1 (= 1.4.4+dfsg-3), linux-libc-dev (= 5.4.0-21.25), login (= 1:4.8.1-1ubuntu4), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.1-1), mawk (= 1.3.4.20200120-2), mime-support (= 3.64ubuntu1), ncurses-base (= 6.2-0ubuntu2), ncurses-bin (= 6.2-0ubuntu2), patch (= 2.7.6-6), perl (= 5.30.0-9build1), perl-base (= 5.30.0-9build1), perl-modules-5.30 (= 5.30.0-9build1), po-debconf (= 1.0.21), python-all (= 2.7.17-2ubuntu4), python-all-dev (= 2.7.17-2ubuntu4), python-atomicwrites (= 1.1.5-2build1), python-attr (= 19.3.0-2), python-configparser (= 3.5.0b2-3build1), python-contextlib2 (= 0.6.0-2), python-funcsigs (= 1.0.2-4build1), python-importlib-metadata (= 1.5.0-1), python-more-itertools (= 4.2.0-1build1), python-packaging (= 20.3-1), python-pathlib2 (= 2.3.5-1ubuntu1), python-pkg-resources (= 44.0.0-2), python-pluggy (= 0.13.0-2), python-py (= 1.8.1-1), python-pyparsing (= 2.4.6-1), python-pytest (= 4.6.9-1), python-scandir (= 1.10.0-2ubuntu3), python-setuptools (= 44.0.0-2), python-six (= 1.14.0-2), python-wcwidth (= 0.1.8+dfsg1-3), python-zipp (= 1.0.0-1), python2 (= 2.7.17-2ubuntu4), python2-dev (= 2.7.17-2ubuntu4), python2-minimal (= 2.7.17-2ubuntu4), python2.7 (= 2.7.17-1ubuntu6), python2.7-dev (= 2.7.17-1ubuntu6), python2.7-minimal (= 2.7.17-1ubuntu6), python3 (= 3.8.2-0ubuntu2), python3-all (= 3.8.2-0ubuntu2), python3-all-dev (= 3.8.2-0ubuntu2), python3-atomicwrites (= 1.1.5-2build1), python3-attr (= 19.3.0-2), python3-dev (= 3.8.2-0ubuntu2), python3-distutils (= 3.8.2-1ubuntu1), python3-importlib-metadata (= 1.5.0-1), python3-lib2to3 (= 3.8.2-1ubuntu1), python3-minimal (= 3.8.2-0ubuntu2), python3-more-itertools (= 4.2.0-1build1), python3-packaging (= 20.3-1), python3-pkg-resources (= 45.2.0-1), python3-pluggy (= 0.13.0-2), python3-py (= 1.8.1-1), python3-pyparsing (= 2.4.6-1), python3-pytest (= 4.6.9-1), python3-setuptools (= 45.2.0-1), python3-six (= 1.14.0-2), python3-wcwidth (= 0.1.8+dfsg1-3), python3-zipp (= 1.0.0-1), python3.8 (= 3.8.2-1ubuntu1), python3.8-dev (= 3.8.2-1ubuntu1), python3.8-minimal (= 3.8.2-1ubuntu1), readline-common (= 8.0-4), samtools (= 1.10-3), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-2.1ubuntu1), tabix (= 1.10.2-3), tar (= 1.30+dfsg-7), tzdata (= 2019c-3ubuntu1), util-linux (= 2.34-0.1ubuntu8), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-2ubuntu1), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1582017834" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python-pysam_0.15.4+ds-1build1_riscv64.deb ------------------------------------------ new Debian package, version 2.0. size 1629480 bytes: control archive=3264 bytes. 814 bytes, 17 lines control 8419 bytes, 88 lines md5sums 161 bytes, 9 lines * postinst #!/bin/sh 262 bytes, 14 lines * prerm #!/bin/sh Package: python-pysam Version: 0.15.4+ds-1build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4760 Depends: libc6 (>= 2.27), libhts3 (>= 1.10), zlib1g (>= 1:1.1.4), python2 (<< 2.8), python2 (>= 2.7~), python2:any (<< 2.8), python2:any (>= 2.7~) Provides: python2.7-pysam Section: python Priority: optional Homepage: https://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2) Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . This package installs the module for Python 2. drwxr-xr-x root/root 0 2020-02-18 09:23 ./ drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/ drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/lib/ drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/lib/python2.7/ drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/ drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam-0.15.4.egg-info/ -rw-r--r-- root/root 1505 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam-0.15.4.egg-info/PKG-INFO -rw-r--r-- root/root 1 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam-0.15.4.egg-info/dependency_links.txt -rw-r--r-- root/root 1 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam-0.15.4.egg-info/not-zip-safe -rw-r--r-- root/root 6 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam-0.15.4.egg-info/top_level.txt drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam/ -rw-r--r-- root/root 8975 2020-01-18 21:20 ./usr/lib/python2.7/dist-packages/pysam/Pileup.py -rw-r--r-- root/root 3235 2020-01-18 21:20 ./usr/lib/python2.7/dist-packages/pysam/__init__.py -rw-r--r-- root/root 434 2020-01-18 21:20 ./usr/lib/python2.7/dist-packages/pysam/bcftools.py -rw-r--r-- root/root 102 2020-01-18 21:20 ./usr/lib/python2.7/dist-packages/pysam/cbcftools_util.h -rw-r--r-- root/root 16 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam/config.py -rw-r--r-- root/root 102 2020-01-18 21:20 ./usr/lib/python2.7/dist-packages/pysam/csamtools_util.h -rw-r--r-- root/root 2565 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam/htslib_util.h drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam/include/ -rw-r--r-- root/root 0 2020-01-18 21:20 ./usr/lib/python2.7/dist-packages/pysam/include/__init__.py drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/ -rw-r--r-- root/root 5022 2020-01-18 21:20 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/HMM.h -rw-r--r-- root/root 5369 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/bam2bcf.h -rw-r--r-- root/root 2030 2020-01-18 21:20 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/bam_sample.h -rw-r--r-- root/root 3470 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/bcftools.h -rw-r--r-- root/root 938 2020-01-18 21:20 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/bcftools.pysam.h -rw-r--r-- root/root 2188 2020-01-18 21:20 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/bin.h -rw-r--r-- root/root 5237 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/call.h -rw-r--r-- root/root 1808 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/cols.h -rw-r--r-- root/root 77 2020-02-18 09:23 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/config.h -rw-r--r-- root/root 1751 2020-01-18 21:20 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./usr/share/lintian/overrides/python-pysam python3-pysam_0.15.4+ds-1build1_riscv64.deb ------------------------------------------- new Debian package, version 2.0. size 1685768 bytes: control archive=3356 bytes. 778 bytes, 17 lines control 8395 bytes, 88 lines md5sums 251 bytes, 12 lines * postinst #!/bin/sh 400 bytes, 12 lines * prerm #!/bin/sh Package: python3-pysam Source: python-pysam Version: 0.15.4+ds-1build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4777 Depends: libc6 (>= 2.27), libhts3 (>= 1.10), zlib1g (>= 1:1.1.4), python3 (<< 3.9), python3 (>= 3.8~), python3:any Section: python Priority: optional Homepage: https://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3) Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . 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-rw-r--r-- root/root 197 2020-01-18 21:20 ./usr/lib/python3/dist-packages/pysam/version.py drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/share/ drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/share/doc/python3-pysam/ -rw-r--r-- root/root 1331 2020-02-18 09:23 ./usr/share/doc/python3-pysam/changelog.Debian.gz -rw-r--r-- root/root 5045 2020-01-23 12:47 ./usr/share/doc/python3-pysam/copyright drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/share/lintian/ drwxr-xr-x root/root 0 2020-02-18 09:23 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 209 2019-08-06 17:35 ./usr/share/lintian/overrides/python3-pysam +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 526068 Build-Time: 8304 Distribution: focal Host Architecture: riscv64 Install-Time: 500 Job: python-pysam_0.15.4+ds-1build1.dsc Machine Architecture: riscv64 Package: python-pysam Package-Time: 8853 Source-Version: 0.15.4+ds-1build1 Space: 526068 Status: successful Version: 0.15.4+ds-1build1 -------------------------------------------------------------------------------- Finished at 2020-04-06T17:41:02Z Build needed 02:27:33, 526068k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19109737 Scanning for processes to kill in build PACKAGEBUILD-19109737 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19109737 Stopping target for build PACKAGEBUILD-19109737 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19109737 Removing build PACKAGEBUILD-19109737