https://launchpad.net/ubuntu/+source/pbbam/0.19.0+dfsg-1ubuntu4/+build/16343464 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-s390x-009 4.4.0-141-generic #167-Ubuntu SMP Wed Dec 5 10:32:22 UTC 2018 s390x Buildd toolchain package versions: launchpad-buildd_166 python-lpbuildd_166 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 1 Feb 22:51:23 ntpdate[1798]: adjust time server 10.211.37.1 offset 0.000280 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=s390x PACKAGEBUILD-16343464 /home/buildd/filecache-default/5f92d5ecab7ce0d953bb2def2bd7e5fe5fb7c904 Creating target for build PACKAGEBUILD-16343464 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=s390x PACKAGEBUILD-16343464 Starting target for build PACKAGEBUILD-16343464 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=s390x PACKAGEBUILD-16343464 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-16343464 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=s390x PACKAGEBUILD-16343464 Updating target for build PACKAGEBUILD-16343464 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main s390x Packages [944 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe s390x Packages [8628 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5217 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main s390x Packages [49.9 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [35.5 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe s390x Packages [213 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [125 kB] Fetched 16.2 MB in 3s (4869 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libreadline7 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libreadline8 The following packages will be upgraded: adduser apt bash binutils binutils-common binutils-s390x-linux-gnu bsdutils ca-certificates coreutils cpp-8 dash debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++-8 gcc-8 gcc-8-base gpg gpg-agent gpgconf gpgv grep gzip init init-system-helpers libapt-pkg5.0 libargon2-1 libasan5 libassuan0 libatomic1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcom-err2 libcomerr2 libdb5.3 libdebconfclient0 libdpkg-perl libext2fs2 libfdisk1 libgcc-8-dev libgcc1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libhogweed4 libitm1 libjson-c3 liblz4-1 liblzma5 libmount1 libmpfr6 libnettle6 libpng16-16 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libstdc++-8-dev libstdc++6 libsystemd0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login lsb-base mount passwd readline-common sed systemd systemd-sysv tar tzdata util-linux xz-utils zlib1g 88 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 47.4 MB of archives. After this operation, 8955 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main s390x debianutils s390x 4.8.6.1 [85.0 kB] Get:2 http://ftpmaster.internal/ubuntu disco/main s390x bash s390x 5.0-2ubuntu1 [610 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main s390x bsdutils s390x 1:2.33.1-0.1ubuntu1 [61.2 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main s390x coreutils s390x 8.30-1ubuntu1 [1216 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main s390x tar s390x 1.30+dfsg-4 [229 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main s390x dpkg s390x 1.19.2ubuntu2 [1080 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main s390x debconf all 1.5.70 [122 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main s390x dash s390x 0.5.10.2-4ubuntu1 [83.6 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main s390x findutils s390x 4.6.0+git+20190105-2 [321 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main s390x grep s390x 3.3-1 [146 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main s390x gzip s390x 1.9-3 [92.7 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main s390x libsmartcols1 s390x 2.33.1-0.1ubuntu1 [85.9 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main s390x libuuid1 s390x 2.33.1-0.1ubuntu1 [21.0 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main s390x libblkid1 s390x 2.33.1-0.1ubuntu1 [123 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main s390x libfdisk1 s390x 2.33.1-0.1ubuntu1 [159 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main s390x libmount1 s390x 2.33.1-0.1ubuntu1 [134 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main s390x fdisk s390x 2.33.1-0.1ubuntu1 [111 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main s390x login s390x 1:4.5-1.1ubuntu1 [262 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main s390x util-linux s390x 2.33.1-0.1ubuntu1 [956 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main s390x sed s390x 4.7-1 [187 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main s390x init-system-helpers all 1.56+nmu1 [38.2 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main s390x libnettle6 s390x 3.4.1-1 [121 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main s390x libhogweed4 s390x 3.4.1-1 [138 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main s390x libgnutls30 s390x 3.6.5-2ubuntu1 [661 kB] Get:25 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libubsan1 s390x 8.2.0-16ubuntu1 [116 kB] Get:26 http://ftpmaster.internal/ubuntu disco-proposed/main s390x gcc-8-base s390x 8.2.0-16ubuntu1 [18.8 kB] Get:27 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libgcc1 s390x 1:8.2.0-16ubuntu1 [25.1 kB] Get:28 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libgomp1 s390x 8.2.0-16ubuntu1 [69.9 kB] Get:29 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libitm1 s390x 8.2.0-16ubuntu1 [26.9 kB] Get:30 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libatomic1 s390x 8.2.0-16ubuntu1 [8424 B] Get:31 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libasan5 s390x 8.2.0-16ubuntu1 [326 kB] Get:32 http://ftpmaster.internal/ubuntu disco-proposed/main s390x cpp-8 s390x 8.2.0-16ubuntu1 [6885 kB] Get:33 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libcc1-0 s390x 8.2.0-16ubuntu1 [44.7 kB] Get:34 http://ftpmaster.internal/ubuntu disco-proposed/main s390x g++-8 s390x 8.2.0-16ubuntu1 [7952 kB] Get:35 http://ftpmaster.internal/ubuntu disco-proposed/main s390x gcc-8 s390x 8.2.0-16ubuntu1 [7706 kB] Get:36 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libgcc-8-dev s390x 8.2.0-16ubuntu1 [648 kB] Get:37 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libstdc++-8-dev s390x 8.2.0-16ubuntu1 [1505 kB] Get:38 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libstdc++6 s390x 8.2.0-16ubuntu1 [397 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main s390x libmpfr6 s390x 4.0.2-1 [229 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main s390x zlib1g s390x 1:1.2.11.dfsg-1ubuntu2 [51.8 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main s390x libbinutils s390x 2.31.1-11ubuntu1 [304 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main s390x binutils-common s390x 2.31.1-11ubuntu1 [194 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main s390x binutils s390x 2.31.1-11ubuntu1 [3328 B] Get:44 http://ftpmaster.internal/ubuntu disco/main s390x binutils-s390x-linux-gnu s390x 2.31.1-11ubuntu1 [1679 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main s390x liblz4-1 s390x 1.8.3-1ubuntu1 [56.1 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main s390x liblzma5 s390x 5.2.4-1 [91.5 kB] Get:47 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libudev1 s390x 240-5ubuntu2 [64.9 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main s390x libzstd1 s390x 1.3.8+dfsg-3 [204 kB] Get:49 http://ftpmaster.internal/ubuntu disco/main s390x libapt-pkg5.0 s390x 1.8.0~beta1 [746 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main s390x libsemanage-common all 2.8-2 [7016 B] Get:51 http://ftpmaster.internal/ubuntu disco/main s390x libsemanage1 s390x 2.8-2 [78.5 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main s390x passwd s390x 1:4.5-1.1ubuntu1 [795 kB] Get:53 http://ftpmaster.internal/ubuntu disco-proposed/main s390x adduser all 3.118ubuntu1 [163 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main s390x libgpg-error0 s390x 1.33-3 [53.7 kB] Get:55 http://ftpmaster.internal/ubuntu disco-proposed/main s390x gpgv s390x 2.2.12-1ubuntu3 [180 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main s390x apt s390x 1.8.0~beta1 [1124 kB] Get:57 http://ftpmaster.internal/ubuntu disco-proposed/main s390x systemd-sysv s390x 240-5ubuntu2 [9388 B] Get:58 http://ftpmaster.internal/ubuntu disco/main s390x mount s390x 2.33.1-0.1ubuntu1 [108 kB] Get:59 http://ftpmaster.internal/ubuntu disco-proposed/main s390x systemd s390x 240-5ubuntu2 [2986 kB] Get:60 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libsystemd0 s390x 240-5ubuntu2 [226 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main s390x libext2fs2 s390x 1.44.5-1 [155 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main s390x e2fsprogs s390x 1.44.5-1 [490 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main s390x init s390x 1.56+nmu1 [6080 B] Get:64 http://ftpmaster.internal/ubuntu disco/main s390x libcap-ng0 s390x 0.7.9-2 [10.6 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main s390x libdb5.3 s390x 5.3.28+dfsg1-0.3 [608 kB] Get:66 http://ftpmaster.internal/ubuntu disco-proposed/main s390x libdebconfclient0 s390x 0.246ubuntu1 [6156 B] Get:67 http://ftpmaster.internal/ubuntu disco/main s390x libcom-err2 s390x 1.44.5-1 [9200 B] Get:68 http://ftpmaster.internal/ubuntu disco/main s390x libss2 s390x 1.44.5-1 [10.6 kB] Get:69 http://ftpmaster.internal/ubuntu disco-proposed/main s390x lsb-base all 10.2018112800ubuntu1 [12.6 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main s390x ca-certificates all 20190110 [146 kB] Get:71 http://ftpmaster.internal/ubuntu disco/main s390x libargon2-1 s390x 0~20171227-0.2 [35.7 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main s390x libjson-c3 s390x 0.12.1+ds-2 [21.4 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main s390x readline-common all 8.0-1 [53.4 kB] Get:74 http://ftpmaster.internal/ubuntu disco/main s390x libreadline8 s390x 8.0-1 [122 kB] Get:75 http://ftpmaster.internal/ubuntu disco/main s390x libsqlite3-0 s390x 3.26.0+fossilbc891ac6b-2 [494 kB] Get:76 http://ftpmaster.internal/ubuntu disco/main s390x tzdata all 2018i-1 [189 kB] Get:77 http://ftpmaster.internal/ubuntu disco/main s390x xz-utils s390x 5.2.4-1 [80.3 kB] Get:78 http://ftpmaster.internal/ubuntu disco/main s390x libgdbm6 s390x 1.18.1-2build1 [27.0 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main s390x libpng16-16 s390x 1.6.36-3 [173 kB] Get:80 http://ftpmaster.internal/ubuntu disco/main s390x dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main s390x libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:82 http://ftpmaster.internal/ubuntu disco/main s390x e2fslibs s390x 1.44.5-1 [2704 B] Get:83 http://ftpmaster.internal/ubuntu disco/main s390x libassuan0 s390x 2.5.2-1 [32.1 kB] Get:84 http://ftpmaster.internal/ubuntu disco-proposed/main s390x gpg s390x 2.2.12-1ubuntu3 [431 kB] Get:85 http://ftpmaster.internal/ubuntu disco-proposed/main s390x gpgconf s390x 2.2.12-1ubuntu3 [115 kB] Get:86 http://ftpmaster.internal/ubuntu disco-proposed/main s390x gpg-agent s390x 2.2.12-1ubuntu3 [209 kB] Get:87 http://ftpmaster.internal/ubuntu disco/main s390x libcomerr2 s390x 1.44.5-1 [2700 B] Get:88 http://ftpmaster.internal/ubuntu disco/main s390x libgdbm-compat4 s390x 1.18.1-2build1 [6264 B] Get:89 http://ftpmaster.internal/ubuntu disco-proposed/main s390x linux-libc-dev s390x 4.19.0-12.13 [1067 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.4 MB in 1s (49.9 MB/s) (Reading database ... 12438 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6.1_s390x.deb ... Unpacking debianutils (4.8.6.1) over (4.8.6) ... Setting up debianutils (4.8.6.1) ... (Reading database ... 12438 files and directories currently installed.) Preparing to unpack .../bash_5.0-2ubuntu1_s390x.deb ... Unpacking bash (5.0-2ubuntu1) over (4.4.18-2ubuntu3) ... Setting up bash (5.0-2ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12438 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.33.1-0.1ubuntu1_s390x.deb ... Unpacking bsdutils (1:2.33.1-0.1ubuntu1) over (1:2.32-0.1ubuntu2) ... Setting up bsdutils (1:2.33.1-0.1ubuntu1) ... (Reading database ... 12438 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-1ubuntu1_s390x.deb ... Unpacking coreutils (8.30-1ubuntu1) over (8.28-1ubuntu2) ... Setting up coreutils (8.30-1ubuntu1) ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-16343464 s390x disco-proposed -c chroot:build-PACKAGEBUILD-16343464 --arch=s390x --dist=disco-proposed --nolog pbbam_0.19.0+dfsg-1ubuntu4.dsc Initiating build PACKAGEBUILD-16343464 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-141-generic #167-Ubuntu SMP Wed Dec 5 10:32:22 UTC 2018 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-s390x-009.buildd +==============================================================================+ | pbbam 0.19.0+dfsg-1ubuntu4 (s390x) 01 Feb 2019 22:51 | +==============================================================================+ Package: pbbam Version: 0.19.0+dfsg-1ubuntu4 Source Version: 0.19.0+dfsg-1ubuntu4 Distribution: disco-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/pbbam-j9M4Ll/pbbam-0.19.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/pbbam-j9M4Ll' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-16343464/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pbbam_0.19.0+dfsg-1ubuntu4.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-Wva4BI/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-Wva4BI/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Wva4BI/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Wva4BI/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Wva4BI/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-Wva4BI/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core 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: libreadline7 Use 'apt autoremove' to remove it. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Wva4BI/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12471 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), dh-exec, d-shlibs, meson, pkg-config, python, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, libgtest-dev, python-cram, samtools Filtered Build-Depends: debhelper (>= 11~), dh-exec, d-shlibs, meson, pkg-config, python, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, libgtest-dev, python-cram, samtools dpkg-deb: building package 'sbuild-build-depends-pbbam-dummy' in '/<>/resolver-oCrj_h/apt_archive/sbuild-build-depends-pbbam-dummy.deb'. Ign:1 copy:/<>/resolver-oCrj_h/apt_archive ./ InRelease Get:2 copy:/<>/resolver-oCrj_h/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-oCrj_h/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-oCrj_h/apt_archive ./ Sources [285 B] Get:5 copy:/<>/resolver-oCrj_h/apt_archive ./ Packages [604 B] Fetched 3008 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install pbbam 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: libreadline7 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libboost-dev libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libgtest-dev libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db meson mime-support ninja-build pkg-config po-debconf python python-cram python-minimal python2 python2-minimal python2.7 python2.7-minimal python3 python3-minimal python3-pkg-resources python3.7 python3.7-minimal samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev libboost-date-time1.67-dev libboost-exception1.67-dev libboost-filesystem1.67-dev libboost-graph1.67-dev libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev libboost-program-options1.67-dev libboost-python1.67-dev libboost-random1.67-dev libboost-regex1.67-dev libboost-serialization1.67-dev libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3-setuptools python3.7-venv python3.7-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libboost-dev libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libgtest-dev libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db meson mime-support ninja-build pkg-config po-debconf python python-cram python-minimal python2 python2-minimal python2.7 python2.7-minimal python3 python3-minimal python3-pkg-resources python3.7 python3.7-minimal samtools sbuild-build-depends-pbbam-dummy zlib1g-dev 0 upgraded, 93 newly installed, 0 to remove and 0 not upgraded. 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http://ftpmaster.internal/ubuntu disco-proposed/universe s390x samtools s390x 1.9-2 [398 kB] Get:93 http://ftpmaster.internal/ubuntu disco/main s390x dh-exec s390x 0.23.1 [24.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 43.0 MB in 2s (27.6 MB/s) Selecting previously unselected package libpython3.7-minimal:s390x. 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Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-3) ... Setting up autotools-dev (20180224.1) ... Setting up libboost1.67-dev:s390x (1.67.0-12) ... Setting up libheimbase1-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up libgtest-dev:s390x (1.8.1-3) ... Setting up libboost-dev:s390x (1.67.0.1) ... Setting up liblzma-dev:s390x (5.2.4-1) ... Setting up libkeyutils1:s390x (1.5.9-9.3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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 ninja-build (1.8.2-1) ... Setting up libpython2.7-stdlib:s390x (2.7.15-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up libmpdec2:s390x (2.4.2-2) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-1ubuntu2) ... Setting up libfile-stripnondeterminism-perl (1.1.0-1) ... Setting up libk5crypto3:s390x (1.17-1) ... Setting up libpython3.7-stdlib:s390x (3.7.2-1build1) ... Setting up libwind0-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up gettext (0.19.8.1-9) ... Setting up libasn1-8-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up groff-base (1.22.4-2) ... Setting up libhcrypto4-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up python2.7 (2.7.15-6) ... Setting up python3.7 (3.7.2-1build1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.35-2) ... Setting up libhx509-5-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.5-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libpython2-stdlib:s390x (2.7.15-4) ... Setting up libkrb5-3:s390x (1.17-1) ... Setting up libkrb5-26-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up libheimntlm0-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up libtool (2.4.6-9) ... Setting up libpython3-stdlib:s390x (3.7.2-1) ... Setting up po-debconf (1.0.21) ... Setting up python3 (3.7.2-1) ... Setting up python3-pkg-resources (40.6.3-1) ... Setting up python2 (2.7.15-4) ... Setting up libgssapi-krb5-2:s390x (1.17-1) ... Setting up libpython-stdlib:s390x (2.7.15-4) ... Setting up libssh-4:s390x (0.8.6-2) ... Setting up meson (0.49.0-2ubuntu1) ... Setting up libgssapi3-heimdal:s390x (7.5.0+dfsg-2.1) ... Setting up python (2.7.15-4) ... Setting up python-cram (0.7-3) ... Setting up libldap-2.4-2:s390x (2.4.47+dfsg-2ubuntu1) ... Setting up libcurl3-gnutls:s390x (7.63.0-1ubuntu1) ... Setting up libhts2:s390x (1.9-10) ... Setting up libhts-dev:s390x (1.9-10) ... Setting up samtools (1.9-2) ... Setting up dh-strip-nondeterminism (1.1.0-1) ... Setting up debhelper (12ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up dh-exec (0.23.1) ... Setting up sbuild-build-depends-pbbam-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-141-generic s390x (s390x) Toolchain package versions: binutils_2.31.1-11ubuntu1 dpkg-dev_1.19.2ubuntu2 g++-8_8.2.0-16ubuntu1 gcc-8_8.2.0-16ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-16ubuntu1 libstdc++6_8.2.0-16ubuntu1 linux-libc-dev_4.19.0-12.13 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-1 apt_1.8.0~beta1 autoconf_2.69-11 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_5.0-2ubuntu1 binutils_2.31.1-11ubuntu1 binutils-common_2.31.1-11ubuntu1 binutils-s390x-linux-gnu_2.31.1-11ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.33.1-0.1ubuntu1 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20190110 coreutils_8.30-1ubuntu1 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-16ubuntu1 d-shlibs_0.84ubuntu2 dash_0.5.10.2-4ubuntu1 debconf_1.5.70 debhelper_12ubuntu1 debianutils_4.8.6.1 dh-autoreconf_19 dh-exec_0.23.1 dh-strip-nondeterminism_1.1.0-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.2ubuntu2 dpkg-dev_1.19.2ubuntu2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1ubuntu1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-16ubuntu1 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-16ubuntu1 gcc-8-base_8.2.0-16ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 googletest_1.8.1-3 gpg_2.2.12-1ubuntu3 gpg-agent_2.2.12-1ubuntu3 gpgconf_2.2.12-1ubuntu3 gpgv_2.2.12-1ubuntu3 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 init_1.56+nmu1 init-system-helpers_1.56+nmu1 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.5 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.8.0~beta1 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.2 libasan5_8.2.0-16ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-2.1 libassuan0_2.5.2-1 libatomic1_8.2.0-16ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.31.1-11ubuntu1 libblkid1_2.33.1-0.1ubuntu1 libboost-dev_1.67.0.1 libboost1.67-dev_1.67.0-12 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-0ubuntu1 libc-dev-bin_2.28-0ubuntu1 libc6_2.28-0ubuntu1 libc6-dev_2.28-0ubuntu1 libcap-ng0_0.7.9-2 libcap2_1:2.25-1.2 libcc1-0_8.2.0-16ubuntu1 libcom-err2_1.44.5-1 libcomerr2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.4-2ubuntu2 libcurl3-gnutls_7.63.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.3 libdebconfclient0_0.246ubuntu1 libdeflate0_1.2-1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.2ubuntu2 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1ubuntu1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.0-1 libgcc-8-dev_8.2.0-16ubuntu1 libgcc1_1:8.2.0-16ubuntu1 libgcrypt20_1.8.4-3ubuntu1 libgdbm-compat4_1.18.1-2build1 libgdbm6_1.18.1-2build1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2ubuntu1 libgomp1_8.2.0-16ubuntu1 libgpg-error0_1.33-3 libgssapi-krb5-2_1.17-1 libgssapi3-heimdal_7.5.0+dfsg-2.1 libgtest-dev_1.8.1-3 libhcrypto4-heimdal_7.5.0+dfsg-2.1 libheimbase1-heimdal_7.5.0+dfsg-2.1 libheimntlm0-heimdal_7.5.0+dfsg-2.1 libhogweed4_3.4.1-1 libhts-dev_1.9-10 libhts2_1.9-10 libhx509-5-heimdal_7.5.0+dfsg-2.1 libicu63_63.1-6 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu3 libisl19_0.20-2 libitm1_8.2.0-16ubuntu1 libjson-c3_0.12.1+ds-2 libk5crypto3_1.17-1 libkeyutils1_1.5.9-9.3 libkmod2_25-1ubuntu2 libkrb5-26-heimdal_7.5.0+dfsg-2.1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libldap-2.4-2_2.4.47+dfsg-2ubuntu1 libldap-common_2.4.47+dfsg-2ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_1.8.3-1ubuntu1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1ubuntu1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4.1-1 libnghttp2-14_1.36.0-1 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-11 libperl5.28_5.28.1-3 libpipeline1_1.5.1-1 libpng16-16_1.6.36-3 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-4 libpython2-stdlib_2.7.15-4 libpython2.7-minimal_2.7.15-6 libpython2.7-stdlib_2.7.15-6 libpython3-stdlib_3.7.2-1 libpython3.7-minimal_3.7.2-1build1 libpython3.7-stdlib_3.7.2-1build1 libreadline7_7.0-5 libreadline8_8.0-1 libroken18-heimdal_7.5.0+dfsg-2.1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1build1 libsasl2-modules-db_2.1.27+dfsg-1build1 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.33.1-0.1ubuntu1 libsqlite3-0_3.26.0+fossilbc891ac6b-2 libss2_1.44.5-1 libssh-4_0.8.6-2 libssl-dev_1.1.1a-1ubuntu2 libssl1.1_1.1.1a-1ubuntu2 libstdc++-8-dev_8.2.0-16ubuntu1 libstdc++6_8.2.0-16ubuntu1 libsystemd0_240-5ubuntu2 libtasn1-6_4.13-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-9 libubsan1_8.2.0-16ubuntu1 libuchardet0_0.0.6-3 libudev1_240-5ubuntu2 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libustr-1.0-1_1.0.4-6 libuuid1_2.33.1-0.1ubuntu1 libwind0-heimdal_7.5.0+dfsg-2.1 libxml2_2.9.4+dfsg1-7ubuntu3 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.0-12.13 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu1 lsb-base_10.2018112800ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-1 mawk_1.3.3-17ubuntu3 meson_0.49.0-2ubuntu1 mime-support_3.60ubuntu1 mount_2.33.1-0.1ubuntu1 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 ninja-build_1.8.2-1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1.1ubuntu1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1build2 pkg-config_0.29.1-0ubuntu2 pkgbinarymangler_143 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python_2.7.15-4 python-cram_0.7-3 python-minimal_2.7.15-4 python2_2.7.15-4 python2-minimal_2.7.15-4 python2.7_2.7.15-6 python2.7-minimal_2.7.15-6 python3_3.7.2-1 python3-minimal_3.7.2-1 python3-pkg-resources_40.6.3-1 python3.7_3.7.2-1build1 python3.7-minimal_3.7.2-1build1 readline-common_8.0-1 samtools_1.9-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbbam-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-5ubuntu2 systemd-sysv_240-5ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-4 tzdata_2018i-1 ubuntu-keyring_2018.09.18.1 util-linux_2.33.1-0.1ubuntu1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu2 zlib1g-dev_1:1.2.11.dfsg-1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Feb 1 22:49:49 2019 UTC gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbbam_0.19.0+dfsg-1ubuntu4.dsc dpkg-source: info: extracting pbbam in pbbam-0.19.0+dfsg dpkg-source: info: unpacking pbbam_0.19.0+dfsg.orig.tar.xz dpkg-source: info: unpacking pbbam_0.19.0+dfsg-1ubuntu4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_gtest_depcheck.patch Check disc 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-16343464 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-16343464 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-16343464 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 0.19.0+dfsg-1ubuntu4 dpkg-buildpackage: info: source distribution disco dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean dh clean --buildsystem=meson debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/pbbam-0.19.0+dfsg' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /<>/pbbam-0.19.0+dfsg/gendata make[1]: Leaving directory '/<>/pbbam-0.19.0+dfsg' dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules build-arch dh build-arch --buildsystem=meson dh_update_autotools_config -a -O--buildsystem=meson dh_autoreconf -a -O--buildsystem=meson dh_auto_configure -a -O--buildsystem=meson cd obj-s390x-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/s390x-linux-gnu --libexecdir=lib/s390x-linux-gnu The Meson build system Version: 0.49.0 Source dir: /<>/pbbam-0.19.0+dfsg Build dir: /<>/pbbam-0.19.0+dfsg/obj-s390x-linux-gnu Build type: native build Project name: PacBioBAM Project version: 0.19.0 Appending CXXFLAGS from environment: '-g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' Appending LDFLAGS from environment: '-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now' Appending CPPFLAGS from environment: '-Wdate-time -D_FORTIFY_SOURCE=2' Native C++ compiler: c++ (gcc 8.2.0 "c++ (Ubuntu 8.2.0-16ubuntu1) 8.2.0") Build machine cpu family: s390x Build machine cpu: s390x Compiler for C++ supports arguments -Wduplicated-cond: YES Compiler for C++ supports arguments -Wduplicated-branches: YES Compiler for C++ supports arguments -Wlogical-op: YES Compiler for C++ supports arguments -Wrestrict: YES Compiler for C++ supports arguments -Wnull-dereference: YES Compiler for C++ supports arguments -Wuseless-cast: YES Compiler for C++ supports arguments -Wdouble-promotion: YES Compiler for C++ supports arguments -Wshadow: YES Compiler for C++ supports arguments -Wformat=1: YES Dependency threads found: YES Dependency Boost found: YES 1.67 Found pkg-config: /usr/bin/pkg-config (0.29.1) Dependency zlib found: YES 1.2.11 Dependency htslib found: YES 1.9 Program python found: YES (/usr/bin/python) Program tools/check-formatting found: YES (/<>/pbbam-0.19.0+dfsg/tools/check-formatting) Program cram found: YES (/usr/bin/cram) Dependency GTest found: YES (prebuilt) Configuring group.fofn using configuration Configuring PbbamTestData.h using configuration Configuring synthetic_movie_all.subreadset.xml using configuration Configuring Bam2SamVersion.h using configuration Configuring bam2sam.t using configuration Configuring PbIndexVersion.h using configuration Configuring PbIndexDumpVersion.h using configuration Configuring pbindexdump_json.t using configuration Configuring pbindexdump_cpp.t using configuration Configuring PbMergeVersion.h using configuration Configuring pbmerge_pacbio_ordering.t using configuration Configuring pbmerge_aligned_ordering.t using configuration Configuring pbmerge_mixed_ordering.t using configuration Configuring pbmerge_dataset.t using configuration Configuring pbmerge_fofn.t using configuration Configuring PbBamifyVersion.h using configuration Program samtools found: YES (/usr/bin/samtools) Configuring pbbamify.t using configuration Build targets in project: 8 Option buildtype is: plain [default: release] Found ninja-1.8.2 at /usr/bin/ninja dh_auto_build -a -O--buildsystem=meson cd obj-s390x-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Accuracy.cpp.o' -MF 'src/25a6634@@pbbam@sha/Accuracy.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Accuracy.cpp.o' -c ../src/Accuracy.cpp [2/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o' -c ../src/BaiIndexedBamReader.cpp [3/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o' -MF 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o' -c ../src/AlignmentPrinter.cpp [4/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamFile.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamFile.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamFile.cpp.o' -c ../src/BamFile.cpp [5/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamHeader.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamHeader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamHeader.cpp.o' -c ../src/BamHeader.cpp [6/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamReader.cpp.o' -c ../src/BamReader.cpp [7/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o' -c ../src/BamRecordBuilder.cpp [8/161] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o' -c 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'src/25a6634@@pbbam@sha/Cigar.cpp.o' 'src/25a6634@@pbbam@sha/CigarOperation.cpp.o' 'src/25a6634@@pbbam@sha/Compare.cpp.o' 'src/25a6634@@pbbam@sha/Config.cpp.o' 'src/25a6634@@pbbam@sha/DataSet.cpp.o' 'src/25a6634@@pbbam@sha/DataSetBaseTypes.cpp.o' 'src/25a6634@@pbbam@sha/DataSetElement.cpp.o' 'src/25a6634@@pbbam@sha/DataSetIO.cpp.o' 'src/25a6634@@pbbam@sha/DataSetTypes.cpp.o' 'src/25a6634@@pbbam@sha/DataSetXsd.cpp.o' 'src/25a6634@@pbbam@sha/EntireFileQuery.cpp.o' 'src/25a6634@@pbbam@sha/FastaReader.cpp.o' 'src/25a6634@@pbbam@sha/FastaSequenceQuery.cpp.o' 'src/25a6634@@pbbam@sha/FastqReader.cpp.o' 'src/25a6634@@pbbam@sha/FileProducer.cpp.o' 'src/25a6634@@pbbam@sha/FileUtils.cpp.o' 'src/25a6634@@pbbam@sha/FofnReader.cpp.o' 'src/25a6634@@pbbam@sha/Frames.cpp.o' 'src/25a6634@@pbbam@sha/GenomicInterval.cpp.o' 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o' 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastaReader.cpp.o' 'src/25a6634@@pbbam@sha/MD5.cpp.o' 'src/25a6634@@pbbam@sha/MemoryUtils.cpp.o' 'src/25a6634@@pbbam@sha/PbiBuilder.cpp.o' 'src/25a6634@@pbbam@sha/PbiFile.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilter.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilterQuery.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilterTypes.cpp.o' 'src/25a6634@@pbbam@sha/PbiIndexedBamReader.cpp.o' 'src/25a6634@@pbbam@sha/PbiIndexIO.cpp.o' 'src/25a6634@@pbbam@sha/PbiRawData.cpp.o' 'src/25a6634@@pbbam@sha/ProgramInfo.cpp.o' 'src/25a6634@@pbbam@sha/QNameQuery.cpp.o' 'src/25a6634@@pbbam@sha/QualityValue.cpp.o' 'src/25a6634@@pbbam@sha/ReadAccuracyQuery.cpp.o' 'src/25a6634@@pbbam@sha/ReadGroupInfo.cpp.o' 'src/25a6634@@pbbam@sha/SamTagCodec.cpp.o' 'src/25a6634@@pbbam@sha/SamWriter.cpp.o' 'src/25a6634@@pbbam@sha/SequenceInfo.cpp.o' 'src/25a6634@@pbbam@sha/SubreadLengthQuery.cpp.o' 'src/25a6634@@pbbam@sha/Validator.cpp.o' 'src/25a6634@@pbbam@sha/ValidationErrors.cpp.o' 'src/25a6634@@pbbam@sha/ValidationException.cpp.o' 'src/25a6634@@pbbam@sha/Version.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwBamRecord.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwCompositeReader.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwReader.cpp.o' 'src/25a6634@@pbbam@sha/VirtualRegionTypeMap.cpp.o' 'src/25a6634@@pbbam@sha/XmlReader.cpp.o' 'src/25a6634@@pbbam@sha/XmlWriter.cpp.o' 'src/25a6634@@pbbam@sha/WhitelistedZmwReadStitcher.cpp.o' 'src/25a6634@@pbbam@sha/ZmwGroupQuery.cpp.o' 'src/25a6634@@pbbam@sha/ZmwReadStitcher.cpp.o' 'src/25a6634@@pbbam@sha/ZmwQuery.cpp.o' 'src/25a6634@@pbbam@sha/ZmwTypeMap.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfVariant.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfFormat.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfHeader.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfReader.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfSort.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfQuery.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfWriter.cpp.o' 'src/25a6634@@pbbam@sha/pugixml_pugixml.cpp.o' -Wl,--no-undefined -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.0.19.0 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now /usr/lib/s390x-linux-gnu/libz.so /usr/lib/s390x-linux-gnu/libhts.so -Wl,--end-group -pthread [83/161] /usr/bin/meson --internal symbolextractor src/libpbbam.so.0.19.0 'src/25a6634@@pbbam@sha/libpbbam.so.0.19.0.symbols' [84/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o' -c ../tests/src/test_BamRecordBuilder.cpp [85/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o' -c ../tests/src/test_AlignmentPrinter.cpp [86/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o' -c ../tests/src/test_BamFile.cpp [87/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o' -c ../tests/src/test_BamRecordImplTags.cpp [88/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o' -c ../tests/src/test_BamRecordImplCore.cpp [89/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' -c ../tests/src/test_BamWriter.cpp [90/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o' -c ../tests/src/test_BarcodeQuery.cpp [91/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -c ../tests/src/test_BamRecordMapping.cpp [92/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o' -c ../tests/src/test_Cigar.cpp [93/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -c ../tests/src/test_BamRecordClipping.cpp [94/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o' -c ../tests/src/test_DataSetCore.cpp [95/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o' -c ../tests/src/test_DataSetQuery.cpp [96/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict 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-Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o' -c ../tests/src/test_Compare.cpp [99/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op 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-Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o' -c ../tests/src/test_EntireFileQuery.cpp [103/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o' -c 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-Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o' -c ../tests/src/test_Fasta.cpp [106/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o' -c 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o' -c ../tests/src/test_Intervals.cpp [109/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o' -c ../tests/src/test_IndexedFastaReader.cpp [110/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o' -c ../tests/src/test_LongCigar.cpp [111/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o' -c ../tests/src/test_PacBioIndex.cpp [112/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o' -c ../tests/src/test_QualityValues.cpp [113/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o' -c ../tests/src/test_QNameQuery.cpp [114/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o' -c ../tests/src/test_Pulse2BaseCache.cpp [115/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o' -c ../tests/src/test_PbiFilterQuery.cpp [116/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o' -c ../tests/src/test_ReadGroupInfo.cpp [117/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o' -c ../tests/src/test_ReadAccuracyQuery.cpp [118/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o' -c ../tests/src/test_StringUtils.cpp [119/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o' -c ../tests/src/test_SequenceUtils.cpp [120/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o' -c ../tests/src/test_SamWriter.cpp [121/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o' -c ../tests/src/test_PbiFilter.cpp [122/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o' -c ../tests/src/test_TimeUtils.cpp [123/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o' -c ../tests/src/test_VcfFile.cpp [124/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o' -c ../tests/src/test_SubreadLengthQuery.cpp [125/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o' -c ../tests/src/test_VcfHeader.cpp [126/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o' -c ../tests/src/test_VcfFormat.cpp [127/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o' -c ../tests/src/test_Validator.cpp [128/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o' -c ../tests/src/test_VcfReader.cpp [129/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o' -c ../tests/src/test_VcfVariant.cpp [130/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o' -c ../tests/src/test_VcfSort.cpp [131/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o' -c ../tests/src/test_VcfQuery.cpp [132/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o' -c ../tests/src/test_Version.cpp [133/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o' -c ../tests/src/test_Tags.cpp [134/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o' -c ../tests/src/test_VcfWriter.cpp [135/161] /usr/bin/python ../tests/scripts/generate_data.py /<>/pbbam-0.19.0+dfsg/tests/data /<>/pbbam-0.19.0+dfsg/obj-s390x-linux-gnu/tests Generating test data in /<>/pbbam-0.19.0+dfsg/obj-s390x-linux-gnu/tests - Creating file: truncated.bam...done. - Creating file: normal.fa...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fq...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating symlink: missing_pbi.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. [136/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o' -c ../tests/src/test_ZmwQuery.cpp [137/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o' -c ../tests/src/test_WhitelistedZmwReadStitcher.cpp [138/161] c++ -Itools/f9d35d4@@bam2sam@exe -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp [139/161] c++ -Itools/f9d35d4@@bam2sam@exe -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o' -MF 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o.d' -o 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o' -c ../tools/bam2sam/src/Bam2Sam.cpp [140/161] c++ -Itools/f9d35d4@@bam2sam@exe -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o' -MF 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o.d' -o 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o' -c ../tools/bam2sam/src/main.cpp [141/161] c++ -o tools/bam2sam 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o' 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--start-group /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so -Wl,--end-group -pthread [142/161] c++ -Itools/f9d35d4@@pbindex@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o' -MF 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o' -c ../tools/pbindex/src/main.cpp [143/161] c++ -Itools/f9d35d4@@pbindex@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o' -MF 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o.d' -o 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o' -c ../tools/pbindex/src/PbIndex.cpp [144/161] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o' -c ../tools/pbindexdump/src/CppFormatter.cpp [145/161] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o' -c ../tests/src/test_ZmwReadStitcher.cpp [146/161] c++ -Itools/f9d35d4@@pbindex@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp [147/161] c++ -o tools/pbindex 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o' 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.19.0 /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/pbbam-0.19.0+dfsg/obj-s390x-linux-gnu/src [148/161] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o' -c ../tools/pbindexdump/src/PbIndexDump.cpp [149/161] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp [150/161] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o' -c ../tools/pbindexdump/src/main.cpp [151/161] c++ -o tests/pbbam_test 'tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamHeader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecord.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetIO.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetXsd.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_EndToEnd.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Fastq.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_FileUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervalQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.19.0 -lgtest -lgtest_main /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/pbbam-0.19.0+dfsg/obj-s390x-linux-gnu/src [152/161] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o' -c ../tools/pbindexdump/src/JsonFormatter.cpp [153/161] c++ -o tools/pbindexdump 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.19.0 /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/pbbam-0.19.0+dfsg/obj-s390x-linux-gnu/src [154/161] c++ -Itools/f9d35d4@@pbmerge@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp [155/161] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp [156/161] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o' -c ../tools/pbbamify/src/main.cpp [157/161] c++ -Itools/f9d35d4@@pbmerge@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o' -MF 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o' -c ../tools/pbmerge/src/main.cpp [158/161] c++ -o tools/pbmerge 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.19.0 /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/pbbam-0.19.0+dfsg/obj-s390x-linux-gnu/src [159/161] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o' -c ../tools/pbbamify/src/PbBamify.cpp [160/161] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o' -c ../tools/pbbamify/src/QueryLookup.cpp [161/161] c++ -o tools/pbbamify 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<>/pbbam-0.19.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.19.0 /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/pbbam-0.19.0+dfsg/obj-s390x-linux-gnu/src debian/rules override_dh_auto_test make[1]: Entering directory '/<>/pbbam-0.19.0+dfsg' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_pacbio_ordering.t.in > tests/src/cram/pbmerge_pacbio_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_mixed_ordering.t.in > tests/src/cram/pbmerge_mixed_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_aligned_ordering.t.in > tests/src/cram/pbmerge_aligned_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbindexdump_json.t.in > tests/src/cram/pbindexdump_json.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbindexdump_cpp.t.in > tests/src/cram/pbindexdump_cpp.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_fofn.t.in > tests/src/cram/pbmerge_fofn.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbbamify.t.in > tests/src/cram/pbbamify.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.19.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.19.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.19.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_dataset.t.in > tests/src/cram/pbmerge_dataset.deb.t mkdir -p /<>/pbbam-0.19.0+dfsg/gendata python tests/scripts/generate_data.py /<>/pbbam-0.19.0+dfsg/tests/data /<>/pbbam-0.19.0+dfsg/gendata Generating test data in /<>/pbbam-0.19.0+dfsg/gendata - Creating file: truncated.bam...done. - Creating file: normal.fa...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fq...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating symlink: missing_pbi.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. # Fix broken PATH synthetic_movie_all_path=`find $PWD -name synthetic_movie_all.subreadset.xml` ; \ sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?${synthetic_movie_all_path}?" tests/src/cram/pbbamify* BINDIR=`dirname $(find $PWD -name pbmerge -type f -executable)`; \ LIBDIR=`find $PWD -name lib -type d`; \ PATH="$BINDIR:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" LD_LIBRARY_PATH="$LIBDIR:" \ cram -v --preserve-env tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbbamify.deb.t tests/src/cram/pbmerge_dataset.deb.t tests/src/cram/pbmerge_pacbio_ordering.deb.t: failed --- tests/src/cram/pbmerge_pacbio_ordering.deb.t +++ tests/src/cram/pbmerge_pacbio_ordering.deb.t.err @@ -104,354 +104,70 @@ Normal Merge: $ $PBMERGE $HQREGION_BAM $SCRAPS_BAM > $MERGED_BAM + ERROR: read group ID not found + [1] $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-0.19.0\tPN:pbmerge\tVN:0.19.0 (esc) $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/100000/0_2659 - ArminsFakeMovie/100000/2659_7034 - ArminsFakeMovie/100000/3025_3047 - ArminsFakeMovie/100000/3047_3095 - ArminsFakeMovie/100000/3095_3116 - ArminsFakeMovie/100000/3628_3650 - ArminsFakeMovie/100000/3650_3700 - ArminsFakeMovie/100000/3700_3722 - ArminsFakeMovie/100000/4267_4289 - ArminsFakeMovie/100000/4289_4335 - ArminsFakeMovie/100000/4335_4356 - ArminsFakeMovie/100000/4864_4888 - ArminsFakeMovie/100000/4888_4939 - ArminsFakeMovie/100000/4939_4960 - ArminsFakeMovie/100000/5477_5498 - ArminsFakeMovie/100000/5498_5546 - ArminsFakeMovie/100000/5546_5571 - ArminsFakeMovie/100000/6087_6116 - ArminsFakeMovie/100000/6116_6173 - ArminsFakeMovie/100000/6173_6199 - ArminsFakeMovie/100000/6719_6740 - ArminsFakeMovie/100000/6740_6790 - ArminsFakeMovie/100000/6790_6812 - ArminsFakeMovie/100000/7034_7035 - ArminsFakeMovie/200000/0_2659 - ArminsFakeMovie/200000/3025_3047 - ArminsFakeMovie/200000/3047_3095 - ArminsFakeMovie/200000/3095_3116 - ArminsFakeMovie/200000/3628_3650 - ArminsFakeMovie/200000/3650_3700 - ArminsFakeMovie/200000/3700_3722 - ArminsFakeMovie/200000/4267_4289 - ArminsFakeMovie/200000/4289_4335 - ArminsFakeMovie/200000/4335_4356 - ArminsFakeMovie/200000/4864_4888 - ArminsFakeMovie/200000/4888_4939 - ArminsFakeMovie/200000/4939_4960 - ArminsFakeMovie/200000/5477_5498 - ArminsFakeMovie/200000/5498_5546 - ArminsFakeMovie/200000/5546_5571 - ArminsFakeMovie/200000/6087_6116 - ArminsFakeMovie/200000/6116_6173 - ArminsFakeMovie/200000/6173_6199 - ArminsFakeMovie/200000/6719_6740 - ArminsFakeMovie/200000/6740_6790 - ArminsFakeMovie/200000/6790_6812 - ArminsFakeMovie/200000/7034_7035 - ArminsFakeMovie/300000/0_2659 - ArminsFakeMovie/300000/3025_3047 - ArminsFakeMovie/300000/3047_3095 - ArminsFakeMovie/300000/3095_3116 - ArminsFakeMovie/300000/3628_3650 - ArminsFakeMovie/300000/3650_3700 - ArminsFakeMovie/300000/3700_3722 - ArminsFakeMovie/300000/4267_4289 - ArminsFakeMovie/300000/4289_4335 - ArminsFakeMovie/300000/4335_4356 - ArminsFakeMovie/300000/4864_4888 - ArminsFakeMovie/300000/4888_4939 - ArminsFakeMovie/300000/4939_4960 - ArminsFakeMovie/300000/5477_5498 - ArminsFakeMovie/300000/5498_5546 - ArminsFakeMovie/300000/5546_5571 - ArminsFakeMovie/300000/6087_6116 - ArminsFakeMovie/300000/6116_6173 - ArminsFakeMovie/300000/6173_6199 - ArminsFakeMovie/300000/6719_6740 - ArminsFakeMovie/300000/6740_6790 - ArminsFakeMovie/300000/6790_6812 - ArminsFakeMovie/300000/7034_7035 $ rm $MERGED_BAM Shuffle Input: $ $PBMERGE $SCRAPS_BAM $HQREGION_BAM > $MERGED_BAM + ERROR: read group ID not found + [1] $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-0.19.0\tPN:pbmerge\tVN:0.19.0 (esc) $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/100000/0_2659 - ArminsFakeMovie/100000/2659_7034 - ArminsFakeMovie/100000/3025_3047 - ArminsFakeMovie/100000/3047_3095 - ArminsFakeMovie/100000/3095_3116 - ArminsFakeMovie/100000/3628_3650 - ArminsFakeMovie/100000/3650_3700 - ArminsFakeMovie/100000/3700_3722 - ArminsFakeMovie/100000/4267_4289 - ArminsFakeMovie/100000/4289_4335 - ArminsFakeMovie/100000/4335_4356 - ArminsFakeMovie/100000/4864_4888 - ArminsFakeMovie/100000/4888_4939 - ArminsFakeMovie/100000/4939_4960 - ArminsFakeMovie/100000/5477_5498 - ArminsFakeMovie/100000/5498_5546 - ArminsFakeMovie/100000/5546_5571 - ArminsFakeMovie/100000/6087_6116 - ArminsFakeMovie/100000/6116_6173 - ArminsFakeMovie/100000/6173_6199 - ArminsFakeMovie/100000/6719_6740 - ArminsFakeMovie/100000/6740_6790 - ArminsFakeMovie/100000/6790_6812 - ArminsFakeMovie/100000/7034_7035 - ArminsFakeMovie/200000/0_2659 - ArminsFakeMovie/200000/3025_3047 - ArminsFakeMovie/200000/3047_3095 - ArminsFakeMovie/200000/3095_3116 - ArminsFakeMovie/200000/3628_3650 - ArminsFakeMovie/200000/3650_3700 - ArminsFakeMovie/200000/3700_3722 - ArminsFakeMovie/200000/4267_4289 - ArminsFakeMovie/200000/4289_4335 - ArminsFakeMovie/200000/4335_4356 - ArminsFakeMovie/200000/4864_4888 - ArminsFakeMovie/200000/4888_4939 - ArminsFakeMovie/200000/4939_4960 - ArminsFakeMovie/200000/5477_5498 - ArminsFakeMovie/200000/5498_5546 - ArminsFakeMovie/200000/5546_5571 - ArminsFakeMovie/200000/6087_6116 - ArminsFakeMovie/200000/6116_6173 - ArminsFakeMovie/200000/6173_6199 - ArminsFakeMovie/200000/6719_6740 - ArminsFakeMovie/200000/6740_6790 - ArminsFakeMovie/200000/6790_6812 - ArminsFakeMovie/200000/7034_7035 - ArminsFakeMovie/300000/0_2659 - ArminsFakeMovie/300000/3025_3047 - ArminsFakeMovie/300000/3047_3095 - ArminsFakeMovie/300000/3095_3116 - ArminsFakeMovie/300000/3628_3650 - ArminsFakeMovie/300000/3650_3700 - ArminsFakeMovie/300000/3700_3722 - ArminsFakeMovie/300000/4267_4289 - ArminsFakeMovie/300000/4289_4335 - ArminsFakeMovie/300000/4335_4356 - ArminsFakeMovie/300000/4864_4888 - ArminsFakeMovie/300000/4888_4939 - ArminsFakeMovie/300000/4939_4960 - ArminsFakeMovie/300000/5477_5498 - ArminsFakeMovie/300000/5498_5546 - ArminsFakeMovie/300000/5546_5571 - ArminsFakeMovie/300000/6087_6116 - ArminsFakeMovie/300000/6116_6173 - ArminsFakeMovie/300000/6173_6199 - ArminsFakeMovie/300000/6719_6740 - ArminsFakeMovie/300000/6740_6790 - ArminsFakeMovie/300000/6790_6812 - ArminsFakeMovie/300000/7034_7035 $ rm $MERGED_BAM Explicit Output Filename (also enables PBI): $ $PBMERGE -o $MERGED_BAM $HQREGION_BAM $SCRAPS_BAM + ERROR: read group ID not found + [1] $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-0.19.0\tPN:pbmerge\tVN:0.19.0 (esc) + [E::hts_open_format] Failed to open file /<>/pbbam-0.19.0+dfsg/gendata/pacbio_ordering_merged.bam + samtools view: failed to open "/<>/pbbam-0.19.0+dfsg/gendata/pacbio_ordering_merged.bam" for reading: No such file or directory + [1] $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/100000/0_2659 - ArminsFakeMovie/100000/2659_7034 - ArminsFakeMovie/100000/3025_3047 - ArminsFakeMovie/100000/3047_3095 - ArminsFakeMovie/100000/3095_3116 - ArminsFakeMovie/100000/3628_3650 - ArminsFakeMovie/100000/3650_3700 - ArminsFakeMovie/100000/3700_3722 - ArminsFakeMovie/100000/4267_4289 - ArminsFakeMovie/100000/4289_4335 - ArminsFakeMovie/100000/4335_4356 - ArminsFakeMovie/100000/4864_4888 - ArminsFakeMovie/100000/4888_4939 - ArminsFakeMovie/100000/4939_4960 - ArminsFakeMovie/100000/5477_5498 - ArminsFakeMovie/100000/5498_5546 - ArminsFakeMovie/100000/5546_5571 - ArminsFakeMovie/100000/6087_6116 - ArminsFakeMovie/100000/6116_6173 - ArminsFakeMovie/100000/6173_6199 - ArminsFakeMovie/100000/6719_6740 - ArminsFakeMovie/100000/6740_6790 - ArminsFakeMovie/100000/6790_6812 - ArminsFakeMovie/100000/7034_7035 - ArminsFakeMovie/200000/0_2659 - ArminsFakeMovie/200000/3025_3047 - ArminsFakeMovie/200000/3047_3095 - ArminsFakeMovie/200000/3095_3116 - ArminsFakeMovie/200000/3628_3650 - ArminsFakeMovie/200000/3650_3700 - ArminsFakeMovie/200000/3700_3722 - ArminsFakeMovie/200000/4267_4289 - ArminsFakeMovie/200000/4289_4335 - ArminsFakeMovie/200000/4335_4356 - ArminsFakeMovie/200000/4864_4888 - ArminsFakeMovie/200000/4888_4939 - ArminsFakeMovie/200000/4939_4960 - ArminsFakeMovie/200000/5477_5498 - ArminsFakeMovie/200000/5498_5546 - ArminsFakeMovie/200000/5546_5571 - ArminsFakeMovie/200000/6087_6116 - ArminsFakeMovie/200000/6116_6173 - ArminsFakeMovie/200000/6173_6199 - ArminsFakeMovie/200000/6719_6740 - ArminsFakeMovie/200000/6740_6790 - ArminsFakeMovie/200000/6790_6812 - ArminsFakeMovie/200000/7034_7035 - ArminsFakeMovie/300000/0_2659 - ArminsFakeMovie/300000/3025_3047 - ArminsFakeMovie/300000/3047_3095 - ArminsFakeMovie/300000/3095_3116 - ArminsFakeMovie/300000/3628_3650 - ArminsFakeMovie/300000/3650_3700 - ArminsFakeMovie/300000/3700_3722 - ArminsFakeMovie/300000/4267_4289 - ArminsFakeMovie/300000/4289_4335 - ArminsFakeMovie/300000/4335_4356 - ArminsFakeMovie/300000/4864_4888 - ArminsFakeMovie/300000/4888_4939 - ArminsFakeMovie/300000/4939_4960 - ArminsFakeMovie/300000/5477_5498 - ArminsFakeMovie/300000/5498_5546 - ArminsFakeMovie/300000/5546_5571 - ArminsFakeMovie/300000/6087_6116 - ArminsFakeMovie/300000/6116_6173 - ArminsFakeMovie/300000/6173_6199 - ArminsFakeMovie/300000/6719_6740 - ArminsFakeMovie/300000/6740_6790 - ArminsFakeMovie/300000/6790_6812 - ArminsFakeMovie/300000/7034_7035 - - $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" - Found - - $ rm $MERGED_BAM - $ rm $MERGED_BAM_PBI - -Explicit Output Filename (with disabled PBI): - - $ $PBMERGE -o $MERGED_BAM --no-pbi $HQREGION_BAM $SCRAPS_BAM - - $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-0.19.0\tPN:pbmerge\tVN:0.19.0 (esc) - - $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/100000/0_2659 - ArminsFakeMovie/100000/2659_7034 - ArminsFakeMovie/100000/3025_3047 - ArminsFakeMovie/100000/3047_3095 - ArminsFakeMovie/100000/3095_3116 - ArminsFakeMovie/100000/3628_3650 - ArminsFakeMovie/100000/3650_3700 - ArminsFakeMovie/100000/3700_3722 - ArminsFakeMovie/100000/4267_4289 - ArminsFakeMovie/100000/4289_4335 - ArminsFakeMovie/100000/4335_4356 - ArminsFakeMovie/100000/4864_4888 - ArminsFakeMovie/100000/4888_4939 - ArminsFakeMovie/100000/4939_4960 - ArminsFakeMovie/100000/5477_5498 - ArminsFakeMovie/100000/5498_5546 - ArminsFakeMovie/100000/5546_5571 - ArminsFakeMovie/100000/6087_6116 - ArminsFakeMovie/100000/6116_6173 - ArminsFakeMovie/100000/6173_6199 - ArminsFakeMovie/100000/6719_6740 - ArminsFakeMovie/100000/6740_6790 - ArminsFakeMovie/100000/6790_6812 - ArminsFakeMovie/100000/7034_7035 - ArminsFakeMovie/200000/0_2659 - ArminsFakeMovie/200000/3025_3047 - ArminsFakeMovie/200000/3047_3095 - ArminsFakeMovie/200000/3095_3116 - ArminsFakeMovie/200000/3628_3650 - ArminsFakeMovie/200000/3650_3700 - ArminsFakeMovie/200000/3700_3722 - ArminsFakeMovie/200000/4267_4289 - ArminsFakeMovie/200000/4289_4335 - ArminsFakeMovie/200000/4335_4356 - ArminsFakeMovie/200000/4864_4888 - ArminsFakeMovie/200000/4888_4939 - ArminsFakeMovie/200000/4939_4960 - ArminsFakeMovie/200000/5477_5498 - ArminsFakeMovie/200000/5498_5546 - ArminsFakeMovie/200000/5546_5571 - ArminsFakeMovie/200000/6087_6116 - ArminsFakeMovie/200000/6116_6173 - ArminsFakeMovie/200000/6173_6199 - ArminsFakeMovie/200000/6719_6740 - ArminsFakeMovie/200000/6740_6790 - ArminsFakeMovie/200000/6790_6812 - ArminsFakeMovie/200000/7034_7035 - ArminsFakeMovie/300000/0_2659 - ArminsFakeMovie/300000/3025_3047 - ArminsFakeMovie/300000/3047_3095 - ArminsFakeMovie/300000/3095_3116 - ArminsFakeMovie/300000/3628_3650 - ArminsFakeMovie/300000/3650_3700 - ArminsFakeMovie/300000/3700_3722 - ArminsFakeMovie/300000/4267_4289 - ArminsFakeMovie/300000/4289_4335 - ArminsFakeMovie/300000/4335_4356 - ArminsFakeMovie/300000/4864_4888 - ArminsFakeMovie/300000/4888_4939 - ArminsFakeMovie/300000/4939_4960 - ArminsFakeMovie/300000/5477_5498 - ArminsFakeMovie/300000/5498_5546 - ArminsFakeMovie/300000/5546_5571 - ArminsFakeMovie/300000/6087_6116 - ArminsFakeMovie/300000/6116_6173 - ArminsFakeMovie/300000/6173_6199 - ArminsFakeMovie/300000/6719_6740 - ArminsFakeMovie/300000/6740_6790 - ArminsFakeMovie/300000/6790_6812 - ArminsFakeMovie/300000/7034_7035 + [E::hts_open_format] Failed to open file /<>/pbbam-0.19.0+dfsg/gendata/pacbio_ordering_merged.bam + samtools view: failed to open "/<>/pbbam-0.19.0+dfsg/gendata/pacbio_ordering_merged.bam" for reading: No such file or directory $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" Not found $ rm $MERGED_BAM + rm: cannot remove '/<>/pbbam-0.19.0+dfsg/gendata/pacbio_ordering_merged.bam': No such file or directory + [1] + $ rm $MERGED_BAM_PBI + rm: cannot remove '/<>/pbbam-0.19.0+dfsg/gendata/pacbio_ordering_merged.bam.pbi': No such file or directory + [1] + +Explicit Output Filename (with disabled PBI): + + $ $PBMERGE -o $MERGED_BAM --no-pbi $HQREGION_BAM $SCRAPS_BAM + ERROR: read group ID not found + [1] + + $ samtools view -H $MERGED_BAM + [E::hts_open_format] Failed to open file /<>/pbbam-0.19.0+dfsg/gendata/pacbio_ordering_merged.bam + samtools view: failed to open "/<>/pbbam-0.19.0+dfsg/gendata/pacbio_ordering_merged.bam" for reading: No such file or directory + [1] + + $ samtools view $MERGED_BAM | cut -f 1 + [E::hts_open_format] Failed to open file /<>/pbbam-0.19.0+dfsg/gendata/pacbio_ordering_merged.bam + samtools view: failed to open "/<>/pbbam-0.19.0+dfsg/gendata/pacbio_ordering_merged.bam" for reading: No such file or directory + + $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" + Not found + + $ rm $MERGED_BAM + rm: cannot remove '/<>/pbbam-0.19.0+dfsg/gendata/pacbio_ordering_merged.bam': No such file or directory + [1] tests/src/cram/pbmerge_mixed_ordering.deb.t: passed tests/src/cram/pbmerge_aligned_ordering.deb.t: passed tests/src/cram/pbindexdump_json.deb.t: passed tests/src/cram/pbindexdump_cpp.deb.t: passed tests/src/cram/pbmerge_fofn.deb.t: passed tests/src/cram/pbbamify.deb.t: failed --- tests/src/cram/pbbamify.deb.t +++ tests/src/cram/pbbamify.deb.t.err @@ -9,123 +9,26 @@ Forward alignments with and without user specified tags, one alignment with undefined mapq, some alignments with basic CIGAR operations, 2 alignemtns with hard clipping, and several invalid alignments (1 without a seq field and 1 not present in the dataset) which should be skipped: $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-1.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | samtools view -h - [Warning] No records found for query 'synthetic_movie_1/10/0_100'. Skipping. - [Warning] Sequence 'synthetic_movie_1/1/0_100' (length 90) is not of the same length as the PacBio BAM sequence (length 100)! Skipping. - [Warning] Found 1 alignments without a seq field which were not converted (most likely secondary alignments). - [INFO] Done processing 15 alignments in 0 min. - @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc) - @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc) - @RG\tID:8d2370c0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_1\tPM:SEQUEL (esc) - @PG\tID:Handmade\tPN:Handmade (esc) - @PG\tID:baz2bam\tPN:baz2bam\tVN:5.0.0.5552\tCL:/opt/pacbio/ppa-5.0.0/bin/baz2bam /data/pb/synthetic_movie_1.baz -o /data/pb/synthetic_movie_1 --metadata /data/pb/.synthetic_movie_1.metadata.xml -j 12 -b 12 --progress --silent --minSubLength 50 --minSnr 3.750000 --adapters /data/pb/synthetic_movie_1.adapters.fasta (esc) - @PG\tID:bazFormat\tPN:bazformat\tVN:1.3.0 (esc) - @PG\tID:bazwriter\tPN:bazwriter\tVN:5.0.0.5552 (esc) - synthetic_movie_1/1/0_100\t0\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t254\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tZE:f:1\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/2/0_101\t0\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/3/0_100\t4\t*\t0\t255\t*\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:3\tRG:Z:8d2370c0 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t8S1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I1=6S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) + Segmentation fault (core dumped) Reverse alignments: 2 primary alignments and 7 secondary, 6 alignments with extended CIGAR and 2 with basic CIGAR strings, 1 alignment with undefined (255) mapq, 2 alignments with hard clipping, 1 alignment with user defined tag. All alignments have a read group assigned which is different than the dataset. $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-2.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_2.subreads.bam | samtools view -h - [INFO] Done processing 9 alignments in 0 min. - @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc) - @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc) - @RG\tID:7a515ee0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_2\tPM:SEQUEL (esc) - @PG\tID:Handmade\tPN:Handmade (esc) - @PG\tID:baz2bam\tPN:baz2bam\tVN:5.0.0.5552\tCL:/opt/pacbio/ppa-5.0.0/bin/baz2bam /data/pb/synthetic_movie_2.baz -o /data/pb/synthetic_movie_2 --metadata /data/pb/.synthetic_movie_2.metadata.xml -j 12 -b 12 --progress --silent --minSubLength 50 --minSnr 3.750000 --adapters /data/pb/synthetic_movie_2.adapters.fasta (esc) - @PG\tID:bazFormat\tPN:bazformat\tVN:1.3.0 (esc) - @PG\tID:bazwriter\tPN:bazwriter\tVN:5.0.0.5552 (esc) - synthetic_movie_2/1000001/0_100\t16\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t254\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tZE:f:1\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000002/0_101\t16\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000002 (esc) - synthetic_movie_2/1000002/0_101\t272\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000002 (esc) - synthetic_movie_2/1000002/0_101\t272\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000002 (esc) - synthetic_movie_2/1000002/0_101\t272\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000002 (esc) + Segmentation fault (core dumped) CCS read: $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-3.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_3.subreads.bam | samtools view -h - [INFO] Done processing 1 alignments in 0 min. - @HD\tVN:1.5\tSO:unknown\tpb:3.0.1 (esc) - @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc) - @RG\tID:67e06f58\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=100-862-200;SEQUENCINGKIT=101-093-700;BASECALLERVERSION=5.0.0.5049;FRAMERATEHZ=80.000000\tPU:synthetic_movie_3\tPM:SEQUEL (esc) - @PG\tID:Handmade\tPN:Handmade (esc) - @PG\tID:ccs-3.0.0\tPN:ccs\tVN:3.0.0\tDS:Generate circular consensus sequences (ccs) from subreads.\tCL:ccs (esc) - synthetic_movie_3/3000001/ccs\t0\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tRG:Z:67e06f58\tnp:i:6\trq:f:0.993687\trs:B:i,8,1,0,0,0,0\tsn:B:f,6.21632,11.7596,4.35394,8.45458\tza:f:nan\tzm:i:3000001\tzs:B:f,nan,nan,nan,nan,nan,nan,-inf,nan,nan (esc) + Segmentation fault (core dumped) No verbose output: $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-1.bam --verbose-level=0 $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | samtools view -h - @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc) - @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc) - @RG\tID:8d2370c0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_1\tPM:SEQUEL (esc) - @PG\tID:Handmade\tPN:Handmade (esc) - @PG\tID:baz2bam\tPN:baz2bam\tVN:5.0.0.5552\tCL:/opt/pacbio/ppa-5.0.0/bin/baz2bam /data/pb/synthetic_movie_1.baz -o /data/pb/synthetic_movie_1 --metadata /data/pb/.synthetic_movie_1.metadata.xml -j 12 -b 12 --progress --silent --minSubLength 50 --minSnr 3.750000 --adapters /data/pb/synthetic_movie_1.adapters.fasta (esc) - @PG\tID:bazFormat\tPN:bazformat\tVN:1.3.0 (esc) - @PG\tID:bazwriter\tPN:bazwriter\tVN:5.0.0.5552 (esc) - synthetic_movie_1/1/0_100\t0\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t254\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tZE:f:1\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/2/0_101\t0\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/3/0_100\t4\t*\t0\t255\t*\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:3\tRG:Z:8d2370c0 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t8S1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I1=6S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) + Segmentation fault (core dumped) Test on a dataset, input contains alignments from all subread sets. $ $PBBAMIFY --input=$DATADIR/pbbamify/input-aligned-all.bam $DATADIR/pbbamify/synthetic-ref-1.fa /<>/pbbam-0.19.0+dfsg/obj-s390x-linux-gnu/tests/synthetic_movie_all.subreadset.xml | samtools view -h - [Warning] No records found for query 'synthetic_movie_1/10/0_100'. Skipping. - [Warning] Sequence 'synthetic_movie_1/1/0_100' (length 90) is not of the same length as the PacBio BAM sequence (length 100)! Skipping. - [Warning] Found 1 alignments without a seq field which were not converted (most likely secondary alignments). - [INFO] Done processing 25 alignments in 0 min. - @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc) - @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc) - @RG\tID:67e06f58\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=100-862-200;SEQUENCINGKIT=101-093-700;BASECALLERVERSION=5.0.0.5049;FRAMERATEHZ=80.000000\tPU:synthetic_movie_3\tPM:SEQUEL (esc) - @RG\tID:7a515ee0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_2\tPM:SEQUEL (esc) - @RG\tID:8d2370c0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_1\tPM:SEQUEL (esc) - @PG\tID:Handmade\tPN:Handmade (esc) - @PG\tID:baz2bam\tPN:baz2bam\tVN:5.0.0.5552\tCL:/opt/pacbio/ppa-5.0.0/bin/baz2bam /data/pb/synthetic_movie_1.baz -o /data/pb/synthetic_movie_1 --metadata /data/pb/.synthetic_movie_1.metadata.xml -j 12 -b 12 --progress --silent --minSubLength 50 --minSnr 3.750000 --adapters /data/pb/synthetic_movie_1.adapters.fasta (esc) - @PG\tID:bazFormat\tPN:bazformat\tVN:1.3.0 (esc) - @PG\tID:bazwriter\tPN:bazwriter\tVN:5.0.0.5552 (esc) - @PG\tID:ccs-3.0.0\tPN:ccs\tVN:3.0.0\tDS:Generate circular consensus sequences (ccs) from subreads.\tCL:ccs (esc) - synthetic_movie_1/1/0_100\t0\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t254\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tZE:f:1\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/2/0_101\t0\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_1/3/0_100\t4\t*\t0\t255\t*\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:3\tRG:Z:8d2370c0 (esc) - synthetic_movie_1/1/0_100\t256\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\tAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1 (esc) - synthetic_movie_1/2/0_101\t256\tsynthetic_ref_1\t30\t60\t8S1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I1=6S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:8d2370c0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:2 (esc) - synthetic_movie_2/1000001/0_100\t16\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t254\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tZE:f:1\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000001/0_100\t272\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100\tqe:i:100\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000001 (esc) - synthetic_movie_2/1000002/0_101\t16\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000002 (esc) - synthetic_movie_2/1000002/0_101\t272\tsynthetic_ref_1\t23\t60\t8=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I7=\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000002 (esc) - synthetic_movie_2/1000002/0_101\t272\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000002 (esc) - synthetic_movie_2/1000002/0_101\t272\tsynthetic_ref_1\t30\t60\t7S1=1X21=3I1X3D13=1D1=1X1=1I9=1X32=1I4=3S\t*\t0\t0\tCGCTATTTTTGAAAATTTTCCGGTTTAAGGAAATTCCGTTCTTCTTCTGAATAACTTAATCTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAAACGAC\t!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\tRG:Z:7a515ee0\tcx:i:3\tip:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tnp:i:1\tpw:B:C,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101\tqe:i:101\tqs:i:0\trq:f:0.8\tsn:B:f,8.34462,15.7107,6.3469,10.3163\tzm:i:1000002 (esc) - synthetic_movie_3/3000001/ccs\t0\tsynthetic_ref_1\t23\t60\t100=\t*\t0\t0\tCGCTATTTATGAAAATTTTCCGGTTTAAGGCGTTTCCGTTCTTCTTCGTCATAACTTAATGTTTTTATTTAAAATACCCTCTGAAAAGAAAGGAAACGAC\tCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\tRG:Z:67e06f58\tnp:i:6\trq:f:0.993687\trs:B:i,8,1,0,0,0,0\tsn:B:f,6.21632,11.7596,4.35394,8.45458\tza:f:nan\tzm:i:3000001\tzs:B:f,nan,nan,nan,nan,nan,nan,-inf,nan,nan (esc) + Segmentation fault (core dumped) No-args: tests/src/cram/pbmerge_dataset.deb.t: failed --- tests/src/cram/pbmerge_dataset.deb.t +++ tests/src/cram/pbmerge_dataset.deb.t.err @@ -52,38 +52,61 @@ Normal Merge from XML: $ $PBMERGE -o $MERGED_BAM $INPUT_XML + ERROR: read group ID not found + [1] $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" - Found + Not found $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" - Found + Not found $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:BAZ_FORMAT\tVN:0.3.0 (esc) - @PG\tID:PPA-BAZ2BAM\tVN:0.1.0 (esc) - @PG\tID:PPA-BAZWRITER\tVN:0.2.0 (esc) - @PG\tID:pbmerge-0.19.0\tPN:pbmerge\tVN:0.19.0 (esc) + [E::hts_open_format] Failed to open file /<>/pbbam-0.19.0+dfsg/gendata/merged.bam + samtools view: failed to open "/<>/pbbam-0.19.0+dfsg/gendata/merged.bam" for reading: No such file or directory + [1] $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/0/4267_4289 - ArminsFakeMovie/0/4289_4335 - ArminsFakeMovie/0/4335_4356 - ArminsFakeMovie/0/4356_4864 - ArminsFakeMovie/0/4864_4888 - ArminsFakeMovie/0/4888_4939 - ArminsFakeMovie/0/4939_4960 - ArminsFakeMovie/0/4960_5477 + [E::hts_open_format] Failed to open file /<>/pbbam-0.19.0+dfsg/gendata/merged.bam + samtools view: failed to open "/<>/pbbam-0.19.0+dfsg/gendata/merged.bam" for reading: No such file or directory $ rm $MERGED_BAM + rm: cannot remove '/<>/pbbam-0.19.0+dfsg/gendata/merged.bam': No such file or directory + [1] $ rm $MERGED_BAM_PBI + rm: cannot remove '/<>/pbbam-0.19.0+dfsg/gendata/merged.bam.pbi': No such file or directory + [1] Normal Merge from XML (disabled PBI): $ $PBMERGE --no-pbi -o $MERGED_BAM $INPUT_XML + ERROR: read group ID not found + [1] + + $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" + Not found + + $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" + Not found + + $ samtools view -H $MERGED_BAM + [E::hts_open_format] Failed to open file /<>/pbbam-0.19.0+dfsg/gendata/merged.bam + samtools view: failed to open "/<>/pbbam-0.19.0+dfsg/gendata/merged.bam" for reading: No such file or directory + [1] + + $ samtools view $MERGED_BAM | cut -f 1 + [E::hts_open_format] Failed to open file /<>/pbbam-0.19.0+dfsg/gendata/merged.bam + samtools view: failed to open "/<>/pbbam-0.19.0+dfsg/gendata/merged.bam" for reading: No such file or directory + + $ rm $MERGED_BAM + rm: cannot remove '/<>/pbbam-0.19.0+dfsg/gendata/merged.bam': No such file or directory + [1] + +Write to stdout: + + $ $PBMERGE --no-pbi $INPUT_XML > $MERGED_BAM + ERROR: read group ID not found + [1] $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" Found @@ -92,53 +115,7 @@ Not found $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:BAZ_FORMAT\tVN:0.3.0 (esc) - @PG\tID:PPA-BAZ2BAM\tVN:0.1.0 (esc) - @PG\tID:PPA-BAZWRITER\tVN:0.2.0 (esc) - @PG\tID:pbmerge-0.19.0\tPN:pbmerge\tVN:0.19.0 (esc) $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/0/4267_4289 - ArminsFakeMovie/0/4289_4335 - ArminsFakeMovie/0/4335_4356 - ArminsFakeMovie/0/4356_4864 - ArminsFakeMovie/0/4864_4888 - ArminsFakeMovie/0/4888_4939 - ArminsFakeMovie/0/4939_4960 - ArminsFakeMovie/0/4960_5477 $ rm $MERGED_BAM - -Write to stdout: - - $ $PBMERGE --no-pbi $INPUT_XML > $MERGED_BAM - - $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" - Found - - $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" - Not found - - $ samtools view -H $MERGED_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:BAZ_FORMAT\tVN:0.3.0 (esc) - @PG\tID:PPA-BAZ2BAM\tVN:0.1.0 (esc) - @PG\tID:PPA-BAZWRITER\tVN:0.2.0 (esc) - @PG\tID:pbmerge-0.19.0\tPN:pbmerge\tVN:0.19.0 (esc) - - $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/0/4267_4289 - ArminsFakeMovie/0/4289_4335 - ArminsFakeMovie/0/4335_4356 - ArminsFakeMovie/0/4356_4864 - ArminsFakeMovie/0/4864_4888 - ArminsFakeMovie/0/4888_4939 - ArminsFakeMovie/0/4939_4960 - ArminsFakeMovie/0/4960_5477 - - $ rm $MERGED_BAM # Ran 8 tests, 0 skipped, 3 failed. make[1]: *** [debian/rules:33: override_dh_auto_test] Error 1 make[1]: Leaving directory '/<>/pbbam-0.19.0+dfsg' make: *** [debian/rules:13: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20190201-2255 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 812032 Build-Time: 195 Distribution: disco-proposed Fail-Stage: build Host Architecture: s390x Install-Time: 13 Job: pbbam_0.19.0+dfsg-1ubuntu4.dsc Machine Architecture: s390x Package: pbbam Package-Time: 210 Source-Version: 0.19.0+dfsg-1ubuntu4 Space: 812032 Status: attempted Version: 0.19.0+dfsg-1ubuntu4 -------------------------------------------------------------------------------- Finished at 20190201-2255 Build needed 00:03:30, 812032k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=s390x PACKAGEBUILD-16343464 Scanning for processes to kill in build PACKAGEBUILD-16343464