https://launchpad.net/ubuntu/+archive/test-rebuild-20191220-focal/+build/18337547 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-003 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:44:14 UTC 2019 s390x Buildd toolchain package versions: launchpad-buildd_183 python-lpbuildd_183 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_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 5 Jan 11:16:25 ntpdate[1854]: adjust time server 10.211.37.1 offset -0.000074 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=s390x PACKAGEBUILD-18337547 --image-type chroot /home/buildd/filecache-default/1ac0229cc48d8f596a1790116aa52d00551197b1 Creating target for build PACKAGEBUILD-18337547 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=s390x PACKAGEBUILD-18337547 Starting target for build PACKAGEBUILD-18337547 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=s390x PACKAGEBUILD-18337547 'deb http://ftpmaster.internal/ubuntu focal main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-18337547 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=s390x PACKAGEBUILD-18337547 Updating target for build PACKAGEBUILD-18337547 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main s390x Packages [916 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main Translation-en [499 kB] Get:4 http://ftpmaster.internal/ubuntu focal/restricted s390x Packages [1288 B] Get:5 http://ftpmaster.internal/ubuntu focal/restricted Translation-en [5768 B] Get:6 http://ftpmaster.internal/ubuntu focal/universe s390x Packages [8337 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5195 kB] Get:8 http://ftpmaster.internal/ubuntu focal/multiverse s390x Packages [119 kB] Get:9 http://ftpmaster.internal/ubuntu focal/multiverse Translation-en [110 kB] Fetched 15.4 MB in 4s (4375 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libhogweed5 libisl22 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-s390x-linux-gnu bsdutils bzip2 cpp-9 debianutils fdisk g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev lsb-base mount ncurses-base ncurses-bin perl perl-base sensible-utils systemd systemd-sysv sysvinit-utils util-linux 91 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 58.1 MB of archives. After this operation, 49.1 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main s390x libc6-dev s390x 2.30-0ubuntu3 [2060 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main s390x libc-dev-bin s390x 2.30-0ubuntu3 [63.9 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main s390x linux-libc-dev s390x 5.3.0-24.26 [1094 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main s390x libisl22 s390x 0.22-2 [546 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main s390x libcc1-0 s390x 9.2.1-21ubuntu1 [46.5 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main s390x binutils-s390x-linux-gnu s390x 2.33.1-6ubuntu3 [1468 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main s390x libbinutils s390x 2.33.1-6ubuntu3 [301 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main s390x binutils-common s390x 2.33.1-6ubuntu3 [203 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main s390x binutils s390x 2.33.1-6ubuntu3 [3328 B] Get:10 http://ftpmaster.internal/ubuntu focal/main s390x gcc-9-base s390x 9.2.1-21ubuntu1 [19.1 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main s390x libgcc1 s390x 1:9.2.1-21ubuntu1 [25.3 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main s390x libgomp1 s390x 9.2.1-21ubuntu1 [83.3 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main s390x libitm1 s390x 9.2.1-21ubuntu1 [27.1 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main s390x libatomic1 s390x 9.2.1-21ubuntu1 [8264 B] Get:15 http://ftpmaster.internal/ubuntu focal/main s390x libasan5 s390x 9.2.1-21ubuntu1 [361 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main s390x libubsan1 s390x 9.2.1-21ubuntu1 [125 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main s390x g++-9 s390x 9.2.1-21ubuntu1 [8609 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main s390x libstdc++-9-dev s390x 9.2.1-21ubuntu1 [1673 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main s390x libgcc-9-dev s390x 9.2.1-21ubuntu1 [704 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main s390x gcc-9 s390x 9.2.1-21ubuntu1 [8095 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main s390x cpp-9 s390x 9.2.1-21ubuntu1 [7454 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main s390x libstdc++6 s390x 9.2.1-21ubuntu1 [504 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main s390x libc6 s390x 2.30-0ubuntu3 [2289 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main s390x base-files s390x 11ubuntu2 [60.0 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main s390x debianutils s390x 4.9.1 [85.7 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main s390x bash s390x 5.0-5ubuntu1 [622 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main s390x bsdutils s390x 1:2.34-0.1ubuntu4 [61.5 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main s390x gzip s390x 1.10-0ubuntu4 [95.8 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main s390x hostname s390x 3.23 [11.1 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main s390x ncurses-bin s390x 6.1+20191019-1ubuntu1 [169 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main s390x perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main s390x libperl5.30 s390x 5.30.0-9 [3782 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main s390x perl s390x 5.30.0-9 [224 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main s390x perl-base s390x 5.30.0-9 [1423 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main s390x bzip2 s390x 1.0.8-2 [33.3 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main s390x libbz2-1.0 s390x 1.0.8-2 [32.6 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main s390x libblkid1 s390x 2.34-0.1ubuntu4 [128 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main s390x libuuid1 s390x 2.34-0.1ubuntu4 [20.5 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main s390x libfdisk1 s390x 2.34-0.1ubuntu4 [160 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main s390x libpcre2-8-0 s390x 10.34-7 [109 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main s390x libselinux1 s390x 3.0-1 [65.6 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main s390x libmount1 s390x 2.34-0.1ubuntu4 [137 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main s390x libncurses6 s390x 6.1+20191019-1ubuntu1 [94.7 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main s390x libtinfo6 s390x 6.1+20191019-1ubuntu1 [83.6 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main s390x libncursesw6 s390x 6.1+20191019-1ubuntu1 [122 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main s390x libsmartcols1 s390x 2.34-0.1ubuntu4 [93.6 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main s390x fdisk s390x 2.34-0.1ubuntu4 [113 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main s390x util-linux s390x 2.34-0.1ubuntu4 [981 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main s390x libdebconfclient0 s390x 0.250ubuntu2 [6152 B] Get:50 http://ftpmaster.internal/ubuntu focal/main s390x base-passwd s390x 3.5.47 [46.7 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main s390x libc-bin s390x 2.30-0ubuntu3 [547 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main s390x ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main s390x lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main s390x sysvinit-utils s390x 2.96-1ubuntu1 [20.6 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main s390x liblz4-1 s390x 1.9.2-2 [53.8 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main s390x systemd-sysv s390x 244-3ubuntu1 [9364 B] Get:57 http://ftpmaster.internal/ubuntu focal/main s390x libacl1 s390x 2.2.53-5ubuntu1 [18.3 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main s390x libapparmor1 s390x 2.13.3-7ubuntu1 [33.0 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main s390x libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:60 http://ftpmaster.internal/ubuntu focal/main s390x libcap-ng0 s390x 0.7.9-2.1 [10.8 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main s390x libaudit1 s390x 1:2.8.5-2ubuntu5 [37.3 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main s390x libcap2 s390x 1:2.27-1 [14.2 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main s390x libudev1 s390x 244-3ubuntu1 [71.8 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main s390x libdevmapper1.02.1 s390x 2:1.02.155-2ubuntu7 [122 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main s390x libjson-c4 s390x 0.13.1+dfsg-6 [27.9 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main s390x libcryptsetup12 s390x 2:2.2.2-1ubuntu1 [160 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main s390x libnettle7 s390x 3.5.1+really3.5.1-2 [124 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main s390x libhogweed5 s390x 3.5.1+really3.5.1-2 [136 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main s390x libp11-kit0 s390x 0.23.18.1-2 [172 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main s390x libtasn1-6 s390x 4.15.0-2 [36.9 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main s390x libgnutls30 s390x 3.6.11.1-2 [684 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main s390x libkmod2 s390x 26-3ubuntu1 [40.0 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main s390x libpam0g s390x 1.3.1-5ubuntu4 [52.9 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main s390x libseccomp2 s390x 2.4.2-2ubuntu1 [38.6 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main s390x mount s390x 2.34-0.1ubuntu4 [110 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main s390x systemd s390x 244-3ubuntu1 [3325 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main s390x libsystemd0 s390x 244-3ubuntu1 [239 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main s390x libzstd1 s390x 1.4.4+dfsg-1 [217 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main s390x libapt-pkg5.90 s390x 1.9.5 [789 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main s390x libgcrypt20 s390x 1.8.5-3ubuntu1 [349 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main s390x gpgv s390x 2.2.17-3ubuntu1 [186 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main s390x apt s390x 1.9.5 [1242 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main s390x libpam-modules-bin s390x 1.3.1-5ubuntu4 [36.5 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main s390x libpam-modules s390x 1.3.1-5ubuntu4 [242 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main s390x libattr1 s390x 1:2.4.48-5 [12.4 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main s390x libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main s390x libsepol1 s390x 3.0-1 [227 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main s390x libsemanage-common all 3.0-1 [9880 B] Get:89 http://ftpmaster.internal/ubuntu focal/main s390x libsemanage1 s390x 3.0-1 [80.3 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main s390x sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main s390x libsqlite3-0 s390x 3.30.1-1ubuntu1 [504 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main s390x gpg s390x 2.2.17-3ubuntu1 [442 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main s390x gpgconf s390x 2.2.17-3ubuntu1 [119 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main s390x gpg-agent s390x 2.2.17-3ubuntu1 [217 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main s390x liblockfile-bin s390x 1.16-1.1 [11.4 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main s390x liblockfile1 s390x 1.16-1.1 [6476 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 58.1 MB in 1s (54.6 MB/s) (Reading database ... 12530 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.30-0ubuntu3_s390x.deb ... Unpacking libc6-dev:s390x (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../1-libc-dev-bin_2.30-0ubuntu3_s390x.deb ... Unpacking libc-dev-bin (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../2-linux-libc-dev_5.3.0-24.26_s390x.deb ... Unpacking linux-libc-dev:s390x (5.3.0-24.26) over (5.3.0-18.19) ... Selecting previously unselected package libisl22:s390x. Preparing to unpack .../3-libisl22_0.22-2_s390x.deb ... Unpacking libisl22:s390x (0.22-2) ... Preparing to unpack .../4-libcc1-0_9.2.1-21ubuntu1_s390x.deb ... Unpacking libcc1-0:s390x (9.2.1-21ubuntu1) over (9.2.1-9ubuntu2) ... Preparing to unpack .../5-binutils-s390x-linux-gnu_2.33.1-6ubuntu3_s390x.deb ... Unpacking binutils-s390x-linux-gnu (2.33.1-6ubuntu3) over (2.33-2ubuntu1) ... Preparing to unpack .../6-libbinutils_2.33.1-6ubuntu3_s390x.deb ... Unpacking libbinutils:s390x (2.33.1-6ubuntu3) over (2.33-2ubuntu1) ... 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Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/update-motd.d/50-motd-news ... Updating /root/.profile to current default. (Reading database ... 12536 files and directories currently installed.) Preparing to unpack .../debianutils_4.9.1_s390x.deb ... Unpacking debianutils (4.9.1) over (4.8.6.3) ... Setting up debianutils (4.9.1) ... (Reading database ... 12536 files and directories currently installed.) Preparing to unpack .../bash_5.0-5ubuntu1_s390x.deb ... Unpacking bash (5.0-5ubuntu1) over (5.0-4ubuntu1) ... Setting up bash (5.0-5ubuntu1) ... 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 ... 12536 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.34-0.1ubuntu4_s390x.deb ... 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Setting up libperl5.30:s390x (5.30.0-9) ... Setting up libisl22:s390x (0.22-2) ... Setting up liblockfile1:s390x (1.16-1.1) ... Setting up libjson-c4:s390x (0.13.1+dfsg-6) ... Setting up libbinutils:s390x (2.33.1-6ubuntu3) ... Setting up libc-dev-bin (2.30-0ubuntu3) ... Setting up libcc1-0:s390x (9.2.1-21ubuntu1) ... Setting up gpg (2.2.17-3ubuntu1) ... Setting up libitm1:s390x (9.2.1-21ubuntu1) ... Setting up libkmod2:s390x (26-3ubuntu1) ... Setting up binutils-s390x-linux-gnu (2.33.1-6ubuntu3) ... Setting up gpg-agent (2.2.17-3ubuntu1) ... Installing new version of config file /etc/logcheck/ignore.d.server/gpg-agent ... Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket. Setting up binutils (2.33.1-6ubuntu3) ... Setting up libgcc-9-dev:s390x (9.2.1-21ubuntu1) ... Setting up perl (5.30.0-9) ... Setting up cpp-9 (9.2.1-21ubuntu1) ... Setting up libc6-dev:s390x (2.30-0ubuntu3) ... Setting up libcryptsetup12:s390x (2:2.2.2-1ubuntu1) ... Setting up gcc-9 (9.2.1-21ubuntu1) ... Setting up libstdc++-9-dev:s390x (9.2.1-21ubuntu1) ... Setting up systemd (244-3ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up g++-9 (9.2.1-21ubuntu1) ... Setting up systemd-sysv (244-3ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18337547 s390x focal -c chroot:build-PACKAGEBUILD-18337547 --arch=s390x --dist=focal --nolog pbbam_0.23.0+dfsg-1.dsc Initiating build PACKAGEBUILD-18337547 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:44:14 UTC 2019 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-s390x-003.buildd +==============================================================================+ | pbbam 0.23.0+dfsg-1 (s390x) 05 Jan 2020 11:16 | +==============================================================================+ Package: pbbam Version: 0.23.0+dfsg-1 Source Version: 0.23.0+dfsg-1 Distribution: focal Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/pbbam-joSgl3/pbbam-0.23.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/pbbam-joSgl3' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18337547/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pbbam_0.23.0+dfsg-1.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-xURuck/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-xURuck/apt_archive ./ InRelease Get:2 copy:/<>/resolver-xURuck/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-xURuck/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-xURuck/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-xURuck/apt_archive ./ Packages [524 B] Fetched 2857 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 packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. 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 860 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-xURuck/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [860 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 860 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14440 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-compat (= 12), dh-exec, d-shlibs, meson, pkg-config, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libgtest-dev, python3-cram, samtools Filtered Build-Depends: debhelper-compat (= 12), dh-exec, d-shlibs, meson, pkg-config, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libgtest-dev, python3-cram, samtools dpkg-deb: building package 'sbuild-build-depends-pbbam-dummy' in '/<>/resolver-_wKfta/apt_archive/sbuild-build-depends-pbbam-dummy.deb'. Ign:1 copy:/<>/resolver-_wKfta/apt_archive ./ InRelease Get:2 copy:/<>/resolver-_wKfta/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-_wKfta/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-_wKfta/apt_archive ./ Sources [291 B] Get:5 copy:/<>/resolver-_wKfta/apt_archive ./ Packages [599 B] Fetched 3009 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 packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. 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 libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl 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 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db meson mime-support ninja-build pkg-config po-debconf python3 python3-cram 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-contract1.67-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 python3-doc python3-tk python3-venv python3-setuptools python3.7-venv python3.7-doc binfmt-support 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 libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl 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 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db meson mime-support ninja-build pkg-config po-debconf python3 python3-cram python3-minimal python3-pkg-resources python3.7 python3.7-minimal samtools sbuild-build-depends-pbbam-dummy zlib1g-dev 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded. 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Setting up ninja-build (1.9.0-3) ... Setting up libkrb5support0:s390x (1.17-6) ... Setting up libsasl2-modules-db:s390x (2.1.27+dfsg-2) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libsigsegv2:s390x (2.12-2) ... Setting up libssl-dev:s390x (1.1.1c-1ubuntu4) ... Setting up autopoint (0.19.8.1-10) ... Setting up pkg-config (0.29.1-0ubuntu3) ... Setting up d-shlibs (0.88) ... Setting up libk5crypto3:s390x (1.17-6) ... Setting up libsasl2-2:s390x (2.1.27+dfsg-2) ... Setting up libroken18-heimdal:s390x (7.7.0+dfsg-1) ... Setting up liblzma-dev:s390x (5.2.4-1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-1ubuntu3) ... Setting up libuchardet0:s390x (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:s390x (1.17-6) ... Setting up libboost-dev:s390x (1.67.0.2) ... Setting up libmpdec2:s390x (2.4.2-2) ... Setting up libbsd0:s390x (0.10.0-1) ... Setting up libelf1:s390x (0.176-1.1) ... Setting up libxml2:s390x (2.9.4+dfsg1-8ubuntu1) ... Setting up libheimbase1-heimdal:s390x (7.7.0+dfsg-1) ... Setting up libfile-stripnondeterminism-perl (1.6.3-1) ... Setting up libpython3.7-stdlib:s390x (3.7.5-2) ... Setting up libgtest-dev:s390x (1.8.1-3) ... Setting up libtool (2.4.6-11) ... Setting up libasn1-8-heimdal:s390x (7.7.0+dfsg-1) ... Setting up m4 (1.4.18-4) ... Setting up libhcrypto4-heimdal:s390x (7.7.0+dfsg-1) ... Setting up libwind0-heimdal:s390x (7.7.0+dfsg-1) ... 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 libgssapi-krb5-2:s390x (1.17-6) ... Setting up libcroco3:s390x (0.6.13-1) ... Setting up libssh-4:s390x (0.9.0-1ubuntu5) ... Setting up autoconf (2.69-11ubuntu1) ... Setting up dh-strip-nondeterminism (1.6.3-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up libpython3-stdlib:s390x (3.7.5-1ubuntu1) ... 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 python3.7 (3.7.5-2) ... Setting up gettext (0.19.8.1-10) ... Setting up libhx509-5-heimdal:s390x (7.7.0+dfsg-1) ... Setting up python3 (3.7.5-1ubuntu1) ... Setting up man-db (2.9.0-2) ... 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 intltool-debian (0.35.0+20060710.5) ... Setting up python3-cram (0.7-4) ... Setting up libkrb5-26-heimdal:s390x (7.7.0+dfsg-1) ... Setting up python3-pkg-resources (41.4.0-1) ... Setting up po-debconf (1.0.21) ... Setting up meson (0.52.0-2) ... Setting up libheimntlm0-heimdal:s390x (7.7.0+dfsg-1) ... Setting up libgssapi3-heimdal:s390x (7.7.0+dfsg-1) ... Setting up libldap-2.4-2:s390x (2.4.48+dfsg-1ubuntu3) ... Setting up libcurl3-gnutls:s390x (7.66.0-1ubuntu1) ... Setting up libhts2:s390x (1.9-12) ... Setting up libhts-dev:s390x (1.9-12) ... Setting up samtools (1.9-7) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.7.1ubuntu1) ... Setting up dh-exec (0.23.2) ... Setting up sbuild-build-depends-pbbam-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-170-generic s390x (s390x) Toolchain package versions: binutils_2.33.1-6ubuntu3 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-21ubuntu1 gcc-9_9.2.1-21ubuntu1 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-21ubuntu1 libstdc++6_9.2.1-21ubuntu1 linux-libc-dev_5.3.0-24.26 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.5 autoconf_2.69-11ubuntu1 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 binutils_2.33.1-6ubuntu3 binutils-common_2.33.1-6ubuntu3 binutils-s390x-linux-gnu_2.33.1-6ubuntu3 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu4 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-21ubuntu1 d-shlibs_0.88 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-exec_0.23.2 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-5 e2fsprogs_1.45.3-4ubuntu2 fakeroot_1.24-1 fdisk_2.34-0.1ubuntu4 file_1:5.37-6 findutils_4.6.0+git+20190209-2ubuntu1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-21ubuntu1 gcc_4:9.2.1-3.1ubuntu1 gcc-9_9.2.1-21ubuntu1 gcc-9-base_9.2.1-21ubuntu1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 googletest_1.8.1-3 gpg_2.2.17-3ubuntu1 gpg-agent_2.2.17-3ubuntu1 gpgconf_2.2.17-3ubuntu1 gpgv_2.2.17-3ubuntu1 grep_3.3-1build1 groff-base_1.22.4-4 gzip_1.10-0ubuntu4 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5ubuntu1 libapparmor1_2.13.3-7ubuntu1 libapt-pkg5.90_1.9.5 libarchive-zip-perl_1.67-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-21ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-1 libassuan0_2.5.3-7ubuntu1 libatomic1_9.2.1-21ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu5 libaudit1_1:2.8.5-2ubuntu5 libbinutils_2.33.1-6ubuntu3 libblkid1_2.34-0.1ubuntu4 libboost-dev_1.67.0.2 libboost1.67-dev_1.67.0-13ubuntu2 libbrotli1_1.0.7-5 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-0ubuntu3 libc-dev-bin_2.30-0ubuntu3 libc6_2.30-0ubuntu3 libc6-dev_2.30-0ubuntu3 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcc1-0_9.2.1-21ubuntu1 libcom-err2_1.45.3-4ubuntu2 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.2-1ubuntu1 libcurl3-gnutls_7.66.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.250ubuntu2 libdebhelper-perl_12.7.1ubuntu1 libdeflate0_1.5-1 libdevmapper1.02.1_2:1.02.155-2ubuntu7 libdpkg-perl_1.19.7ubuntu2 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.3-4ubuntu2 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu4 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-21ubuntu1 libgcc1_1:9.2.1-21ubuntu1 libgcrypt20_1.8.5-3ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.63.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-21ubuntu1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6 libgssapi3-heimdal_7.7.0+dfsg-1 libgtest-dev_1.8.1-3 libhcrypto4-heimdal_7.7.0+dfsg-1 libheimbase1-heimdal_7.7.0+dfsg-1 libheimntlm0-heimdal_7.7.0+dfsg-1 libhogweed4_3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.9-12 libhts2_1.9-12 libhx509-5-heimdal_7.7.0+dfsg-1 libicu63_63.2-2 libidn2-0_2.2.0-2 libip4tc2_1.8.3-2ubuntu5 libisl21_0.21-2 libisl22_0.22-2 libitm1_9.2.1-21ubuntu1 libjson-c4_0.13.1+dfsg-6 libk5crypto3_1.17-6 libkeyutils1_1.6-6ubuntu1 libkmod2_26-3ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-1 libkrb5-3_1.17-6 libkrb5support0_1.17-6 libldap-2.4-2_2.4.48+dfsg-1ubuntu3 libldap-common_2.4.48+dfsg-1ubuntu3 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1ubuntu4 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1ubuntu1 libncursesw6_6.1+20191019-1ubuntu1 libnettle6_3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.28_5.28.1-6build1 libperl5.30_5.30.0-9 libpipeline1_1.5.1-3 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libpsl5_0.20.2-2 libpython3-stdlib_3.7.5-1ubuntu1 libpython3.7-minimal_3.7.5-2 libpython3.7-stdlib_3.7.5-2 libreadline8_8.0-3 libroken18-heimdal_7.7.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2ubuntu1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu4 libsqlite3-0_3.30.1-1ubuntu1 libss2_1.45.3-4ubuntu2 libssh-4_0.9.0-1ubuntu5 libssl-dev_1.1.1c-1ubuntu4 libssl1.1_1.1.1c-1ubuntu4 libstdc++-9-dev_9.2.1-21ubuntu1 libstdc++6_9.2.1-21ubuntu1 libsub-override-perl_0.09-2 libsystemd0_244-3ubuntu1 libtasn1-6_4.15.0-2 libtinfo6_6.1+20191019-1ubuntu1 libtool_2.4.6-11 libubsan1_9.2.1-21ubuntu1 libuchardet0_0.0.6-3 libudev1_244-3ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu4 libwind0-heimdal_7.7.0+dfsg-1 libxml2_2.9.4+dfsg1-8ubuntu1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.3.0-24.26 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu4 logsave_1.45.3-4ubuntu2 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17ubuntu3 meson_0.52.0-2 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu4 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 ninja-build_1.9.0-3 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkg-config_0.29.1-0ubuntu3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 python3_3.7.5-1ubuntu1 python3-cram_0.7-4 python3-minimal_3.7.5-1ubuntu1 python3-pkg-resources_41.4.0-1 python3.7_3.7.5-2 python3.7-minimal_3.7.5-2 readline-common_8.0-3 samtools_1.9-7 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+nmu1 systemd_244-3ubuntu1 systemd-sysv_244-3ubuntu1 sysvinit-utils_2.96-1ubuntu1 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 util-linux_2.34-0.1ubuntu4 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Aug 5 04:30:36 2019 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbbam_0.23.0+dfsg-1.dsc dpkg-source: info: extracting pbbam in pbbam-0.23.0+dfsg dpkg-source: info: unpacking pbbam_0.23.0+dfsg.orig.tar.xz dpkg-source: info: unpacking pbbam_0.23.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_gtest_depcheck.patch dpkg-source: info: applying use_debian_packaged_python3-cram.patch dpkg-source: info: applying python3.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-18337547 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18337547 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18337547 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 0.23.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable 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-0.23.0+dfsg' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /<>/pbbam-0.23.0+dfsg/gendata make[1]: Leaving directory '/<>/pbbam-0.23.0+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 The Meson build system Version: 0.52.0 Source dir: /<>/pbbam-0.23.0+dfsg Build dir: /<>/pbbam-0.23.0+dfsg/obj-s390x-linux-gnu Build type: native build Project name: PacBioBAM Project version: 0.23.0 Appending CXXFLAGS from environment: '-g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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' Appending CXXFLAGS from environment: '-g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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' C++ compiler for the host machine: c++ (gcc 9.2.1 "c++ (Ubuntu 9.2.1-21ubuntu1) 9.2.1 20191130") C++ linker for the host machine: GNU ld.bfd 2.33.1 Host machine cpu family: s390x Host 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 Run-time dependency threads found: YES Run-time dependency Boost found: YES 1.67 Found pkg-config: /usr/bin/pkg-config (0.29.1) Run-time dependency zlib found: YES 1.2.11 Run-time dependency htslib found: YES 1.9 Program python3 found: YES (/usr/bin/python3) Program tools/check-formatting found: YES (/<>/pbbam-0.23.0+dfsg/tools/check-formatting) Program cram3 found: YES (/usr/bin/cram3) Run-time 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-1.9.0 at /usr/bin/ninja dh_auto_build -a -O--buildsystem=meson cd obj-s390x-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [2/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [3/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [4/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [5/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [6/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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/BamFileMerger.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamFileMerger.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamFileMerger.cpp.o' -c ../src/BamFileMerger.cpp [7/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [8/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [9/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 ../src/BamRecordImpl.cpp [10/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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/BamRecordView.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecordView.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecordView.cpp.o' -c ../src/BamRecordView.cpp [11/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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/BamRecordTags.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecordTags.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecordTags.cpp.o' -c ../src/BamRecordTags.cpp [12/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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/BamWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamWriter.cpp.o' -c ../src/BamWriter.cpp [13/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+dfsg=. 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-I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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/GenomicIntervalQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o' -c ../src/GenomicIntervalQuery.cpp [48/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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/IndexedBamWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o' -c ../src/IndexedBamWriter.cpp ../src/IndexedBamWriter.cpp: In member function ‘std::vector PacBio::BAM::internal::PbiBuilder2::LoadGzi()’: ../src/IndexedBamWriter.cpp:585:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 585 | fread(&entry.vAddress, sizeof(entry.vAddress), 1, gziFile.get()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/IndexedBamWriter.cpp:586:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 586 | fread(&entry.uAddress, sizeof(entry.uAddress), 1, gziFile.get()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [49/179] c++ 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'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/IRecordWriter.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/QualityValues.cpp.o' 'src/25a6634@@pbbam@sha/ReadAccuracyQuery.cpp.o' 'src/25a6634@@pbbam@sha/ReadGroupInfo.cpp.o' 'src/25a6634@@pbbam@sha/RecordType.cpp.o' 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'src/25a6634@@pbbam@sha/ZmwQuery.cpp.o' 'src/25a6634@@pbbam@sha/ZmwTypeMap.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfFile.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfFormat.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfHeader.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfHeaderTypes.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfQuery.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfReader.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfSort.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfVariant.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfWriter.cpp.o' 'src/25a6634@@pbbam@sha/pugixml_pugixml.cpp.o' -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.0.23.0 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread /usr/lib/s390x-linux-gnu/libz.so /usr/lib/s390x-linux-gnu/libhts.so -Wl,--end-group [102/179] /usr/bin/meson --internal symbolextractor src/libpbbam.so.0.23.0 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-I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [140/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [141/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [142/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [143/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond 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../tests/src/test_VcfReader.cpp [145/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [146/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [147/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 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-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 [153/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [154/179] c++ -Itools/f9d35d4@@bam2sam@exe -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [155/179] /usr/bin/python3 ../tests/scripts/generate_data.py /<>/pbbam-0.23.0+dfsg/tests/data /<>/pbbam-0.23.0+dfsg/obj-s390x-linux-gnu/tests Generating test data in /<>/pbbam-0.23.0+dfsg/obj-s390x-linux-gnu/tests - Creating file: truncated.bam...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fa...done. - Creating file: normal.fq...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: missing_pbi.bam...done. 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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_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 [158/179] c++ -Itools/f9d35d4@@pbindex@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [159/179] c++ -Itools/f9d35d4@@bam2sam@exe -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [160/179] c++ -o tools/bam2sam 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o' 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-fdebug-prefix-map=/<>/pbbam-0.23.0+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 [178/179] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+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 [179/179] 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,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.23.0 /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/pbbam-0.23.0+dfsg/obj-s390x-linux-gnu/src debian/rules override_dh_auto_test make[1]: Entering directory '/<>/pbbam-0.23.0+dfsg' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.23.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.23.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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-0.23.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.23.0+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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.23.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.23.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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-0.23.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.23.0+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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.23.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.23.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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-0.23.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.23.0+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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-0.23.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.23.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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-0.23.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-0.23.0+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 dh_auto_configure -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 Directory already configured. Just run your build command (e.g. ninja) and Meson will regenerate as necessary. If ninja fails, run "ninja reconfigure" or "meson --reconfigure" to force Meson to regenerate. If build failures persist, run "meson setup --wipe" to rebuild from scratch using the same options as passed when configuring the build. To change option values, run "meson configure" instead. mkdir -p /<>/pbbam-0.23.0+dfsg/gendata python3 tests/scripts/generate_data.py /<>/pbbam-0.23.0+dfsg/tests/data /<>/pbbam-0.23.0+dfsg/gendata Generating test data in /<>/pbbam-0.23.0+dfsg/gendata - Creating file: truncated.bam...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fa...done. - Creating file: normal.fq...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: missing_pbi.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:" \ cram3 -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 @@ -104,6 +104,8 @@ Normal Merge: $ $PBMERGE $HQREGION_BAM $SCRAPS_BAM > $MERGED_BAM + ERROR: bad numeric conversion: positive overflow + [1] $ samtools view -H $MERGED_BAM @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) @@ -115,82 +117,14 @@ @PG\tID:pbmerge-0.23.0\tPN:pbmerge\tVN:0.23.0 (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: bad numeric conversion: positive overflow + [1] $ samtools view -H $MERGED_BAM @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) @@ -202,82 +136,14 @@ @PG\tID:pbmerge-0.23.0\tPN:pbmerge\tVN:0.23.0 (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: bad numeric conversion: positive overflow + [1] $ samtools view -H $MERGED_BAM @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) @@ -289,76 +155,6 @@ @PG\tID:pbmerge-0.23.0\tPN:pbmerge\tVN:0.23.0 (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 $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" Found @@ -369,6 +165,8 @@ Explicit Output Filename (with disabled PBI): $ $PBMERGE -o $MERGED_BAM --no-pbi $HQREGION_BAM $SCRAPS_BAM + ERROR: bad numeric conversion: positive overflow + [1] $ samtools view -H $MERGED_BAM @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) @@ -380,76 +178,6 @@ @PG\tID:pbmerge-0.23.0\tPN:pbmerge\tVN:0.23.0 (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 $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" Not found 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-0.23.0+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 @@ -52,6 +52,8 @@ Normal Merge from XML: $ $PBMERGE -o $MERGED_BAM $INPUT_XML + ERROR: BamHeader: read group ID not found: + [1] $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" Found @@ -69,14 +71,6 @@ @PG\tID:pbmerge-0.23.0\tPN:pbmerge\tVN:0.23.0 (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 $ rm $MERGED_BAM_PBI @@ -101,14 +95,14 @@ @PG\tID:pbmerge-0.23.0\tPN:pbmerge\tVN:0.23.0 (esc) $ samtools view $MERGED_BAM | cut -f 1 + ArminsFakeMovie/0/4356_4864 + ArminsFakeMovie/0/4960_5477 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 @@ -132,13 +126,13 @@ @PG\tID:pbmerge-0.23.0\tPN:pbmerge\tVN:0.23.0 (esc) $ samtools view $MERGED_BAM | cut -f 1 + ArminsFakeMovie/0/4356_4864 + ArminsFakeMovie/0/4960_5477 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:22: override_dh_auto_test] Error 1 make[1]: Leaving directory '/<>/pbbam-0.23.0+dfsg' make: *** [debian/rules:13: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200105-1119 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 866768 Build-Time: 128 Distribution: focal Fail-Stage: build Host Architecture: s390x Install-Time: 10 Job: pbbam_0.23.0+dfsg-1.dsc Machine Architecture: s390x Package: pbbam Package-Time: 139 Source-Version: 0.23.0+dfsg-1 Space: 866768 Status: attempted Version: 0.23.0+dfsg-1 -------------------------------------------------------------------------------- Finished at 20200105-1119 Build needed 00:02:19, 866768k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=s390x PACKAGEBUILD-18337547 Scanning for processes to kill in build PACKAGEBUILD-18337547