https://launchpad.net/ubuntu/+source/pbbam/2.4.0+dfsg-1build1/+build/27789654 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-012 5.4.0-176-generic #196-Ubuntu SMP Fri Mar 22 16:47:16 UTC 2024 s390x Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 10 Apr 22:58:26 ntpdate[1910]: adjust time server 10.211.37.1 offset 0.000133 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27789654 --image-type chroot /home/buildd/filecache-default/c23f799bb684944311373fdcead5a58221fa6ef7 Creating target for build PACKAGEBUILD-27789654 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27789654 Starting target for build PACKAGEBUILD-27789654 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27789654 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27789654 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27789654 Updating target for build PACKAGEBUILD-27789654 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [89.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x Packages [1340 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x Packages [14.6 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6071 kB] Get:9 http://ftpmaster.internal/ubuntu noble-updates/universe s390x Packages [2868 B] Get:10 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [948 B] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [329 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [139 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [733 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [283 kB] Fetched 24.6 MB in 4s (6250 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: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-s390x-linux-gnu cpp-s390x-linux-gnu g++-13-s390x-linux-gnu g++-s390x-linux-gnu gcc-13-s390x-linux-gnu gcc-14-base gcc-s390x-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: advancecomp apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-s390x-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 170 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 107 MB of archives. After this operation, 76.3 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libnsl-dev s390x 1.3.0-3build3 [73.1 kB] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcrypt-dev s390x 1:4.4.36-4build1 [119 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu7 [66.4 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libc6-dev s390x 2.39-0ubuntu8 [1629 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libc-dev-bin s390x 2.39-0ubuntu8 [20.2 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-dev s390x 1.3.4+ds-1.1build1 [197 kB] Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x libnss-nisplus s390x 1.3-5build1 [23.8 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc3t64 s390x 1.3.4+ds-1.1build1 [85.9 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libgssapi-krb5-2 s390x 1.20.1-6ubuntu2 [149 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libkrb5-3 s390x 1.20.1-6ubuntu2 [360 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libk5crypto3 s390x 1.20.1-6ubuntu2 [90.3 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libkrb5support0 s390x 1.20.1-6ubuntu2 [34.7 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libacl1 s390x 2.3.2-1build1 [18.0 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libapparmor1 s390x 4.0.0-beta3-0ubuntu3 [50.8 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libcap-ng0 s390x 0.8.4-2build2 [15.8 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libaudit1 s390x 1:3.1.2-2.1build1 [48.9 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblkid1 s390x 2.39.3-9ubuntu5 [128 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcap2 s390x 1:2.66-5ubuntu2 [31.8 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcrypt1 s390x 1:4.4.36-4build1 [88.9 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgpg-error-l10n all 1.47-3build2 [8064 B] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgpg-error0 s390x 1.47-3build2 [75.6 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgcrypt20 s390x 1.10.3-2build1 [501 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main s390x liblzma5 s390x 5.6.1+really5.4.5-1 [135 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libzstd1 s390x 1.5.5+dfsg2-2build1 [341 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkmod2 s390x 31+20240202-2ubuntu6 [56.4 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblz4-1 s390x 1.9.4-1build1 [79.4 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpcre2-8-0 s390x 10.42-4ubuntu2 [245 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libselinux1 s390x 3.5-2ubuntu2 [84.8 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmount1 s390x 2.39.3-9ubuntu5 [138 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main s390x perl-modules-5.38 all 5.38.2-3.2build2 [3110 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-6build1 [763 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm6t64 s390x 1.23-5.1build1 [36.5 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm-compat4t64 s390x 1.23-5.1build1 [6890 B] Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libperl5.38t64 s390x 5.38.2-3.2build2 [5006 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main s390x perl s390x 5.38.2-3.2build2 [231 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main s390x perl-base s390x 5.38.2-3.2build2 [1968 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main s390x liblocale-gettext-perl s390x 1.07-6ubuntu5 [15.8 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libtext-iconv-perl s390x 1.7-8build3 [13.8 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main s390x libtext-charwidth-perl s390x 0.04-11build3 [9518 B] Get:42 http://ftpmaster.internal/ubuntu noble/main s390x libc6 s390x 2.39-0ubuntu8 [2847 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libc-bin s390x 2.39-0ubuntu8 [654 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main s390x openssl s390x 3.0.13-0ubuntu3 [1009 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main s390x libsystemd-shared s390x 255.4-1ubuntu7 [2131 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcryptsetup12 s390x 2:2.7.0-1ubuntu4 [264 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main s390x libssl3t64 s390x 3.0.13-0ubuntu3 [1675 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main s390x systemd-dev all 255.4-1ubuntu7 [104 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main s390x systemd-sysv s390x 255.4-1ubuntu7 [11.9 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main s390x systemd s390x 255.4-1ubuntu7 [3534 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main s390x libsystemd0 s390x 255.4-1ubuntu7 [443 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules-bin s390x 1.5.3-5ubuntu4 [57.2 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules s390x 1.5.3-5ubuntu4 [289 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libnettle8t64 s390x 3.9.1-2.2build1 [210 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main s390x libhogweed6t64 s390x 3.9.1-2.2build1 [204 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libp11-kit0 s390x 0.25.3-4ubuntu2 [320 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libunistring5 s390x 1.1-2build1 [550 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main s390x libgnutls30t64 s390x 3.8.3-1.1ubuntu3 [944 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main s390x libapt-pkg6.0t64 s390x 2.7.14build2 [1014 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bzip2 s390x 1.0.8-5.1 [35.5 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libbz2-1.0 s390x 1.0.8-5.1 [40.0 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main s390x gcc-14-base s390x 14-20240330-1ubuntu2 [47.4 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-s1 s390x 14-20240330-1ubuntu2 [35.9 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++6 s390x 14-20240330-1ubuntu2 [905 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main s390x libudev1 s390x 255.4-1ubuntu7 [178 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxxhash0 s390x 0.8.2-2build1 [24.1 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g s390x 1:1.3.dfsg-3.1ubuntu2 [75.9 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libffi8 s390x 3.4.6-1build1 [23.1 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libidn2-0 s390x 2.3.7-2build1 [67.3 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtasn1-6 s390x 4.19.0-3build1 [48.5 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main s390x libdebconfclient0 s390x 0.271ubuntu3 [11.4 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main s390x base-passwd s390x 3.6.3build1 [51.5 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libassuan0 s390x 2.5.6-1build1 [38.3 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main s390x libsqlite3-0 s390x 3.45.1-1ubuntu2 [747 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main s390x gpg s390x 2.4.4-2ubuntu17 [589 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main s390x libreadline8t64 s390x 8.2-4build1 [171 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main s390x readline-common all 8.2-4build1 [56.5 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libncursesw6 s390x 6.4+20240113-1ubuntu2 [161 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtinfo6 s390x 6.4+20240113-1ubuntu2 [117 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main s390x gpg-agent s390x 2.4.4-2ubuntu17 [240 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main s390x gpgconf s390x 2.4.4-2ubuntu17 [111 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main s390x pinentry-curses s390x 1.2.1-3ubuntu5 [37.6 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main s390x init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main s390x libnpth0t64 s390x 1.6-3.1build1 [8204 B] Get:85 http://ftpmaster.internal/ubuntu noble/main s390x gpgv s390x 2.4.4-2ubuntu17 [165 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main s390x libseccomp2 s390x 2.5.5-1ubuntu3 [53.4 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main s390x apt-utils s390x 2.7.14build2 [214 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main s390x apt s390x 2.7.14build2 [1390 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main s390x debconf-i18n all 1.5.86 [205 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main s390x debconf all 1.5.86 [124 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main s390x libpam0g s390x 1.5.3-5ubuntu4 [69.7 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libargon2-1 s390x 0~20190702+dfsg-4build1 [54.1 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main s390x libdevmapper1.02.1 s390x 2:1.02.185-3ubuntu3 [142 kB] Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libjson-c5 s390x 0.17-1build1 [37.2 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libuuid1 s390x 2.39.3-9ubuntu5 [35.9 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfdisk1 s390x 2.39.3-9ubuntu5 [151 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main s390x mount s390x 2.39.3-9ubuntu5 [119 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcom-err2 s390x 1.47.0-2.4~exp1ubuntu4 [22.9 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkeyutils1 s390x 1.6.3-3build1 [9556 B] Get:101 http://ftpmaster.internal/ubuntu noble/main s390x libnsl2 s390x 1.3.0-3build3 [44.1 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main s390x linux-libc-dev s390x 6.8.0-22.22 [1592 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main s390x base-files s390x 13ubuntu9 [73.7 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17build1 [90.2 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main s390x bash s390x 5.2.21-2ubuntu4 [845 kB] Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdutils s390x 1:2.39.3-9ubuntu5 [96.4 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main s390x coreutils s390x 9.4-3ubuntu6 [1483 kB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main s390x tar s390x 1.35+dfsg-3build1 [269 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main s390x dpkg s390x 1.22.6ubuntu6 [1278 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main s390x dash s390x 0.5.12-6ubuntu5 [95.0 kB] Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main s390x diffutils s390x 1:3.10-1build1 [188 kB] Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main s390x findutils s390x 4.9.0-5build1 [305 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main s390x grep s390x 3.11-4build1 [173 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gzip s390x 1.12-1ubuntu3 [107 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main s390x hostname s390x 3.23+nmu2ubuntu2 [11.2 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main s390x login s390x 1:4.13+dfsg1-4ubuntu3 [202 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ncurses-bin s390x 6.4+20240113-1ubuntu2 [198 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main s390x sed s390x 4.9-2build1 [198 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main s390x util-linux s390x 2.39.3-9ubuntu5 [1142 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main s390x ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main s390x sysvinit-utils s390x 3.08-6ubuntu3 [34.8 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main s390x logsave s390x 1.47.0-2.4~exp1ubuntu4 [22.6 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libext2fs2t64 s390x 1.47.0-2.4~exp1ubuntu4 [234 kB] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main s390x e2fsprogs s390x 1.47.0-2.4~exp1ubuntu4 [614 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main s390x optipng s390x 0.7.8+ds-1build2 [114 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main s390x libpng16-16t64 s390x 1.6.43-5build1 [200 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main s390x init s390x 1.66ubuntu1 [6188 B] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsmartcols1 s390x 2.39.3-9ubuntu5 [68.1 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main s390x uuid-runtime s390x 2.39.3-9ubuntu5 [33.4 kB] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libattr1 s390x 1:2.5.2-1build1 [11.7 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmd0 s390x 1.1.0-2build1 [24.6 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main s390x libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage-common all 3.5-1build5 [10.1 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsepol2 s390x 3.5-2build1 [315 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage2 s390x 3.5-1build5 [96.8 kB] Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main s390x passwd s390x 1:4.13+dfsg1-4ubuntu3 [857 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main s390x libproc2-0 s390x 2:4.0.4-4ubuntu3 [59.8 kB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libss2 s390x 1.47.0-2.4~exp1ubuntu4 [17.2 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main s390x mawk s390x 1.3.4.20240123-1build1 [133 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main s390x procps s390x 2:4.0.4-4ubuntu3 [724 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main s390x sensible-utils all 0.0.22 [22.5 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main s390x ca-certificates all 20240203 [159 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main s390x krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main s390x tzdata all 2024a-2ubuntu1 [273 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main s390x bash-completion all 1:2.11-8 [180 kB] Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdextrautils s390x 2.39.3-9ubuntu5 [76.3 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main s390x libgpm2 s390x 1.20.7-11 [14.7 kB] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libip4tc2 s390x 1.8.10-3ubuntu2 [24.2 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main s390x libjansson4 s390x 2.14-2build2 [33.2 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main s390x psmisc s390x 23.7-1build1 [178 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main s390x xz-utils s390x 5.6.1+really5.4.5-1 [269 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main s390x advancecomp s390x 2.5-1build1 [205 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main s390x libctf0 s390x 2.42-4ubuntu2 [98.4 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main s390x libctf-nobfd0 s390x 2.42-4ubuntu2 [100 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main s390x binutils-s390x-linux-gnu s390x 2.42-4ubuntu2 [2270 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main s390x libbinutils s390x 2.42-4ubuntu2 [479 kB] Get:157 http://ftpmaster.internal/ubuntu noble/main s390x binutils s390x 2.42-4ubuntu2 [3042 B] Get:158 http://ftpmaster.internal/ubuntu noble/main s390x binutils-common s390x 2.42-4ubuntu2 [217 kB] Get:159 http://ftpmaster.internal/ubuntu noble/main s390x libsframe1 s390x 2.42-4ubuntu2 [14.2 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main s390x libubsan1 s390x 14-20240330-1ubuntu2 [1186 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240330-1ubuntu2 [151 kB] Get:162 http://ftpmaster.internal/ubuntu noble/main s390x libitm1 s390x 14-20240330-1ubuntu2 [31.1 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 14-20240330-1ubuntu2 [9386 B] Get:164 http://ftpmaster.internal/ubuntu noble/main s390x libasan8 s390x 14-20240330-1ubuntu2 [2994 kB] Get:165 http://ftpmaster.internal/ubuntu noble/main s390x g++-13 s390x 13.2.0-23ubuntu3 [14.5 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13 s390x 13.2.0-23ubuntu3 [469 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++-13-dev s390x 13.2.0-23ubuntu3 [2494 kB] Get:168 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-13-dev s390x 13.2.0-23ubuntu3 [1003 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main s390x libcc1-0 s390x 14-20240330-1ubuntu2 [49.8 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13 s390x 13.2.0-23ubuntu3 [1026 B] Get:171 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-base s390x 13.2.0-23ubuntu3 [48.6 kB] Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libisl23 s390x 0.26-3build1 [713 kB] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmpfr6 s390x 4.2.1-1build1 [322 kB] Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmpc3 s390x 1.3.1-1build1 [58.4 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-s390x-linux-gnu s390x 13.2.0-23ubuntu3 [19.1 MB] Get:176 http://ftpmaster.internal/ubuntu noble/main s390x g++-13-s390x-linux-gnu s390x 13.2.0-23ubuntu3 [11.3 MB] Get:177 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13-s390x-linux-gnu s390x 13.2.0-23ubuntu3 [9936 kB] Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main s390x g++ s390x 4:13.2.0-7ubuntu2 [1096 B] Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gcc s390x 4:13.2.0-7ubuntu2 [5008 B] Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main s390x cpp s390x 4:13.2.0-7ubuntu2 [22.4 kB] Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main s390x cpp-s390x-linux-gnu s390x 4:13.2.0-7ubuntu2 [5404 B] Get:182 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gcc-s390x-linux-gnu s390x 4:13.2.0-7ubuntu2 [1202 B] Get:183 http://ftpmaster.internal/ubuntu noble-proposed/main s390x g++-s390x-linux-gnu s390x 4:13.2.0-7ubuntu2 [956 B] Get:184 http://ftpmaster.internal/ubuntu noble/main s390x dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:185 http://ftpmaster.internal/ubuntu noble/main s390x libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:186 http://ftpmaster.internal/ubuntu noble-proposed/main s390x patch s390x 2.7.6-7build3 [113 kB] Get:187 http://ftpmaster.internal/ubuntu noble-proposed/main s390x make s390x 4.3-4.1build2 [196 kB] Get:188 http://ftpmaster.internal/ubuntu noble/main s390x lto-disabled-list all 47 [12.4 kB] Get:189 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfakeroot s390x 1.33-1build1 [32.0 kB] Get:190 http://ftpmaster.internal/ubuntu noble-proposed/main s390x fakeroot s390x 1.33-1build1 [67.6 kB] Get:191 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblockfile-bin s390x 1.17-1build3 [11.6 kB] Get:192 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblockfile1 s390x 1.17-1build3 [7028 B] Get:193 http://ftpmaster.internal/ubuntu noble-proposed/main s390x lockfile-progs s390x 0.1.19build2 [8406 B] Preconfiguring packages ... Fetched 107 MB in 5s (20.9 MB/s) (Reading database ... 13395 files and directories currently installed.) Preparing to unpack .../0-libnsl-dev_1.3.0-3build3_s390x.deb ... Unpacking libnsl-dev:s390x (1.3.0-3build3) over (1.3.0-2build2) ... Preparing to unpack .../1-libcrypt-dev_1%3a4.4.36-4build1_s390x.deb ... Unpacking libcrypt-dev:s390x (1:4.4.36-4build1) over (1:4.4.36-2) ... Preparing to unpack .../2-rpcsvc-proto_1.4.2-0ubuntu7_s390x.deb ... Unpacking rpcsvc-proto (1.4.2-0ubuntu7) over (1.4.2-0ubuntu6) ... Preparing to unpack .../3-libc6-dev_2.39-0ubuntu8_s390x.deb ... Unpacking libc6-dev:s390x (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Preparing to unpack .../4-libc-dev-bin_2.39-0ubuntu8_s390x.deb ... Unpacking libc-dev-bin (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Preparing to unpack .../5-libtirpc-common_1.3.4+ds-1.1build1_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.1build1) over (1.3.3+ds-1) ... Preparing to unpack .../6-libtirpc-dev_1.3.4+ds-1.1build1_s390x.deb ... 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(Reading database ... 14816 files and directories currently installed.) Removing libgdbm6:s390x (1.23-3) ... Selecting previously unselected package libgdbm6t64:s390x. (Reading database ... 14811 files and directories currently installed.) Preparing to unpack .../libgdbm6t64_1.23-5.1build1_s390x.deb ... Unpacking libgdbm6t64:s390x (1.23-5.1build1) ... dpkg: libgdbm-compat4:s390x: dependency problems, but removing anyway as you requested: libperl5.36:s390x depends on libgdbm-compat4 (>= 1.18-3). (Reading database ... 14817 files and directories currently installed.) Removing libgdbm-compat4:s390x (1.23-3) ... Selecting previously unselected package libgdbm-compat4t64:s390x. (Reading database ... 14812 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4t64_1.23-5.1build1_s390x.deb ... Unpacking libgdbm-compat4t64:s390x (1.23-5.1build1) ... Selecting previously unselected package libperl5.38t64:s390x. 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Selecting previously unselected package libssl3t64:s390x. (Reading database ... 15333 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.0.13-0ubuntu3_s390x.deb ... Unpacking libssl3t64:s390x (3.0.13-0ubuntu3) ... Setting up libssl3t64:s390x (3.0.13-0ubuntu3) ... (Reading database ... 15346 files and directories currently installed.) Preparing to unpack .../systemd-dev_255.4-1ubuntu7_all.deb ... Unpacking systemd-dev (255.4-1ubuntu7) over (253.5-1ubuntu6) ... Preparing to unpack .../systemd-sysv_255.4-1ubuntu7_s390x.deb ... Unpacking systemd-sysv (255.4-1ubuntu7) over (253.5-1ubuntu6) ... Preparing to unpack .../systemd_255.4-1ubuntu7_s390x.deb ... Unpacking systemd (255.4-1ubuntu7) over (253.5-1ubuntu6) ... dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sockets.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/multi-user.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/journald.conf.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty Preparing to unpack .../libsystemd0_255.4-1ubuntu7_s390x.deb ... 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(Reading database ... 15481 files and directories currently installed.) Removing libhogweed6:s390x (3.9.1-2) ... dpkg: libnettle8:s390x: dependency problems, but removing anyway as you requested: libgnutls30:s390x depends on libnettle8 (>= 3.7~). Removing libnettle8:s390x (3.9.1-2) ... Selecting previously unselected package libnettle8t64:s390x. (Reading database ... 15469 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.9.1-2.2build1_s390x.deb ... Unpacking libnettle8t64:s390x (3.9.1-2.2build1) ... Setting up libnettle8t64:s390x (3.9.1-2.2build1) ... Selecting previously unselected package libhogweed6t64:s390x. (Reading database ... 15477 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2build1_s390x.deb ... Unpacking libhogweed6t64:s390x (3.9.1-2.2build1) ... Setting up libhogweed6t64:s390x (3.9.1-2.2build1) ... (Reading database ... 15483 files and directories currently installed.) 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Setting up libgnutls30t64:s390x (3.8.3-1.1ubuntu3) ... dpkg: libapt-pkg6.0:s390x: dependency problems, but removing anyway as you requested: apt-utils depends on libapt-pkg6.0 (>= 2.7.3). apt depends on libapt-pkg6.0 (>= 2.7.3). (Reading database ... 15490 files and directories currently installed.) Removing libapt-pkg6.0:s390x (2.7.3) ... Selecting previously unselected package libapt-pkg6.0t64:s390x. (Reading database ... 15441 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.7.14build2_s390x.deb ... Unpacking libapt-pkg6.0t64:s390x (2.7.14build2) ... Setting up libapt-pkg6.0t64:s390x (2.7.14build2) ... (Reading database ... 15491 files and directories currently installed.) Preparing to unpack .../bzip2_1.0.8-5.1_s390x.deb ... Unpacking bzip2 (1.0.8-5.1) over (1.0.8-5build1) ... dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') Preparing to unpack .../libbz2-1.0_1.0.8-5.1_s390x.deb ... Unpacking libbz2-1.0:s390x (1.0.8-5.1) over (1.0.8-5build1) ... Setting up libbz2-1.0:s390x (1.0.8-5.1) ... Selecting previously unselected package gcc-14-base:s390x. (Reading database ... 15491 files and directories currently installed.) 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(Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.2-2build1_s390x.deb ... Unpacking libxxhash0:s390x (0.8.2-2build1) over (0.8.1-1) ... Setting up libxxhash0:s390x (0.8.2-2build1) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu2_s390x.deb ... Unpacking zlib1g:s390x (1:1.3.dfsg-3.1ubuntu2) over (1:1.2.13.dfsg-1ubuntu5) ... Setting up zlib1g:s390x (1:1.3.dfsg-3.1ubuntu2) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.6-1build1_s390x.deb ... Unpacking libffi8:s390x (3.4.6-1build1) over (3.4.4-1) ... Setting up libffi8:s390x (3.4.6-1build1) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.7-2build1_s390x.deb ... Unpacking libidn2-0:s390x (2.3.7-2build1) over (2.3.4-1) ... Setting up libidn2-0:s390x (2.3.7-2build1) ... 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(Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libsqlite3-0_3.45.1-1ubuntu2_s390x.deb ... Unpacking libsqlite3-0:s390x (3.45.1-1ubuntu2) over (3.42.0-1) ... Preparing to unpack .../gpg_2.4.4-2ubuntu17_s390x.deb ... Unpacking gpg (2.4.4-2ubuntu17) over (2.2.40-1.1ubuntu1) ... dpkg: libreadline8:s390x: dependency problems, but removing anyway as you requested: gpgconf depends on libreadline8 (>= 6.0). (Reading database ... 15496 files and directories currently installed.) Removing libreadline8:s390x (8.2-1.3) ... Selecting previously unselected package libreadline8t64:s390x. (Reading database ... 15484 files and directories currently installed.) Preparing to unpack .../libreadline8t64_8.2-4build1_s390x.deb ... Adding 'diversion of /lib/s390x-linux-gnu/libhistory.so.8 to /lib/s390x-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/s390x-linux-gnu/libhistory.so.8.2 to /lib/s390x-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/s390x-linux-gnu/libreadline.so.8 to /lib/s390x-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/s390x-linux-gnu/libreadline.so.8.2 to /lib/s390x-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:s390x (8.2-4build1) ... Preparing to unpack .../readline-common_8.2-4build1_all.deb ... Unpacking readline-common (8.2-4build1) over (8.2-1.3) ... Preparing to unpack .../libncursesw6_6.4+20240113-1ubuntu2_s390x.deb ... Unpacking libncursesw6:s390x (6.4+20240113-1ubuntu2) over (6.4+20230625-2) ... Preparing to unpack .../libtinfo6_6.4+20240113-1ubuntu2_s390x.deb ... 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(both '/usr/bin/gunzip' and '/usr/bin/uncompress') dpkg: warning: old file '/bin/gunzip' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') Setting up gzip (1.12-1ubuntu3) ... (Reading database ... 15495 files and directories currently installed.) Preparing to unpack .../hostname_3.23+nmu2ubuntu2_s390x.deb ... Unpacking hostname (3.23+nmu2ubuntu2) over (3.23+nmu1ubuntu1) ... Setting up hostname (3.23+nmu2ubuntu2) ... (Reading database ... 15495 files and directories currently installed.) Preparing to unpack .../login_1%3a4.13+dfsg1-4ubuntu3_s390x.deb ... Unpacking login (1:4.13+dfsg1-4ubuntu3) over (1:4.13+dfsg1-1ubuntu1) ... Setting up login (1:4.13+dfsg1-4ubuntu3) ... Installing new version of config file /etc/login.defs ... Installing new version of config file /etc/pam.d/login ... (Reading database ... 15495 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20240113-1ubuntu2_s390x.deb ... 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Setting up uuid-runtime (2.39.3-9ubuntu5) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libcrypt-dev:s390x (1:4.4.36-4build1) ... Setting up libasan8:s390x (14-20240330-1ubuntu2) ... Setting up procps (2:4.0.4-4ubuntu3) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1build1) ... Setting up libkrb5-3:s390x (1.20.1-6ubuntu2) ... Setting up liblockfile1:s390x (1.17-1build3) ... Setting up libperl5.38t64:s390x (5.38.2-3.2build2) ... Setting up libbinutils:s390x (2.42-4ubuntu2) ... Setting up libisl23:s390x (0.26-3build1) ... Setting up libc-dev-bin (2.39-0ubuntu8) ... Setting up openssl (3.0.13-0ubuntu3) ... Setting up libgpg-error-l10n (1.47-3build2) ... Setting up readline-common (8.2-4build1) ... Setting up libcc1-0:s390x (14-20240330-1ubuntu2) ... Setting up liblocale-gettext-perl (1.07-6ubuntu5) ... Setting up libitm1:s390x (14-20240330-1ubuntu2) ... Setting up libctf0:s390x (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up apt-utils (2.7.14build2) ... Setting up binutils-s390x-linux-gnu (2.42-4ubuntu2) ... Setting up debconf-i18n (1.5.86) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... Setting up binutils (2.42-4ubuntu2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-3.2build2) ... Setting up cpp-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19build2) ... Setting up libgssapi-krb5-2:s390x (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu6) ... Setting up libreadline8t64:s390x (8.2-4build1) ... Setting up libgcc-13-dev:s390x (13.2.0-23ubuntu3) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:s390x (2.39-0ubuntu8) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up libstdc++-13-dev:s390x (13.2.0-23ubuntu3) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up cpp-13 (13.2.0-23ubuntu3) ... Setting up cpp-s390x-linux-gnu (4:13.2.0-7ubuntu2) ... Setting up libtirpc3t64:s390x (1.3.4+ds-1.1build1) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:s390x (1.3.4+ds-1.1build1) ... Setting up gcc-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-s390x-linux-gnu (4:13.2.0-7ubuntu2) ... Setting up g++-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-13 (13.2.0-23ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu2) ... Setting up libnsl2:s390x (1.3.0-3build3) ... Setting up g++-13 (13.2.0-23ubuntu3) ... Setting up g++-s390x-linux-gnu (4:13.2.0-7ubuntu2) ... Setting up libnss-nisplus:s390x (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu2) ... Setting up g++ (4:13.2.0-7ubuntu2) ... Setting up libnsl-dev:s390x (1.3.0-3build3) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15545 files and directories currently installed.) Purging configuration files for libssl3:s390x (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27789654 s390x noble-proposed -c chroot:build-PACKAGEBUILD-27789654 --arch=s390x --dist=noble-proposed --nolog pbbam_2.4.0+dfsg-1build1.dsc Initiating build PACKAGEBUILD-27789654 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-176-generic #196-Ubuntu SMP Fri Mar 22 16:47:16 UTC 2024 s390x sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-s390x-012.buildd +==============================================================================+ | pbbam 2.4.0+dfsg-1build1 (s390x) Wed, 10 Apr 2024 22:59:02 +0000 | +==============================================================================+ Package: pbbam Version: 2.4.0+dfsg-1build1 Source Version: 2.4.0+dfsg-1build1 Distribution: noble-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27789654/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/pbbam-YCU5FI/resolver-Tc3iX6' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pbbam_2.4.0+dfsg-1build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/pbbam-YCU5FI/pbbam-2.4.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/pbbam-YCU5FI' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>> 2.2.0), python3-cram, libgtest-dev, samtools, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>> 2.2.0), python3-cram, libgtest-dev, samtools, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [470 B] Get:5 copy:/<>/apt_archive ./ Packages [542 B] Fetched 1969 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data d-shlibs debhelper debugedit dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libarchive13t64 libboost-dev libboost1.83-dev libbrotli1 libcurl3t64-gnutls libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libelf1t64 libexpat1 libfile-stripnondeterminism-perl libgtest-dev libhts-dev libhts3t64 libhtscodecs2 libicu74 libjsoncpp25 libldap2 liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libpbcopper-dev libpbcopper2.3.0 libpipeline1 libpkgconf3 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 libuv1t64 libxml2 m4 man-db media-types meson netbase ninja-build pkg-config pkgconf pkgconf-bin po-debconf python3 python3-cram python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-minimal samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-serialization1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev 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 python-setuptools-doc python3.12-venv python3.12-doc binfmt-support cwltool Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data d-shlibs debhelper debugedit dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libarchive13t64 libboost-dev libboost1.83-dev libbrotli1 libcurl3t64-gnutls libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libelf1t64 libexpat1 libfile-stripnondeterminism-perl libgtest-dev libhts-dev libhts3t64 libhtscodecs2 libicu74 libjsoncpp25 libldap2 liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libpbcopper-dev libpbcopper2.3.0 libpipeline1 libpkgconf3 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 libuv1t64 libxml2 m4 man-db media-types meson netbase ninja-build pkg-config pkgconf pkgconf-bin po-debconf python3 python3-cram python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-minimal samtools sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 67.5 MB of archives. After this operation, 364 MB of additional disk space will be used. 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http://ftpmaster.internal/ubuntu noble/main s390x python3 s390x 3.12.2-0ubuntu2 [24.1 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libelf1t64 s390x 0.190-1.1build4 [69.7 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libicu74 s390x 74.2-1ubuntu3 [10.9 MB] Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libxml2 s390x 2.9.14+dfsg-1.3ubuntu3 [818 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main s390x python3-pkg-resources all 68.1.2-2ubuntu1 [168 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libmagic-mgc s390x 1:5.45-3build1 [305 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libmagic1t64 s390x 1:5.45-3build1 [93.2 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x file s390x 1:5.45-3build1 [22.2 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gettext-base s390x 0.21-14ubuntu2 [39.4 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libuchardet0 s390x 0.0.8-1build1 [76.7 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x groff-base s390x 1.23.0-3build2 [1049 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libncurses6 s390x 6.4+20240113-1ubuntu2 [124 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libnghttp2-14 s390x 1.59.0-1build2 [77.8 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libpipeline1 s390x 1.5.7-2 [25.0 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libpsl5t64 s390x 0.21.2-1.1build1 [57.7 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libuv1t64 s390x 1.48.0-1.1build1 [101 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main s390x man-db s390x 2.12.0-4build2 [1253 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main s390x m4 s390x 1.4.19-4build1 [256 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main s390x autoconf all 2.71-3 [339 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x autotools-dev all 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noble/main s390x libsub-override-perl all 0.10-1 [10.0 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main s390x libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main s390x dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libdw1t64 s390x 0.190-1.1build4 [286 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main s390x debugedit s390x 1:5.0-5build2 [50.5 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main s390x dwz s390x 0.15-1build6 [122 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gettext s390x 0.21-14ubuntu2 [915 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main s390x debhelper all 13.14.1ubuntu5 [869 kB] Get:60 http://ftpmaster.internal/ubuntu noble/universe s390x googletest all 1.14.0-1 [521 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main s390x libboost1.83-dev s390x 1.83.0-2.1ubuntu3 [10.7 MB] Get:62 http://ftpmaster.internal/ubuntu noble/main s390x libboost-dev s390x 1.83.0.1ubuntu2 [4310 B] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcurl3t64-gnutls s390x 8.5.0-2ubuntu10 [356 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcurl4-gnutls-dev s390x 8.5.0-2ubuntu10 [466 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdeflate0 s390x 1.19-1build1 [46.1 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdeflate-dev s390x 1.19-1build1 [52.4 kB] Get:67 http://ftpmaster.internal/ubuntu noble/universe s390x libgtest-dev s390x 1.14.0-1 [266 kB] Get:68 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] Get:69 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3t64 s390x 1.19+ds-1.1build3 [474 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main s390x liblzma-dev s390x 5.6.1+really5.4.5-1 [184 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g-dev s390x 1:1.3.dfsg-3.1ubuntu2 [904 kB] Get:72 http://ftpmaster.internal/ubuntu noble/universe s390x libhts-dev s390x 1.19+ds-1.1build3 [5962 kB] Get:73 http://ftpmaster.internal/ubuntu noble/universe s390x libpbcopper2.3.0 s390x 2.3.0+dfsg-2 [608 kB] Get:74 http://ftpmaster.internal/ubuntu noble/universe s390x libpbcopper-dev s390x 2.3.0+dfsg-2 [1188 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpkgconf3 s390x 1.8.1-2build1 [31.4 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main s390x libssl-dev s390x 3.0.13-0ubuntu3 [2131 kB] Get:77 http://ftpmaster.internal/ubuntu noble/universe s390x ninja-build s390x 1.11.1-2 [135 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main s390x python3-setuptools all 68.1.2-2ubuntu1 [396 kB] Get:79 http://ftpmaster.internal/ubuntu noble/universe s390x meson all 1.3.2-1ubuntu1 [604 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main s390x pkgconf-bin s390x 1.8.1-2build1 [21.3 kB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main s390x pkgconf s390x 1.8.1-2build1 [16.8 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main s390x pkg-config s390x 1.8.1-2build1 [7264 B] Get:83 http://ftpmaster.internal/ubuntu noble/universe s390x python3-cram all 0.7-5 [17.9 kB] Get:84 http://ftpmaster.internal/ubuntu noble/universe s390x samtools s390x 1.19.2-1build2 [612 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main s390x dh-exec s390x 0.29build1 [25.9 kB] Preconfiguring packages ... Fetched 67.5 MB in 3s (26.0 MB/s) Selecting previously unselected package libpython3.12-minimal:s390x. (Reading database ... 15545 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.2-5ubuntu3_s390x.deb ... Unpacking libpython3.12-minimal:s390x (3.12.2-5ubuntu3) ... Selecting previously unselected package libexpat1:s390x. Preparing to unpack .../libexpat1_2.6.1-2build1_s390x.deb ... Unpacking libexpat1:s390x (2.6.1-2build1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.2-5ubuntu3_s390x.deb ... Unpacking python3.12-minimal (3.12.2-5ubuntu3) ... Setting up libpython3.12-minimal:s390x (3.12.2-5ubuntu3) ... Setting up libexpat1:s390x (2.6.1-2build1) ... Setting up python3.12-minimal (3.12.2-5ubuntu3) ... Selecting previously unselected package python3-minimal. (Reading database ... 15863 files and directories currently installed.) 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Processing triggers for libc-bin (2.39-0ubuntu8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-176-generic #196-Ubuntu SMP Fri Mar 22 16:47:16 UTC 2024 s390x (s390x) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu3 gcc-13_13.2.0-23ubuntu3 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 linux-libc-dev_6.8.0-22.22 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13ubuntu9 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-s390x-linux-gnu_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu5 bsdutils_1:2.39.3-9ubuntu5 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 cmake_3.28.3-1build6 cmake-data_3.28.3-1build6 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu2 cpp-13_13.2.0-23ubuntu3 cpp-13-s390x-linux-gnu_13.2.0-23ubuntu3 cpp-s390x-linux-gnu_4:13.2.0-7ubuntu2 d-shlibs_0.106 dash_0.5.12-6ubuntu5 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 dh-autoreconf_20 dh-exec_0.29build1 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 dpkg_1.22.6ubuntu6 dpkg-dev_1.22.6ubuntu6 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.33-1build1 file_1:5.45-3build1 findutils_4.9.0-5build1 g++_4:13.2.0-7ubuntu2 g++-13_13.2.0-23ubuntu3 g++-13-s390x-linux-gnu_13.2.0-23ubuntu3 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libboost-dev_1.83.0.1ubuntu2 libboost1.83-dev_1.83.0-2.1ubuntu3 libbrotli1_1.1.0-2build2 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-0ubuntu8 libc-dev-bin_2.39-0ubuntu8 libc6_2.39-0ubuntu8 libc6-dev_2.39-0ubuntu8 libcap-ng0_0.8.4-2build2 libcap2_1:2.66-5ubuntu2 libcc1-0_14-20240330-1ubuntu2 libcom-err2_1.47.0-2.4~exp1ubuntu4 libcrypt-dev_1:4.4.36-4build1 libcrypt1_1:4.4.36-4build1 libcryptsetup12_2:2.7.0-1ubuntu4 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libcurl3t64-gnutls_8.5.0-2ubuntu10 libcurl4-gnutls-dev_8.5.0-2ubuntu10 libcurl4t64_8.5.0-2ubuntu10 libdb5.3t64_5.3.28+dfsg2-6build1 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdeflate-dev_1.19-1build1 libdeflate0_1.19-1build1 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdpkg-perl_1.22.6ubuntu6 libdw1t64_0.190-1.1build4 libelf1t64_0.190-1.1build4 libexpat1_2.6.1-2build1 libext2fs2t64_1.47.0-2.4~exp1ubuntu4 libfakeroot_1.33-1build1 libfdisk1_2.39.3-9ubuntu5 libffi8_3.4.6-1build1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-23ubuntu3 libgcc-s1_14-20240330-1ubuntu2 libgcrypt20_1.10.3-2build1 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30t64_3.8.3-1.1ubuntu3 libgomp1_14-20240330-1ubuntu2 libgpg-error-l10n_1.47-3build2 libgpg-error0_1.47-3build2 libgpm2_1.20.7-11 libgssapi-krb5-2_1.20.1-6ubuntu2 libgtest-dev_1.14.0-1 libhogweed6t64_3.9.1-2.2build1 libhts-dev_1.19+ds-1.1build3 libhts3t64_1.19+ds-1.1build3 libhtscodecs2_1.6.0-1 libicu74_74.2-1ubuntu3 libidn2-0_2.3.7-2build1 libip4tc2_1.8.10-3ubuntu2 libisl23_0.26-3build1 libitm1_14-20240330-1ubuntu2 libjansson4_2.14-2build2 libjson-c5_0.17-1build1 libjsoncpp25_1.9.5-6build1 libk5crypto3_1.20.1-6ubuntu2 libkeyutils1_1.6.3-3build1 libkmod2_31+20240202-2ubuntu6 libkrb5-3_1.20.1-6ubuntu2 libkrb5support0_1.20.1-6ubuntu2 libldap2_2.6.7+dfsg-1~exp1ubuntu8 liblocale-gettext-perl_1.07-6ubuntu5 liblockfile-bin_1.17-1build3 liblockfile1_1.17-1build3 liblz4-1_1.9.4-1build1 liblzma-dev_5.6.1+really5.4.5-1 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3build1 libmagic1t64_1:5.45-3build1 libmd0_1.1.0-2build1 libmount1_2.39.3-9ubuntu5 libmpc3_1.3.1-1build1 libmpfr6_4.2.1-1build1 libncurses6_6.4+20240113-1ubuntu2 libncursesw6_6.4+20240113-1ubuntu2 libnettle8t64_3.9.1-2.2build1 libnghttp2-14_1.59.0-1build2 libnpth0t64_1.6-3.1build1 libnsl-dev_1.3.0-3build3 libnsl2_1.3.0-3build3 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-5build1 libp11-kit0_0.25.3-4ubuntu2 libpam-modules_1.5.3-5ubuntu4 libpam-modules-bin_1.5.3-5ubuntu4 libpam-runtime_1.5.3-5ubuntu4 libpam0g_1.5.3-5ubuntu4 libpbcopper-dev_2.3.0+dfsg-2 libpbcopper2.3.0_2.3.0+dfsg-2 libpcre2-8-0_10.42-4ubuntu2 libperl5.36_5.36.0-9ubuntu1 libperl5.38t64_5.38.2-3.2build2 libpipeline1_1.5.7-2 libpkgconf3_1.8.1-2build1 libpng16-16t64_1.6.43-5build1 libproc2-0_2:4.0.4-4ubuntu3 libpsl5t64_0.21.2-1.1build1 libpython3-stdlib_3.12.2-0ubuntu2 libpython3.12-minimal_3.12.2-5ubuntu3 libpython3.12-stdlib_3.12.2-5ubuntu3 libreadline8t64_8.2-4build1 librhash0_1.4.3-3build1 librtmp1_2.4+20151223.gitfa8646d.1-2build7 libsasl2-2_2.1.28+dfsg1-5ubuntu3 libsasl2-modules-db_2.1.28+dfsg1-5ubuntu3 libseccomp2_2.5.5-1ubuntu3 libselinux1_3.5-2ubuntu2 libsemanage-common_3.5-1build5 libsemanage2_3.5-1build5 libsepol2_3.5-2build1 libsframe1_2.42-4ubuntu2 libsmartcols1_2.39.3-9ubuntu5 libsqlite3-0_3.45.1-1ubuntu2 libss2_1.47.0-2.4~exp1ubuntu4 libssh-4_0.10.6-2build2 libssl-dev_3.0.13-0ubuntu3 libssl3t64_3.0.13-0ubuntu3 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 libsub-override-perl_0.10-1 libsystemd-shared_255.4-1ubuntu7 libsystemd0_255.4-1ubuntu7 libtasn1-6_4.19.0-3build1 libtext-charwidth-perl_0.04-11build3 libtext-iconv-perl_1.7-8build3 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20240113-1ubuntu2 libtirpc-common_1.3.4+ds-1.1build1 libtirpc-dev_1.3.4+ds-1.1build1 libtirpc3t64_1.3.4+ds-1.1build1 libtool_2.4.7-7build1 libubsan1_14-20240330-1ubuntu2 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policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-4ubuntu3 psmisc_23.7-1build1 python3_3.12.2-0ubuntu2 python3-cram_0.7-5 python3-minimal_3.12.2-0ubuntu2 python3-pkg-resources_68.1.2-2ubuntu1 python3-setuptools_68.1.2-2ubuntu1 python3.12_3.12.2-5ubuntu3 python3.12-minimal_3.12.2-5ubuntu3 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu7 samtools_1.19.2-1build2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2build1 sensible-utils_0.0.22 systemd_255.4-1ubuntu7 systemd-dev_255.4-1ubuntu7 systemd-sysv_255.4-1ubuntu7 sysvinit-utils_3.08-6ubuntu3 tar_1.35+dfsg-3build1 tzdata_2024a-2ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-9ubuntu5 uuid-runtime_2.39.3-9ubuntu5 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pbbam Binary: pbbamtools, libpbbam2.4.0, libpbbam-dev Architecture: any Version: 2.4.0+dfsg-1build1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://pbbam.readthedocs.org/en/latest/index.html Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/pbbam Vcs-Git: https://salsa.debian.org/med-team/pbbam.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 13), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>> 2.2.0), python3-cram, libgtest-dev , samtools Package-List: libpbbam-dev deb libdevel optional arch=any libpbbam2.4.0 deb libs optional arch=any pbbamtools deb science optional arch=any Checksums-Sha1: c18a5477be1369d03c515bf59103d3233785d583 7826464 pbbam_2.4.0+dfsg.orig.tar.xz e39e2fc09c574d8a6b2d9f065603d985020c7e80 9060 pbbam_2.4.0+dfsg-1build1.debian.tar.xz Checksums-Sha256: e991e5f5470976f2ad0cca93658a273989738ca48cce4f024fd074cc1e8cbe2b 7826464 pbbam_2.4.0+dfsg.orig.tar.xz 8696ed2b075f62fb6adb42772ff6e394a8507b9b1e6ef02ec52b94632d1a0919 9060 pbbam_2.4.0+dfsg-1build1.debian.tar.xz Files: 315039ff474e762e609442ca84988512 7826464 pbbam_2.4.0+dfsg.orig.tar.xz 6cf4657153b01d2a03ff5ca19099f544 9060 pbbam_2.4.0+dfsg-1build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEETQvhLw5HdtiqzpaW5mx3Wuv+bH0FAmXSStIACgkQ5mx3Wuv+ bH2DBxAAhdGLtNJeJOB6tsT/y5J43qkqs7uEGsa8+oJBC3sIS9gFLIi7Ku3wPPj0 gqYAqp9Q2bYB59K3laiQiI0m9cKQkIFvrwGSmbIYydAkiLB6DbK+823e2U4lMgN3 uF79/GfPAhB8yNJK/P/ZgVDlWF5CJcZeUUGfN7TPmJFYYwZwYWyvQWoYGR/KHcK1 VfIez9fguznr84pV00QaJiL4UKNh5oCi2As1GS2RAK52raJcY5wrEFk65hWsm/tB X+0DGvRHoHLHBzFh9kywEImtZTf+v9jGDbRTQlblxXGMnjZxjGXFskLdZBpP6j/s VgXduc6ws1bx7idQg67A5+f8QGlLCQ/8V9eXGHnSF+4dX0F7JbFvHHqhRvanY0xD A3mVqgzABaY5yXsjguR2Yfe+7cXDsMAwBWvoh2YYRNMcZACCUyUpbUfpIlY5Vawt DXIG2OHTeyDkmxmS9I7/7qgJL+Ucpc19/wA2h5fpfjm46ZNj4nUnFPN4V/goa9Qa 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User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27789654 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27789654 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27789654 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 2.4.0+dfsg-1build1 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x debian/rules clean dh clean --buildsystem=meson debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /<>/gendata make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules binary-arch dh binary-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 && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/s390x-linux-gnu -Dpython.bytecompile=-1 The Meson build system Version: 1.3.2 Source dir: /<> Build dir: /<>/obj-s390x-linux-gnu Build type: native build Project name: PacBioBAM Project version: 2.4.0 C compiler for the host machine: cc (gcc 13.2.0 "cc (Ubuntu 13.2.0-23ubuntu3) 13.2.0") C linker for the host machine: cc ld.bfd 2.42 C++ compiler for the host machine: c++ (gcc 13.2.0 "c++ (Ubuntu 13.2.0-23ubuntu3) 13.2.0") C++ linker for the host machine: c++ ld.bfd 2.42 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 Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1 Run-time dependency Boost found: YES 1.83.0 (/usr/include) Run-time dependency zlib found: YES 1.3 Run-time dependency htslib found: YES 1.19 Run-time dependency pbcopper found: YES 2.3.0 Configuring PbbamVersion.cpp using configuration Configuring LibraryVersion.h using configuration Program tools/check-formatting found: YES (/<>/tools/check-formatting) Program python3 found: YES (/usr/bin/python3) Program cram3 found: YES (/usr/bin/cram3) Run-time dependency GTest found: YES 1.14.0 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 Configuring CcsKineticsBystrandifyVersion.h using configuration Build targets in project: 12 PacBioBAM 2.4.0 User defined options buildtype : plain libdir : lib/s390x-linux-gnu localstatedir : /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload python.bytecompile: -1 Found ninja-1.11.1 at /usr/bin/ninja dh_auto_build -a -O--buildsystem=meson cd obj-s390x-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/226] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 2.4.0 /<>/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [2/226] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 2.4.0 /<>/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [3/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o -MF src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o.d -o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o -c src/PbbamGitHash.cpp [4/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection 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src/libpbbam.so.2.4.0.p/Config.cpp.o.d -o src/libpbbam.so.2.4.0.p/Config.cpp.o -c ../src/Config.cpp [25/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/CollectionMetadata.cpp.o -MF src/libpbbam.so.2.4.0.p/CollectionMetadata.cpp.o.d -o src/libpbbam.so.2.4.0.p/CollectionMetadata.cpp.o -c ../src/CollectionMetadata.cpp [26/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/CompositeFastaReader.cpp.o -MF src/libpbbam.so.2.4.0.p/CompositeFastaReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/CompositeFastaReader.cpp.o -c ../src/CompositeFastaReader.cpp [27/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/DataSetElement.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetElement.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetElement.cpp.o -c ../src/DataSetElement.cpp [28/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/CompositeBamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/CompositeBamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/CompositeBamReader.cpp.o -c ../src/CompositeBamReader.cpp [29/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/DataSetIO.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetIO.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetIO.cpp.o -c ../src/DataSetIO.cpp [30/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/DataSetBaseTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetBaseTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetBaseTypes.cpp.o -c ../src/DataSetBaseTypes.cpp [31/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/DataSet.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSet.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSet.cpp.o -c ../src/DataSet.cpp [32/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ErrnoReason.cpp.o -MF src/libpbbam.so.2.4.0.p/ErrnoReason.cpp.o.d -o src/libpbbam.so.2.4.0.p/ErrnoReason.cpp.o -c ../src/ErrnoReason.cpp [33/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o -c ../src/DataSetXsd.cpp [34/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o -MF src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o.d -o src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o -c ../src/FaiIndex.cpp [35/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o -MF src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o.d -o src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o -c ../src/FaiZmwChunker.cpp [36/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/EntireFileQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/EntireFileQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/EntireFileQuery.cpp.o -c ../src/EntireFileQuery.cpp [37/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp In file included from /usr/include/c++/13/map:62, from ../include/pbbam/ProgramInfo.h:6, from ../include/pbbam/BamHeader.h:6, from ../include/pbbam/BamFile.h:6, from ../include/pbbam/DataSetTypes.h:6, from ../src/DataSetTypes.cpp:3: In constructor ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Reuse_or_alloc_node::_Reuse_or_alloc_node(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_tree.h:1800:25, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:446:11: warning: array subscript 25 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 446 | : _M_root(__t._M_root()), _M_nodes(__t._M_rightmost()), _M_t(__t) | ^~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 200 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In constructor ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Reuse_or_alloc_node::_Reuse_or_alloc_node(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_tree.h:1800:25, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:446:35: warning: array subscript 27 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 446 | : _M_root(__t._M_root()), _M_nodes(__t._M_rightmost()), _M_t(__t) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 216 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘void std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_tree.h:1801:20, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:208:27: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 208 | _M_header._M_parent = 0; | ~~~~~~~~~~~~~~~~~~~~^~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘void std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_tree.h:1801:20, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:209:27: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 209 | _M_header._M_left = &_M_header; | ^~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘void std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_tree.h:1801:20, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:209:25: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 209 | _M_header._M_left = &_M_header; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘void std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_tree.h:1801:20, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:210:26: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 210 | _M_header._M_right = &_M_header; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘void std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_tree.h:1801:20, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:211:21: warning: array subscript 4 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 211 | _M_node_count = 0; | ~~~~~~~~~~~~~~^~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree_node<_Val>* std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_copy(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&, _NodeGen&) [with bool _MoveValues = false; _NodeGen = std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node; _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_tree.h:1804:38, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:893:25: warning: array subscript 26 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 893 | _M_leftmost() = _S_minimum(__root); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 208 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree_node<_Val>* std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_copy(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&, _NodeGen&) [with bool _MoveValues = false; _NodeGen = std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node; _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_tree.h:1804:38, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:894:26: warning: array subscript 27 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 894 | _M_rightmost() = _S_maximum(__root); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 216 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree_node<_Val>* std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_copy(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&, _NodeGen&) [with bool _MoveValues = false; _NodeGen = std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node; _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_tree.h:1804:38, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:895:33: warning: array subscript 3 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 895 | _M_impl._M_node_count = __x._M_impl._M_node_count; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 184 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::operator=(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’, inlined from ‘std::map<_Key, _Tp, _Compare, _Alloc>& std::map<_Key, _Tp, _Compare, _Alloc>::operator=(const std::map<_Key, _Tp, _Compare, _Alloc>&) [with _Key = PacBio::BAM::XsdType; _Tp = PacBio::BAM::NamespaceInfo; _Compare = std::less; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:1804:23: warning: array subscript 25 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 1804 | _M_root() = _M_copy<__as_lvalue>(__x, __roan); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 200 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In file included from ../include/pbbam/internal/DataSetElement.h:6, from ../include/pbbam/internal/DataSetBaseTypes.h:6, from ../include/pbbam/CollectionMetadata.h:6, from ../include/pbbam/DataSetTypes.h:7: In member function ‘PacBio::BAM::NamespaceRegistry& PacBio::BAM::NamespaceRegistry::operator=(const PacBio::BAM::NamespaceRegistry&)’, inlined from ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: ../include/pbbam/DataSetXsd.h:65:20: warning: array subscript 3 is outside array bounds of ‘void [184]’ [-Warray-bounds=] 65 | class PBBAM_EXPORT NamespaceRegistry | ^~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase* PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 184 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ [38/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o -c ../src/FastaSequence.cpp [39/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FastaReader.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastaReader.cpp.o -c ../src/FastaReader.cpp [40/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FastaCache.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaCache.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastaCache.cpp.o -c ../src/FastaCache.cpp [41/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FastqSequence.cpp.o -MF src/libpbbam.so.2.4.0.p/FastqSequence.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastqSequence.cpp.o -c ../src/FastqSequence.cpp [42/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FastaWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaWriter.cpp.o.d -o 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-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/MemoryUtils.cpp.o -MF src/libpbbam.so.2.4.0.p/MemoryUtils.cpp.o.d -o src/libpbbam.so.2.4.0.p/MemoryUtils.cpp.o -c ../src/MemoryUtils.cpp [64/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o -c ../src/PbiBuilder.cpp [65/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiFile.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFile.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFile.cpp.o -c ../src/PbiFile.cpp [66/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o -c ../src/PbiBuilderBase.cpp [67/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o -c ../src/PbiFilterQuery.cpp In file included from /usr/include/c++/13/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/BamFile.h:6, from ../include/pbbam/DataSet.h:6, from ../include/pbbam/PbiFilter.h:6, from ../include/pbbam/PbiFilterQuery.h:6, from ../src/PbiFilterQuery.cpp:3: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:88:18, inlined from ‘constexpr void std::_Destroy(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:149:22, inlined from ‘static constexpr void std::_Destroy_aux< >::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; bool = false]’ at /usr/include/c++/13/bits/stl_construct.h:163:19, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_construct.h:196:11, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/alloc_traits.h:948:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, inlined from ‘PacBio::BAM::PbiFilter::PbiFilter(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:199:55, inlined from ‘PacBio::BAM::PbiFilterCompositeBamReader& PacBio::BAM::PbiFilterCompositeBamReader::Filter(const PacBio::BAM::PbiFilter&) [with OrderByType = PacBio::BAM::Compare::None]’ at ../include/pbbam/internal/CompositeBamReader.inl:147:17: /usr/include/c++/13/bits/unique_ptr.h:403:19: warning: potential null pointer dereference [-Wnull-dereference] 403 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ [68/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o -c ../src/PbiIndexedBamReader.cpp In file included from /usr/include/c++/13/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/BamFile.h:6, from ../include/pbbam/PbiIndexedBamReader.h:6, from ../src/PbiIndexedBamReader.cpp:3: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:88:18, inlined from ‘constexpr void std::_Destroy(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:149:22, inlined from ‘static constexpr void std::_Destroy_aux< >::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; bool = false]’ at /usr/include/c++/13/bits/stl_construct.h:163:19, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_construct.h:196:11, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/alloc_traits.h:948:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, inlined from ‘PacBio::BAM::PbiFilter& PacBio::BAM::PbiFilter::operator=(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:203:28, inlined from ‘void PacBio::BAM::PbiIndexedBamReader::PbiIndexedBamReaderPrivate::Filter(PacBio::BAM::PbiFilter)’ at ../src/PbiIndexedBamReader.cpp:36:35: /usr/include/c++/13/bits/unique_ptr.h:403:19: warning: potential null pointer dereference [-Wnull-dereference] 403 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ [69/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o -c ../src/PbiFilterTypes.cpp [70/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o -c ../src/PbiIndexIO.cpp [71/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o -c ../src/PbiFilter.cpp [72/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o -c ../src/ProgramInfo.cpp [73/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/RecordType.cpp.o -MF src/libpbbam.so.2.4.0.p/RecordType.cpp.o.d -o src/libpbbam.so.2.4.0.p/RecordType.cpp.o -c ../src/RecordType.cpp [74/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o -MF src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o.d -o src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o -c ../src/RunMetadata.cpp [75/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o -c ../src/PbiRawData.cpp [76/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o -MF src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o.d -o src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o -c ../src/RunMetadataParser.cpp [77/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/SamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/SamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamReader.cpp.o -c ../src/SamReader.cpp [78/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o -MF src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o -c ../src/SamTagCodec.cpp ../src/SamTagCodec.cpp: In static member function ‘static PacBio::BAM::TagCollection PacBio::BAM::SamTagCodec::Decode(const std::string&)’: ../src/SamTagCodec.cpp:79:63: warning: ignoring return value of ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::const_reference std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator[](size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; const_reference = const char&; size_type = long unsigned int]’, declared with attribute ‘nodiscard’ [-Wunused-result] 79 | tags[name] = Tag{static_cast(remainder[0], TagModifier::ASCII_CHAR)}; | ^ In file included from /usr/include/c++/13/string:54, from ../include/pbbam/Tag.h:7, from ../include/pbbam/TagCollection.h:6, from ../include/pbbam/SamTagCodec.h:6, from ../src/SamTagCodec.cpp:3: /usr/include/c++/13/bits/basic_string.h:1236:7: note: declared here 1236 | operator[] (size_type __pos) const _GLIBCXX_NOEXCEPT | ^~~~~~~~ [79/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o -MF src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o.d -o src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o -c ../src/StringUtilities.cpp [80/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o -c ../src/SequenceInfo.cpp [81/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o -c ../src/ReadGroupInfo.cpp [82/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/SamWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/SamWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamWriter.cpp.o -c ../src/SamWriter.cpp [83/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/TagCollection.cpp.o -MF src/libpbbam.so.2.4.0.p/TagCollection.cpp.o.d -o src/libpbbam.so.2.4.0.p/TagCollection.cpp.o -c ../src/TagCollection.cpp [84/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o -MF src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o.d -o src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o -c ../src/TimeUtils.cpp [85/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o -c ../src/TextFileWriter.cpp [86/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o -MF src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o.d -o src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o -c ../src/ValidationErrors.cpp [87/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ValidationException.cpp.o -MF src/libpbbam.so.2.4.0.p/ValidationException.cpp.o.d -o src/libpbbam.so.2.4.0.p/ValidationException.cpp.o -c ../src/ValidationException.cpp [88/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o -MF src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o -c ../src/TextFileReader.cpp [89/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/Version.cpp.o -MF src/libpbbam.so.2.4.0.p/Version.cpp.o.d -o src/libpbbam.so.2.4.0.p/Version.cpp.o -c ../src/Version.cpp [90/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/Tag.cpp.o -MF src/libpbbam.so.2.4.0.p/Tag.cpp.o.d -o src/libpbbam.so.2.4.0.p/Tag.cpp.o -c ../src/Tag.cpp [91/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/Validator.cpp.o -MF src/libpbbam.so.2.4.0.p/Validator.cpp.o.d -o src/libpbbam.so.2.4.0.p/Validator.cpp.o -c ../src/Validator.cpp [92/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o -c ../src/VirtualRegion.cpp [93/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o -c ../src/VirtualRegionTypeMap.cpp [94/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o -c ../src/VirtualZmwBamRecord.cpp [95/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o -c ../src/VirtualZmwCompositeReader.cpp [96/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o -c ../src/VirtualZmwReader.cpp [97/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o -c ../src/XmlWriter.cpp [98/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/XmlReader.cpp.o -MF src/libpbbam.so.2.4.0.p/XmlReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/XmlReader.cpp.o -c ../src/XmlReader.cpp [99/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o -c ../src/ZmwChunkedFastaReader.cpp ../src/ZmwChunkedFastaReader.cpp: In constructor ‘PacBio::BAM::ZmwChunkedFastaReader::ZmwChunkedFastaReaderPrivate::ZmwChunkedFastaReaderPrivate(const std::string&, size_t)’: ../src/ZmwChunkedFastaReader.cpp:78:48: warning: redundant move in initialization [-Wredundant-move] 78 | : reader_{MakeFastaReaderImpl(std::move(fn), numChunks)} | ~~~~~~~~~^~~~ ../src/ZmwChunkedFastaReader.cpp:78:48: note: remove ‘std::move’ call [100/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o -c ../src/ZmwChunkedFastxBgzfReader.cpp [101/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o -c ../src/ZmwChunkedFastxReaderImpl.cpp [102/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o -c ../src/WhitelistedZmwReadStitcher.cpp [103/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o -c ../src/ZmwChunkedFastxTextReader.cpp [104/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o -c ../src/ZmwChunkedFastqReader.cpp ../src/ZmwChunkedFastqReader.cpp: In constructor ‘PacBio::BAM::ZmwChunkedFastqReader::ZmwChunkedFastqReaderPrivate::ZmwChunkedFastqReaderPrivate(const std::string&, size_t)’: ../src/ZmwChunkedFastqReader.cpp:78:48: warning: redundant move in initialization [-Wredundant-move] 78 | : reader_{MakeFastqReaderImpl(std::move(fn), numChunks)} | ~~~~~~~~~^~~~ ../src/ZmwChunkedFastqReader.cpp:78:48: note: remove ‘std::move’ call [105/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o -c ../src/ZmwTypeMap.cpp [106/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o -MF src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o -c ../src/bed/BedReader.cpp [107/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o -c ../src/ZmwReadStitcher.cpp [108/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o -c ../src/ZmwQuery.cpp In file included from /usr/include/c++/13/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/BamFile.h:6, from ../include/pbbam/internal/QueryBase.h:6, from ../include/pbbam/ZmwQuery.h:6, from ../src/ZmwQuery.cpp:3: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:88:18, inlined from ‘constexpr void std::_Destroy(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:149:22, inlined from ‘static constexpr void std::_Destroy_aux< >::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; bool = false]’ at /usr/include/c++/13/bits/stl_construct.h:163:19, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_construct.h:196:11, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/alloc_traits.h:948:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, inlined from ‘PacBio::BAM::PbiFilter::PbiFilter(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:199:55, inlined from ‘PacBio::BAM::PbiFilterCompositeBamReader& PacBio::BAM::PbiFilterCompositeBamReader::Filter(const PacBio::BAM::PbiFilter&) [with OrderByType = PacBio::BAM::Compare::Zmw]’ at ../include/pbbam/internal/CompositeBamReader.inl:147:17: /usr/include/c++/13/bits/unique_ptr.h:403:19: warning: potential null pointer dereference [-Wnull-dereference] 403 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ [109/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o -c ../src/ZmwGroupQuery.cpp [110/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o -c ../src/bed/BedWriter.cpp [111/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o -c ../src/vcf/VcfFile.cpp [112/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o -c ../src/csv/CsvWriter.cpp [113/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o -c ../src/vcf/VcfHeaderTypes.cpp [114/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o -c ../src/vcf/VcfHeader.cpp [115/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o -c ../src/vcf/VcfFormat.cpp [116/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o -MF src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o -c ../src/csv/CsvReader.cpp [117/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o -c ../src/vcf/VcfReader.cpp [118/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o -c ../src/vcf/VcfQuery.cpp [119/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o -c ../src/vcf/VcfWriter.cpp [120/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -MF src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o.d -o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -c src/PbbamVersion.cpp [121/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o -c ../src/vcf/VcfVariant.cpp ../src/vcf/VcfVariant.cpp: In member function ‘PacBio::VCF::VcfVariant& PacBio::VCF::VcfVariant::RemoveInfoField(const std::string&)’: ../src/vcf/VcfVariant.cpp:250:35: warning: redundant move in initialization [-Wredundant-move] 250 | AddInfoField(std::move(field)); | ~~~~~~~~~^~~~~~~ ../src/vcf/VcfVariant.cpp:250:35: note: remove ‘std::move’ call [122/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o -c ../src/vcf/VcfSort.cpp [123/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamReader.cpp.o -MF tests/pbbam_test.p/src_test_BamReader.cpp.o.d -o tests/pbbam_test.p/src_test_BamReader.cpp.o -c ../tests/src/test_BamReader.cpp [124/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection 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-Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o -MF src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o.d -o src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o -c ../src/pugixml/pugixml.cpp [126/226] c++ -o src/libpbbam.so.2.4.0 src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o src/libpbbam.so.2.4.0.p/AlignmentPrinter.cpp.o src/libpbbam.so.2.4.0.p/BaiIndexCache.cpp.o src/libpbbam.so.2.4.0.p/BaiIndexedBamReader.cpp.o src/libpbbam.so.2.4.0.p/BamFile.cpp.o src/libpbbam.so.2.4.0.p/BamFileMerger.cpp.o src/libpbbam.so.2.4.0.p/BamHeader.cpp.o src/libpbbam.so.2.4.0.p/BamReader.cpp.o src/libpbbam.so.2.4.0.p/BamRecord.cpp.o src/libpbbam.so.2.4.0.p/BamRecordImpl.cpp.o src/libpbbam.so.2.4.0.p/BamRecordTags.cpp.o src/libpbbam.so.2.4.0.p/BamRecordView.cpp.o src/libpbbam.so.2.4.0.p/BamTagCodec.cpp.o src/libpbbam.so.2.4.0.p/BamWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipFastaWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipFastqWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipWriter.cpp.o src/libpbbam.so.2.4.0.p/ChemistryTable.cpp.o src/libpbbam.so.2.4.0.p/CollectionMetadata.cpp.o src/libpbbam.so.2.4.0.p/Compare.cpp.o src/libpbbam.so.2.4.0.p/CompositeBamReader.cpp.o src/libpbbam.so.2.4.0.p/CompositeFastaReader.cpp.o src/libpbbam.so.2.4.0.p/Config.cpp.o src/libpbbam.so.2.4.0.p/DataSet.cpp.o src/libpbbam.so.2.4.0.p/DataSetBaseTypes.cpp.o src/libpbbam.so.2.4.0.p/DataSetElement.cpp.o src/libpbbam.so.2.4.0.p/DataSetIO.cpp.o src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o src/libpbbam.so.2.4.0.p/EntireFileQuery.cpp.o src/libpbbam.so.2.4.0.p/ErrnoReason.cpp.o src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o src/libpbbam.so.2.4.0.p/FastaCache.cpp.o src/libpbbam.so.2.4.0.p/FastaReader.cpp.o src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o src/libpbbam.so.2.4.0.p/FastaSequenceQuery.cpp.o src/libpbbam.so.2.4.0.p/FastaWriter.cpp.o src/libpbbam.so.2.4.0.p/FastqReader.cpp.o src/libpbbam.so.2.4.0.p/FastqSequence.cpp.o src/libpbbam.so.2.4.0.p/FastqWriter.cpp.o src/libpbbam.so.2.4.0.p/FileProducer.cpp.o src/libpbbam.so.2.4.0.p/FileUtils.cpp.o src/libpbbam.so.2.4.0.p/FofnReader.cpp.o src/libpbbam.so.2.4.0.p/FormatUtils.cpp.o src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.2.4.0.p/IFastaWriter.cpp.o src/libpbbam.so.2.4.0.p/IFastqWriter.cpp.o src/libpbbam.so.2.4.0.p/IndexedBamWriter.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastaReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o src/libpbbam.so.2.4.0.p/IRecordWriter.cpp.o src/libpbbam.so.2.4.0.p/KSeqReader.cpp.o src/libpbbam.so.2.4.0.p/LibraryInfo.cpp.o src/libpbbam.so.2.4.0.p/MD5.cpp.o src/libpbbam.so.2.4.0.p/MemoryUtils.cpp.o src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o src/libpbbam.so.2.4.0.p/PbiFile.cpp.o src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.2.4.0.p/RecordType.cpp.o src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o src/libpbbam.so.2.4.0.p/SamReader.cpp.o src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o src/libpbbam.so.2.4.0.p/SamWriter.cpp.o src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o src/libpbbam.so.2.4.0.p/Tag.cpp.o src/libpbbam.so.2.4.0.p/TagCollection.cpp.o src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o src/libpbbam.so.2.4.0.p/Validator.cpp.o src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o src/libpbbam.so.2.4.0.p/ValidationException.cpp.o src/libpbbam.so.2.4.0.p/Version.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.2.4.0.p/XmlReader.cpp.o src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.2.4.0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -pthread /usr/lib/s390x-linux-gnu/libz.so /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libpbcopper.so -Wl,--end-group [127/226] /usr/bin/meson --internal symbolextractor /<>/obj-s390x-linux-gnu src/libpbbam.so.2.4.0 src/libpbbam.so.2.4.0 src/libpbbam.so.2.4.0.p/libpbbam.so.2.4.0.symbols [128/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -c ../tests/src/test_BamRecordImplTags.cpp [129/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o -c ../tests/src/test_BamRecordImplCore.cpp ../tests/src/test_BamRecordImplCore.cpp: In member function ‘virtual void BAM_BamRecordImplCore_can_be_move_constructed_Test::TestBody()’: ../tests/src/test_BamRecordImplCore.cpp:425:73: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 425 | BamRecordImpl bam(std::move(BamRecordImplCoreTests::CreateBamImpl())); | ^ ../tests/src/test_BamRecordImplCore.cpp:425:73: note: remove ‘std::move’ call [130/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecord.cpp.o -MF tests/pbbam_test.p/src_test_BamRecord.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecord.cpp.o -c ../tests/src/test_BamRecord.cpp ../tests/src/test_BamRecord.cpp: In member function ‘virtual void BAM_BamRecord_can_be_constructed_from_bamrecordimpl_Test::TestBody()’: ../tests/src/test_BamRecord.cpp:771:29: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 771 | BamRecord bam3(std::move(BamRecordTests::CreateBamImpl())); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/src/test_BamRecord.cpp:771:29: note: remove ‘std::move’ call ../tests/src/test_BamRecord.cpp:797:21: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 797 | bam4 = std::move(BamRecordTests::CreateBamImpl()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/src/test_BamRecord.cpp:797:21: note: remove ‘std::move’ call [131/226] c++ 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-Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o -MF tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o.d -o tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o -c ../tests/src/test_ReadGroupInfo.cpp [171/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o -MF tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o.d -o tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o -c ../tests/src/test_PbiFilterQuery.cpp [172/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_RunMetadata.cpp.o -MF tests/pbbam_test.p/src_test_RunMetadata.cpp.o.d -o tests/pbbam_test.p/src_test_RunMetadata.cpp.o -c ../tests/src/test_RunMetadata.cpp [173/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_SamIO.cpp.o -MF tests/pbbam_test.p/src_test_SamIO.cpp.o.d -o tests/pbbam_test.p/src_test_SamIO.cpp.o -c ../tests/src/test_SamIO.cpp In file included from /usr/include/c++/13/ios:45, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from ../include/pbbam/exception/InvalidSequencingChemistryException.h:7, from ../include/pbbam/ReadGroupInfo.h:6, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/SamReader.h:6, from ../tests/src/test_SamIO.cpp:1: In member function ‘std::basic_streambuf<_CharT, _Traits>::char_type* std::basic_streambuf<_CharT, _Traits>::egptr() const [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘std::basic_streambuf<_CharT, _Traits>::int_type std::basic_streambuf<_CharT, _Traits>::sbumpc() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/13/streambuf:326:49, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/13/bits/streambuf_iterator.h:173:17, inlined from ‘constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::input_iterator_tag) [with _InIterator = std::istreambuf_iterator >; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.tcc:182:6, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(_InputIterator, _InputIterator, const _Alloc&) [with _InputIterator = std::istreambuf_iterator >; = void; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:765:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/streambuf:495:30: warning: potential null pointer dereference [-Wnull-dereference] 495 | egptr() const { return _M_in_end; } | ^~~~~~~~~ In member function ‘std::basic_streambuf<_CharT, _Traits>::char_type* std::basic_streambuf<_CharT, _Traits>::gptr() const [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘std::basic_streambuf<_CharT, _Traits>::int_type std::basic_streambuf<_CharT, _Traits>::sbumpc() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/13/streambuf:326:33, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/13/bits/streambuf_iterator.h:173:17, inlined from ‘constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::input_iterator_tag) [with _InIterator = std::istreambuf_iterator >; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.tcc:182:6, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(_InputIterator, _InputIterator, const _Alloc&) [with _InputIterator = std::istreambuf_iterator >; = void; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:765:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/streambuf:492:30: warning: potential null pointer dereference [-Wnull-dereference] 492 | gptr() const { return _M_in_cur; } | ^~~~~~~~~ In member function ‘std::basic_streambuf<_CharT, _Traits>::char_type* std::basic_streambuf<_CharT, _Traits>::egptr() const [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘std::basic_streambuf<_CharT, _Traits>::int_type std::basic_streambuf<_CharT, _Traits>::sbumpc() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/13/streambuf:326:49, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/13/bits/streambuf_iterator.h:173:17, inlined from ‘constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::input_iterator_tag) [with _InIterator = std::istreambuf_iterator >; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.tcc:209:6, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(_InputIterator, _InputIterator, const _Alloc&) [with _InputIterator = std::istreambuf_iterator >; = void; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:765:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/streambuf:495:30: warning: potential null pointer dereference [-Wnull-dereference] 495 | egptr() const { return _M_in_end; } | ^~~~~~~~~ In member function ‘std::basic_streambuf<_CharT, _Traits>::char_type* std::basic_streambuf<_CharT, _Traits>::gptr() const [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘std::basic_streambuf<_CharT, _Traits>::int_type std::basic_streambuf<_CharT, _Traits>::sbumpc() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/13/streambuf:326:33, inlined from ‘std::istreambuf_iterator<_CharT, _Traits>& std::istreambuf_iterator<_CharT, _Traits>::operator++() [with _CharT = char; _Traits = std::char_traits]’ at /usr/include/c++/13/bits/streambuf_iterator.h:173:17, inlined from ‘constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::input_iterator_tag) [with _InIterator = std::istreambuf_iterator >; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.tcc:209:6, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(_InputIterator, _InputIterator, const _Alloc&) [with _InputIterator = std::istreambuf_iterator >; = void; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/basic_string.h:765:16, inlined from ‘virtual void BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/streambuf:492:30: warning: potential null pointer dereference [-Wnull-dereference] 492 | gptr() const { return _M_in_cur; } | ^~~~~~~~~ [174/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_PbiFilter.cpp.o -MF tests/pbbam_test.p/src_test_PbiFilter.cpp.o.d -o tests/pbbam_test.p/src_test_PbiFilter.cpp.o -c ../tests/src/test_PbiFilter.cpp [175/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_SequenceUtils.cpp.o -MF tests/pbbam_test.p/src_test_SequenceUtils.cpp.o.d -o tests/pbbam_test.p/src_test_SequenceUtils.cpp.o -c ../tests/src/test_SequenceUtils.cpp [176/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_StringUtils.cpp.o -MF tests/pbbam_test.p/src_test_StringUtils.cpp.o.d -o tests/pbbam_test.p/src_test_StringUtils.cpp.o -c ../tests/src/test_StringUtils.cpp [177/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_SegmentReads.cpp.o -MF tests/pbbam_test.p/src_test_SegmentReads.cpp.o.d -o tests/pbbam_test.p/src_test_SegmentReads.cpp.o -c ../tests/src/test_SegmentReads.cpp [178/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_TextFileWriter.cpp.o -MF tests/pbbam_test.p/src_test_TextFileWriter.cpp.o.d -o tests/pbbam_test.p/src_test_TextFileWriter.cpp.o -c ../tests/src/test_TextFileWriter.cpp [179/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_TextFileReader.cpp.o -MF tests/pbbam_test.p/src_test_TextFileReader.cpp.o.d -o tests/pbbam_test.p/src_test_TextFileReader.cpp.o -c ../tests/src/test_TextFileReader.cpp [180/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_TimeUtils.cpp.o -MF tests/pbbam_test.p/src_test_TimeUtils.cpp.o.d -o tests/pbbam_test.p/src_test_TimeUtils.cpp.o -c ../tests/src/test_TimeUtils.cpp [181/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfFile.cpp.o -MF tests/pbbam_test.p/src_test_VcfFile.cpp.o.d -o tests/pbbam_test.p/src_test_VcfFile.cpp.o -c ../tests/src/test_VcfFile.cpp [182/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfHeader.cpp.o -MF tests/pbbam_test.p/src_test_VcfHeader.cpp.o.d -o tests/pbbam_test.p/src_test_VcfHeader.cpp.o -c ../tests/src/test_VcfHeader.cpp [183/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfFormat.cpp.o -MF tests/pbbam_test.p/src_test_VcfFormat.cpp.o.d -o tests/pbbam_test.p/src_test_VcfFormat.cpp.o -c ../tests/src/test_VcfFormat.cpp [184/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_Validator.cpp.o -MF tests/pbbam_test.p/src_test_Validator.cpp.o.d -o tests/pbbam_test.p/src_test_Validator.cpp.o -c ../tests/src/test_Validator.cpp [185/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfReader.cpp.o -MF tests/pbbam_test.p/src_test_VcfReader.cpp.o.d -o tests/pbbam_test.p/src_test_VcfReader.cpp.o -c ../tests/src/test_VcfReader.cpp [186/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_Tags.cpp.o -MF tests/pbbam_test.p/src_test_Tags.cpp.o.d -o tests/pbbam_test.p/src_test_Tags.cpp.o -c ../tests/src/test_Tags.cpp In file included from ../tests/src/test_Tags.cpp:14: In function ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = unsigned int; T2 = unsigned int]’, inlined from ‘static testing::AssertionResult testing::internal::EqHelper::Compare(const char*, const char*, const T1&, const T2&) [with T1 = unsigned int; T2 = unsigned int; typename std::enable_if<((! std::is_integral<_Tp>::value) || (! std::is_pointer<_Dp>::value))>::type* = 0]’ at /usr/include/gtest/gtest.h:1398:64, inlined from ‘virtual void BAM_Tag_can_describe_uint32_tag_Test::TestBody()’ at ../tests/src/test_Tags.cpp:391:5: /usr/include/gtest/gtest.h:1379:3: warning: ‘v2’ may be used uninitialized [-Wmaybe-uninitialized] 1379 | if (lhs == rhs) { | ^~ ../tests/src/test_Tags.cpp: In member function ‘virtual void BAM_Tag_can_describe_uint32_tag_Test::TestBody()’: ../tests/src/test_Tags.cpp:375:14: note: ‘v2’ was declared here 375 | uint32_t v2; | ^~ In function ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = short unsigned int; T2 = short unsigned int]’, inlined from ‘static testing::AssertionResult testing::internal::EqHelper::Compare(const char*, const char*, const T1&, const T2&) [with T1 = short unsigned int; T2 = short unsigned int; typename std::enable_if<((! std::is_integral<_Tp>::value) || (! std::is_pointer<_Dp>::value))>::type* = 0]’ at /usr/include/gtest/gtest.h:1398:64, inlined from ‘virtual void BAM_Tag_can_describe_uint16_tag_Test::TestBody()’ at ../tests/src/test_Tags.cpp:343:5: /usr/include/gtest/gtest.h:1379:3: warning: ‘v2’ may be used uninitialized [-Wmaybe-uninitialized] 1379 | if (lhs == rhs) { | ^~ ../tests/src/test_Tags.cpp: In member function ‘virtual void BAM_Tag_can_describe_uint16_tag_Test::TestBody()’: ../tests/src/test_Tags.cpp:327:14: note: ‘v2’ was declared here 327 | uint16_t v2; | ^~ [187/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfSort.cpp.o -MF tests/pbbam_test.p/src_test_VcfSort.cpp.o.d -o tests/pbbam_test.p/src_test_VcfSort.cpp.o -c ../tests/src/test_VcfSort.cpp [188/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfQuery.cpp.o -MF tests/pbbam_test.p/src_test_VcfQuery.cpp.o.d -o tests/pbbam_test.p/src_test_VcfQuery.cpp.o -c ../tests/src/test_VcfQuery.cpp [189/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfWriter.cpp.o -MF tests/pbbam_test.p/src_test_VcfWriter.cpp.o.d -o tests/pbbam_test.p/src_test_VcfWriter.cpp.o -c ../tests/src/test_VcfWriter.cpp [190/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfVariant.cpp.o -MF tests/pbbam_test.p/src_test_VcfVariant.cpp.o.d -o tests/pbbam_test.p/src_test_VcfVariant.cpp.o -c ../tests/src/test_VcfVariant.cpp [191/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_Version.cpp.o -MF tests/pbbam_test.p/src_test_Version.cpp.o.d -o tests/pbbam_test.p/src_test_Version.cpp.o -c ../tests/src/test_Version.cpp [192/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o -MF tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o -c ../tests/src/test_ZmwChunkedFastxReader.cpp [193/226] /usr/bin/python3 ../tests/scripts/generate_data.py /<>/tests/data /<>/obj-s390x-linux-gnu/tests Generating test data in /<>/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. [194/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o -c ../tests/src/test_WhitelistedZmwReadStitcher.cpp [195/226] c++ -Itests/zero_byte_check/zero_byte_check.p -Itests/zero_byte_check -I../tests/zero_byte_check -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/zero_byte_check/zero_byte_check.p/main.cpp.o -MF tests/zero_byte_check/zero_byte_check.p/main.cpp.o.d -o tests/zero_byte_check/zero_byte_check.p/main.cpp.o -c ../tests/zero_byte_check/main.cpp [196/226] c++ -o tests/zero_byte_check/zero_byte_check tests/zero_byte_check/zero_byte_check.p/main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/<>/obj-s390x-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so /usr/lib/s390x-linux-gnu/libpbcopper.so -Wl,--end-group [197/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -MF tests/pbbam_test.p/src_test_ZmwQuery.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -c ../tests/src/test_ZmwQuery.cpp [198/226] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_main.cpp.o -MF tools/bam2sam.p/bam2sam_src_main.cpp.o.d -o tools/bam2sam.p/bam2sam_src_main.cpp.o -c ../tools/bam2sam/src/main.cpp [199/226] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -c ../tools/bam2sam/src/Bam2SamWorkflow.cpp [200/226] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -c ../tools/bam2sam/src/Bam2SamSettings.cpp [201/226] c++ -o tools/bam2sam tools/bam2sam.p/bam2sam_src_main.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,--start-group /usr/lib/s390x-linux-gnu/libhts.so -pthread /usr/lib/s390x-linux-gnu/libz.so /usr/lib/s390x-linux-gnu/libpbcopper.so -Wl,--end-group [202/226] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_main.cpp.o -MF tools/pbindex.p/pbindex_src_main.cpp.o.d -o tools/pbindex.p/pbindex_src_main.cpp.o -c ../tools/pbindex/src/main.cpp [203/226] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o -c ../tools/pbindex/src/PbIndexSettings.cpp [204/226] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -c ../tools/pbindex/src/PbIndexWorkflow.cpp [205/226] c++ -o tools/pbindex tools/pbindex.p/pbindex_src_main.cpp.o tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-s390x-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so /usr/lib/s390x-linux-gnu/libpbcopper.so -Wl,--end-group [206/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -c ../tests/src/test_ZmwReadStitcher.cpp In file included from /usr/include/c++/13/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/BamRecord.h:6, from ../include/pbbam/virtual/ZmwReadStitcher.h:6, from ../tests/src/test_ZmwReadStitcher.cpp:1: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:88:18, inlined from ‘constexpr void std::_Destroy(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:149:22, inlined from ‘static constexpr void std::_Destroy_aux< >::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; bool = false]’ at /usr/include/c++/13/bits/stl_construct.h:163:19, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_construct.h:196:11, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/alloc_traits.h:948:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, inlined from ‘PacBio::BAM::PbiFilter::PbiFilter(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:199:55, inlined from ‘virtual void BAM_ZmwReadStitcher_can_stitch_from_filtered_bams_Test::TestBody()’ at ../tests/src/test_ZmwReadStitcher.cpp:115:36: /usr/include/c++/13/bits/unique_ptr.h:403:19: warning: potential null pointer dereference [-Wnull-dereference] 403 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ [207/226] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o -c ../tools/pbindexdump/src/CppFormatter.cpp [208/226] c++ -o tests/pbbam_test tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o tests/pbbam_test.p/src_test_BamFile.cpp.o tests/pbbam_test.p/src_test_BamHeader.cpp.o tests/pbbam_test.p/src_test_BamReader.cpp.o tests/pbbam_test.p/src_test_BamRecord.cpp.o tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o tests/pbbam_test.p/src_test_BamRecordMapping.cpp.o tests/pbbam_test.p/src_test_BamWriter.cpp.o tests/pbbam_test.p/src_test_BedReader.cpp.o tests/pbbam_test.p/src_test_BedWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastaWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastqWriter.cpp.o tests/pbbam_test.p/src_test_BgzipWriter.cpp.o tests/pbbam_test.p/src_test_CollectionMetadata.cpp.o tests/pbbam_test.p/src_test_Compare.cpp.o tests/pbbam_test.p/src_test_CompositeBamReaders.cpp.o tests/pbbam_test.p/src_test_Csv.cpp.o tests/pbbam_test.p/src_test_DataSetCore.cpp.o tests/pbbam_test.p/src_test_DataSetGenomicIntervals.cpp.o tests/pbbam_test.p/src_test_DataSetIO.cpp.o tests/pbbam_test.p/src_test_DataSetQuery.cpp.o tests/pbbam_test.p/src_test_DataSetXsd.cpp.o tests/pbbam_test.p/src_test_EndToEnd.cpp.o tests/pbbam_test.p/src_test_EntireFileQuery.cpp.o tests/pbbam_test.p/src_test_FaiIndex.cpp.o tests/pbbam_test.p/src_test_FaiZmwChunker.cpp.o tests/pbbam_test.p/src_test_FastaCache.cpp.o tests/pbbam_test.p/src_test_FastaReader.cpp.o tests/pbbam_test.p/src_test_FastaSequence.cpp.o tests/pbbam_test.p/src_test_FastaSequenceQuery.cpp.o tests/pbbam_test.p/src_test_FastaWriter.cpp.o tests/pbbam_test.p/src_test_FastqReader.cpp.o tests/pbbam_test.p/src_test_FastqSequence.cpp.o tests/pbbam_test.p/src_test_FastqWriter.cpp.o tests/pbbam_test.p/src_test_FileUtils.cpp.o tests/pbbam_test.p/src_test_GenomicIntervalQuery.cpp.o tests/pbbam_test.p/src_test_IndexedBamWriter.cpp.o tests/pbbam_test.p/src_test_IndexedFastaReader.cpp.o tests/pbbam_test.p/src_test_IndexedFastqReader.cpp.o tests/pbbam_test.p/src_test_LongCigar.cpp.o tests/pbbam_test.p/src_test_PacBioIndex.cpp.o tests/pbbam_test.p/src_test_PbiFilter.cpp.o tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o tests/pbbam_test.p/src_test_Pulse2BaseCache.cpp.o tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o tests/pbbam_test.p/src_test_RunMetadata.cpp.o tests/pbbam_test.p/src_test_SamIO.cpp.o tests/pbbam_test.p/src_test_SegmentReads.cpp.o tests/pbbam_test.p/src_test_SequenceUtils.cpp.o tests/pbbam_test.p/src_test_StringUtils.cpp.o tests/pbbam_test.p/src_test_Tags.cpp.o tests/pbbam_test.p/src_test_TextFileReader.cpp.o tests/pbbam_test.p/src_test_TextFileWriter.cpp.o tests/pbbam_test.p/src_test_TimeUtils.cpp.o tests/pbbam_test.p/src_test_Validator.cpp.o tests/pbbam_test.p/src_test_VcfFile.cpp.o tests/pbbam_test.p/src_test_VcfFormat.cpp.o tests/pbbam_test.p/src_test_VcfHeader.cpp.o tests/pbbam_test.p/src_test_VcfReader.cpp.o tests/pbbam_test.p/src_test_VcfSort.cpp.o tests/pbbam_test.p/src_test_VcfQuery.cpp.o tests/pbbam_test.p/src_test_VcfVariant.cpp.o tests/pbbam_test.p/src_test_VcfWriter.cpp.o tests/pbbam_test.p/src_test_Version.cpp.o tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-s390x-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/s390x-linux-gnu/libgtest_main.a /usr/lib/s390x-linux-gnu/libgtest.a /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so /usr/lib/s390x-linux-gnu/libpbcopper.so -Wl,--end-group [209/226] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o -c ../tools/pbindexdump/src/PbIndexDumpSettings.cpp [210/226] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -c ../tools/pbindexdump/src/PbIndexDumpWorkflow.cpp [211/226] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_main.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_main.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -c ../tools/pbindexdump/src/main.cpp [212/226] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_main.cpp.o -MF tools/pbmerge.p/pbmerge_src_main.cpp.o.d -o tools/pbmerge.p/pbmerge_src_main.cpp.o -c ../tools/pbmerge/src/main.cpp [213/226] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o -c ../tools/pbmerge/src/PbMergeSettings.cpp [214/226] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -c ../tools/pbindexdump/src/JsonFormatter.cpp [215/226] c++ -o tools/pbindexdump tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-s390x-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so /usr/lib/s390x-linux-gnu/libpbcopper.so -Wl,--end-group [216/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o -c ../tools/pbbamify/src/PbBamifySettings.cpp [217/226] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -c ../tools/pbmerge/src/PbMergeWorkflow.cpp [218/226] c++ -o tools/pbmerge tools/pbmerge.p/pbmerge_src_main.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-s390x-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so /usr/lib/s390x-linux-gnu/libpbcopper.so -Wl,--end-group [219/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_main.cpp.o -MF tools/pbbamify.p/pbbamify_src_main.cpp.o.d -o tools/pbbamify.p/pbbamify_src_main.cpp.o -c ../tools/pbbamify/src/main.cpp [220/226] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/main.cpp [221/226] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifySettings.cpp [222/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -MF tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o.d -o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -c ../tools/pbbamify/src/QueryLookup.cpp [223/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o -c ../tools/pbbamify/src/PbBamifyWorkflow.cpp [224/226] c++ -o tools/pbbamify tools/pbbamify.p/pbbamify_src_main.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-s390x-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so /usr/lib/s390x-linux-gnu/libpbcopper.so -Wl,--end-group [225/226] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp In file included from /usr/include/c++/13/memory:78, from /usr/include/pbcopper/logging/LogMessage.h:8, from /usr/include/pbcopper/logging/Logging.h:8, from /usr/include/pbcopper/cli2/Results.h:12, from ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.h:4, from ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:1: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:88:18, inlined from ‘constexpr void std::_Destroy(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:149:22, inlined from ‘static constexpr void std::_Destroy_aux< >::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; bool = false]’ at /usr/include/c++/13/bits/stl_construct.h:163:19, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/13/bits/stl_construct.h:196:11, inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/alloc_traits.h:948:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, inlined from ‘PacBio::BAM::PbiFilter::PbiFilter(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:199:55, inlined from ‘std::__detail::__unique_ptr_t<_Tp> std::make_unique(_Args&& ...) [with _Tp = PacBio::BAM::PbiIndexedBamReader; _Args = {const PacBio::BAM::PbiFilter&, PacBio::BAM::BamFile}]’ at /usr/include/c++/13/bits/unique_ptr.h:1070:30: /usr/include/c++/13/bits/unique_ptr.h:403:19: warning: potential null pointer dereference [-Wnull-dereference] 403 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ [226/226] c++ -o tools/ccs-kinetics-bystrandify tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-s390x-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/s390x-linux-gnu/libhts.so /usr/lib/s390x-linux-gnu/libz.so /usr/lib/s390x-linux-gnu/libpbcopper.so -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/<>' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_dataset.t.in > tests/src/cram/pbmerge_dataset.deb.t 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@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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 dh_auto_configure -O--buildsystem=meson cd obj-s390x-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/s390x-linux-gnu -Dpython.bytecompile=-1 Directory already configured. Just run your build command (e.g. ninja) and Meson will regenerate as necessary. Run "meson setup --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. mkdir -p /<>/gendata python3 tests/scripts/generate_data.py /<>/tests/data /<>/gendata Generating test data in /<>/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/pbbamify.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbmerge_dataset.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbbamify.deb.t: failed --- tests/src/cram/pbbamify.deb.t +++ tests/src/cram/pbbamify.deb.t.err @@ -9,91 +9,47 @@ 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: $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-1.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | samtools view -h | grep -v '@PG ID:samtools' - @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: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:Handmade\tPN:Handmade (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) + [main_samview] fail to read the header from "-". + Segmentation fault (core dumped) + [1] $ grep -c "WARN" pbbamify.log - 3 + 0 + [1] $ grep -c "INFO" pbbamify.log - 1 + 0 + [1] $ rm pbbamify.log 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. $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-2.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_2.subreads.bam | samtools view -h | grep -v '@PG ID:samtools' - @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: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) - @PG\tID:Handmade\tPN:Handmade (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) + [main_samview] fail to read the header from "-". + Segmentation fault (core dumped) + [1] $ grep -c "INFO" pbbamify.log - 1 + 0 + [1] $ rm pbbamify.log CCS read: $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-3.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_3.subreads.bam | samtools view -h | grep -v '@PG ID:samtools' - @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:ccs-3.0.0\tPN:ccs\tVN:3.0.0\tDS:Generate circular consensus sequences (ccs) from subreads.\tCL:ccs (esc) - @PG\tID:Handmade\tPN:Handmade (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) + [main_samview] fail to read the header from "-". + Segmentation fault (core dumped) + [1] $ grep -c "INFO" pbbamify.log - 1 + 0 + [1] $ rm pbbamify.log No verbose output: $ $PBBAMIFY --log-file=pbbamify.log --input=$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 | grep -v '@PG ID:samtools' - @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: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:Handmade\tPN:Handmade (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) + [main_samview] fail to read the header from "-". + Segmentation fault (core dumped) + [1] $ grep -n "INFO" pbbamify.log [1] @@ -102,43 +58,16 @@ Test on a dataset, input contains alignments from all subread sets. $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-all.bam $DATADIR/pbbamify/synthetic-ref-1.fa /<>/obj-s390x-linux-gnu/tests/synthetic_movie_all.subreadset.xml | samtools view -h | grep -v '@PG ID:samtools' - @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: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) - @PG\tID:Handmade\tPN:Handmade (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) + [main_samview] fail to read the header from "-". + Segmentation fault (core dumped) + [1] $ grep -c "WARN" pbbamify.log - 3 + 0 + [1] $ grep -c "INFO" pbbamify.log - 1 + 0 + [1] $ rm pbbamify.log No-args: tests/src/cram/pbindexdump_cpp.deb.t: passed tests/src/cram/pbindexdump_json.deb.t: passed tests/src/cram/pbmerge_aligned_ordering.deb.t: passed 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 + >|> 20240410 23:04:08.225 -|- FATAL -|- Run at ../src/cli2/CLI.cpp:152 -|- 0x3ff956f4740|| -|- pbmerge ERROR: [pbbam] BAM header ERROR: read group ID not found: + [1] $ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found" Found @@ -69,14 +71,6 @@ @PG\tID:pbmerge-2.4.0\tPN:pbmerge\tVN:2.4.0 (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-2.4.0\tPN:pbmerge\tVN:2.4.0 (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-2.4.0\tPN:pbmerge\tVN:2.4.0 (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 tests/src/cram/pbmerge_fofn.deb.t: passed tests/src/cram/pbmerge_mixed_ordering.deb.t: passed tests/src/cram/pbmerge_pacbio_ordering.deb.t: failed --- tests/src/cram/pbmerge_pacbio_ordering.deb.t +++ tests/src/cram/pbmerge_pacbio_ordering.deb.t.err @@ -104,354 +104,72 @@ Normal Merge: $ $PBMERGE $HQREGION_BAM $SCRAPS_BAM > $MERGED_BAM + Segmentation fault (core dumped) + [139] $ samtools view -H $MERGED_BAM | grep -v 'CL:samtools view -H ' - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-2.4.0\tPN:pbmerge\tVN:2.4.0 (esc) + [main_samview] fail to read the header from "/<>/gendata/pacbio_ordering_merged.bam". + [1] $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/100000/0_2659 - ArminsFakeMovie/100000/2659_7034 - ArminsFakeMovie/100000/3025_3047 - ArminsFakeMovie/100000/3047_3095 - ArminsFakeMovie/100000/3095_3116 - ArminsFakeMovie/100000/3628_3650 - ArminsFakeMovie/100000/3650_3700 - ArminsFakeMovie/100000/3700_3722 - ArminsFakeMovie/100000/4267_4289 - ArminsFakeMovie/100000/4289_4335 - ArminsFakeMovie/100000/4335_4356 - ArminsFakeMovie/100000/4864_4888 - ArminsFakeMovie/100000/4888_4939 - ArminsFakeMovie/100000/4939_4960 - ArminsFakeMovie/100000/5477_5498 - ArminsFakeMovie/100000/5498_5546 - ArminsFakeMovie/100000/5546_5571 - ArminsFakeMovie/100000/6087_6116 - ArminsFakeMovie/100000/6116_6173 - ArminsFakeMovie/100000/6173_6199 - ArminsFakeMovie/100000/6719_6740 - ArminsFakeMovie/100000/6740_6790 - ArminsFakeMovie/100000/6790_6812 - ArminsFakeMovie/100000/7034_7035 - ArminsFakeMovie/200000/0_2659 - ArminsFakeMovie/200000/3025_3047 - ArminsFakeMovie/200000/3047_3095 - ArminsFakeMovie/200000/3095_3116 - ArminsFakeMovie/200000/3628_3650 - ArminsFakeMovie/200000/3650_3700 - ArminsFakeMovie/200000/3700_3722 - ArminsFakeMovie/200000/4267_4289 - ArminsFakeMovie/200000/4289_4335 - ArminsFakeMovie/200000/4335_4356 - ArminsFakeMovie/200000/4864_4888 - ArminsFakeMovie/200000/4888_4939 - ArminsFakeMovie/200000/4939_4960 - ArminsFakeMovie/200000/5477_5498 - ArminsFakeMovie/200000/5498_5546 - ArminsFakeMovie/200000/5546_5571 - ArminsFakeMovie/200000/6087_6116 - ArminsFakeMovie/200000/6116_6173 - ArminsFakeMovie/200000/6173_6199 - ArminsFakeMovie/200000/6719_6740 - ArminsFakeMovie/200000/6740_6790 - ArminsFakeMovie/200000/6790_6812 - ArminsFakeMovie/200000/7034_7035 - ArminsFakeMovie/300000/0_2659 - ArminsFakeMovie/300000/3025_3047 - ArminsFakeMovie/300000/3047_3095 - ArminsFakeMovie/300000/3095_3116 - ArminsFakeMovie/300000/3628_3650 - ArminsFakeMovie/300000/3650_3700 - ArminsFakeMovie/300000/3700_3722 - ArminsFakeMovie/300000/4267_4289 - ArminsFakeMovie/300000/4289_4335 - ArminsFakeMovie/300000/4335_4356 - ArminsFakeMovie/300000/4864_4888 - ArminsFakeMovie/300000/4888_4939 - ArminsFakeMovie/300000/4939_4960 - ArminsFakeMovie/300000/5477_5498 - ArminsFakeMovie/300000/5498_5546 - ArminsFakeMovie/300000/5546_5571 - ArminsFakeMovie/300000/6087_6116 - ArminsFakeMovie/300000/6116_6173 - ArminsFakeMovie/300000/6173_6199 - ArminsFakeMovie/300000/6719_6740 - ArminsFakeMovie/300000/6740_6790 - ArminsFakeMovie/300000/6790_6812 - ArminsFakeMovie/300000/7034_7035 + [main_samview] fail to read the header from "/<>/gendata/pacbio_ordering_merged.bam". $ rm $MERGED_BAM Shuffle Input: $ $PBMERGE $SCRAPS_BAM $HQREGION_BAM > $MERGED_BAM + Segmentation fault (core dumped) + [139] $ samtools view -H $MERGED_BAM | grep -v 'CL:samtools view -H ' - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-2.4.0\tPN:pbmerge\tVN:2.4.0 (esc) + [main_samview] fail to read the header from "/<>/gendata/pacbio_ordering_merged.bam". + [1] $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/100000/0_2659 - ArminsFakeMovie/100000/2659_7034 - ArminsFakeMovie/100000/3025_3047 - ArminsFakeMovie/100000/3047_3095 - ArminsFakeMovie/100000/3095_3116 - ArminsFakeMovie/100000/3628_3650 - ArminsFakeMovie/100000/3650_3700 - ArminsFakeMovie/100000/3700_3722 - ArminsFakeMovie/100000/4267_4289 - ArminsFakeMovie/100000/4289_4335 - ArminsFakeMovie/100000/4335_4356 - ArminsFakeMovie/100000/4864_4888 - ArminsFakeMovie/100000/4888_4939 - ArminsFakeMovie/100000/4939_4960 - ArminsFakeMovie/100000/5477_5498 - ArminsFakeMovie/100000/5498_5546 - ArminsFakeMovie/100000/5546_5571 - ArminsFakeMovie/100000/6087_6116 - ArminsFakeMovie/100000/6116_6173 - ArminsFakeMovie/100000/6173_6199 - ArminsFakeMovie/100000/6719_6740 - ArminsFakeMovie/100000/6740_6790 - ArminsFakeMovie/100000/6790_6812 - ArminsFakeMovie/100000/7034_7035 - ArminsFakeMovie/200000/0_2659 - ArminsFakeMovie/200000/3025_3047 - ArminsFakeMovie/200000/3047_3095 - ArminsFakeMovie/200000/3095_3116 - ArminsFakeMovie/200000/3628_3650 - ArminsFakeMovie/200000/3650_3700 - ArminsFakeMovie/200000/3700_3722 - ArminsFakeMovie/200000/4267_4289 - ArminsFakeMovie/200000/4289_4335 - ArminsFakeMovie/200000/4335_4356 - ArminsFakeMovie/200000/4864_4888 - ArminsFakeMovie/200000/4888_4939 - ArminsFakeMovie/200000/4939_4960 - ArminsFakeMovie/200000/5477_5498 - ArminsFakeMovie/200000/5498_5546 - ArminsFakeMovie/200000/5546_5571 - ArminsFakeMovie/200000/6087_6116 - ArminsFakeMovie/200000/6116_6173 - ArminsFakeMovie/200000/6173_6199 - ArminsFakeMovie/200000/6719_6740 - ArminsFakeMovie/200000/6740_6790 - ArminsFakeMovie/200000/6790_6812 - ArminsFakeMovie/200000/7034_7035 - ArminsFakeMovie/300000/0_2659 - ArminsFakeMovie/300000/3025_3047 - ArminsFakeMovie/300000/3047_3095 - ArminsFakeMovie/300000/3095_3116 - ArminsFakeMovie/300000/3628_3650 - ArminsFakeMovie/300000/3650_3700 - ArminsFakeMovie/300000/3700_3722 - ArminsFakeMovie/300000/4267_4289 - ArminsFakeMovie/300000/4289_4335 - ArminsFakeMovie/300000/4335_4356 - ArminsFakeMovie/300000/4864_4888 - ArminsFakeMovie/300000/4888_4939 - ArminsFakeMovie/300000/4939_4960 - ArminsFakeMovie/300000/5477_5498 - ArminsFakeMovie/300000/5498_5546 - ArminsFakeMovie/300000/5546_5571 - ArminsFakeMovie/300000/6087_6116 - ArminsFakeMovie/300000/6116_6173 - ArminsFakeMovie/300000/6173_6199 - ArminsFakeMovie/300000/6719_6740 - ArminsFakeMovie/300000/6740_6790 - ArminsFakeMovie/300000/6790_6812 - ArminsFakeMovie/300000/7034_7035 + [main_samview] fail to read the header from "/<>/gendata/pacbio_ordering_merged.bam". $ rm $MERGED_BAM Explicit Output Filename (also enables PBI): $ $PBMERGE -o $MERGED_BAM $HQREGION_BAM $SCRAPS_BAM + Segmentation fault (core dumped) + [139] $ samtools view -H $MERGED_BAM | grep -v 'CL:samtools view -H ' - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-2.4.0\tPN:pbmerge\tVN:2.4.0 (esc) + [main_samview] fail to read the header from "/<>/gendata/pacbio_ordering_merged.bam". + [1] $ samtools view $MERGED_BAM | cut -f 1 - ArminsFakeMovie/100000/0_2659 - ArminsFakeMovie/100000/2659_7034 - ArminsFakeMovie/100000/3025_3047 - ArminsFakeMovie/100000/3047_3095 - ArminsFakeMovie/100000/3095_3116 - ArminsFakeMovie/100000/3628_3650 - ArminsFakeMovie/100000/3650_3700 - ArminsFakeMovie/100000/3700_3722 - ArminsFakeMovie/100000/4267_4289 - ArminsFakeMovie/100000/4289_4335 - ArminsFakeMovie/100000/4335_4356 - ArminsFakeMovie/100000/4864_4888 - ArminsFakeMovie/100000/4888_4939 - ArminsFakeMovie/100000/4939_4960 - ArminsFakeMovie/100000/5477_5498 - ArminsFakeMovie/100000/5498_5546 - ArminsFakeMovie/100000/5546_5571 - ArminsFakeMovie/100000/6087_6116 - ArminsFakeMovie/100000/6116_6173 - ArminsFakeMovie/100000/6173_6199 - ArminsFakeMovie/100000/6719_6740 - ArminsFakeMovie/100000/6740_6790 - ArminsFakeMovie/100000/6790_6812 - ArminsFakeMovie/100000/7034_7035 - ArminsFakeMovie/200000/0_2659 - ArminsFakeMovie/200000/3025_3047 - ArminsFakeMovie/200000/3047_3095 - ArminsFakeMovie/200000/3095_3116 - ArminsFakeMovie/200000/3628_3650 - ArminsFakeMovie/200000/3650_3700 - ArminsFakeMovie/200000/3700_3722 - ArminsFakeMovie/200000/4267_4289 - ArminsFakeMovie/200000/4289_4335 - ArminsFakeMovie/200000/4335_4356 - ArminsFakeMovie/200000/4864_4888 - ArminsFakeMovie/200000/4888_4939 - ArminsFakeMovie/200000/4939_4960 - ArminsFakeMovie/200000/5477_5498 - ArminsFakeMovie/200000/5498_5546 - ArminsFakeMovie/200000/5546_5571 - ArminsFakeMovie/200000/6087_6116 - ArminsFakeMovie/200000/6116_6173 - ArminsFakeMovie/200000/6173_6199 - ArminsFakeMovie/200000/6719_6740 - ArminsFakeMovie/200000/6740_6790 - ArminsFakeMovie/200000/6790_6812 - ArminsFakeMovie/200000/7034_7035 - ArminsFakeMovie/300000/0_2659 - ArminsFakeMovie/300000/3025_3047 - ArminsFakeMovie/300000/3047_3095 - ArminsFakeMovie/300000/3095_3116 - ArminsFakeMovie/300000/3628_3650 - ArminsFakeMovie/300000/3650_3700 - ArminsFakeMovie/300000/3700_3722 - ArminsFakeMovie/300000/4267_4289 - ArminsFakeMovie/300000/4289_4335 - ArminsFakeMovie/300000/4335_4356 - ArminsFakeMovie/300000/4864_4888 - ArminsFakeMovie/300000/4888_4939 - ArminsFakeMovie/300000/4939_4960 - ArminsFakeMovie/300000/5477_5498 - ArminsFakeMovie/300000/5498_5546 - ArminsFakeMovie/300000/5546_5571 - ArminsFakeMovie/300000/6087_6116 - ArminsFakeMovie/300000/6116_6173 - ArminsFakeMovie/300000/6173_6199 - ArminsFakeMovie/300000/6719_6740 - ArminsFakeMovie/300000/6740_6790 - ArminsFakeMovie/300000/6790_6812 - ArminsFakeMovie/300000/7034_7035 - - $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" - Found - - $ rm $MERGED_BAM - $ rm $MERGED_BAM_PBI - -Explicit Output Filename (with disabled PBI): - - $ $PBMERGE -o $MERGED_BAM --no-pbi $HQREGION_BAM $SCRAPS_BAM - - $ samtools view -H $MERGED_BAM | grep -v 'CL:samtools view -H ' - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) - @PG\tID:pbmerge-2.4.0\tPN:pbmerge\tVN:2.4.0 (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 + [main_samview] fail to read the header from "/<>/gendata/pacbio_ordering_merged.bam". $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" Not found $ rm $MERGED_BAM + $ rm $MERGED_BAM_PBI + rm: cannot remove '/<>/gendata/pacbio_ordering_merged.bam.pbi': No such file or directory + [1] + +Explicit Output Filename (with disabled PBI): + + $ $PBMERGE -o $MERGED_BAM --no-pbi $HQREGION_BAM $SCRAPS_BAM + Segmentation fault (core dumped) + [139] + + $ samtools view -H $MERGED_BAM | grep -v 'CL:samtools view -H ' + [E::hts_open_format] Failed to open file "/<>/gendata/pacbio_ordering_merged.bam" : No such file or directory + samtools view: failed to open "/<>/gendata/pacbio_ordering_merged.bam" for reading: No such file or directory + [1] + + $ samtools view $MERGED_BAM | cut -f 1 + [E::hts_open_format] Failed to open file "/<>/gendata/pacbio_ordering_merged.bam" : No such file or directory + samtools view: failed to open "/<>/gendata/pacbio_ordering_merged.bam" for reading: No such file or directory + + $ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found" + Not found + + $ rm $MERGED_BAM + rm: cannot remove '/<>/gendata/pacbio_ordering_merged.bam': No such file or directory + [1] # Ran 8 tests, 0 skipped, 3 failed. make[1]: *** [debian/rules:22: override_dh_auto_test] Error 1 make[1]: Leaving directory '/<>' make: *** [debian/rules:13: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2024-04-10T23:04:09Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: 688076 Build-Time: 290 Distribution: noble-proposed Fail-Stage: build Host Architecture: s390x Install-Time: 15 Job: pbbam_2.4.0+dfsg-1build1.dsc Machine Architecture: s390x Package: pbbam Package-Time: 307 Source-Version: 2.4.0+dfsg-1build1 Space: 688076 Status: attempted Version: 2.4.0+dfsg-1build1 -------------------------------------------------------------------------------- Finished at 2024-04-10T23:04:09Z Build needed 00:05:07, 688076k disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27789654 Scanning for processes to kill in build PACKAGEBUILD-27789654