https://launchpad.net/ubuntu/+source/samtools/1.17-1/+build/26332609 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-002 5.4.0-152-generic #169-Ubuntu SMP Tue Jun 6 22:22:48 UTC 2023 ppc64le Buildd toolchain package versions: launchpad-buildd_233~634~ubuntu20.04.1 python3-lpbuildd_233~634~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. Syncing the system clock with the buildd NTP service... 23 Jun 07:05:46 ntpdate[2207]: adjust time server 10.211.37.1 offset -0.014731 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=ppc64el PACKAGEBUILD-26332609 --image-type chroot /home/buildd/filecache-default/7984b9498478de1d58b749dc057a3cf5e3226d68 Creating target for build PACKAGEBUILD-26332609 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=ppc64el PACKAGEBUILD-26332609 Starting target for build PACKAGEBUILD-26332609 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=ppc64el PACKAGEBUILD-26332609 'deb http://ftpmaster.internal/ubuntu mantic main universe' 'deb http://ftpmaster.internal/ubuntu mantic-security main universe' 'deb http://ftpmaster.internal/ubuntu mantic-updates main universe' 'deb http://ftpmaster.internal/ubuntu mantic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-26332609 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=ppc64el PACKAGEBUILD-26332609 Updating target for build PACKAGEBUILD-26332609 Get:1 http://ftpmaster.internal/ubuntu mantic InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu mantic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main ppc64el Packages [1344 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe ppc64el Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5936 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main ppc64el Packages [54.5 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [25.3 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe ppc64el Packages [457 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [163 kB] Fetched 23.4 MB in 13s (1783 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-13-base libproc2-0 The following packages will be upgraded: adduser advancecomp apt base-files bash binutils binutils-common binutils-powerpc64le-linux-gnu bsdutils ca-certificates coreutils cpp cpp-12 dash debconf diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-12 gcc gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep hostname libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libfdisk1 libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgssapi-krb5-2 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblzma5 libmd0 libmount1 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev logsave lsb-base lto-disabled-list mawk mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tar tzdata usrmerge util-linux util-linux-extra xz-utils zlib1g 137 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 110 MB of archives. After this operation, 998 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu mantic/main ppc64el libcrypt-dev ppc64el 1:4.4.35-1 [143 kB] Get:2 http://ftpmaster.internal/ubuntu mantic/main ppc64el libc6-dev ppc64el 2.37-0ubuntu2 [2057 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main ppc64el libc-dev-bin ppc64el 2.37-0ubuntu2 [20.9 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main ppc64el libcrypt1 ppc64el 1:4.4.35-1 [107 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main ppc64el linux-libc-dev ppc64el 6.3.0-7.7 [1533 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main ppc64el libc6 ppc64el 2.37-0ubuntu2 [3192 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main ppc64el libc-bin ppc64el 2.37-0ubuntu2 [736 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main ppc64el gcc-13-base ppc64el 13.1.0-6ubuntu1 [42.0 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main ppc64el libgcc-s1 ppc64el 13.1.0-6ubuntu1 [38.5 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main ppc64el base-files ppc64el 13ubuntu1 [74.2 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main ppc64el bash ppc64el 5.2.15-2ubuntu1 [956 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main ppc64el bsdutils ppc64el 1:2.38.1-5ubuntu2 [95.5 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main ppc64el coreutils ppc64el 9.1-1ubuntu2 [1508 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main ppc64el liblzma5 ppc64el 5.4.1-0.2 [154 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main ppc64el libgcrypt20 ppc64el 1.10.1-3ubuntu1 [718 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main ppc64el libstdc++6 ppc64el 13.1.0-6ubuntu1 [872 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main ppc64el libacl1 ppc64el 2.3.1-3 [20.4 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main ppc64el libapparmor1 ppc64el 3.0.8-1ubuntu3 [51.0 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main ppc64el libaudit-common all 1:3.0.9-1 [5142 B] Get:20 http://ftpmaster.internal/ubuntu mantic/main ppc64el libcap-ng0 ppc64el 0.8.3-1build2 [16.0 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main ppc64el libaudit1 ppc64el 1:3.0.9-1 [51.2 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main ppc64el libblkid1 ppc64el 2.38.1-5ubuntu2 [135 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main ppc64el libcap2 ppc64el 1:2.66-4ubuntu1 [34.4 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main ppc64el libperl5.36 ppc64el 5.36.0-7ubuntu1 [4849 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main ppc64el perl ppc64el 5.36.0-7ubuntu1 [235 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main ppc64el perl-base ppc64el 5.36.0-7ubuntu1 [1858 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main ppc64el perl-modules-5.36 all 5.36.0-7ubuntu1 [2984 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main ppc64el libdb5.3 ppc64el 5.3.28+dfsg2-1 [847 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main ppc64el zlib1g ppc64el 1:1.2.13.dfsg-1ubuntu4 [70.1 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main ppc64el debconf all 1.5.82 [125 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main ppc64el libssl3 ppc64el 3.0.9-1ubuntu1 [2139 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main ppc64el libzstd1 ppc64el 1.5.4+dfsg2-5 [375 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main ppc64el libkmod2 ppc64el 30+20221128-1ubuntu1 [59.8 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main ppc64el libpcre2-8-0 ppc64el 10.42-1 [256 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main ppc64el libselinux1 ppc64el 3.4-1build4 [96.6 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main ppc64el libmount1 ppc64el 2.38.1-5ubuntu2 [145 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main ppc64el libpam0g ppc64el 1.5.2-6ubuntu1 [73.4 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main ppc64el libseccomp2 ppc64el 2.5.4-1ubuntu3 [61.6 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main ppc64el systemd-sysv ppc64el 252.5-2ubuntu3 [11.5 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main ppc64el systemd ppc64el 252.5-2ubuntu3 [3198 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main ppc64el libsystemd-shared ppc64el 252.5-2ubuntu3 [2027 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main ppc64el libargon2-1 ppc64el 0~20190702+dfsg-3 [21.8 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main ppc64el libudev1 ppc64el 252.5-2ubuntu3 [172 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.185-2ubuntu1 [179 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main ppc64el libuuid1 ppc64el 2.38.1-5ubuntu2 [36.4 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main ppc64el libcryptsetup12 ppc64el 2:2.6.1-4ubuntu1 [343 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main ppc64el libfdisk1 ppc64el 2.38.1-5ubuntu2 [167 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main ppc64el libp11-kit0 ppc64el 0.24.1-2ubuntu1 [258 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main ppc64el mount ppc64el 2.38.1-5ubuntu2 [119 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main ppc64el libsystemd0 ppc64el 252.5-2ubuntu3 [467 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main ppc64el libapt-pkg6.0 ppc64el 2.7.1 [970 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main ppc64el tar ppc64el 1.34+dfsg-1.2ubuntu1 [354 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main ppc64el dpkg ppc64el 1.21.22ubuntu1 [1469 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main ppc64el dash ppc64el 0.5.12-2ubuntu1 [105 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main ppc64el diffutils ppc64el 1:3.8-4 [196 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main ppc64el findutils ppc64el 4.9.0-4ubuntu1 [328 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main ppc64el grep ppc64el 3.8-5 [170 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main ppc64el hostname ppc64el 3.23+nmu1ubuntu1 [11.1 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main ppc64el ncurses-bin ppc64el 6.4-4 [197 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main ppc64el sed ppc64el 4.9-1 [208 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main ppc64el libsmartcols1 ppc64el 2.38.1-5ubuntu2 [71.4 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main ppc64el util-linux-extra ppc64el 2.38.1-5ubuntu2 [88.9 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main ppc64el util-linux ppc64el 2.38.1-5ubuntu2 [1140 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main ppc64el ncurses-base all 6.4-4 [23.3 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main ppc64el sysvinit-utils ppc64el 3.06-4ubuntu1 [34.2 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main ppc64el lsb-base all 11.6 [4606 B] Get:67 http://ftpmaster.internal/ubuntu mantic-proposed/main ppc64el adduser all 3.134ubuntu1 [136 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main ppc64el gpgv ppc64el 2.2.40-1.1ubuntu1 [174 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main ppc64el libgnutls30 ppc64el 3.7.9-2ubuntu1 [1054 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main ppc64el apt ppc64el 2.7.1 [1369 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main ppc64el libpam-modules-bin ppc64el 1.5.2-6ubuntu1 [51.9 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main ppc64el libpam-modules ppc64el 1.5.2-6ubuntu1 [323 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main ppc64el logsave ppc64el 1.47.0-1ubuntu1 [14.7 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main ppc64el libext2fs2 ppc64el 1.47.0-1ubuntu1 [255 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main ppc64el e2fsprogs ppc64el 1.47.0-1ubuntu1 [652 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main ppc64el libattr1 ppc64el 1:2.5.1-4 [13.2 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main ppc64el libdebconfclient0 ppc64el 0.267ubuntu1 [7796 B] Get:78 http://ftpmaster.internal/ubuntu mantic/main ppc64el libmd0 ppc64el 1.1.0-1 [30.2 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/main ppc64el libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main ppc64el libsemanage-common all 3.4-1build4 [9852 B] Get:81 http://ftpmaster.internal/ubuntu mantic/main ppc64el libsepol2 ppc64el 3.4-2.1 [382 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main ppc64el libsemanage2 ppc64el 3.4-1build4 [113 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main ppc64el libncurses6 ppc64el 6.4-4 [145 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main ppc64el libncursesw6 ppc64el 6.4-4 [179 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main ppc64el libtinfo6 ppc64el 6.4-4 [126 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main ppc64el usrmerge all 35ubuntu1 [58.2 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main ppc64el libcom-err2 ppc64el 1.47.0-1ubuntu1 [14.6 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main ppc64el libproc2-0 ppc64el 2:4.0.3-1ubuntu1 [62.1 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main ppc64el libss2 ppc64el 1.47.0-1ubuntu1 [17.5 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main ppc64el mawk ppc64el 1.3.4.20230525-1 [122 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/main ppc64el procps ppc64el 2:4.0.3-1ubuntu1 [632 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main ppc64el sensible-utils all 0.0.20 [19.6 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main ppc64el openssl ppc64el 3.0.9-1ubuntu1 [1205 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main ppc64el ca-certificates all 20230311ubuntu1 [152 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main ppc64el libgssapi-krb5-2 ppc64el 1.20.1-2 [181 kB] Get:96 http://ftpmaster.internal/ubuntu mantic/main ppc64el libkrb5-3 ppc64el 1.20.1-2 [425 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main ppc64el libkrb5support0 ppc64el 1.20.1-2 [37.2 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main ppc64el libk5crypto3 ppc64el 1.20.1-2 [106 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main ppc64el readline-common all 8.2-1.3 [55.7 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main ppc64el libreadline8 ppc64el 8.2-1.3 [175 kB] Get:101 http://ftpmaster.internal/ubuntu mantic/main ppc64el libsqlite3-0 ppc64el 3.40.1-2 [751 kB] Get:102 http://ftpmaster.internal/ubuntu mantic/main ppc64el tzdata all 2023c-4exp1ubuntu1 [271 kB] Get:103 http://ftpmaster.internal/ubuntu mantic/main ppc64el xz-utils ppc64el 5.4.1-0.2 [277 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main ppc64el advancecomp ppc64el 2.5-1 [235 kB] Get:105 http://ftpmaster.internal/ubuntu mantic-proposed/main ppc64el libctf0 ppc64el 2.40.50.20230622-1ubuntu1 [109 kB] Get:106 http://ftpmaster.internal/ubuntu mantic-proposed/main ppc64el libctf-nobfd0 ppc64el 2.40.50.20230622-1ubuntu1 [109 kB] Get:107 http://ftpmaster.internal/ubuntu mantic-proposed/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.40.50.20230622-1ubuntu1 [2448 kB] Get:108 http://ftpmaster.internal/ubuntu mantic-proposed/main ppc64el libbinutils ppc64el 2.40.50.20230622-1ubuntu1 [730 kB] Get:109 http://ftpmaster.internal/ubuntu mantic-proposed/main ppc64el binutils ppc64el 2.40.50.20230622-1ubuntu1 [3082 B] Get:110 http://ftpmaster.internal/ubuntu mantic-proposed/main ppc64el binutils-common ppc64el 2.40.50.20230622-1ubuntu1 [227 kB] Get:111 http://ftpmaster.internal/ubuntu mantic/main ppc64el libisl23 ppc64el 0.26-3 [864 kB] Get:112 http://ftpmaster.internal/ubuntu mantic/main ppc64el libmpfr6 ppc64el 4.2.0-1 [343 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main ppc64el g++-12 ppc64el 12.3.0-3ubuntu1 [11.4 MB] Get:114 http://ftpmaster.internal/ubuntu mantic/main ppc64el gcc-12 ppc64el 12.3.0-3ubuntu1 [19.8 MB] Get:115 http://ftpmaster.internal/ubuntu mantic/main ppc64el cpp-12 ppc64el 12.3.0-3ubuntu1 [10.1 MB] Get:116 http://ftpmaster.internal/ubuntu mantic/main ppc64el libubsan1 ppc64el 13.1.0-6ubuntu1 [1133 kB] Get:117 http://ftpmaster.internal/ubuntu mantic/main ppc64el libstdc++-12-dev ppc64el 12.3.0-3ubuntu1 [2301 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/main ppc64el libgomp1 ppc64el 13.1.0-6ubuntu1 [155 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main ppc64el libitm1 ppc64el 13.1.0-6ubuntu1 [32.6 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/main ppc64el libatomic1 ppc64el 13.1.0-6ubuntu1 [10.6 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main ppc64el libasan8 ppc64el 13.1.0-6ubuntu1 [2827 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/main ppc64el liblsan0 ppc64el 13.1.0-6ubuntu1 [1232 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/main ppc64el libquadmath0 ppc64el 13.1.0-6ubuntu1 [156 kB] Get:124 http://ftpmaster.internal/ubuntu mantic/main ppc64el libgcc-12-dev ppc64el 12.3.0-3ubuntu1 [1512 kB] Get:125 http://ftpmaster.internal/ubuntu mantic/main ppc64el libtsan2 ppc64el 13.1.0-6ubuntu1 [2647 kB] Get:126 http://ftpmaster.internal/ubuntu mantic/main ppc64el libcc1-0 ppc64el 13.1.0-6ubuntu1 [48.8 kB] Get:127 http://ftpmaster.internal/ubuntu mantic/main ppc64el gcc-12-base ppc64el 12.3.0-3ubuntu1 [42.8 kB] Get:128 http://ftpmaster.internal/ubuntu mantic/main ppc64el g++ ppc64el 4:12.2.0-3ubuntu1 [1116 B] Get:129 http://ftpmaster.internal/ubuntu mantic/main ppc64el gcc ppc64el 4:12.2.0-3ubuntu1 [5194 B] Get:130 http://ftpmaster.internal/ubuntu mantic/main ppc64el cpp ppc64el 4:12.2.0-3ubuntu1 [27.8 kB] Get:131 http://ftpmaster.internal/ubuntu mantic/main ppc64el dpkg-dev all 1.21.22ubuntu1 [1118 kB] Get:132 http://ftpmaster.internal/ubuntu mantic/main ppc64el libdpkg-perl all 1.21.22ubuntu1 [247 kB] Get:133 http://ftpmaster.internal/ubuntu mantic/main ppc64el lto-disabled-list all 41 [12.4 kB] Get:134 http://ftpmaster.internal/ubuntu mantic/main ppc64el libfakeroot ppc64el 1.31-1.2 [34.0 kB] Get:135 http://ftpmaster.internal/ubuntu mantic/main ppc64el fakeroot ppc64el 1.31-1.2 [62.1 kB] Get:136 http://ftpmaster.internal/ubuntu mantic/main ppc64el gpg ppc64el 2.2.40-1.1ubuntu1 [646 kB] Get:137 http://ftpmaster.internal/ubuntu mantic/main ppc64el gpgconf ppc64el 2.2.40-1.1ubuntu1 [106 kB] Get:138 http://ftpmaster.internal/ubuntu mantic/main ppc64el gpg-agent ppc64el 2.2.40-1.1ubuntu1 [253 kB] Get:139 http://ftpmaster.internal/ubuntu mantic/main ppc64el pkgbinarymangler all 153 [16.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 110 MB in 39s (2843 kB/s) (Reading database ... 13031 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.35-1_ppc64el.deb ... Unpacking libcrypt-dev:ppc64el (1:4.4.35-1) over (1:4.4.33-1) ... Preparing to unpack .../libc6-dev_2.37-0ubuntu2_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libc-dev-bin_2.37-0ubuntu2_ppc64el.deb ... Unpacking libc-dev-bin (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libcrypt1_1%3a4.4.35-1_ppc64el.deb ... Unpacking libcrypt1:ppc64el (1:4.4.35-1) over (1:4.4.33-1) ... Setting up libcrypt1:ppc64el (1:4.4.35-1) ... (Reading database ... 13031 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_6.3.0-7.7_ppc64el.deb ... Unpacking linux-libc-dev:ppc64el (6.3.0-7.7) over (5.19.0-21.21) ... Preparing to unpack .../libc6_2.37-0ubuntu2_ppc64el.deb ... Unpacking libc6:ppc64el (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Setting up libc6:ppc64el (2.37-0ubuntu2) ... 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Setting up libctf-nobfd0:ppc64el (2.40.50.20230622-1ubuntu1) ... Setting up libcom-err2:ppc64el (1.47.0-1ubuntu1) ... Setting up libgomp1:ppc64el (13.1.0-6ubuntu1) ... Setting up libfakeroot:ppc64el (1.31-1.2) ... Setting up libkrb5support0:ppc64el (1.20.1-2) ... Setting up gcc-12-base:ppc64el (12.3.0-3ubuntu1) ... Setting up tzdata (2023c-4exp1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jun 23 07:07:01 UTC 2023. Universal Time is now: Fri Jun 23 07:07:01 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.31-1.2) ... Setting up perl-modules-5.36 (5.36.0-7ubuntu1) ... Setting up libmpfr6:ppc64el (4.2.0-1) ... Setting up libncurses6:ppc64el (6.4-4) ... Setting up xz-utils (5.4.1-0.2) ... Setting up libquadmath0:ppc64el (13.1.0-6ubuntu1) ... Setting up libproc2-0:ppc64el (2:4.0.3-1ubuntu1) ... Setting up libatomic1:ppc64el (13.1.0-6ubuntu1) ... Setting up libss2:ppc64el (1.47.0-1ubuntu1) ... Setting up libncursesw6:ppc64el (6.4-4) ... Setting up libk5crypto3:ppc64el (1.20.1-2) ... Setting up logsave (1.47.0-1ubuntu1) ... Setting up libfdisk1:ppc64el (2.38.1-5ubuntu2) ... Setting up libubsan1:ppc64el (13.1.0-6ubuntu1) ... Setting up advancecomp (2.5-1) ... Setting up libdevmapper1.02.1:ppc64el (2:1.02.185-2ubuntu1) ... Setting up mount (2.38.1-5ubuntu2) ... Setting up sensible-utils (0.0.20) ... Setting up libcrypt-dev:ppc64el (1:4.4.35-1) ... Setting up libasan8:ppc64el (13.1.0-6ubuntu1) ... Setting up procps (2:4.0.3-1ubuntu1) ... Setting up libcryptsetup12:ppc64el (2:2.6.1-4ubuntu1) ... Setting up mawk (1.3.4.20230525-1) ... Setting up libkrb5-3:ppc64el (1.20.1-2) ... Setting up libtsan2:ppc64el (13.1.0-6ubuntu1) ... Setting up libbinutils:ppc64el (2.40.50.20230622-1ubuntu1) ... Setting up libisl23:ppc64el (0.26-3) ... Setting up libc-dev-bin (2.37-0ubuntu2) ... Setting up openssl (3.0.9-1ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.2-1.3) ... Setting up libcc1-0:ppc64el (13.1.0-6ubuntu1) ... Setting up libperl5.36:ppc64el (5.36.0-7ubuntu1) ... Setting up liblsan0:ppc64el (13.1.0-6ubuntu1) ... Setting up libitm1:ppc64el (13.1.0-6ubuntu1) ... Setting up libkmod2:ppc64el (30+20221128-1ubuntu1) ... Setting up libctf0:ppc64el (2.40.50.20230622-1ubuntu1) ... Setting up cpp-12 (12.3.0-3ubuntu1) ... Setting up pkgbinarymangler (153) ... Setting up libreadline8:ppc64el (8.2-1.3) ... Setting up e2fsprogs (1.47.0-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up ca-certificates (20230311ubuntu1) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 19 added, 6 removed; done. Setting up perl (5.36.0-7ubuntu1) ... Setting up libgcc-12-dev:ppc64el (12.3.0-3ubuntu1) ... Setting up libgssapi-krb5-2:ppc64el (1.20.1-2) ... Setting up libsystemd-shared:ppc64el (252.5-2ubuntu3) ... Setting up libdpkg-perl (1.21.22ubuntu1) ... Setting up cpp (4:12.2.0-3ubuntu1) ... Setting up gpgconf (2.2.40-1.1ubuntu1) ... Setting up libc6-dev:ppc64el (2.37-0ubuntu2) ... Setting up binutils-powerpc64le-linux-gnu (2.40.50.20230622-1ubuntu1) ... Setting up gpg (2.2.40-1.1ubuntu1) ... Setting up gpg-agent (2.2.40-1.1ubuntu1) ... Setting up libstdc++-12-dev:ppc64el (12.3.0-3ubuntu1) ... Setting up systemd (252.5-2ubuntu3) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up binutils (2.40.50.20230622-1ubuntu1) ... Setting up dpkg-dev (1.21.22ubuntu1) ... Setting up gcc-12 (12.3.0-3ubuntu1) ... Setting up g++-12 (12.3.0-3ubuntu1) ... Setting up systemd-sysv (252.5-2ubuntu3) ... Setting up gcc (4:12.2.0-3ubuntu1) ... Setting up g++ (4:12.2.0-3ubuntu1) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for ca-certificates (20230311ubuntu1) ... 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-26332609 ppc64el mantic-proposed -c chroot:build-PACKAGEBUILD-26332609 --arch=ppc64el --dist=mantic-proposed --nolog samtools_1.17-1.dsc Initiating build PACKAGEBUILD-26332609 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-152-generic #169-Ubuntu SMP Tue Jun 6 22:22:48 UTC 2023 ppc64le sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-ppc64el-002.buildd +==============================================================================+ | samtools 1.17-1 (ppc64el) Fri, 23 Jun 2023 07:07:07 +0000 | +==============================================================================+ Package: samtools Version: 1.17-1 Source Version: 1.17-1 Distribution: mantic-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26332609/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-ekWXtq/resolver-WXpWpb' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- samtools_1.17-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/samtools-ekWXtq/samtools-1.17' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-ekWXtq' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix, liblzma-dev, libbz2-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix, liblzma-dev, libbz2-dev, 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 [461 B] Get:5 copy:/<>/apt_archive ./ Packages [539 B] Fetched 1957 B in 0s (81.1 kB/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 additional packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bash-completion bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72 libio-pty-perl libldap2 liblzma-dev libmagic-mgc libmagic1 libncurses-dev libnghttp2-14 libpipeline1 libpkgconf3 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config pkgconf pkgconf-bin po-debconf tabix zlib1g-dev Suggested packages: gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev liblzma-doc ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bash-completion bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72 libio-pty-perl libldap2 liblzma-dev libmagic-mgc libmagic1 libncurses-dev libnghttp2-14 libpipeline1 libpkgconf3 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy tabix zlib1g-dev 0 upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 31.7 MB of archives. After this operation, 113 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [760 B] Get:2 http://ftpmaster.internal/ubuntu mantic/universe ppc64el autoconf-archive all 20220903-3 [681 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main ppc64el libelf1 ppc64el 0.188-2.1 [63.2 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main ppc64el libicu72 ppc64el 72.1-3ubuntu2 [11.1 MB] Get:5 http://ftpmaster.internal/ubuntu mantic/main ppc64el libxml2 ppc64el 2.9.14+dfsg-1.2 [822 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main ppc64el bash-completion all 1:2.11-6ubuntu1 [179 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main ppc64el bsdextrautils ppc64el 2.38.1-5ubuntu2 [76.4 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main ppc64el libmagic-mgc ppc64el 1:5.44-3 [293 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main ppc64el libmagic1 ppc64el 1:5.44-3 [104 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main ppc64el file ppc64el 1:5.44-3 [22.4 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main ppc64el gettext-base ppc64el 0.21-12 [42.3 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main ppc64el libuchardet0 ppc64el 0.0.7-1build2 [80.4 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main ppc64el groff-base ppc64el 1.22.4-10 [1004 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main ppc64el libnghttp2-14 ppc64el 1.54.0-1 [87.3 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main ppc64el libpipeline1 ppc64el 1.5.7-1 [25.8 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main ppc64el libpsl5 ppc64el 0.21.2-1 [60.6 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main ppc64el man-db ppc64el 2.11.2-2 [1258 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main ppc64el m4 ppc64el 1.4.19-3 [275 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main ppc64el autoconf all 2.71-3 [339 kB] Get:20 http://ftpmaster.internal/ubuntu mantic/main ppc64el autotools-dev all 20220109.1 [44.9 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main ppc64el automake all 1:1.16.5-1.3 [558 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main ppc64el autopoint all 0.21-12 [422 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main ppc64el libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main ppc64el libtool all 2.4.7-5 [166 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main ppc64el dh-autoreconf all 20 [16.1 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main ppc64el libsub-override-perl all 0.09-4 [8706 B] Get:28 http://ftpmaster.internal/ubuntu mantic/main ppc64el libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main ppc64el dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:30 http://ftpmaster.internal/ubuntu mantic/main ppc64el libdw1 ppc64el 0.188-2.1 [284 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main ppc64el debugedit ppc64el 1:5.0-5 [51.1 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main ppc64el dwz ppc64el 0.15-1 [139 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main ppc64el gettext ppc64el 0.21-12 [970 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main ppc64el debhelper all 13.11.4ubuntu3 [925 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main ppc64el libbrotli1 ppc64el 1.0.9-2build8 [370 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main ppc64el libbz2-dev ppc64el 1.0.8-5build1 [49.3 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main ppc64el libsasl2-modules-db ppc64el 2.1.28+dfsg1-1 [22.6 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main ppc64el libsasl2-2 ppc64el 2.1.28+dfsg1-1 [68.3 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main ppc64el libldap2 ppc64el 2.6.3+dfsg-1~exp1ubuntu2 [217 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build4 [65.5 kB] Get:43 http://ftpmaster.internal/ubuntu mantic-proposed/main ppc64el libssh-4 ppc64el 0.10.5-2 [239 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main ppc64el libcurl3-gnutls ppc64el 7.88.1-10ubuntu1 [369 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main ppc64el libcurl4-gnutls-dev ppc64el 7.88.1-10ubuntu1 [476 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main ppc64el libdeflate0 ppc64el 1.15-1 [53.0 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main ppc64el libdeflate-dev ppc64el 1.15-1 [60.6 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/universe ppc64el libhtscodecs2 ppc64el 1.5.0-1 [106 kB] Get:49 http://ftpmaster.internal/ubuntu mantic-proposed/universe ppc64el libhts3 ppc64el 1.17+ds-1 [543 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main ppc64el liblzma-dev ppc64el 5.4.1-0.2 [202 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main ppc64el zlib1g-dev ppc64el 1:1.2.13.dfsg-1ubuntu4 [901 kB] Get:52 http://ftpmaster.internal/ubuntu mantic-proposed/universe ppc64el libhts-dev ppc64el 1.17+ds-1 [6146 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main ppc64el libio-pty-perl ppc64el 1:1.17-1 [32.8 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main ppc64el libncurses-dev ppc64el 6.4-4 [479 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main ppc64el libpkgconf3 ppc64el 1.8.1-2 [36.9 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main ppc64el pkgconf-bin ppc64el 1.8.1-2 [22.0 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main ppc64el pkgconf ppc64el 1.8.1-2 [16.7 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main ppc64el pkg-config ppc64el 1.8.1-2 [7170 B] Get:59 http://ftpmaster.internal/ubuntu mantic-proposed/universe ppc64el tabix ppc64el 1.17+ds-1 [681 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 31.7 MB in 22s (1433 kB/s) Selecting previously unselected package autoconf-archive. (Reading database ... 12513 files and directories currently installed.) Preparing to unpack .../00-autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libelf1:ppc64el. Preparing to unpack .../01-libelf1_0.188-2.1_ppc64el.deb ... Unpacking libelf1:ppc64el (0.188-2.1) ... Selecting previously unselected package libicu72:ppc64el. Preparing to unpack .../02-libicu72_72.1-3ubuntu2_ppc64el.deb ... Unpacking libicu72:ppc64el (72.1-3ubuntu2) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../03-libxml2_2.9.14+dfsg-1.2_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.14+dfsg-1.2) ... Selecting previously unselected package bash-completion. Preparing to unpack .../04-bash-completion_1%3a2.11-6ubuntu1_all.deb ... Unpacking bash-completion (1:2.11-6ubuntu1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../05-bsdextrautils_2.38.1-5ubuntu2_ppc64el.deb ... Unpacking bsdextrautils (2.38.1-5ubuntu2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.44-3_ppc64el.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:ppc64el. Preparing to unpack .../07-libmagic1_1%3a5.44-3_ppc64el.deb ... Unpacking libmagic1:ppc64el (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.44-3_ppc64el.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-12_ppc64el.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:ppc64el. Preparing to unpack .../10-libuchardet0_0.0.7-1build2_ppc64el.deb ... Unpacking libuchardet0:ppc64el (0.0.7-1build2) ... Selecting previously unselected package groff-base. Preparing to unpack .../11-groff-base_1.22.4-10_ppc64el.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package libnghttp2-14:ppc64el. Preparing to unpack .../12-libnghttp2-14_1.54.0-1_ppc64el.deb ... Unpacking libnghttp2-14:ppc64el (1.54.0-1) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../13-libpipeline1_1.5.7-1_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.5.7-1) ... Selecting previously unselected package libpsl5:ppc64el. Preparing to unpack .../14-libpsl5_0.21.2-1_ppc64el.deb ... Unpacking libpsl5:ppc64el (0.21.2-1) ... Selecting previously unselected package man-db. Preparing to unpack .../15-man-db_2.11.2-2_ppc64el.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../16-m4_1.4.19-3_ppc64el.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../17-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. 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Preparing to unpack .../58-sbuild-build-depends-main-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:ppc64el (1.5.0-1) ... Setting up libpipeline1:ppc64el (1.5.7-1) ... Setting up libncurses-dev:ppc64el (6.4-4) ... Setting up libpsl5:ppc64el (0.21.2-1) ... Setting up libicu72:ppc64el (72.1-3ubuntu2) ... Setting up bsdextrautils (2.38.1-5ubuntu2) ... Setting up libio-pty-perl (1:1.17-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4ubuntu3) ... Setting up libbrotli1:ppc64el (1.0.9-2build8) ... Setting up libnghttp2-14:ppc64el (1.54.0-1) ... Setting up libmagic1:ppc64el (1:5.44-3) ... Setting up libdeflate0:ppc64el (1.15-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up autoconf-archive (20220903-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:ppc64el (2.1.28+dfsg1-1) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:ppc64el (1.8.1-2) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build4) ... Setting up bash-completion (1:2.11-6ubuntu1) ... Setting up autopoint (0.21-12) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libsasl2-2:ppc64el (2.1.28+dfsg1-1) ... Setting up libssh-4:ppc64el (0.10.5-2) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:ppc64el (5.4.1-0.2) ... Setting up zlib1g-dev:ppc64el (1:1.2.13.dfsg-1ubuntu4) ... Setting up libuchardet0:ppc64el (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libdeflate-dev:ppc64el (1.15-1) ... Setting up tabix (1.17+ds-1) ... Setting up libelf1:ppc64el (0.188-2.1) ... Setting up libxml2:ppc64el (2.9.14+dfsg-1.2) ... Setting up libldap2:ppc64el (2.6.3+dfsg-1~exp1ubuntu2) ... Setting up libbz2-dev:ppc64el (1.0.8-5build1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:ppc64el (0.188-2.1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libcurl3-gnutls:ppc64el (7.88.1-10ubuntu1) ... Setting up libcurl4-gnutls-dev:ppc64el (7.88.1-10ubuntu1) ... Setting up pkgconf:ppc64el (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:ppc64el (1.8.1-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up debugedit (1:5.0-5) ... Setting up libhts3:ppc64el (1.17+ds-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:ppc64el (1.17+ds-1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up debhelper (13.11.4ubuntu3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-152-generic #169-Ubuntu SMP Tue Jun 6 22:22:48 UTC 2023 ppc64el (ppc64le) Toolchain package versions: binutils_2.40.50.20230622-1ubuntu1 dpkg-dev_1.21.22ubuntu1 g++-12_12.3.0-3ubuntu1 gcc-12_12.3.0-3ubuntu1 libc6-dev_2.37-0ubuntu2 libstdc++-12-dev_12.3.0-3ubuntu1 libstdc++6_13.1.0-6ubuntu1 linux-libc-dev_6.3.0-7.7 Package versions: adduser_3.134ubuntu1 advancecomp_2.5-1 apt_2.7.1 autoconf_2.71-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_13ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 bash-completion_1:2.11-6ubuntu1 binutils_2.40.50.20230622-1ubuntu1 binutils-common_2.40.50.20230622-1ubuntu1 binutils-powerpc64le-linux-gnu_2.40.50.20230622-1ubuntu1 bsdextrautils_2.38.1-5ubuntu2 bsdutils_1:2.38.1-5ubuntu2 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-3ubuntu1 cpp-12_12.3.0-3ubuntu1 dash_0.5.12-2ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.21.22ubuntu1 dpkg-dev_1.21.22ubuntu1 dwz_0.15-1 e2fsprogs_1.47.0-1ubuntu1 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-4ubuntu1 g++_4:12.2.0-3ubuntu1 g++-12_12.3.0-3ubuntu1 gcc_4:12.2.0-3ubuntu1 gcc-12_12.3.0-3ubuntu1 gcc-12-base_12.3.0-3ubuntu1 gcc-13-base_13.1.0-6ubuntu1 gettext_0.21-12 gettext-base_0.21-12 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapparmor1_3.0.8-1ubuntu3 libapt-pkg6.0_2.7.1 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-3 libasan8_13.1.0-6ubuntu1 libassuan0_2.5.5-5 libatomic1_13.1.0-6ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40.50.20230622-1ubuntu1 libblkid1_2.38.1-5ubuntu2 libbrotli1_1.0.9-2build8 libbz2-1.0_1.0.8-5build1 libbz2-dev_1.0.8-5build1 libc-bin_2.37-0ubuntu2 libc-dev-bin_2.37-0ubuntu2 libc6_2.37-0ubuntu2 libc6-dev_2.37-0ubuntu2 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-4ubuntu1 libcc1-0_13.1.0-6ubuntu1 libcom-err2_1.47.0-1ubuntu1 libcrypt-dev_1:4.4.35-1 libcrypt1_1:4.4.35-1 libcryptsetup12_2:2.6.1-4ubuntu1 libctf-nobfd0_2.40.50.20230622-1ubuntu1 libctf0_2.40.50.20230622-1ubuntu1 libcurl3-gnutls_7.88.1-10ubuntu1 libcurl4-gnutls-dev_7.88.1-10ubuntu1 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.267ubuntu1 libdebhelper-perl_13.11.4ubuntu3 libdeflate-dev_1.15-1 libdeflate0_1.15-1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.21.22ubuntu1 libdw1_0.188-2.1 libelf1_0.188-2.1 libext2fs2_1.47.0-1ubuntu1 libfakeroot_1.31-1.2 libfdisk1_2.38.1-5ubuntu2 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-3ubuntu1 libgcc-s1_13.1.0-6ubuntu1 libgcrypt20_1.10.1-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.9-2ubuntu1 libgomp1_13.1.0-6ubuntu1 libgpg-error0_1.46-1 libgssapi-krb5-2_1.20.1-2 libhogweed6_3.8.1-2 libhts-dev_1.17+ds-1 libhts3_1.17+ds-1 libhtscodecs2_1.5.0-1 libicu72_72.1-3ubuntu2 libidn2-0_2.3.3-1build1 libio-pty-perl_1:1.17-1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.26-3 libitm1_13.1.0-6ubuntu1 libjansson4_2.14-2 libjson-c5_0.16-2 libk5crypto3_1.20.1-2 libkeyutils1_1.6.3-2 libkmod2_30+20221128-1ubuntu1 libkrb5-3_1.20.1-2 libkrb5support0_1.20.1-2 libldap2_2.6.3+dfsg-1~exp1ubuntu2 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_13.1.0-6ubuntu1 liblz4-1_1.9.4-1 liblzma-dev_5.4.1-0.2 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.1.0-1 libmount1_2.38.1-5ubuntu2 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libncurses-dev_6.4-4 libncurses6_6.4-4 libncursesw6_6.4-4 libnettle8_3.8.1-2 libnghttp2-14_1.54.0-1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libp11-kit0_0.24.1-2ubuntu1 libpam-modules_1.5.2-6ubuntu1 libpam-modules-bin_1.5.2-6ubuntu1 libpam-runtime_1.5.2-6ubuntu1 libpam0g_1.5.2-6ubuntu1 libpcre2-8-0_10.42-1 libperl5.36_5.36.0-7ubuntu1 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-2 libpng16-16_1.6.39-2 libproc2-0_2:4.0.3-1ubuntu1 libprocps8_2:3.3.17-7ubuntu1 libpsl5_0.21.2-1 libquadmath0_13.1.0-6ubuntu1 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg1-1 libsasl2-modules-db_2.1.28+dfsg1-1 libseccomp2_2.5.4-1ubuntu3 libselinux1_3.4-1build4 libsemanage-common_3.4-1build4 libsemanage2_3.4-1build4 libsepol2_3.4-2.1 libsmartcols1_2.38.1-5ubuntu2 libsqlite3-0_3.40.1-2 libss2_1.47.0-1ubuntu1 libssh-4_0.10.5-2 libssl3_3.0.9-1ubuntu1 libstdc++-12-dev_12.3.0-3ubuntu1 libstdc++6_13.1.0-6ubuntu1 libsub-override-perl_0.09-4 libsystemd-shared_252.5-2ubuntu3 libsystemd0_252.5-2ubuntu3 libtasn1-6_4.19.0-2 libtinfo6_6.4-4 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libtsan2_13.1.0-6ubuntu1 libubsan1_13.1.0-6ubuntu1 libuchardet0_0.0.7-1build2 libudev1_252.5-2ubuntu3 libunistring2_1.0-2 libuuid1_2.38.1-5ubuntu2 libxml2_2.9.14+dfsg-1.2 libxxhash0_0.8.1-1 libzstd1_1.5.4+dfsg2-5 linux-libc-dev_6.3.0-7.7 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-1ubuntu1 lsb-base_11.6 lto-disabled-list_41 m4_1.4.19-3 make_4.3-4.1build1 man-db_2.11.2-2 mawk_1.3.4.20230525-1 mount_2.38.1-5ubuntu2 ncurses-base_6.4-4 ncurses-bin_6.4-4 openssl_3.0.9-1ubuntu1 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-7ubuntu1 perl-base_5.36.0-7ubuntu1 perl-modules-5.36_5.36.0-7ubuntu1 pinentry-curses_1.2.1-1ubuntu1 pkg-config_1.8.1-2 pkgbinarymangler_153 pkgconf_1.8.1-2 pkgconf-bin_1.8.1-2 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.3-1ubuntu1 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 systemd_252.5-2ubuntu3 systemd-sysv_252.5-2ubuntu3 sysvinit-utils_3.06-4ubuntu1 tabix_1.17+ds-1 tar_1.34+dfsg-1.2ubuntu1 tzdata_2023c-4exp1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_35ubuntu1 util-linux_2.38.1-5ubuntu2 util-linux-extra_2.38.1-5ubuntu2 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1ubuntu4 zlib1g-dev_1:1.2.13.dfsg-1ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: samtools Binary: samtools, samtools-test Architecture: any all Version: 1.17-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://www.htslib.org/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/samtools Vcs-Git: https://salsa.debian.org/med-team/samtools.git Testsuite: autopkgtest Testsuite-Triggers: tabix Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl , libncurses-dev, libhts-dev (>= 1.17~), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix, liblzma-dev, libbz2-dev Package-List: samtools deb science optional arch=any samtools-test deb science optional arch=all Checksums-Sha1: d1268bc344dfa232f8da9ff7b6f0daf7e25d4135 5459752 samtools_1.17.orig.tar.gz 9acd81361fad894450e6943c5d4faf2b334e09d5 22852 samtools_1.17-1.debian.tar.xz Checksums-Sha256: f76ec1880468ecaa5341a7256ae896f2cfb191193dbb683046776fb81e18af49 5459752 samtools_1.17.orig.tar.gz f4101dea7163f452f86363831eb43ae3a6921e54847e99081301106fd392d136 22852 samtools_1.17-1.debian.tar.xz Files: 1da0897ae626b75769e31efa9b8bf7a0 5459752 samtools_1.17.orig.tar.gz 071e15168e5850892703c53ccf502d53 22852 samtools_1.17-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmSUs24UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqCwxAAoya/uuqWmg9RqZLjywB3j9N384a0 UyulDt3+uKzixKf42gVQYt/DnqqpXoocCuHqjYqhrJbWQ712VhZOw2Blz5bqkL0r fbbRYg45hvm6zqSgzAzO8bYizIatkA8Fo5LNn9pLqAtZmcFHbsZlZCKdpcWSWKW+ NqF8tlRy9Rl6sOEncCOAfz7jrYvGeZgTCkwGb97EV2qNFqan0ZSwhT1hzaF2YKjW EGl3QSckPg+eJSApfLd+F43Eq1M9mwk9E5vVFMTyNlED5XVNI/lL3slRVYUhxuMl Zuxd1hbEH7aYFnnnhUH1zoDYQiFEkS9edTH+TK4Hhkm6ini0hOxmZXZNbbXwy9TW AWRKJRswSzoIkLQTippbjIloku7wV/pEf9aCQg6qgqPafjAsEMPn1oAHpB1hTLiU omZ8fZwwfD2+lhdwUG0iHP0hnJ/UerhqJd6YXD7wIhq9ION9UtHvVOrQ+F0O7ajM UBIbnaSHnhEODdvLe7qarEV9OnAHW2jJymje/7tz/RHofJydqJH4h5BWsxgITDLU lvfCSngLd6U/t+zxoiFFh9CIGwxxS0skk/CszQeVv7hx61Hbwo+k4M3JZzvz1VNE Q1a8lx0VOjhLwK1T58TQ45xwo6B+kyekb6r33Hbx/tZJy5eLO/pK3SzWbNKg0+XZ 4ORUGHuZYEIwwls= =bnPv -----END PGP SIGNATURE----- gpgv: Signature made Thu Jun 22 20:47:42 2023 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./samtools_1.17-1.dsc: no acceptable signature found dpkg-source: info: extracting samtools in /<> dpkg-source: info: unpacking samtools_1.17.orig.tar.gz dpkg-source: info: unpacking samtools_1.17-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible.patch dpkg-source: info: applying samtools-fasta-q-whatis.patch dpkg-source: info: applying typos.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-26332609 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26332609 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26332609 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 samtools dpkg-buildpackage: info: source version 1.17-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el dpkg-source: info: using options from samtools-1.17/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -f config.mk touch config.mk dh_auto_clean -- make -j4 distclean make[2]: Entering directory '/<>' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* cd test/reference && rm -f mpileup.*.fai rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview rm -f config.cache config.h config.log config.mk config.status rm -f TAGS rm -rf autom4te.cache make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files rm -fr -- debian/samtools/ debian/tmp/ debian/samtools-test/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal autoconf configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system ./configure --build=powerpc64le-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/powerpc64le-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j4 "CFLAGS=-g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>' gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.17"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c sed -i -e 's@/<>@«BUILDPATH»@g' version.h gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_samples.o bam_samples.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_consensus.o bam_consensus.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus_pileup.o consensus_pileup.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reference.o reference.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reset.o reset.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cram_size.o cram_size.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/samtools-1.17-1 -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o bam.o gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o samtools bam_aux.o bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_plbuf.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o bam_samples.o bam_consensus.o consensus_pileup.o reference.o reset.o cram_size.o ./lz4/lz4.o libst.a -lhts -lcurses -lm -lz -lpthread make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test -- BGZIP=/usr/bin/bgzip make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 BGZIP=/usr/bin/bgzip make[2]: Entering directory '/<>' test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip ${TEST_OPTS:-} test_reference: /<>/samtools reference test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 -e test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 -r 17:1000-1500 test/reference/mpileup.1.tmp.cram .. ok test_reference: /<>/samtools reference -@ 2 -r 17:1000-1500 -e test/reference/mpileup.1.tmp.cram .. ok /usr/bin/bgzip -c -b 65272 -s 5 /tmp/EVABEoGsaH/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/EVABEoGsaH/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/EVABEoGsaH/bgzip.dat.gz .. ok /<>/samtools faidx /tmp/EVABEoGsaH/faidx.fa 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/EVABEoGsaH/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/EVABEoGsaH/faidx.fa 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/EVABEoGsaH/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/EVABEoGsaH/faidx.fa 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/EVABEoGsaH/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/EVABEoGsaH/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /<>/samtools faidx /tmp/EVABEoGsaH/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /<>/samtools fqidx /tmp/EVABEoGsaH/fqidx.fq 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/EVABEoGsaH/fqidx.fq.gz 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/EVABEoGsaH/fqidx.fq 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/EVABEoGsaH/fqidx.fq.gz 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/EVABEoGsaH/fqidx.fq 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/EVABEoGsaH/fqidx.fq.gz 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/EVABEoGsaH/fqidx.fq 1:99998-100007 .. ok .. ok /<>/samtools fqidx /tmp/EVABEoGsaH/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /<>/test/dat/dict.fa .. ok test_dict: /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/EVABEoGsaH/dict.fa.gz .. ok test_dict: cat /<>/test/dat/dict.fa | /<>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /<>/samtools dict -AH < /<>/test/dat/dict.alias.fa .. ok test_dict: /<>/samtools dict -H -l /<>/test/dat/dict.alt < /<>/test/dat/dict.alias.fa .. ok test_index: /<>/samtools view /tmp/EVABEoGsaH/large_chrom.bam ref2 .. ok test_index: /<>/samtools view /tmp/EVABEoGsaH/large_chrom.bam ref2:1-541556283 .. ok test_index: /<>/samtools index /<>/test/dat/test_input_1_a.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/EVABEoGsaH/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/EVABEoGsaH/test_input_1_b.bam.bai .. ok test_index: /<>/samtools merge -O sam - -X -cp -R ref2 /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_a.bam.bai /tmp/EVABEoGsaH/test_input_1_b.bam.bai .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/EVABEoGsaH/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /<>/samtools index /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam .. ok test_index: /<>/samtools index -M /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.bam /tmp/EVABEoGsaH/auto_indexed.csi && cat /tmp/EVABEoGsaH/auto_indexed.csi .. ok test_index: /<>/samtools index /<>/test/dat/auto_indexed.tmp.cram /tmp/EVABEoGsaH/auto_indexed.crai && cat /tmp/EVABEoGsaH/auto_indexed.crai .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.sam /tmp/EVABEoGsaH/auto_indexed.csi && cat /tmp/EVABEoGsaH/auto_indexed.csi .. ok test_index: /<>/samtools view -@ 2 /tmp/EVABEoGsaH/large_chrom.bam ref2 .. ok test_index: /<>/samtools view -@ 2 /tmp/EVABEoGsaH/large_chrom.bam ref2:1-541556283 .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/test_input_1_a.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/EVABEoGsaH/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/EVABEoGsaH/test_input_1_b.bam.bai .. ok test_index: /<>/samtools merge -@ 2 -O sam - -X -cp -R ref2 /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_a.bam.bai /tmp/EVABEoGsaH/test_input_1_b.bam.bai .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/EVABEoGsaH/test_input_1_b_opt.bam.bai ref2 .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam .. ok test_index: /<>/samtools index -@ 2 -M /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam && cat /<>/test/dat/test_input_1_a.bam.bai .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.bam /tmp/EVABEoGsaH/auto_indexed.csi && cat /tmp/EVABEoGsaH/auto_indexed.csi .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/auto_indexed.tmp.cram /tmp/EVABEoGsaH/auto_indexed.crai && cat /tmp/EVABEoGsaH/auto_indexed.crai .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.sam /tmp/EVABEoGsaH/auto_indexed.csi && cat /tmp/EVABEoGsaH/auto_indexed.csi .. ok test_mpileup: /<>/samtools mpileup -b /tmp/EVABEoGsaH/mpileup.bam.list -f /tmp/EVABEoGsaH/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/EVABEoGsaH/mpileup.cram.list -f /tmp/EVABEoGsaH/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/EVABEoGsaH/mpileup.bam.urllist -f /tmp/EVABEoGsaH/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/EVABEoGsaH/mpileup.cram.urllist -f /tmp/EVABEoGsaH/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/EVABEoGsaH/mpileup.ref.fa.gz -r17:1050-1060 /tmp/EVABEoGsaH/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/EVABEoGsaH/mpileup.ref.fa.gz -r17:1050-1060 /tmp/EVABEoGsaH/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup /<>/test/mpileup/overlap.bam | grep 128814202 .. ok test_usage: samtools samtools has subcommands: dict, faidx, fqidx, index, calmd, fixmate, reheader, targetcut, addreplacerg, markdup, ampliconclip, collate, cat, consensus, merge, mpileup, sort, split, quickcheck, fastq, fasta, import, reference, reset, bedcov, coverage, depth, flagstat, idxstats, phase, stats, ampliconstats, flags, head, tview, view, depad, samples, help, version .. ok test_usage_subcommand: samtools dict Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools faidx .. ok test_usage_subcommand: samtools fqidx .. ok test_usage_subcommand: samtools index .. ok test_usage_subcommand: samtools calmd Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools fixmate .. ok test_usage_subcommand: samtools reheader Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools targetcut Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools addreplacerg .. ok test_usage_subcommand: samtools markdup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools ampliconclip Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools collate .. ok test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools consensus .. ok test_usage_subcommand: samtools merge .. ok test_usage_subcommand: samtools mpileup Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools sort .. ok test_usage_subcommand: samtools split .. ok test_usage_subcommand: samtools quickcheck .. ok test_usage_subcommand: samtools fastq .. ok test_usage_subcommand: samtools fasta .. ok test_usage_subcommand: samtools import .. ok test_usage_subcommand: samtools reference .. ok test_usage_subcommand: samtools reset .. ok test_usage_subcommand: samtools bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth .. ok test_usage_subcommand: samtools flagstat .. ok test_usage_subcommand: samtools idxstats .. ok test_usage_subcommand: samtools phase Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools stats .. ok test_usage_subcommand: samtools ampliconstats .. ok test_usage_subcommand: samtools flags .. ok test_usage_subcommand: samtools head .. ok test_usage_subcommand: samtools tview Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools view .. ok test_usage_subcommand: samtools depad Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools samples Usage on stderr rather than stdout .. expected failure test_view: Generating test data file .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/EVABEoGsaH/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/EVABEoGsaH/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/EVABEoGsaH/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/EVABEoGsaH/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/EVABEoGsaH/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/EVABEoGsaH/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/EVABEoGsaH/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/EVABEoGsaH/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/EVABEoGsaH/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/EVABEoGsaH/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/EVABEoGsaH/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/EVABEoGsaH/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/EVABEoGsaH/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/EVABEoGsaH/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/EVABEoGsaH/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/EVABEoGsaH/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/EVABEoGsaH/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/EVABEoGsaH/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/EVABEoGsaH/view.001.forn (SAM input) .. ok 68: Count -N /tmp/EVABEoGsaH/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/EVABEoGsaH/view.001.forn (BAM input) .. ok 70: Count -N /tmp/EVABEoGsaH/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/EVABEoGsaH/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/EVABEoGsaH/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok 74: Count -d BC (SAM input) .. ok 75: Filter -d BC (BAM input) .. ok 76: Count -d BC (BAM input) .. ok 77: Filter -d BC (CRAM input) .. ok 78: Count -d BC (CRAM input) .. ok 79: Filter -d BC:TGCA (SAM input) .. ok 80: Count -d BC:TGCA (SAM input) .. ok 81: Filter -d BC:TGCA (BAM input) .. ok 82: Count -d BC:TGCA (BAM input) .. ok 83: Filter -d BC:TGCA (CRAM input) .. ok 84: Count -d BC:TGCA (CRAM input) .. ok 85: Filter -D BC:/tmp/EVABEoGsaH/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/EVABEoGsaH/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/EVABEoGsaH/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/EVABEoGsaH/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/EVABEoGsaH/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/EVABEoGsaH/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/EVABEoGsaH/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/EVABEoGsaH/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/EVABEoGsaH/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/EVABEoGsaH/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/EVABEoGsaH/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/EVABEoGsaH/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/EVABEoGsaH/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/EVABEoGsaH/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/EVABEoGsaH/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/EVABEoGsaH/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/EVABEoGsaH/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/EVABEoGsaH/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/EVABEoGsaH/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/EVABEoGsaH/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/EVABEoGsaH/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/EVABEoGsaH/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/EVABEoGsaH/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/EVABEoGsaH/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok 110: Count -d NE:TGCA (SAM input) .. ok 111: Filter -d NE:TGCA (BAM input) .. ok 112: Count -d NE:TGCA (BAM input) .. ok 113: Filter -d NE:TGCA (CRAM input) .. ok 114: Count -d NE:TGCA (CRAM input) .. ok 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/EVABEoGsaH/view.test115.sam -h -d TGCA /tmp/EVABEoGsaH/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/EVABEoGsaH/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/EVABEoGsaH/view.test117.sam -h -d TGCA /tmp/EVABEoGsaH/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/EVABEoGsaH/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -o /tmp/EVABEoGsaH/view.test119.sam -h -d TGCA /tmp/EVABEoGsaH/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /<>/samtools view -c -d TGCA /tmp/EVABEoGsaH/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/EVABEoGsaH/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EVABEoGsaH/view.001.fobc" Failed command: /<>/samtools view -o /tmp/EVABEoGsaH/view.test121.sam -h -D BClong:/tmp/EVABEoGsaH/view.001.fobc /tmp/EVABEoGsaH/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/EVABEoGsaH/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EVABEoGsaH/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/EVABEoGsaH/view.001.fobc /tmp/EVABEoGsaH/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/EVABEoGsaH/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EVABEoGsaH/view.001.fobc" Failed command: /<>/samtools view -o /tmp/EVABEoGsaH/view.test123.sam -h -D BClong:/tmp/EVABEoGsaH/view.001.fobc /tmp/EVABEoGsaH/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/EVABEoGsaH/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EVABEoGsaH/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/EVABEoGsaH/view.001.fobc /tmp/EVABEoGsaH/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/EVABEoGsaH/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EVABEoGsaH/view.001.fobc" Failed command: /<>/samtools view -o /tmp/EVABEoGsaH/view.test125.sam -h -D BClong:/tmp/EVABEoGsaH/view.001.fobc /tmp/EVABEoGsaH/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/EVABEoGsaH/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/EVABEoGsaH/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/EVABEoGsaH/view.001.fobc /tmp/EVABEoGsaH/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -o /tmp/EVABEoGsaH/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/EVABEoGsaH/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/EVABEoGsaH/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -o /tmp/EVABEoGsaH/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/EVABEoGsaH/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/EVABEoGsaH/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -o /tmp/EVABEoGsaH/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/EVABEoGsaH/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /<>/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/EVABEoGsaH/view.test006.cram --no-PG .. expected failure 133: Filter -d NM:13 (SAM input) .. ok 134: Count -d NM:13 (SAM input) .. ok 135: Filter -d NM:13 (BAM input) .. ok 136: Count -d NM:13 (BAM input) .. ok 137: Filter -d NM:13 (CRAM input) .. ok 138: Count -d NM:13 (CRAM input) .. ok 139: Filter -d ab:z (SAM input) .. ok 140: Count -d ab:z (SAM input) .. ok 141: Filter -d ab:z (BAM input) .. ok 142: Count -d ab:z (BAM input) .. ok 143: Filter -d ab:z (CRAM input) .. ok 144: Count -d ab:z (CRAM input) .. ok 145: Filter -l Library 2 (SAM input) .. ok 146: Count -l Library 2 (SAM input) .. ok 147: Filter -l Library 2 (BAM input) .. ok 148: Count -l Library 2 (BAM input) .. ok 149: Filter -l Library 2 (CRAM input) .. ok 150: Count -l Library 2 (CRAM input) .. ok 151: Filter -l Library 3 (SAM input) .. ok 152: Count -l Library 3 (SAM input) .. ok 153: Filter -l Library 3 (BAM input) .. ok 154: Count -l Library 3 (BAM input) .. ok 155: Filter -l Library 3 (CRAM input) .. ok 156: Count -l Library 3 (CRAM input) .. ok 157: Filter -q 50 (SAM input) .. ok 158: Count -q 50 (SAM input) .. ok 159: Filter -q 50 (BAM input) .. ok 160: Count -q 50 (BAM input) .. ok 161: Filter -q 50 (CRAM input) .. ok 162: Count -q 50 (CRAM input) .. ok 163: Filter -q 99 (SAM input) .. ok 164: Count -q 99 (SAM input) .. ok 165: Filter -q 99 (BAM input) .. ok 166: Count -q 99 (BAM input) .. ok 167: Filter -q 99 (CRAM input) .. ok 168: Count -q 99 (CRAM input) .. ok 169: Filter -q 100 (SAM input) .. ok 170: Count -q 100 (SAM input) .. ok 171: Filter -q 100 (BAM input) .. ok 172: Count -q 100 (BAM input) .. ok 173: Filter -q 100 (CRAM input) .. ok 174: Count -q 100 (CRAM input) .. ok 175: Filter -x fa (SAM input) .. ok 176: Count -x fa (SAM input) .. ok 177: Filter -x fa (BAM input) .. ok 178: Count -x fa (BAM input) .. ok 179: Filter -x fa (CRAM input) .. ok 180: Count -x fa (CRAM input) .. ok 181: Filter -x fa -x ha (SAM input) .. ok 182: Count -x fa -x ha (SAM input) .. ok 183: Filter -x fa -x ha (BAM input) .. ok 184: Count -x fa -x ha (BAM input) .. ok 185: Filter -x fa -x ha (CRAM input) .. ok 186: Count -x fa -x ha (CRAM input) .. ok 187: Filter -x fa,ha (SAM input) .. ok 188: Count -x fa,ha (SAM input) .. ok 189: Filter -x fa,ha (BAM input) .. ok 190: Count -x fa,ha (BAM input) .. ok 191: Filter -x fa,ha (CRAM input) .. ok 192: Count -x fa,ha (CRAM input) .. ok 193: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 194: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 195: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 196: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 197: Filter -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 198: Count -x ^RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 199: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 200: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (SAM input).. ok 201: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 202: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (BAM input).. ok 203: Filter --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 204: Count --keep-tag RG,BC,NM,MD,H0,aa,ab,za,ba,bb,bc,bd,be,bf,bg,ia (CRAM input).. ok 205: Filter -x fa -r grp2 (SAM input) .. ok 206: Count -x fa -r grp2 (SAM input) .. ok 207: Filter -x fa -r grp2 (BAM input) .. ok 208: Count -x fa -r grp2 (BAM input) .. ok 209: Filter -x fa -r grp2 (CRAM input) .. ok 210: Count -x fa -r grp2 (CRAM input) .. ok 211: Filter -x RG -r grp2 (SAM input) .. ok 212: Count -x RG -r grp2 (SAM input) .. ok 213: Filter -x RG -r grp2 (BAM input) .. ok 214: Count -x RG -r grp2 (BAM input) .. ok 215: Filter -x RG -r grp2 (CRAM input) .. ok 216: Count -x RG -r grp2 (CRAM input) .. ok 217: Filter -m 10 (SAM input) .. ok 218: Count -m 10 (SAM input) .. ok 219: Filter -m 10 (BAM input) .. ok 220: Count -m 10 (BAM input) .. ok 221: Filter -m 10 (CRAM input) .. ok 222: Count -m 10 (CRAM input) .. ok 223: Filter -m 11 (SAM input) .. ok 224: Count -m 11 (SAM input) .. ok 225: Filter -m 11 (BAM input) .. ok 226: Count -m 11 (BAM input) .. ok 227: Filter -m 11 (CRAM input) .. ok 228: Count -m 11 (CRAM input) .. ok 229: Filter -m 15 (SAM input) .. ok 230: Count -m 15 (SAM input) .. ok 231: Filter -m 15 (BAM input) .. ok 232: Count -m 15 (BAM input) .. ok 233: Filter -m 15 (CRAM input) .. ok 234: Count -m 15 (CRAM input) .. ok 235: Filter -m 16 (SAM input) .. ok 236: Count -m 16 (SAM input) .. ok 237: Filter -m 16 (BAM input) .. ok 238: Count -m 16 (BAM input) .. ok 239: Filter -m 16 (CRAM input) .. ok 240: Count -m 16 (CRAM input) .. ok 241: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 242: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 243: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 244: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 245: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 246: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 247: Filter -e [BC] (SAM input) .. ok 248: Count -e [BC] (SAM input) .. ok 249: Filter -e [BC] (BAM input) .. ok 250: Count -e [BC] (BAM input) .. ok 251: Filter -e [BC] (CRAM input) .. ok 252: Count -e [BC] (CRAM input) .. ok 253: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 254: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 255: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 256: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 257: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 258: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 259: Filter -e mapq >= 50 (SAM input) .. ok 260: Count -e mapq >= 50 (SAM input) .. ok 261: Filter -e mapq >= 50 (BAM input) .. ok 262: Count -e mapq >= 50 (BAM input) .. ok 263: Filter -e mapq >= 50 (CRAM input) .. ok 264: Count -e mapq >= 50 (CRAM input) .. ok 265: Filter -e mapq >= 99 (SAM input) .. ok 266: Count -e mapq >= 99 (SAM input) .. ok 267: Filter -e mapq >= 99 (BAM input) .. ok 268: Count -e mapq >= 99 (BAM input) .. ok 269: Filter -e mapq >= 99 (CRAM input) .. ok 270: Count -e mapq >= 99 (CRAM input) .. ok 271: Filter -e mapq >= 100 (SAM input) .. ok 272: Count -e mapq >= 100 (SAM input) .. ok 273: Filter -e mapq >= 100 (BAM input) .. ok 274: Count -e mapq >= 100 (BAM input) .. ok 275: Filter -e mapq >= 100 (CRAM input) .. ok 276: Count -e mapq >= 100 (CRAM input) .. ok 277: 1bp reads file SAM -> BAM -> SAM .. ok 278: 1bp reads file SAM -> CRAM -> SAM .. ok 278: Region Z (BAM input) .. ok 279: Count Z (BAM input) .. ok 280: Region Z (CRAM input) .. ok 281: Count Z (CRAM input) .. ok 282: Region Z:30 (BAM input) .. ok 283: Count Z:30 (BAM input) .. ok 284: Region Z:30 (CRAM input) .. ok 285: Count Z:30 (CRAM input) .. ok 286: Region Z:20-40 (BAM input) .. ok 287: Count Z:20-40 (BAM input) .. ok 288: Region Z:20-40 (CRAM input) .. ok 289: Count Z:20-40 (CRAM input) .. ok 290: Region ref1 (BAM input) .. ok 291: Count ref1 (BAM input) .. ok 292: Region ref1 (CRAM input) .. ok 293: Count ref1 (CRAM input) .. ok 294: Region ref1:15 (BAM input) .. ok 295: Count ref1:15 (BAM input) .. ok 296: Region ref1:15 (CRAM input) .. ok 297: Count ref1:15 (CRAM input) .. ok 298: Region ref1:15-45 (BAM input) .. ok 299: Count ref1:15-45 (BAM input) .. ok 300: Region ref1:15-45 (CRAM input) .. ok 301: Count ref1:15-45 (CRAM input) .. ok 302: Region ref1:15-45 ref2 (BAM input) .. ok 303: Count ref1:15-45 ref2 (BAM input) .. ok 304: Region ref1:15-45 ref2 (CRAM input) .. ok 305: Count ref1:15-45 ref2 (CRAM input) .. ok 306: Region ref1:15-45 ref2:16 (BAM input) .. ok 307: Count ref1:15-45 ref2:16 (BAM input) .. ok 308: Region ref1:15-45 ref2:16 (CRAM input) .. ok 309: Count ref1:15-45 ref2:16 (CRAM input) .. ok 310: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 311: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 312: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 313: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 314: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 315: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 316: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 317: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 318: Region -f 128 ref1 (BAM input) .. ok 319: Count -f 128 ref1 (BAM input) .. ok 320: Region -f 128 ref1 (CRAM input) .. ok 321: Count -f 128 ref1 (CRAM input) .. ok 322: Region -q 50 ref1:15-45 (BAM input) .. ok 323: Count -q 50 ref1:15-45 (BAM input) .. ok 324: Region -q 50 ref1:15-45 (CRAM input) .. ok 325: Count -q 50 ref1:15-45 (CRAM input) .. ok 326: Region -r grp2 ref1:15-45 (BAM input) .. ok 327: Count -r grp2 ref1:15-45 (BAM input) .. ok 328: Region -r grp2 ref1:15-45 (CRAM input) .. ok 329: Count -r grp2 ref1:15-45 (CRAM input) .. ok 330: Region * (BAM input) .. ok 331: Count * (BAM input) .. ok 332: Region * (CRAM input) .. ok 333: Count * (CRAM input) .. ok 334: Region -L /<>/test/dat/view.002.01.bed (BAM input).. ok 335: Count -L /<>/test/dat/view.002.01.bed (BAM input).. ok 336: Region -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 337: Count -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 338: Region -L /<>/test/dat/view.002.02.bed (BAM input).. ok 339: Count -L /<>/test/dat/view.002.02.bed (BAM input).. ok 340: Region -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 341: Count -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 342: Region -L /<>/test/dat/view.001.01.bed (BAM input).. ok 343: Count -L /<>/test/dat/view.001.01.bed (BAM input).. ok 344: Region -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 345: Count -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 346: Region -L /<>/test/dat/view.001.02.bed (BAM input).. ok 347: Count -L /<>/test/dat/view.001.02.bed (BAM input).. ok 348: Region -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 349: Count -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 350: Region -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 351: Count -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 352: Region -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 353: Count -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 354: Region -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 355: Count -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 356: Region -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 357: Count -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 358: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 359: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 360: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 361: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 362: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 363: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 364: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 365: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 366: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 367: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 368: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 369: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 370: Region -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 371: Count -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 372: Region -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 373: Count -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 374: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 375: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 376: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 377: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 378: Region -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 379: Count -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 380: Region -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 381: Count -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 382: Region -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 383: Count -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 384: Region -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 385: Count -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 386: Region -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 387: Count -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 388: Region -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 389: Count -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 390: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 391: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 392: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 393: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 394: Region -L /<>/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 395: Count -L /<>/test/dat/view.001.01.bed -M --unmap (BAM input).. ok 396: Region -L /<>/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 397: Count -L /<>/test/dat/view.001.01.bed -M --unmap (CRAM input).. ok 398: Region -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 399: Count -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (BAM input).. ok 400: Region -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 401: Count -L /<>/test/dat/view.001.01.bed -M --unmap ref1:11-30 (CRAM input).. ok 402: Make BAM with no M5/UR tags .. ok 403: Add @SQ with -t (SAM -> SAM) .. ok 404: Add @SQ with -T (SAM -> SAM) .. ok 405: Add @SQ with -t (BAM -> SAM) .. ok 406: Add @SQ with -T (BAM -> SAM) .. ok 407: Add @SQ with -t (SAM -> BAM) .. ok 408: Add @SQ with -T (SAM -> BAM) .. ok 409: Add @SQ with -t (BAM -> BAM) .. ok 410: Add @SQ with -T (BAM -> BAM) .. ok 411: Add @SQ with -t (SAM -> CRAM) .. ok 412: Add @SQ with -T (SAM -> CRAM) .. ok 413: Add @SQ with -t (BAM -> CRAM) .. ok 414: Add @SQ with -T (BAM -> CRAM) .. ok 415: Make CRAM with no UR field .. ok 416: Decoding CRAM with no UR field via -T .. ok 417: CIGAR B-operator removal .. ok 418: Big SAM -> BAM .. ok 419: Big SAM -> BAM (2 threads) .. ok 420: Big SAM -> BAM (4 threads) .. ok 421: Big SAM -> CRAM .. ok 422: Big SAM -> CRAM (2 threads) .. ok 423: Big SAM -> CRAM (4 threads) .. ok 424: Subsample 0.2 (SAM input) ............ ok 425: Subsample 0.5 (SAM input) ............ ok 426: Subsample 0.8 (SAM input) ............ ok 427: Subsample 0.2 (BAM input) ............ ok 428: Subsample 0.5 (BAM input) ............ ok 429: Subsample 0.8 (BAM input) ............ ok 430: Subsample 0.2 (CRAM input) ............ ok 431: Subsample 0.5 (CRAM input) ............ ok 432: Subsample 0.8 (CRAM input) ............ ok 433: SAM add PG .. ok 434: Unset dup flag, remove dt and do tags .. ok 435: Unmap dup flagged reads. .. ok 436: Unmap dup flagged reads. .. ok 437: fetch pairs .. ok 438: fetch pairs .. ok 439: fetch pairs .. ok test_head: /<>/samtools head /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 0 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 1 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 5 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 29 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 30 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -n 0 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -n 1 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -n 5 /<>/test/dat/view.001.sam .. ok test_head: /<>/samtools head -h 5 -n 5 < /<>/test/dat/view.001.sam .. ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_import: /<>/samtools import -0 test/bam2fq/1.1.fq.expected | /<>/samtools fastq -0 /<>/test/0.fq .. ok test_import: /<>/samtools import -s test/bam2fq/1.1.fq.expected | /<>/samtools fastq -0 /<>/test/0.fq .. ok test_import: /<>/samtools import -s test/bam2fq/5.s.fq.expected | /<>/samtools fastq -s /<>/test/s.fq .. ok test_import: /<>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /<>/samtools fastq -N -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /<>/samtools fastq -i --index-format 'i*i*' -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /<>/samtools fastq --barcode-tag OX -i --index-format 'i*i*' -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /<>/samtools fastq -N -T RG,BC,QT -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /<>/samtools fastq -N -T RG,BC,QT,MD,ia -1 /<>/test/1.fq -2 /<>/test/2.fq .. ok test_import: /<>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /<>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /<>/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /<>/samtools import test/import/2.interleaved.fq -T "" .. ok test_import: /<>/samtools import test/import/3.interleaved.fq -i .. ok test_import: /<>/samtools import test/import/4.aux.fq -T "*" .. ok test_import: /<>/samtools import test/import/4.aux.fq -T "" .. ok test_import: /<>/samtools import test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /<>/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq .. ok test_import: /<>/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.002.sam .. ok test_bam2fq: /<>/samtools fastq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.003.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.010.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /<>/test/bc_split.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -N -t -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -N -t -T MD,ia -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -i --index-format 'i*i*' -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.703.sam .. ok test_bam2fq: /<>/samtools fastq -N -1 /<>/test/o.fq -2 /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fasta -N -1 /<>/test/o.fa -2 /<>/test/o.fa /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -s /tmp/EVABEoGsaH/bam2fq.discard.s.fq -0 /tmp/EVABEoGsaH/bam2fq.discard.0.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -T ba,bb,bc,bd,be,bf,bg /<>/test/dat/bam2fq.013.sam .. ok test_bam2fq: /<>/samtools fastq --index-format 'i8n1i8' --i1 /<>/test/i1.fq --i2 /<>/test/i2.fq -0 /<>/test/0.fq /<>/test/dat/bam2fq.014.sam .. ok test_bam2fq: /<>/samtools fastq -N -T '*' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -T '' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -t -T '*' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /<>/samtools fastq -@ 2 -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.002.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.003.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /<>/test/bc.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.010.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /<>/test/bc_split.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -t -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -t -T MD,ia -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.004.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /<>/test/i.fq -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -i --index-format 'i*i*' -s /<>/test/s.fq -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.005.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -1 /<>/test/1.fq -2 /<>/test/2.fq /<>/test/dat/bam2fq.703.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -1 /<>/test/o.fq -2 /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fasta -@ 2 -N -1 /<>/test/o.fa -2 /<>/test/o.fa /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -s /tmp/EVABEoGsaH/bam2fq.discard.s.fq -0 /tmp/EVABEoGsaH/bam2fq.discard.0.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /<>/test/dat/bam2fq.013.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 --index-format 'i8n1i8' --i1 /<>/test/i1.fq --i2 /<>/test/i2.fq -0 /<>/test/0.fq /<>/test/dat/bam2fq.014.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -T '*' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -T '' /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -t -T '*' /<>/test/dat/bam2fq.001.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa -i 0 /<>/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/stat/test.fa /<>/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -S RG -r /<>/test/stat/test.fa /<>/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -S RG -r /<>/test/stat/test.fa /<>/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -t /<>/test/stat/11.stats.targets /<>/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /<>/samtools stats -g 4 -t /<>/test/stat/11.stats.targets /<>/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /<>/samtools stats -g 4 /<>/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -t /<>/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -p -t /<>/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -t /<>/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/12_overlaps.bam -p -t /<>/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /<>/samtools stats /<>/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /<>/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /<>/samtools stats -I s1 /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -I grp2 /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -I grp3 /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -I Sample /<>/test/stat/11_target.bam | tail -n+4 .. ok test_stats: /<>/samtools stats -r /<>/test/mpileup/ce.fa /<>/test/stat/15.big_del.sam | tail -n+4 .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_c.bam .. ok test_merge: /<>/samtools merge -s 1 -O sam -b /tmp/Qj02ErgQhx - /<>/test/dat/test_input_1_a.bam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_b.bam .. ok test_merge: /<>/samtools merge -r -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -cp -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam .. ok test_merge: /<>/samtools merge -s 1 -O sam - /<>/test/dat/test_input_1_a_regex.sam /<>/test/dat/test_input_1_b_regex.sam .. ok test_merge: /<>/samtools merge -o - -s 1 -O sam /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/EVABEoGsaH/merge.tag.1.bam /tmp/EVABEoGsaH/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/EVABEoGsaH/merge.tag.3.bam /tmp/EVABEoGsaH/merge.tag.4.bam .. ok test_merge: /<>/samtools merge --no-PG -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /<>/samtools merge --no-PG -O SAM -L /<>/test/merge/merge.bed - /tmp/EVABEoGsaH/merge.bed.1.bam /tmp/EVABEoGsaH/merge.bed.2.bam .. ok test_merge: /<>/samtools merge --no-PG -r -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a.bam /<>/test/dat/test_input_1_b.bam /<>/test/dat/test_input_1_c.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam -b /tmp/CO6OiFdrEK - /<>/test/dat/test_input_1_a.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_b.bam .. ok test_merge: /<>/samtools merge -@ 2 -r -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -cp -s 1 -O sam - /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -O sam - /<>/test/dat/test_input_1_a_regex.sam /<>/test/dat/test_input_1_b_regex.sam .. ok test_merge: /<>/samtools merge -@ 2 -o - -s 1 -O sam /<>/test/dat/test_input_1_a.sam /<>/test/dat/test_input_1_b.sam /<>/test/dat/test_input_1_c.sam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/EVABEoGsaH/merge.tag.1.bam /tmp/EVABEoGsaH/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/EVABEoGsaH/merge.tag.3.bam /tmp/EVABEoGsaH/merge.tag.4.bam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -O SAM -L /<>/test/merge/merge.bed - /tmp/EVABEoGsaH/merge.bed.1.bam /tmp/EVABEoGsaH/merge.bed.2.bam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -r -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_sort: /<>/samtools sort /<>/test/dat/test_input_1_a.bam /tmp/EVABEoGsaH/sortout .. ok test_sort: /<>/samtools sort -f /<>/test/dat/test_input_1_a.bam /tmp/EVABEoGsaH/sortout.bam .. ok test_sort: /<>/samtools sort -o /<>/test/dat/test_input_1_a.bam /tmp/EVABEoGsaH/sorttmp .. ok test_sort: /<>/samtools sort -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -n -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -n -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -t AS -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -t FI -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort --template-coordinate -m 10M /<>/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 /<>/test/dat/test_input_1_a.bam /tmp/EVABEoGsaH/sortout .. ok test_sort: /<>/samtools sort -@ 2 -f /<>/test/dat/test_input_1_a.bam /tmp/EVABEoGsaH/sortout.bam .. ok test_sort: /<>/samtools sort -@ 2 -o /<>/test/dat/test_input_1_a.bam /tmp/EVABEoGsaH/sorttmp .. ok test_sort: /<>/samtools sort -@ 2 -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -n -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -n -t RG -m 10M /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t AS -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t FI -m 10M /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 --template-coordinate -m 10M /<>/test/sort/template-coordinate.sort.sam -O SAM -o - .. ok test_collate: /<>/samtools collate --output-fmt=sam -O /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -o /<>/test/collate/collate1.tmp.sam /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -o /<>/test/collate/collate2.tmp.sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate2.tmp .. ok test_collate: /<>/samtools collate --output-fmt=sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate3.tmp .. ok test_collate: /<>/samtools collate --output-fmt=sam -f /<>/test/collate/fast_collate.sam -o /<>/test/collate/1_fast_collate.sam .. ok test_collate: /<>/samtools collate --output-fmt=sam -f -r 4 /<>/test/collate/fast_collate.sam -o /<>/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -O /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -@ 2 -o /<>/test/collate/collate1.tmp.sam /<>/test/dat/test_input_1_d.sam .. ok test_collate: /<>/samtools collate -@ 2 -o /<>/test/collate/collate2.tmp.sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate2.tmp .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam /<>/test/dat/test_input_1_d.sam /<>/test/collate/collate3.tmp .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -f /<>/test/collate/fast_collate.sam -o /<>/test/collate/1_fast_collate.sam .. ok test_collate: /<>/samtools collate -@ 2 --output-fmt=sam -f -r 4 /<>/test/collate/fast_collate.sam -o /<>/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /<>/samtools fixmate -z off -O sam /<>/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /<>/samtools fixmate -cO sam /<>/test/fixmate/5_ct.sam - .. ok test_fixmate: /<>/samtools fixmate -cO sam /<>/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /<>/samtools fixmate -z off -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -z off -O sam /<>/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/sanitize.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /<>/samtools fixmate -@ 2 -z off -O sam /<>/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -cO sam /<>/test/fixmate/5_ct.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -cO sam /<>/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -z off -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -z off -O sam /<>/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/sanitize.sam - .. ok /<>/samtools calmd -uAr /<>/test/dat/mpileup.1.sam /<>/test/dat/mpileup.ref.fa .. ok /<>/samtools calmd -@ 2 -uAr /<>/test/dat/mpileup.1.sam /<>/test/dat/mpileup.ref.fa .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.bam .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.cram .. ok test_idxstat: /<>/samtools idxstats /<>/test/dat/test_input_1_a.sam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /<>/samtools quickcheck /<>/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /<>/samtools quickcheck -v /<>/test/quickcheck/1.quickcheck.badeof.bam /<>/test/quickcheck/2.quickcheck.badheader.bam /<>/test/quickcheck/3.quickcheck.ok.bam /<>/test/quickcheck/4.quickcheck.ok.bam /<>/test/quickcheck/5.quickcheck.scramble30.truncated.cram /<>/test/quickcheck/6.quickcheck.cram21.ok.cram /<>/test/quickcheck/7.quickcheck.cram30.ok.cram /<>/test/quickcheck/8.quickcheck.cram21.truncated.cram /<>/test/quickcheck/9.quickcheck.cram30.truncated.cram /<>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /<>/samtools quickcheck -uv /<>/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.bam | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v21.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v30.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader --in-place /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v21.cram && /<>/samtools view -h --no-PG /<>/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader --in-place /<>/test/reheader/hdr.sam /<>/test/dat/view.001.tmp.v30.cram && /<>/samtools view -h --no-PG /<>/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<>/test/dat/view.001.tmp.bam | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /<>/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /<>/test/dat/view.001.tmp.v30.cram | /<>/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m overwrite_all /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m orphan_only /<>/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -R '1#9' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m overwrite_all /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m orphan_only /<>/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -R '1#9' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /<>/test/addrprg/1_fixup.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /<>/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /<>/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /<>/test/addrprg/1_fixup.sam .. ok test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/3_missing_mc.sam - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. samtools markdup: error, unable to assign pair hash key. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/4_missing_ms.sam - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/5_markdup.sam - .. ok test_markdup: /<>/samtools markdup -O sam -r --no-PG /<>/test/markdup/6_remove_dups.sam - .. ok test_markdup: /<>/samtools markdup -S -O sam --no-PG /<>/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /<>/test/markdup/8_optical_dup.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<>/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t -O sam --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /<>/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /<>/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t --barcode-name -O sam --no-PG /<>/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /<>/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /<>/samtools markdup -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /<>/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /<>/samtools markdup -d 100 --mode s -t --use-read-groups -O sam --no-PG /<>/test/markdup/17_read_group.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: samtools markdup: error, queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/2_bad_order.sam - ERR: samtools markdup: error, not in coordinate sorted order. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/3_missing_mc.sam - ERR: samtools markdup: error, no MC tag. Please run samtools fixmate on file first. samtools markdup: error, unable to assign pair hash key. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/4_missing_ms.sam - ERR: samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. samtools markdup: error, no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /<>/samtools markdup -@ 2 -O sam --no-PG /<>/test/markdup/5_markdup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -O sam -r --no-PG /<>/test/markdup/6_remove_dups.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -O sam --no-PG /<>/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /<>/test/markdup/8_optical_dup.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /<>/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+):([[:digit:]]+)$' --no-PG -S /<>/test/markdup/10_optical_chain.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+):([[:print:]]+)' --coords-order xyt --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --read-coords '^([0-9]+):([0-9]+)' --coords-order xy --no-PG /<>/test/markdup/11_optical_dup_regex.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 2500 --mode s -t -O sam --read-coords '([[:digit:]]+):([[:digit:]]+)$' --coords-order xy --no-PG /<>/test/markdup/12_optical_chain_regex.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-tag BX -O sam --no-PG /<>/test/markdup/13_optical_barcode_tag.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-name -O sam --no-PG /<>/test/markdup/14_optical_barcode_name.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]+):([0-9]+)' --coords-order xy -O sam --no-PG /<>/test/markdup/15_optical_barcode_rgx_name.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -S -d 100 --mode s -t --barcode-rgx '^([!-9;-?A-~]+):[0-9]+:' --read-coords '^[!-9;-?A-~]+:([0-9]{4})([0-9]{4})' --coords-order xy -O sam --no-PG /<>/test/markdup/16_optical_barcode_rgx_name_test_2.sam - .. ok test_markdup: /<>/samtools markdup -@ 2 -d 100 --mode s -t --use-read-groups -O sam --no-PG /<>/test/markdup/17_read_group.sam - .. ok test_bedcov: /<>/samtools bedcov /<>/test/bedcov/bedcov.bed /<>/test/bedcov/bedcov.bam .. ok test_bedcov: /<>/samtools bedcov -j /<>/test/bedcov/bedcov.bed /<>/test/bedcov/bedcov.bam .. ok test_bedcov: /<>/samtools bedcov -g512 -G2048 /<>/test/bedcov/bedcov_gG.bed /<>/test/bedcov/bedcov.bam .. ok test_bedcov: /<>/samtools bedcov -c /<>/test/bedcov/bedcov_gG.bed /<>/test/bedcov/bedcov.bam .. ok test_split: /<>/samtools split --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_split: /<>/samtools split -@ 2 --output-fmt sam -u /<>/test/split/split.tmp.unk.sam -f /<>/test/split/split.tmp.%!.%. /<>/test/split/split.sam .. ok test_large_positions: /<>/samtools view -h --no-PG /tmp/EVABEoGsaH/longref.sam.gz .. ok test_large_positions: /<>/samtools view -h --no-PG /tmp/EVABEoGsaH/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /<>/samtools view -h --no-PG -L /<>/test/large_pos/test.bed /tmp/EVABEoGsaH/longref.sam.gz .. ok test_large_positions: /<>/samtools sort -O sam --no-PG -m 10M /<>/test/large_pos/longref_name.sam .. ok test_large_positions: /<>/samtools merge -O sam --no-PG - /<>/test/large_pos/longref.sam /<>/test/large_pos/longref2.sam .. ok test_large_positions: /<>/samtools depth /<>/test/large_pos/longref.sam .. ok test_large_positions: /<>/samtools depth -b /<>/test/large_pos/test.bed /<>/test/large_pos/longref.sam .. ok test_large_positions: /<>/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/EVABEoGsaH/longref.sam.gz .. ok test_large_positions: /<>/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /<>/samtools fixmate -O sam --no-PG - - | /<>/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip --no-PG --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test2.bed /<>/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /<>/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam --hard-clip -b /<>/test/ampliconclip/ac_test2.bed /<>/test/ampliconclip/4_total_hc_data.sam .. ok test_ampliconstats: /<>/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconclip/1_hard_clipped.expected.sam /<>/test/ampliconclip/1_soft_clipped.expected.sam /<>/test/ampliconclip/1_soft_clipped_strand.expected.sam /<>/test/ampliconclip/2_both_clipped.expected.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /<>/samtools ampliconstats -@ 2 -c 0 /<>/test/ampliconclip/multi_ref.bed /<>/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_ampliconstats: /<>/samtools ampliconstats -@ 2 -c 0 /<>/test/ampliconclip/ac_test.bed /<>/test/ampliconstats/mixed_clipped.sam | grep -E -v 'Samtools version|Command line' .. ok test_reset: cat /<>/test/dat/mpileup.1.sam | /<>/samtools reset | /<>/samtools view .. ok test_reset: /<>/samtools reset < /<>/test/dat/mpileup.1.sam | /<>/samtools view .. ok test_reset: /<>/samtools reset /<>/test/dat/mpileup.1.sam | /<>/samtools view .. ok test_reset: cat /<>/test/dat/mpileup.1.sam | /<>/samtools reset -o /<>/test/reset/output.sam .. ok test_reset: /<>/samtools reset -o /<>/test/reset/output.sam /<>/test/dat/test_input_1_a.bam .. ok test_reset: /<>/samtools reset -o /<>/test/reset/output.sam /<>/test/dat/test_input_1_a.cram .. ok test_reset: /<>/samtools reset --reject-PG bwa_index /<>/test/dat/mpileup.1.sam -o /<>/test/reset/output.sam; grep /<>/test/reset/output.sam -e"@PG ID:samtools PN:samtools" | wc -l | sed 's/ //g' .. ok test_reset: /<>/samtools reset --reject-PG sam_to_fixed_bam /<>/test/dat/mpileup.1.sam -o /<>/test/reset/output.sam; grep /<>/test/reset/output.sam -e"@PG ID:" | wc -l | sed 's/ //g' .. ok test_reset: /<>/samtools reset --reject-PG bwa_index --no-PG /<>/test/dat/mpileup.1.sam -o /<>/test/reset/output.sam; grep /<>/test/reset/output.sam -e"@PG" .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --keep-tag RG -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --keep-tag X0,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD --keep-tag X0,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --remove-tag X0,X1,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG -x X0,X1,MD -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset --reject-PG bwa /<>/test/dat/mpileup.1.sam --no-RG --remove-tag ^X0,MD --keep-tag X1 -o /<>/test/reset/output .. ok test_reset: /<>/samtools reset /<>/test/reset/seq.sam -o /<>/test/reset/output .. ok Number of tests: total .. 909 passed .. 865 failed .. 0 expected failure .. 44 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && AWK="mawk" ../regression.sh mpileup.reg === Testing mpileup.reg regressions === [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" [W::cram_encode_aux] Missing @RG header for RG "ERR162872" EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 118 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="mawk" ../regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 53 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/consensus && AWK="mawk" ../regression.sh consensus.reg === Testing consensus.reg regressions === Expected passes: 65 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS cd test/cram_size && AWK="mawk" ../regression.sh cram_size.reg === Testing cram_size.reg regressions === Expected passes: 3 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 => PASS make[2]: Leaving directory '/<>' rm -fr -- /tmp/dh-xdg-rundir-MMoOy2BF make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a rm -f -- debian/samtools.substvars rm -fr -- debian/.debhelper/generated/samtools/ debian/samtools/ debian/tmp/ rm -f debian/samtools.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- \ prefix=/usr install -m0755 -d /<>/debian/tmp make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/<>' mkdir -p -m 755 /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/share/man/man1 install -p samtools /<>/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /<>/debian/tmp/usr/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /<>/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /<>/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/<>' make clean make[2]: Entering directory '/<>' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai view.*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* cd test/reference && rm -f mpileup.*.fai rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/samtools.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install install -m0755 -d debian/samtools//usr cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/ install -m0755 -d debian/samtools//usr/share/man cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/ install -m0755 -d debian/samtools/usr/share/commonwl/ cp --reflink=auto -a ./debian/samtools-faidx.cwl ./debian/samtools-index.cwl ./debian/samtools-rmdup.cwl ./debian/samtools-sort.cwl ./debian/samtools-view.cwl debian/samtools/usr/share/commonwl// install -m0755 -d debian/samtools/usr/share/man/man1 cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/ # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done # Disable the executable bit on a dataset. if [ -d debian/samtools-test ] \ ; then chmod 0644 debian/samtools-test/usr/share/samtools/test/ampliconclip/ac_test.bed \ ; fi make[1]: Leaving directory '/<>' dh_installdocs -a install -m0755 -d debian/samtools/usr/share/doc/samtools install -m0755 -d debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./AUTHORS debian/samtools/usr/share/doc/samtools cp --reflink=auto -a ./README debian/samtools/usr/share/doc/samtools chmod -R u\+rw,go=rX debian/samtools/usr/share/doc install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright rm -f debian/samtools.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs NEWS install -m0755 -d debian/samtools/usr/share/doc/samtools install -p -m0644 debian/.debhelper/generated/samtools/dh_installchangelogs.dch.trimmed debian/samtools/usr/share/doc/samtools/changelog.Debian install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian install -p -m0644 NEWS debian/samtools/usr/share/doc/samtools/changelog make[1]: Leaving directory '/<>' dh_installexamples -a install -m0755 -d debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/00README.txt debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/ex1.sam.gz debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.fa debian/samtools/usr/share/doc/samtools/examples cp --reflink=auto -a ./examples/toy.sam debian/samtools/usr/share/doc/samtools/examples rm -f debian/samtools.debhelper.log debian/rules execute_before_dh_installman make[1]: Entering directory '/<>' # Fix whatis entries for subcommands; "samtools subcommand \- desc." # will confuse the lexer, but "samtools-subcommand \- desc." will work. sed -i '/^\.SH NAME/{n;s/^\([^ ]\+\) \([^ ]\+\) \\- /\1-\2 \\- /}' \ debian/*/usr/share/man/man*/*.* # .EX expects a indentation width. sed -i 's/^.EX$/.EX 8/' debian/*/usr/share/man/man*/*.* make[1]: Leaving directory '/<>' dh_installman -a rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 man-recode --to-code UTF-8 --suffix .dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 mv debian/samtools/usr/share/man/man1/samtools-depad.1.dh-new debian/samtools/usr/share/man/man1/samtools-depad.1 mv debian/samtools/usr/share/man/man1/samtools-depth.1.dh-new debian/samtools/usr/share/man/man1/samtools-depth.1 mv debian/samtools/usr/share/man/man1/samtools-dict.1.dh-new debian/samtools/usr/share/man/man1/samtools-dict.1 mv debian/samtools/usr/share/man/man1/samtools-faidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-faidx.1 mv debian/samtools/usr/share/man/man1/samtools-fasta.1.dh-new debian/samtools/usr/share/man/man1/samtools-fasta.1 mv debian/samtools/usr/share/man/man1/samtools-fixmate.1.dh-new debian/samtools/usr/share/man/man1/samtools-fixmate.1 mv debian/samtools/usr/share/man/man1/samtools-flags.1.dh-new debian/samtools/usr/share/man/man1/samtools-flags.1 mv debian/samtools/usr/share/man/man1/samtools-flagstat.1.dh-new debian/samtools/usr/share/man/man1/samtools-flagstat.1 mv debian/samtools/usr/share/man/man1/samtools-fqidx.1.dh-new debian/samtools/usr/share/man/man1/samtools-fqidx.1 mv debian/samtools/usr/share/man/man1/samtools-head.1.dh-new debian/samtools/usr/share/man/man1/samtools-head.1 mv debian/samtools/usr/share/man/man1/samtools-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 debian/samtools/usr/share/man/man1/samtools-faidx.1 debian/samtools/usr/share/man/man1/samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fixmate.1 debian/samtools/usr/share/man/man1/samtools-flags.1 debian/samtools/usr/share/man/man1/samtools-flagstat.1 debian/samtools/usr/share/man/man1/samtools-fqidx.1 debian/samtools/usr/share/man/man1/samtools-head.1 debian/samtools/usr/share/man/man1/samtools-idxstats.1 mv debian/samtools/usr/share/man/man1/ace2sam.1.dh-new debian/samtools/usr/share/man/man1/ace2sam.1 mv debian/samtools/usr/share/man/man1/samtools-addreplacerg.1.dh-new debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconclip.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 mv debian/samtools/usr/share/man/man1/samtools-ampliconstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 mv debian/samtools/usr/share/man/man1/samtools-bedcov.1.dh-new debian/samtools/usr/share/man/man1/samtools-bedcov.1 mv debian/samtools/usr/share/man/man1/samtools-calmd.1.dh-new debian/samtools/usr/share/man/man1/samtools-calmd.1 mv debian/samtools/usr/share/man/man1/samtools-cat.1.dh-new debian/samtools/usr/share/man/man1/samtools-cat.1 mv debian/samtools/usr/share/man/man1/samtools-collate.1.dh-new debian/samtools/usr/share/man/man1/samtools-collate.1 mv debian/samtools/usr/share/man/man1/samtools-consensus.1.dh-new debian/samtools/usr/share/man/man1/samtools-consensus.1 mv debian/samtools/usr/share/man/man1/samtools-coverage.1.dh-new debian/samtools/usr/share/man/man1/samtools-coverage.1 mv debian/samtools/usr/share/man/man1/samtools-cram-size.1.dh-new debian/samtools/usr/share/man/man1/samtools-cram-size.1 chmod 0644 -- debian/samtools/usr/share/man/man1/ace2sam.1 debian/samtools/usr/share/man/man1/samtools-addreplacerg.1 debian/samtools/usr/share/man/man1/samtools-ampliconclip.1 debian/samtools/usr/share/man/man1/samtools-ampliconstats.1 debian/samtools/usr/share/man/man1/samtools-bedcov.1 debian/samtools/usr/share/man/man1/samtools-calmd.1 debian/samtools/usr/share/man/man1/samtools-cat.1 debian/samtools/usr/share/man/man1/samtools-collate.1 debian/samtools/usr/share/man/man1/samtools-consensus.1 debian/samtools/usr/share/man/man1/samtools-coverage.1 debian/samtools/usr/share/man/man1/samtools-cram-size.1 mv debian/samtools/usr/share/man/man1/samtools-import.1.dh-new debian/samtools/usr/share/man/man1/samtools-import.1 mv debian/samtools/usr/share/man/man1/samtools-index.1.dh-new debian/samtools/usr/share/man/man1/samtools-index.1 mv debian/samtools/usr/share/man/man1/samtools-markdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-markdup.1 mv debian/samtools/usr/share/man/man1/samtools-merge.1.dh-new debian/samtools/usr/share/man/man1/samtools-merge.1 mv debian/samtools/usr/share/man/man1/samtools-mpileup.1.dh-new debian/samtools/usr/share/man/man1/samtools-mpileup.1 mv debian/samtools/usr/share/man/man1/samtools-phase.1.dh-new debian/samtools/usr/share/man/man1/samtools-phase.1 mv debian/samtools/usr/share/man/man1/samtools-quickcheck.1.dh-new debian/samtools/usr/share/man/man1/samtools-quickcheck.1 mv debian/samtools/usr/share/man/man1/samtools-reference.1.dh-new debian/samtools/usr/share/man/man1/samtools-reference.1 mv debian/samtools/usr/share/man/man1/samtools-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-reset.1.dh-new debian/samtools/usr/share/man/man1/samtools-reset.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-import.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.1 debian/samtools/usr/share/man/man1/samtools-merge.1 debian/samtools/usr/share/man/man1/samtools-mpileup.1 debian/samtools/usr/share/man/man1/samtools-phase.1 debian/samtools/usr/share/man/man1/samtools-quickcheck.1 debian/samtools/usr/share/man/man1/samtools-reference.1 debian/samtools/usr/share/man/man1/samtools-reheader.1 debian/samtools/usr/share/man/man1/samtools-reset.1 debian/samtools/usr/share/man/man1/samtools-rmdup.1 mv debian/samtools/usr/share/man/man1/samtools-samples.1.dh-new debian/samtools/usr/share/man/man1/samtools-samples.1 mv debian/samtools/usr/share/man/man1/samtools-sort.1.dh-new debian/samtools/usr/share/man/man1/samtools-sort.1 mv debian/samtools/usr/share/man/man1/samtools-split.1.dh-new debian/samtools/usr/share/man/man1/samtools-split.1 mv debian/samtools/usr/share/man/man1/samtools-stats.1.dh-new debian/samtools/usr/share/man/man1/samtools-stats.1 mv debian/samtools/usr/share/man/man1/samtools-targetcut.1.dh-new debian/samtools/usr/share/man/man1/samtools-targetcut.1 mv debian/samtools/usr/share/man/man1/samtools-tview.1.dh-new debian/samtools/usr/share/man/man1/samtools-tview.1 mv debian/samtools/usr/share/man/man1/samtools-view.1.dh-new debian/samtools/usr/share/man/man1/samtools-view.1 mv debian/samtools/usr/share/man/man1/samtools.1.dh-new debian/samtools/usr/share/man/man1/samtools.1 mv debian/samtools/usr/share/man/man1/samtools.pl.1.dh-new debian/samtools/usr/share/man/man1/samtools.pl.1 mv debian/samtools/usr/share/man/man1/wgsim.1.dh-new debian/samtools/usr/share/man/man1/wgsim.1 chmod 0644 -- debian/samtools/usr/share/man/man1/samtools-samples.1 debian/samtools/usr/share/man/man1/samtools-sort.1 debian/samtools/usr/share/man/man1/samtools-split.1 debian/samtools/usr/share/man/man1/samtools-stats.1 debian/samtools/usr/share/man/man1/samtools-targetcut.1 debian/samtools/usr/share/man/man1/samtools-tview.1 debian/samtools/usr/share/man/man1/samtools-view.1 debian/samtools/usr/share/man/man1/samtools.1 debian/samtools/usr/share/man/man1/samtools.pl.1 debian/samtools/usr/share/man/man1/wgsim.1 dh_lintian -a install -m0755 -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools dh_perl -a mv debian/samtools.substvars.new debian/samtools.substvars dh_link -a rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 ln -s samtools-fasta.1 debian/samtools/usr/share/man/man1/samtools-fastq.1 dh_strip_nondeterminism -a Using 1687465915 as canonical time Normalizing debian/samtools/usr/share/doc/samtools/examples/ex1.sam.gz using File::StripNondeterminism::handlers::gzip dh_compress -a cd debian/samtools chmod a-x usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 gzip -9nf usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/README usr/share/doc/samtools/changelog usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools-addreplacerg.1 usr/share/man/man1/samtools-ampliconclip.1 usr/share/man/man1/samtools-ampliconstats.1 usr/share/man/man1/samtools-bedcov.1 usr/share/man/man1/samtools-calmd.1 usr/share/man/man1/samtools-cat.1 usr/share/man/man1/samtools-collate.1 usr/share/man/man1/samtools-consensus.1 usr/share/man/man1/samtools-coverage.1 usr/share/man/man1/samtools-cram-size.1 usr/share/man/man1/samtools-depad.1 usr/share/man/man1/samtools-depth.1 usr/share/man/man1/samtools-dict.1 usr/share/man/man1/samtools-faidx.1 usr/share/man/man1/samtools-fasta.1 usr/share/man/man1/samtools-fixmate.1 usr/share/man/man1/samtools-flags.1 usr/share/man/man1/samtools-flagstat.1 usr/share/man/man1/samtools-fqidx.1 usr/share/man/man1/samtools-head.1 usr/share/man/man1/samtools-idxstats.1 usr/share/man/man1/samtools-import.1 usr/share/man/man1/samtools-index.1 usr/share/man/man1/samtools-markdup.1 usr/share/man/man1/samtools-merge.1 usr/share/man/man1/samtools-mpileup.1 usr/share/man/man1/samtools-phase.1 usr/share/man/man1/samtools-quickcheck.1 usr/share/man/man1/samtools-reference.1 usr/share/man/man1/samtools-reheader.1 usr/share/man/man1/samtools-reset.1 usr/share/man/man1/samtools-rmdup.1 usr/share/man/man1/samtools-samples.1 usr/share/man/man1/samtools-sort.1 usr/share/man/man1/samtools-split.1 usr/share/man/man1/samtools-stats.1 usr/share/man/man1/samtools-targetcut.1 usr/share/man/man1/samtools-tview.1 usr/share/man/man1/samtools-view.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1 cd '/<>' rm -f debian/samtools/usr/share/man/man1/samtools-fastq.1 debian/samtools/usr/share/man/man1/samtools-fastq.1.gz ln -s samtools-fasta.1.gz debian/samtools/usr/share/man/man1/samtools-fastq.1.gz dh_fixperms -a find debian/samtools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools/usr/share/man debian/samtools/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -a dh_dwz -a install -m0755 -d debian/samtools/usr/lib/debug/.dwz/powerpc64le-linux-gnu dwz -mdebian/samtools/usr/lib/debug/.dwz/powerpc64le-linux-gnu/samtools.debug -M/usr/lib/debug/.dwz/powerpc64le-linux-gnu/samtools.debug -- debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim dwz: debian/samtools/usr/bin/samtools: DWARF compression not beneficial - old size 719020 new size 728144 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/powerpc64le-linux-gnu/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/powerpc64le-linux-gnu/samtools.debug dh_strip -a debugedit --build-id --build-id-seed=samtools/1.17-1 debian/samtools/usr/bin/samtools 1ca1b488a78d61a4bad90eee0e60d3a8eba7d4ae install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c/a1b488a78d61a4bad90eee0e60d3a8eba7d4ae.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c/a1b488a78d61a4bad90eee0e60d3a8eba7d4ae.debug strip --remove-section=.comment --remove-section=.note -o /tmp/2jRxB5qseG/strip39FaLk debian/samtools/usr/bin/samtools chmod --reference debian/samtools/usr/bin/samtools /tmp/2jRxB5qseG/strip39FaLk cat '/tmp/2jRxB5qseG/strip39FaLk' > 'debian/samtools/usr/bin/samtools' chmod --reference /tmp/2jRxB5qseG/strip39FaLk debian/samtools/usr/bin/samtools objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1c/a1b488a78d61a4bad90eee0e60d3a8eba7d4ae.debug debian/samtools/usr/bin/samtools /tmp/2jRxB5qseG/objcopy_pF3cZ chmod --reference debian/samtools/usr/bin/samtools /tmp/2jRxB5qseG/objcopy_pF3cZ cat '/tmp/2jRxB5qseG/objcopy_pF3cZ' > 'debian/samtools/usr/bin/samtools' chmod --reference /tmp/2jRxB5qseG/objcopy_pF3cZ debian/samtools/usr/bin/samtools debugedit --build-id --build-id-seed=samtools/1.17-1 debian/samtools/usr/bin/wgsim debugedit: debian/samtools/usr/bin/wgsim: Unknown DWARF DW_FORM_0x1f20 334c34194d91b2091b0c4b8f4800b44207aedb05 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/33 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/33/4c34194d91b2091b0c4b8f4800b44207aedb05.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/33/4c34194d91b2091b0c4b8f4800b44207aedb05.debug strip --remove-section=.comment --remove-section=.note -o /tmp/2jRxB5qseG/stripCYQwGZ debian/samtools/usr/bin/wgsim chmod --reference debian/samtools/usr/bin/wgsim /tmp/2jRxB5qseG/stripCYQwGZ cat '/tmp/2jRxB5qseG/stripCYQwGZ' > 'debian/samtools/usr/bin/wgsim' chmod --reference /tmp/2jRxB5qseG/stripCYQwGZ debian/samtools/usr/bin/wgsim objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/33/4c34194d91b2091b0c4b8f4800b44207aedb05.debug debian/samtools/usr/bin/wgsim /tmp/2jRxB5qseG/objcopyNcexdk chmod --reference debian/samtools/usr/bin/wgsim /tmp/2jRxB5qseG/objcopyNcexdk cat '/tmp/2jRxB5qseG/objcopyNcexdk' > 'debian/samtools/usr/bin/wgsim' chmod --reference /tmp/2jRxB5qseG/objcopyNcexdk debian/samtools/usr/bin/wgsim debugedit --build-id --build-id-seed=samtools/1.17-1 debian/samtools/usr/bin/md5sum-lite debugedit: debian/samtools/usr/bin/md5sum-lite: Unknown DWARF DW_FORM_0x1f20 e1874609fb6bc25cbeb983ce185a4acf40da9755 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e1 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e1/874609fb6bc25cbeb983ce185a4acf40da9755.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e1/874609fb6bc25cbeb983ce185a4acf40da9755.debug strip --remove-section=.comment --remove-section=.note -o /tmp/2jRxB5qseG/stripizcPCQ debian/samtools/usr/bin/md5sum-lite chmod --reference debian/samtools/usr/bin/md5sum-lite /tmp/2jRxB5qseG/stripizcPCQ cat '/tmp/2jRxB5qseG/stripizcPCQ' > 'debian/samtools/usr/bin/md5sum-lite' chmod --reference /tmp/2jRxB5qseG/stripizcPCQ debian/samtools/usr/bin/md5sum-lite objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e1/874609fb6bc25cbeb983ce185a4acf40da9755.debug debian/samtools/usr/bin/md5sum-lite /tmp/2jRxB5qseG/objcopyaxt6IP chmod --reference debian/samtools/usr/bin/md5sum-lite /tmp/2jRxB5qseG/objcopyaxt6IP cat '/tmp/2jRxB5qseG/objcopyaxt6IP' > 'debian/samtools/usr/bin/md5sum-lite' chmod --reference /tmp/2jRxB5qseG/objcopyaxt6IP debian/samtools/usr/bin/md5sum-lite debugedit --build-id --build-id-seed=samtools/1.17-1 debian/samtools/usr/bin/md5fa debugedit: debian/samtools/usr/bin/md5fa: Unknown DWARF DW_FORM_0x1f20 98b4a18866ed6fe97b21f8e9b7086a2e89c370e1 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/98 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/98/b4a18866ed6fe97b21f8e9b7086a2e89c370e1.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/98/b4a18866ed6fe97b21f8e9b7086a2e89c370e1.debug strip --remove-section=.comment --remove-section=.note -o /tmp/2jRxB5qseG/striph3xdYP debian/samtools/usr/bin/md5fa chmod --reference debian/samtools/usr/bin/md5fa /tmp/2jRxB5qseG/striph3xdYP cat '/tmp/2jRxB5qseG/striph3xdYP' > 'debian/samtools/usr/bin/md5fa' chmod --reference /tmp/2jRxB5qseG/striph3xdYP debian/samtools/usr/bin/md5fa objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/98/b4a18866ed6fe97b21f8e9b7086a2e89c370e1.debug debian/samtools/usr/bin/md5fa /tmp/2jRxB5qseG/objcopy7q8LJt chmod --reference debian/samtools/usr/bin/md5fa /tmp/2jRxB5qseG/objcopy7q8LJt cat '/tmp/2jRxB5qseG/objcopy7q8LJt' > 'debian/samtools/usr/bin/md5fa' chmod --reference /tmp/2jRxB5qseG/objcopy7q8LJt debian/samtools/usr/bin/md5fa debugedit --build-id --build-id-seed=samtools/1.17-1 debian/samtools/usr/bin/ace2sam debugedit: debian/samtools/usr/bin/ace2sam: Unknown DWARF DW_FORM_0x1f20 fa28e7c2220950ff0ed1ea2e07d8fc4ff9d9230d install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fa objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fa/28e7c2220950ff0ed1ea2e07d8fc4ff9d9230d.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fa/28e7c2220950ff0ed1ea2e07d8fc4ff9d9230d.debug strip --remove-section=.comment --remove-section=.note -o /tmp/2jRxB5qseG/stripv_Q8r0 debian/samtools/usr/bin/ace2sam chmod --reference debian/samtools/usr/bin/ace2sam /tmp/2jRxB5qseG/stripv_Q8r0 cat '/tmp/2jRxB5qseG/stripv_Q8r0' > 'debian/samtools/usr/bin/ace2sam' chmod --reference /tmp/2jRxB5qseG/stripv_Q8r0 debian/samtools/usr/bin/ace2sam objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fa/28e7c2220950ff0ed1ea2e07d8fc4ff9d9230d.debug debian/samtools/usr/bin/ace2sam /tmp/2jRxB5qseG/objcopyQ0LpiU chmod --reference debian/samtools/usr/bin/ace2sam /tmp/2jRxB5qseG/objcopyQ0LpiU cat '/tmp/2jRxB5qseG/objcopyQ0LpiU' > 'debian/samtools/usr/bin/ace2sam' chmod --reference /tmp/2jRxB5qseG/objcopyQ0LpiU debian/samtools/usr/bin/ace2sam debugedit --build-id --build-id-seed=samtools/1.17-1 debian/samtools/usr/bin/maq2sam-long debugedit: debian/samtools/usr/bin/maq2sam-long: Unknown DWARF DW_FORM_0x1f20 790e8a3ca22f487afd0cfd57f736b45c60d3e60f install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/79 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/79/0e8a3ca22f487afd0cfd57f736b45c60d3e60f.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/79/0e8a3ca22f487afd0cfd57f736b45c60d3e60f.debug strip --remove-section=.comment --remove-section=.note -o /tmp/2jRxB5qseG/stripWottR7 debian/samtools/usr/bin/maq2sam-long chmod --reference debian/samtools/usr/bin/maq2sam-long /tmp/2jRxB5qseG/stripWottR7 cat '/tmp/2jRxB5qseG/stripWottR7' > 'debian/samtools/usr/bin/maq2sam-long' chmod --reference /tmp/2jRxB5qseG/stripWottR7 debian/samtools/usr/bin/maq2sam-long objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/79/0e8a3ca22f487afd0cfd57f736b45c60d3e60f.debug debian/samtools/usr/bin/maq2sam-long /tmp/2jRxB5qseG/objcopystpsrf chmod --reference debian/samtools/usr/bin/maq2sam-long /tmp/2jRxB5qseG/objcopystpsrf cat '/tmp/2jRxB5qseG/objcopystpsrf' > 'debian/samtools/usr/bin/maq2sam-long' chmod --reference /tmp/2jRxB5qseG/objcopystpsrf debian/samtools/usr/bin/maq2sam-long debugedit --build-id --build-id-seed=samtools/1.17-1 debian/samtools/usr/bin/maq2sam-short debugedit: debian/samtools/usr/bin/maq2sam-short: Unknown DWARF DW_FORM_0x1f20 6d1016683d094011b872190b4f417d86b826a883 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6d objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6d/1016683d094011b872190b4f417d86b826a883.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6d/1016683d094011b872190b4f417d86b826a883.debug strip --remove-section=.comment --remove-section=.note -o /tmp/2jRxB5qseG/stripExP5qm debian/samtools/usr/bin/maq2sam-short chmod --reference debian/samtools/usr/bin/maq2sam-short /tmp/2jRxB5qseG/stripExP5qm cat '/tmp/2jRxB5qseG/stripExP5qm' > 'debian/samtools/usr/bin/maq2sam-short' chmod --reference /tmp/2jRxB5qseG/stripExP5qm debian/samtools/usr/bin/maq2sam-short objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6d/1016683d094011b872190b4f417d86b826a883.debug debian/samtools/usr/bin/maq2sam-short /tmp/2jRxB5qseG/objcopyLHwe28 chmod --reference debian/samtools/usr/bin/maq2sam-short /tmp/2jRxB5qseG/objcopyLHwe28 cat '/tmp/2jRxB5qseG/objcopyLHwe28' > 'debian/samtools/usr/bin/maq2sam-short' chmod --reference /tmp/2jRxB5qseG/objcopyLHwe28 debian/samtools/usr/bin/maq2sam-short install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/powerpc64le-linux-gnu debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/samtools/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/samtools/usr/lib/debug install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym install -m0755 -d debian/.debhelper/samtools dh_makeshlibs -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short dh_installdeb -a install -m0755 -d debian/samtools/DEBIAN dh_gencontrol -a install -m0755 -d debian/samtools/DEBIAN echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=1ca1b488a78d61a4bad90eee0e60d3a8eba7d4ae 334c34194d91b2091b0c4b8f4800b44207aedb05 6d1016683d094011b872190b4f417d86b826a883 790e8a3ca22f487afd0cfd57f736b45c60d3e60f 98b4a18866ed6fe97b21f8e9b7086a2e89c370e1 e1874609fb6bc25cbeb983ce185a4acf40da9755 fa28e7c2220950ff0ed1ea2e07d8fc4ff9d9230d" -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/control dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools dpkg-gencontrol: warning: package samtools: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools/DEBIAN/control dh_md5sums -a install -m0755 -d debian/samtools/DEBIAN cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums install -m0755 -d debian/.debhelper/samtools/dbgsym-root/DEBIAN cd debian/.debhelper/samtools/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --root-owner-group --build debian/samtools .. dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root debian/.debhelper/scratch-space/build-samtools INFO: pkgstriptranslations version 153 INFO: pkgstriptranslations version 153 pkgstriptranslations: processing samtools (in debian/samtools); do_strip: , oemstrip: pkgstriptranslations: processing samtools-dbgsym (in debian/.debhelper/samtools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/samtools/DEBIAN/control, package samtools, directory debian/samtools .. removing usr/share/doc/samtools/changelog.gz pkgstripfiles: processing control file: debian/.debhelper/samtools/dbgsym-root/DEBIAN/control, package samtools-dbgsym, directory debian/.debhelper/samtools/dbgsym-root dpkg-deb: building package 'samtools-dbgsym' in 'debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.17-1_ppc64el.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package samtools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'samtools' in '../samtools_1.17-1_ppc64el.deb'. Renaming samtools-dbgsym_1.17-1_ppc64el.deb to samtools-dbgsym_1.17-1_ppc64el.ddeb mv debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.17-1_ppc64el.deb ../samtools-dbgsym_1.17-1_ppc64el.ddeb dpkg-genbuildinfo --build=any -O../samtools_1.17-1_ppc64el.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../samtools_1.17-1_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.17/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-06-23T07:08:43Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ samtools_1.17-1_ppc64el.changes: -------------------------------- Format: 1.8 Date: Thu, 22 Jun 2023 22:31:55 +0200 Source: samtools Binary: samtools Built-For-Profiles: noudeb Architecture: ppc64el Version: 1.17-1 Distribution: mantic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: samtools - processing sequence alignments in SAM, BAM and CRAM formats Changes: samtools (1.17-1) unstable; urgency=medium . * Migrate samtools to unstable. 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wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: samtools Binary: samtools samtools-dbgsym Architecture: ppc64el Version: 1.17-1 Checksums-Md5: 2c8bcbc0e7039881f378c2fda90fe236 875770 samtools-dbgsym_1.17-1_ppc64el.ddeb a04dec04ed5121b92a020fd1de5f2bbc 643336 samtools_1.17-1_ppc64el.deb Checksums-Sha1: 67eebe4ac516c14db18e9f17fd062c93b17f70a3 875770 samtools-dbgsym_1.17-1_ppc64el.ddeb 37580358a1e3397f0ce320197be5f0e916f7ec76 643336 samtools_1.17-1_ppc64el.deb Checksums-Sha256: df76e1e0b0a6963b474624af97fa9a8995d4521cf875d3ee90df0fb99cf22afa 875770 samtools-dbgsym_1.17-1_ppc64el.ddeb ced1d38d3228449b1455d66529f4bcdacc446648f825ef172ccc9d6989a81afb 643336 samtools_1.17-1_ppc64el.deb Build-Origin: Ubuntu Build-Architecture: ppc64el Build-Date: Fri, 23 Jun 2023 07:08:43 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), autoconf-archive (= 20220903-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-12), autotools-dev (= 20220109.1), base-files (= 13ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), bash-completion (= 1:2.11-6ubuntu1), binutils (= 2.40.50.20230622-1ubuntu1), binutils-common (= 2.40.50.20230622-1ubuntu1), binutils-powerpc64le-linux-gnu (= 2.40.50.20230622-1ubuntu1), bsdextrautils (= 2.38.1-5ubuntu2), bsdutils (= 1:2.38.1-5ubuntu2), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 9.1-1ubuntu2), cpp (= 4:12.2.0-3ubuntu1), cpp-12 (= 12.3.0-3ubuntu1), dash (= 0.5.12-2ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.4ubuntu3), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), dpkg (= 1.21.22ubuntu1), dpkg-dev (= 1.21.22ubuntu1), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-4ubuntu1), g++ (= 4:12.2.0-3ubuntu1), g++-12 (= 12.3.0-3ubuntu1), gcc (= 4:12.2.0-3ubuntu1), gcc-12 (= 12.3.0-3ubuntu1), gcc-12-base (= 12.3.0-3ubuntu1), gcc-13-base (= 13.1.0-6ubuntu1), gettext (= 0.21-12), gettext-base (= 0.21-12), grep (= 3.8-5), groff-base (= 1.22.4-10), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 13.1.0-6ubuntu1), libatomic1 (= 13.1.0-6ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.9-1), libaudit1 (= 1:3.0.9-1), libbinutils (= 2.40.50.20230622-1ubuntu1), libblkid1 (= 2.38.1-5ubuntu2), libbrotli1 (= 1.0.9-2build8), libbz2-1.0 (= 1.0.8-5build1), libbz2-dev (= 1.0.8-5build1), libc-bin (= 2.37-0ubuntu2), libc-dev-bin (= 2.37-0ubuntu2), libc6 (= 2.37-0ubuntu2), libc6-dev (= 2.37-0ubuntu2), libcap-ng0 (= 0.8.3-1build2), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.1.0-6ubuntu1), libcom-err2 (= 1.47.0-1ubuntu1), libcrypt-dev (= 1:4.4.35-1), libcrypt1 (= 1:4.4.35-1), libctf-nobfd0 (= 2.40.50.20230622-1ubuntu1), libctf0 (= 2.40.50.20230622-1ubuntu1), libcurl3-gnutls (= 7.88.1-10ubuntu1), libcurl4-gnutls-dev (= 7.88.1-10ubuntu1), libdb5.3 (= 5.3.28+dfsg2-1), libdebconfclient0 (= 0.267ubuntu1), libdebhelper-perl (= 13.11.4ubuntu3), libdeflate-dev (= 1.15-1), libdeflate0 (= 1.15-1), libdpkg-perl (= 1.21.22ubuntu1), libdw1 (= 0.188-2.1), libelf1 (= 0.188-2.1), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-12-dev (= 12.3.0-3ubuntu1), libgcc-s1 (= 13.1.0-6ubuntu1), libgcrypt20 (= 1.10.1-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgnutls30 (= 3.7.9-2ubuntu1), libgomp1 (= 13.1.0-6ubuntu1), libgpg-error0 (= 1.46-1), libgssapi-krb5-2 (= 1.20.1-2), libhogweed6 (= 3.8.1-2), libhts-dev (= 1.17+ds-1), libhts3 (= 1.17+ds-1), libhtscodecs2 (= 1.5.0-1), libicu72 (= 72.1-3ubuntu2), libidn2-0 (= 2.3.3-1build1), libio-pty-perl (= 1:1.17-1), libisl23 (= 0.26-3), libitm1 (= 13.1.0-6ubuntu1), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-2), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-2), libkrb5support0 (= 1.20.1-2), libldap2 (= 2.6.3+dfsg-1~exp1ubuntu2), liblsan0 (= 13.1.0-6ubuntu1), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.1-0.2), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.1.0-1), libmount1 (= 2.38.1-5ubuntu2), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.0-1), libncurses-dev (= 6.4-4), libncurses6 (= 6.4-4), libncursesw6 (= 6.4-4), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.54.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libp11-kit0 (= 0.24.1-2ubuntu1), libpam-modules (= 1.5.2-6ubuntu1), libpam-modules-bin (= 1.5.2-6ubuntu1), libpam-runtime (= 1.5.2-6ubuntu1), libpam0g (= 1.5.2-6ubuntu1), libpcre2-8-0 (= 10.42-1), libperl5.36 (= 5.36.0-7ubuntu1), libpipeline1 (= 1.5.7-1), libpkgconf3 (= 1.8.1-2), libpsl5 (= 0.21.2-1), libquadmath0 (= 13.1.0-6ubuntu1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-1), libsasl2-modules-db (= 2.1.28+dfsg1-1), libseccomp2 (= 2.5.4-1ubuntu3), libselinux1 (= 3.4-1build4), libsmartcols1 (= 2.38.1-5ubuntu2), libssh-4 (= 0.10.5-2), libssl3 (= 3.0.9-1ubuntu1), libstdc++-12-dev (= 12.3.0-3ubuntu1), libstdc++6 (= 13.1.0-6ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.5-2ubuntu3), libtasn1-6 (= 4.19.0-2), libtinfo6 (= 6.4-4), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libtsan2 (= 13.1.0-6ubuntu1), libubsan1 (= 13.1.0-6ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.5-2ubuntu3), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-5ubuntu2), libxml2 (= 2.9.14+dfsg-1.2), libzstd1 (= 1.5.4+dfsg2-5), linux-libc-dev (= 6.3.0-7.7), login (= 1:4.13+dfsg1-1ubuntu1), lto-disabled-list (= 41), m4 (= 1.4.19-3), make (= 4.3-4.1build1), man-db (= 2.11.2-2), mawk (= 1.3.4.20230525-1), ncurses-base (= 6.4-4), ncurses-bin (= 6.4-4), patch (= 2.7.6-7build2), perl (= 5.36.0-7ubuntu1), perl-base (= 5.36.0-7ubuntu1), perl-modules-5.36 (= 5.36.0-7ubuntu1), pkg-config (= 1.8.1-2), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.06-4ubuntu1), tabix (= 1.17+ds-1), tar (= 1.34+dfsg-1.2ubuntu1), usrmerge (= 35ubuntu1), util-linux (= 2.38.1-5ubuntu2), util-linux-extra (= 2.38.1-5ubuntu2), xz-utils (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-1ubuntu4), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1687465915" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ samtools_1.17-1_ppc64el.deb --------------------------- new Debian package, version 2.0. size 643336 bytes: control archive=2915 bytes. 913 bytes, 18 lines control 5608 bytes, 82 lines md5sums Package: samtools Version: 1.17-1 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1784 Depends: libc6 (>= 2.34), libhts3 (>= 1.17), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.1.4) Suggests: cwltool Section: science Priority: optional Homepage: https://www.htslib.org/ Description: processing sequence alignments in SAM, BAM and CRAM formats Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence Alignment/Map) and CRAM formats, does sorting, merging and indexing, and allows one to retrieve reads in any regions swiftly. It is designed to work on a stream, and is able to open a BAM or CRAM (not SAM) file on a remote FTP or HTTP server. drwxr-xr-x root/root 0 2023-06-22 20:31 ./ drwxr-xr-x root/root 0 2023-06-22 20:31 ./usr/ drwxr-xr-x root/root 0 2023-06-22 20:31 ./usr/bin/ -rwxr-xr-x root/root 67752 2023-06-22 20:31 ./usr/bin/ace2sam -rwxr-xr-x root/root 5443 2023-06-22 20:31 ./usr/bin/blast2sam.pl -rwxr-xr-x root/root 3360 2023-06-22 20:31 ./usr/bin/bowtie2sam.pl -rwxr-xr-x root/root 17996 2023-06-22 20:31 ./usr/bin/export2sam.pl -rwxr-xr-x root/root 3300 2023-06-22 20:31 ./usr/bin/fasta-sanitize.pl -rwxr-xr-x root/root 6121 2023-06-22 20:31 ./usr/bin/interpolate_sam.pl -rwxr-xr-x root/root 67752 2023-06-22 20:31 ./usr/bin/maq2sam-long -rwxr-xr-x root/root 67752 2023-06-22 20:31 ./usr/bin/maq2sam-short -rwxr-xr-x root/root 67752 2023-06-22 20:31 ./usr/bin/md5fa -rwxr-xr-x root/root 67752 2023-06-22 20:31 ./usr/bin/md5sum-lite -rwxr-xr-x root/root 7969 2023-06-22 20:31 ./usr/bin/novo2sam.pl -rwxr-xr-x root/root 44331 2023-06-22 20:31 ./usr/bin/plot-ampliconstats -rwxr-xr-x root/root 50549 2023-06-22 20:31 ./usr/bin/plot-bamstats -rwxr-xr-x root/root 3204 2023-06-22 20:31 ./usr/bin/psl2sam.pl -rwxr-xr-x root/root 8957 2023-06-22 20:31 ./usr/bin/sam2vcf.pl -rwxr-xr-x root/root 861472 2023-06-22 20:31 ./usr/bin/samtools -rwxr-xr-x root/root 16474 2023-06-22 20:31 ./usr/bin/samtools.pl -rwxr-xr-x root/root 11333 2023-06-22 20:31 ./usr/bin/seq_cache_populate.pl -rwxr-xr-x root/root 3905 2023-06-22 20:31 ./usr/bin/soap2sam.pl -rwxr-xr-x root/root 67888 2023-06-22 20:31 ./usr/bin/wgsim -rwxr-xr-x root/root 12542 2023-06-22 20:31 ./usr/bin/wgsim_eval.pl -rwxr-xr-x root/root 3579 2023-06-22 20:31 ./usr/bin/zoom2sam.pl drwxr-xr-x root/root 0 2023-06-22 20:31 ./usr/share/ drwxr-xr-x root/root 0 2023-06-22 20:31 ./usr/share/commonwl/ -rwxr-xr-x root/root 1906 2023-06-11 13:09 ./usr/share/commonwl/samtools-faidx.cwl -rwxr-xr-x root/root 1979 2023-06-11 13:09 ./usr/share/commonwl/samtools-index.cwl -rwxr-xr-x root/root 1627 2023-06-11 13:09 ./usr/share/commonwl/samtools-rmdup.cwl -rwxr-xr-x root/root 2834 2023-06-11 13:09 ./usr/share/commonwl/samtools-sort.cwl -rwxr-xr-x root/root 6224 2023-06-11 13:09 ./usr/share/commonwl/samtools-view.cwl drwxr-xr-x root/root 0 2023-06-22 20:31 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-06-22 20:31 ./usr/share/doc/samtools/ -rw-r--r-- root/root 828 2023-02-21 12:24 ./usr/share/doc/samtools/AUTHORS -rw-r--r-- root/root 369 2023-06-11 13:09 ./usr/share/doc/samtools/NEWS.Debian.gz -rw-r--r-- root/root 497 2023-06-11 13:09 ./usr/share/doc/samtools/README.Debian -rw-r--r-- root/root 2479 2023-02-21 12:24 ./usr/share/doc/samtools/README.gz -rw-r--r-- root/root 1777 2023-06-22 20:31 ./usr/share/doc/samtools/changelog.Debian.gz -rw-r--r-- root/root 2250 2023-06-11 13:09 ./usr/share/doc/samtools/copyright drwxr-xr-x root/root 0 2023-06-22 20:31 ./usr/share/doc/samtools/examples/ -rw-r--r-- root/root 1315 2023-02-21 12:24 ./usr/share/doc/samtools/examples/00README.txt -rw-r--r-- root/root 3225 2023-02-21 12:24 ./usr/share/doc/samtools/examples/ex1.fa -rw-r--r-- root/root 114565 2023-06-22 20:31 ./usr/share/doc/samtools/examples/ex1.sam.gz -rw-r--r-- root/root 98 2023-02-21 12:24 ./usr/share/doc/samtools/examples/toy.fa -rw-r--r-- root/root 786 2023-02-21 12:24 ./usr/share/doc/samtools/examples/toy.sam drwxr-xr-x root/root 0 2023-06-22 20:31 ./usr/share/lintian/ drwxr-xr-x root/root 0 2023-06-22 20:31 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 168 2023-06-12 18:58 ./usr/share/lintian/overrides/samtools drwxr-xr-x root/root 0 2023-06-22 20:31 ./usr/share/man/ drwxr-xr-x root/root 0 2023-06-22 20:31 ./usr/share/man/man1/ -rw-r--r-- root/root 462 2023-06-22 20:31 ./usr/share/man/man1/ace2sam.1.gz -rw-r--r-- root/root 1639 2023-06-22 20:31 ./usr/share/man/man1/samtools-addreplacerg.1.gz -rw-r--r-- root/root 2314 2023-06-22 20:31 ./usr/share/man/man1/samtools-ampliconclip.1.gz 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+------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build Type: any Build-Space: 30368 Build-Time: 68 Distribution: mantic-proposed Host Architecture: ppc64el Install-Time: 28 Job: samtools_1.17-1.dsc Machine Architecture: ppc64el Package: samtools Package-Time: 96 Source-Version: 1.17-1 Space: 30368 Status: successful Version: 1.17-1 -------------------------------------------------------------------------------- Finished at 2023-06-23T07:08:43Z Build needed 00:01:36, 30368k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=ppc64el PACKAGEBUILD-26332609 Scanning for processes to kill in build PACKAGEBUILD-26332609