https://launchpad.net/ubuntu/+source/samtools/1.17-1/+build/26332608 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-arm64-038 5.4.0-149-generic #166-Ubuntu SMP Tue Apr 18 16:52:10 UTC 2023 aarch64 Buildd toolchain package versions: launchpad-buildd_232~632~ubuntu20.04.1 python3-lpbuildd_232~632~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 07:05:31 ntpdate[1879]: adjust time server 10.211.37.1 offset -0.012453 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=armhf PACKAGEBUILD-26332608 --image-type chroot /home/buildd/filecache-default/232c5f007faca678b94fe1cafd15f5ae1164056a Creating target for build PACKAGEBUILD-26332608 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=armhf PACKAGEBUILD-26332608 Starting target for build PACKAGEBUILD-26332608 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=armhf PACKAGEBUILD-26332608 '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-26332608 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=armhf PACKAGEBUILD-26332608 Updating target for build PACKAGEBUILD-26332608 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 armhf Packages [1330 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe armhf Packages [14.4 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5936 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main armhf Packages [42.8 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [25.3 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe armhf Packages [421 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [163 kB] Fetched 23.4 MB in 11s (2211 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-arm-linux-gnueabihf binutils-common 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 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblzma5 libmd0 libmount1 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 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 133 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 89.5 MB of archives. After this operation, 32.8 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu mantic/main armhf libcrypt-dev armhf 1:4.4.35-1 [120 kB] Get:2 http://ftpmaster.internal/ubuntu mantic/main armhf libc6-dev armhf 2.37-0ubuntu2 [1339 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main armhf libc-dev-bin armhf 2.37-0ubuntu2 [18.9 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main armhf libcrypt1 armhf 1:4.4.35-1 [92.5 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main armhf linux-libc-dev armhf 6.3.0-7.7 [1503 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main armhf libc6 armhf 2.37-0ubuntu2 [2465 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main armhf libc-bin armhf 2.37-0ubuntu2 [533 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main armhf gcc-13-base armhf 13.1.0-6ubuntu1 [41.9 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main armhf libgcc-s1 armhf 13.1.0-6ubuntu1 [41.4 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main armhf base-files armhf 13ubuntu1 [73.7 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main armhf bash armhf 5.2.15-2ubuntu1 [671 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main armhf bsdutils armhf 1:2.38.1-5ubuntu2 [96.3 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main armhf coreutils armhf 9.1-1ubuntu2 [1290 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main armhf liblzma5 armhf 5.4.1-0.2 [109 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main armhf libgcrypt20 armhf 1.10.1-3ubuntu1 [448 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main armhf libstdc++6 armhf 13.1.0-6ubuntu1 [697 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main armhf libacl1 armhf 2.3.1-3 [15.1 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main armhf libapparmor1 armhf 3.0.8-1ubuntu3 [41.8 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main armhf libaudit-common all 1:3.0.9-1 [5142 B] Get:20 http://ftpmaster.internal/ubuntu mantic/main armhf libcap-ng0 armhf 0.8.3-1build2 [13.5 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main armhf libaudit1 armhf 1:3.0.9-1 [43.0 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main armhf libblkid1 armhf 2.38.1-5ubuntu2 [145 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main armhf libcap2 armhf 1:2.66-4ubuntu1 [25.2 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main armhf libperl5.36 armhf 5.36.0-7ubuntu1 [4025 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main armhf perl armhf 5.36.0-7ubuntu1 [235 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main armhf perl-base armhf 5.36.0-7ubuntu1 [1636 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main armhf perl-modules-5.36 all 5.36.0-7ubuntu1 [2984 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main armhf libdb5.3 armhf 5.3.28+dfsg2-1 [662 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main armhf zlib1g armhf 1:1.2.13.dfsg-1ubuntu4 [48.9 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main armhf debconf all 1.5.82 [125 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main armhf libssl3 armhf 3.0.9-1ubuntu1 [1571 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main armhf libzstd1 armhf 1.5.4+dfsg2-5 [257 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main armhf libkmod2 armhf 30+20221128-1ubuntu1 [41.9 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main armhf libpcre2-8-0 armhf 10.42-1 [197 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main armhf libselinux1 armhf 3.4-1build4 [69.2 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main armhf libmount1 armhf 2.38.1-5ubuntu2 [152 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main armhf libpam0g armhf 1.5.2-6ubuntu1 [60.5 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main armhf libseccomp2 armhf 2.5.4-1ubuntu3 [48.8 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main armhf systemd-sysv armhf 252.5-2ubuntu3 [11.5 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main armhf systemd armhf 252.5-2ubuntu3 [2985 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main armhf libsystemd-shared armhf 252.5-2ubuntu3 [1746 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main armhf libargon2-1 armhf 0~20190702+dfsg-3 [20.9 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main armhf libudev1 armhf 252.5-2ubuntu3 [142 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main armhf libdevmapper1.02.1 armhf 2:1.02.185-2ubuntu1 [135 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main armhf libuuid1 armhf 2.38.1-5ubuntu2 [31.9 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main armhf libcryptsetup12 armhf 2:2.6.1-4ubuntu1 [216 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main armhf libfdisk1 armhf 2.38.1-5ubuntu2 [186 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main armhf libp11-kit0 armhf 0.24.1-2ubuntu1 [212 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main armhf mount armhf 2.38.1-5ubuntu2 [125 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main armhf libsystemd0 armhf 252.5-2ubuntu3 [366 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main armhf libapt-pkg6.0 armhf 2.7.1 [925 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main armhf tar armhf 1.34+dfsg-1.2ubuntu1 [270 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main armhf dpkg armhf 1.21.22ubuntu1 [1348 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main armhf dash armhf 0.5.12-2ubuntu1 [79.0 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main armhf diffutils armhf 1:3.8-4 [167 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main armhf findutils armhf 4.9.0-4ubuntu1 [294 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main armhf grep armhf 3.8-5 [155 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main armhf hostname armhf 3.23+nmu1ubuntu1 [10.2 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main armhf ncurses-bin armhf 6.4-4 [175 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main armhf sed armhf 4.9-1 [191 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main armhf libsmartcols1 armhf 2.38.1-5ubuntu2 [103 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main armhf util-linux-extra armhf 2.38.1-5ubuntu2 [98.3 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main armhf util-linux armhf 2.38.1-5ubuntu2 [1160 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main armhf ncurses-base all 6.4-4 [23.3 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main armhf sysvinit-utils armhf 3.06-4ubuntu1 [32.5 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main armhf lsb-base all 11.6 [4606 B] Get:67 http://ftpmaster.internal/ubuntu mantic-proposed/main armhf adduser all 3.134ubuntu1 [136 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main armhf gpgv armhf 2.2.40-1.1ubuntu1 [195 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main armhf libgnutls30 armhf 3.7.9-2ubuntu1 [949 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main armhf apt armhf 2.7.1 [1343 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main armhf libpam-modules-bin armhf 1.5.2-6ubuntu1 [42.5 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main armhf libpam-modules armhf 1.5.2-6ubuntu1 [265 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main armhf logsave armhf 1.47.0-1ubuntu1 [13.7 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main armhf libext2fs2 armhf 1.47.0-1ubuntu1 [193 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main armhf e2fsprogs armhf 1.47.0-1ubuntu1 [572 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main armhf libattr1 armhf 1:2.5.1-4 [11.2 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main armhf libdebconfclient0 armhf 0.267ubuntu1 [7382 B] Get:78 http://ftpmaster.internal/ubuntu mantic/main armhf libmd0 armhf 1.1.0-1 [23.1 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/main armhf libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main armhf libsemanage-common all 3.4-1build4 [9852 B] Get:81 http://ftpmaster.internal/ubuntu mantic/main armhf libsepol2 armhf 3.4-2.1 [262 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main armhf libsemanage2 armhf 3.4-1build4 [83.8 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main armhf libncurses6 armhf 6.4-4 [87.6 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main armhf libncursesw6 armhf 6.4-4 [119 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main armhf libtinfo6 armhf 6.4-4 [86.6 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main armhf usrmerge all 35ubuntu1 [58.2 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main armhf libcom-err2 armhf 1.47.0-1ubuntu1 [13.6 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main armhf libproc2-0 armhf 2:4.0.3-1ubuntu1 [46.4 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main armhf libss2 armhf 1.47.0-1ubuntu1 [14.5 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main armhf mawk armhf 1.3.4.20230525-1 [102 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/main armhf procps armhf 2:4.0.3-1ubuntu1 [599 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main armhf sensible-utils all 0.0.20 [19.6 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main armhf openssl armhf 3.0.9-1ubuntu1 [1159 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main armhf ca-certificates all 20230311ubuntu1 [152 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main armhf libgssapi-krb5-2 armhf 1.20.1-2 [118 kB] Get:96 http://ftpmaster.internal/ubuntu mantic/main armhf libkrb5-3 armhf 1.20.1-2 [320 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main armhf libkrb5support0 armhf 1.20.1-2 [30.9 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main armhf libk5crypto3 armhf 1.20.1-2 [78.3 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main armhf readline-common all 8.2-1.3 [55.7 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main armhf libreadline8 armhf 8.2-1.3 [128 kB] Get:101 http://ftpmaster.internal/ubuntu mantic/main armhf libsqlite3-0 armhf 3.40.1-2 [566 kB] Get:102 http://ftpmaster.internal/ubuntu mantic/main armhf tzdata all 2023c-4exp1ubuntu1 [271 kB] Get:103 http://ftpmaster.internal/ubuntu mantic/main armhf xz-utils armhf 5.4.1-0.2 [269 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main armhf advancecomp armhf 2.5-1 [192 kB] Get:105 http://ftpmaster.internal/ubuntu mantic-proposed/main armhf libctf0 armhf 2.40.50.20230622-1ubuntu1 [86.1 kB] Get:106 http://ftpmaster.internal/ubuntu mantic-proposed/main armhf libctf-nobfd0 armhf 2.40.50.20230622-1ubuntu1 [85.9 kB] Get:107 http://ftpmaster.internal/ubuntu mantic-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.40.50.20230622-1ubuntu1 [2776 kB] Get:108 http://ftpmaster.internal/ubuntu mantic-proposed/main armhf libbinutils armhf 2.40.50.20230622-1ubuntu1 [485 kB] Get:109 http://ftpmaster.internal/ubuntu mantic-proposed/main armhf binutils armhf 2.40.50.20230622-1ubuntu1 [3074 B] Get:110 http://ftpmaster.internal/ubuntu mantic-proposed/main armhf binutils-common armhf 2.40.50.20230622-1ubuntu1 [227 kB] Get:111 http://ftpmaster.internal/ubuntu mantic/main armhf libisl23 armhf 0.26-3 [595 kB] Get:112 http://ftpmaster.internal/ubuntu mantic/main armhf libmpfr6 armhf 4.2.0-1 [228 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main armhf g++-12 armhf 12.3.0-3ubuntu1 [9317 kB] Get:114 http://ftpmaster.internal/ubuntu mantic/main armhf gcc-12 armhf 12.3.0-3ubuntu1 [16.2 MB] Get:115 http://ftpmaster.internal/ubuntu mantic/main armhf cpp-12 armhf 12.3.0-3ubuntu1 [8156 kB] Get:116 http://ftpmaster.internal/ubuntu mantic/main armhf libubsan1 armhf 13.1.0-6ubuntu1 [1072 kB] Get:117 http://ftpmaster.internal/ubuntu mantic/main armhf libgomp1 armhf 13.1.0-6ubuntu1 [120 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/main armhf libatomic1 armhf 13.1.0-6ubuntu1 [7762 B] Get:119 http://ftpmaster.internal/ubuntu mantic/main armhf libasan8 armhf 13.1.0-6ubuntu1 [2741 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/main armhf libstdc++-12-dev armhf 12.3.0-3ubuntu1 [2251 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main armhf libgcc-12-dev armhf 12.3.0-3ubuntu1 [857 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/main armhf libcc1-0 armhf 13.1.0-6ubuntu1 [43.7 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/main armhf gcc-12-base armhf 12.3.0-3ubuntu1 [42.8 kB] Get:124 http://ftpmaster.internal/ubuntu mantic/main armhf g++ armhf 4:12.2.0-3ubuntu1 [1108 B] Get:125 http://ftpmaster.internal/ubuntu mantic/main armhf gcc armhf 4:12.2.0-3ubuntu1 [5184 B] Get:126 http://ftpmaster.internal/ubuntu mantic/main armhf cpp armhf 4:12.2.0-3ubuntu1 [27.8 kB] Get:127 http://ftpmaster.internal/ubuntu mantic/main armhf dpkg-dev all 1.21.22ubuntu1 [1118 kB] Get:128 http://ftpmaster.internal/ubuntu mantic/main armhf libdpkg-perl all 1.21.22ubuntu1 [247 kB] Get:129 http://ftpmaster.internal/ubuntu mantic/main armhf lto-disabled-list all 41 [12.4 kB] Get:130 http://ftpmaster.internal/ubuntu mantic/main armhf libfakeroot armhf 1.31-1.2 [27.4 kB] Get:131 http://ftpmaster.internal/ubuntu mantic/main armhf fakeroot armhf 1.31-1.2 [61.5 kB] Get:132 http://ftpmaster.internal/ubuntu mantic/main armhf gpg armhf 2.2.40-1.1ubuntu1 [482 kB] Get:133 http://ftpmaster.internal/ubuntu mantic/main armhf gpgconf armhf 2.2.40-1.1ubuntu1 [120 kB] Get:134 http://ftpmaster.internal/ubuntu mantic/main armhf gpg-agent armhf 2.2.40-1.1ubuntu1 [236 kB] Get:135 http://ftpmaster.internal/ubuntu mantic/main armhf pkgbinarymangler all 153 [16.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 89.5 MB in 6s (15.5 MB/s) (Reading database ... 12825 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.35-1_armhf.deb ... Unpacking libcrypt-dev:armhf (1:4.4.35-1) over (1:4.4.33-1) ... Preparing to unpack .../libc6-dev_2.37-0ubuntu2_armhf.deb ... Unpacking libc6-dev:armhf (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libc-dev-bin_2.37-0ubuntu2_armhf.deb ... Unpacking libc-dev-bin (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libcrypt1_1%3a4.4.35-1_armhf.deb ... Unpacking libcrypt1:armhf (1:4.4.35-1) over (1:4.4.33-1) ... Setting up libcrypt1:armhf (1:4.4.35-1) ... (Reading database ... 12825 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_6.3.0-7.7_armhf.deb ... Unpacking linux-libc-dev:armhf (6.3.0-7.7) over (5.19.0-21.21) ... Preparing to unpack .../libc6_2.37-0ubuntu2_armhf.deb ... Unpacking libc6:armhf (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Setting up libc6:armhf (2.37-0ubuntu2) ... (Reading database ... 12829 files and directories currently installed.) 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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-26332608 armhf mantic-proposed -c chroot:build-PACKAGEBUILD-26332608 --arch=armhf --dist=mantic-proposed --nolog samtools_1.17-1.dsc Initiating build PACKAGEBUILD-26332608 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-149-generic #166-Ubuntu SMP Tue Apr 18 16:52:10 UTC 2023 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-arm64-038.buildd +==============================================================================+ | samtools 1.17-1 (armhf) Fri, 23 Jun 2023 07:06:11 +0000 | +==============================================================================+ Package: samtools Version: 1.17-1 Source Version: 1.17-1 Distribution: mantic-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26332608/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-Q1JTKa/resolver-X1TvoM' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- samtools_1.17-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/samtools-Q1JTKa/samtools-1.17' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-Q1JTKa' 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 [537 B] Fetched 1955 B in 0s (105 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. 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librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build4 [52.8 kB] Get:43 http://ftpmaster.internal/ubuntu mantic-proposed/main armhf libssh-4 armhf 0.10.5-2 [166 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main armhf libcurl3-gnutls armhf 7.88.1-10ubuntu1 [262 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main armhf libcurl4-gnutls-dev armhf 7.88.1-10ubuntu1 [374 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main armhf libdeflate0 armhf 1.15-1 [39.6 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main armhf libdeflate-dev armhf 1.15-1 [46.3 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/universe armhf libhtscodecs2 armhf 1.5.0-1 [67.5 kB] Get:49 http://ftpmaster.internal/ubuntu mantic-proposed/universe armhf libhts3 armhf 1.17+ds-1 [381 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main armhf liblzma-dev armhf 5.4.1-0.2 [165 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1ubuntu4 [880 kB] Get:52 http://ftpmaster.internal/ubuntu mantic-proposed/universe armhf libhts-dev armhf 1.17+ds-1 [1679 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main armhf libio-pty-perl armhf 1:1.17-1 [31.9 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main armhf libncurses-dev armhf 6.4-4 [344 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main armhf libpkgconf3 armhf 1.8.1-2 [26.3 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main armhf pkgconf-bin armhf 1.8.1-2 [20.6 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main armhf pkgconf armhf 1.8.1-2 [16.7 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main armhf pkg-config armhf 1.8.1-2 [7170 B] Get:59 http://ftpmaster.internal/ubuntu mantic-proposed/universe armhf tabix armhf 1.17+ds-1 [411 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 24.6 MB in 4s (6249 kB/s) Selecting previously unselected package autoconf-archive. 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Setting up libtool (2.4.7-5) ... Setting up libcurl3-gnutls:armhf (7.88.1-10ubuntu1) ... Setting up libcurl4-gnutls-dev:armhf (7.88.1-10ubuntu1) ... Setting up pkgconf:armhf (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:armhf (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:armhf (1.17+ds-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:armhf (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 (armhf included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-149-generic #166-Ubuntu SMP Tue Apr 18 16:52:10 UTC 2023 arm64 (armv7l) 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-arm-linux-gnueabihf_2.40.50.20230622-1ubuntu1 binutils-common_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 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 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 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 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-26332608 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26332608 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26332608 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 armhf 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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... 64 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 -O2 -ffile-prefix-map=/<>=. -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 -Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>' gcc -g -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -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 sed -i -e 's@/<>@«BUILDPATH»@g' version.h gcc -g -O2 -ffile-prefix-map=/<>=. -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 cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/<>=. -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 gcc -g -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 gcc -g -O2 -ffile-prefix-map=/<>=. -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 cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 gcc -g -O2 -ffile-prefix-map=/<>=. -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 cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 gcc -g -O2 -ffile-prefix-map=/<>=. -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 cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 gcc -g -O2 -ffile-prefix-map=/<>=. -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 cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -O2 -ffile-prefix-map=/<>=. -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 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-Bsymbolic-functions -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 -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 -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 -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 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-Bsymbolic-functions -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 gcc -L./lz4 -Wl,-Bsymbolic-functions -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 -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 -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 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/VFyRpwoi9N/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/VFyRpwoi9N/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/VFyRpwoi9N/bgzip.dat.gz .. ok /<>/samtools faidx /tmp/VFyRpwoi9N/faidx.fa 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/VFyRpwoi9N/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/VFyRpwoi9N/faidx.fa 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/VFyRpwoi9N/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/VFyRpwoi9N/faidx.fa 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/VFyRpwoi9N/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/VFyRpwoi9N/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /<>/samtools faidx /tmp/VFyRpwoi9N/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /<>/samtools fqidx /tmp/VFyRpwoi9N/fqidx.fq 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/VFyRpwoi9N/fqidx.fq.gz 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/VFyRpwoi9N/fqidx.fq 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/VFyRpwoi9N/fqidx.fq.gz 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/VFyRpwoi9N/fqidx.fq 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/VFyRpwoi9N/fqidx.fq.gz 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/VFyRpwoi9N/fqidx.fq 1:99998-100007 .. ok .. ok /<>/samtools fqidx /tmp/VFyRpwoi9N/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/VFyRpwoi9N/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/VFyRpwoi9N/large_chrom.bam ref2 .. ok test_index: /<>/samtools view /tmp/VFyRpwoi9N/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/VFyRpwoi9N/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/VFyRpwoi9N/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/VFyRpwoi9N/test_input_1_b.bam.bai .. ok test_index: /<>/samtools view -X /<>/test/dat/test_input_1_b.bam /tmp/VFyRpwoi9N/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/VFyRpwoi9N/auto_indexed.csi && cat /tmp/VFyRpwoi9N/auto_indexed.csi .. ok test_index: /<>/samtools index /<>/test/dat/auto_indexed.tmp.cram /tmp/VFyRpwoi9N/auto_indexed.crai && cat /tmp/VFyRpwoi9N/auto_indexed.crai .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.sam /tmp/VFyRpwoi9N/auto_indexed.csi && cat /tmp/VFyRpwoi9N/auto_indexed.csi .. ok test_index: /<>/samtools view -@ 2 /tmp/VFyRpwoi9N/large_chrom.bam ref2 .. ok test_index: /<>/samtools view -@ 2 /tmp/VFyRpwoi9N/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/VFyRpwoi9N/test_input_1_b.bam.bai ref2 .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/VFyRpwoi9N/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/VFyRpwoi9N/test_input_1_b.bam.bai .. ok test_index: /<>/samtools view -@ 2 -X /<>/test/dat/test_input_1_b.bam /tmp/VFyRpwoi9N/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/VFyRpwoi9N/auto_indexed.csi && cat /tmp/VFyRpwoi9N/auto_indexed.csi .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/auto_indexed.tmp.cram /tmp/VFyRpwoi9N/auto_indexed.crai && cat /tmp/VFyRpwoi9N/auto_indexed.crai .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.sam /tmp/VFyRpwoi9N/auto_indexed.csi && cat /tmp/VFyRpwoi9N/auto_indexed.csi .. ok test_mpileup: /<>/samtools mpileup -b /tmp/VFyRpwoi9N/mpileup.bam.list -f /tmp/VFyRpwoi9N/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/VFyRpwoi9N/mpileup.cram.list -f /tmp/VFyRpwoi9N/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/VFyRpwoi9N/mpileup.bam.urllist -f /tmp/VFyRpwoi9N/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/VFyRpwoi9N/mpileup.cram.urllist -f /tmp/VFyRpwoi9N/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/VFyRpwoi9N/mpileup.ref.fa.gz -r17:1050-1060 /tmp/VFyRpwoi9N/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/VFyRpwoi9N/mpileup.ref.fa.gz -r17:1050-1060 /tmp/VFyRpwoi9N/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/VFyRpwoi9N/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/VFyRpwoi9N/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/VFyRpwoi9N/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/VFyRpwoi9N/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/VFyRpwoi9N/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/VFyRpwoi9N/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/VFyRpwoi9N/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/VFyRpwoi9N/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/VFyRpwoi9N/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/VFyRpwoi9N/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/VFyRpwoi9N/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/VFyRpwoi9N/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/VFyRpwoi9N/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/VFyRpwoi9N/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/VFyRpwoi9N/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/VFyRpwoi9N/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/VFyRpwoi9N/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/VFyRpwoi9N/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/VFyRpwoi9N/view.001.forn (SAM input) .. ok 68: Count -N /tmp/VFyRpwoi9N/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/VFyRpwoi9N/view.001.forn (BAM input) .. ok 70: Count -N /tmp/VFyRpwoi9N/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/VFyRpwoi9N/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/VFyRpwoi9N/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/VFyRpwoi9N/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/VFyRpwoi9N/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/VFyRpwoi9N/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/VFyRpwoi9N/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/VFyRpwoi9N/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/VFyRpwoi9N/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/VFyRpwoi9N/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/VFyRpwoi9N/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/VFyRpwoi9N/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/VFyRpwoi9N/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/VFyRpwoi9N/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/VFyRpwoi9N/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/VFyRpwoi9N/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/VFyRpwoi9N/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/VFyRpwoi9N/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/VFyRpwoi9N/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/VFyRpwoi9N/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/VFyRpwoi9N/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/VFyRpwoi9N/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/VFyRpwoi9N/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/VFyRpwoi9N/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/VFyRpwoi9N/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/VFyRpwoi9N/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/VFyRpwoi9N/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/VFyRpwoi9N/view.test115.sam -h -d TGCA /tmp/VFyRpwoi9N/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/VFyRpwoi9N/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/VFyRpwoi9N/view.test117.sam -h -d TGCA /tmp/VFyRpwoi9N/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/VFyRpwoi9N/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/VFyRpwoi9N/view.test119.sam -h -d TGCA /tmp/VFyRpwoi9N/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/VFyRpwoi9N/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/VFyRpwoi9N/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VFyRpwoi9N/view.001.fobc" Failed command: /<>/samtools view -o /tmp/VFyRpwoi9N/view.test121.sam -h -D BClong:/tmp/VFyRpwoi9N/view.001.fobc /tmp/VFyRpwoi9N/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/VFyRpwoi9N/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VFyRpwoi9N/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/VFyRpwoi9N/view.001.fobc /tmp/VFyRpwoi9N/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/VFyRpwoi9N/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VFyRpwoi9N/view.001.fobc" Failed command: /<>/samtools view -o /tmp/VFyRpwoi9N/view.test123.sam -h -D BClong:/tmp/VFyRpwoi9N/view.001.fobc /tmp/VFyRpwoi9N/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/VFyRpwoi9N/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VFyRpwoi9N/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/VFyRpwoi9N/view.001.fobc /tmp/VFyRpwoi9N/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/VFyRpwoi9N/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VFyRpwoi9N/view.001.fobc" Failed command: /<>/samtools view -o /tmp/VFyRpwoi9N/view.test125.sam -h -D BClong:/tmp/VFyRpwoi9N/view.001.fobc /tmp/VFyRpwoi9N/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/VFyRpwoi9N/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/VFyRpwoi9N/view.001.fobc" Failed command: /<>/samtools view -c -D BClong:/tmp/VFyRpwoi9N/view.001.fobc /tmp/VFyRpwoi9N/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/VFyRpwoi9N/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/VFyRpwoi9N/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/VFyRpwoi9N/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/VFyRpwoi9N/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/VFyRpwoi9N/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/VFyRpwoi9N/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/VFyRpwoi9N/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/VFyRpwoi9N/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/VFyRpwoi9N/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/VFyRpwoi9N/bam2fq.discard.s.fq -0 /tmp/VFyRpwoi9N/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/VFyRpwoi9N/bam2fq.discard.s.fq -0 /tmp/VFyRpwoi9N/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/87GguMkUHC - /<>/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/VFyRpwoi9N/merge.tag.1.bam /tmp/VFyRpwoi9N/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/VFyRpwoi9N/merge.tag.3.bam /tmp/VFyRpwoi9N/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/VFyRpwoi9N/merge.bed.1.bam /tmp/VFyRpwoi9N/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/Spob81U2jQ - /<>/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/VFyRpwoi9N/merge.tag.1.bam /tmp/VFyRpwoi9N/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/VFyRpwoi9N/merge.tag.3.bam /tmp/VFyRpwoi9N/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/VFyRpwoi9N/merge.bed.1.bam /tmp/VFyRpwoi9N/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/VFyRpwoi9N/sortout .. ok test_sort: /<>/samtools sort -f /<>/test/dat/test_input_1_a.bam /tmp/VFyRpwoi9N/sortout.bam .. ok test_sort: /<>/samtools sort -o /<>/test/dat/test_input_1_a.bam /tmp/VFyRpwoi9N/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/VFyRpwoi9N/sortout .. ok test_sort: /<>/samtools sort -@ 2 -f /<>/test/dat/test_input_1_a.bam /tmp/VFyRpwoi9N/sortout.bam .. ok test_sort: /<>/samtools sort -@ 2 -o /<>/test/dat/test_input_1_a.bam /tmp/VFyRpwoi9N/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/VFyRpwoi9N/longref.sam.gz .. ok test_large_positions: /<>/samtools view -h --no-PG /tmp/VFyRpwoi9N/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /<>/samtools view -h --no-PG -L /<>/test/large_pos/test.bed /tmp/VFyRpwoi9N/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/VFyRpwoi9N/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-7Qff0d8d 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/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 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/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 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/arm-linux-gnueabihf dwz -mdebian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/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 684466 new size 706176 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug chmod 0644 -- debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug dh_strip -a 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_0x1f21 c593c76bc62f0be2a5d126570a12e20e21498115 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c5 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c5/93c76bc62f0be2a5d126570a12e20e21498115.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c5/93c76bc62f0be2a5d126570a12e20e21498115.debug strip --remove-section=.comment --remove-section=.note -o /tmp/5yFSdOJh5B/stripGMDih8 debian/samtools/usr/bin/ace2sam chmod --reference debian/samtools/usr/bin/ace2sam /tmp/5yFSdOJh5B/stripGMDih8 cat '/tmp/5yFSdOJh5B/stripGMDih8' > 'debian/samtools/usr/bin/ace2sam' chmod --reference /tmp/5yFSdOJh5B/stripGMDih8 debian/samtools/usr/bin/ace2sam objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c5/93c76bc62f0be2a5d126570a12e20e21498115.debug debian/samtools/usr/bin/ace2sam /tmp/5yFSdOJh5B/objcopyM4kKmI chmod --reference debian/samtools/usr/bin/ace2sam /tmp/5yFSdOJh5B/objcopyM4kKmI cat '/tmp/5yFSdOJh5B/objcopyM4kKmI' > 'debian/samtools/usr/bin/ace2sam' chmod --reference /tmp/5yFSdOJh5B/objcopyM4kKmI debian/samtools/usr/bin/ace2sam 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 3fdbc5b1d12572aee42c63535df84ff49c9da001 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3f objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3f/dbc5b1d12572aee42c63535df84ff49c9da001.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3f/dbc5b1d12572aee42c63535df84ff49c9da001.debug strip --remove-section=.comment --remove-section=.note -o /tmp/5yFSdOJh5B/strip6PrzXg debian/samtools/usr/bin/maq2sam-short chmod --reference debian/samtools/usr/bin/maq2sam-short /tmp/5yFSdOJh5B/strip6PrzXg cat '/tmp/5yFSdOJh5B/strip6PrzXg' > 'debian/samtools/usr/bin/maq2sam-short' chmod --reference /tmp/5yFSdOJh5B/strip6PrzXg debian/samtools/usr/bin/maq2sam-short objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3f/dbc5b1d12572aee42c63535df84ff49c9da001.debug debian/samtools/usr/bin/maq2sam-short /tmp/5yFSdOJh5B/objcopyh4q3d7 chmod --reference debian/samtools/usr/bin/maq2sam-short /tmp/5yFSdOJh5B/objcopyh4q3d7 cat '/tmp/5yFSdOJh5B/objcopyh4q3d7' > 'debian/samtools/usr/bin/maq2sam-short' chmod --reference /tmp/5yFSdOJh5B/objcopyh4q3d7 debian/samtools/usr/bin/maq2sam-short 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_0x1f21 be32849df02ebf065488439ee19d8a033c60de38 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/be objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/be/32849df02ebf065488439ee19d8a033c60de38.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/be/32849df02ebf065488439ee19d8a033c60de38.debug strip --remove-section=.comment --remove-section=.note -o /tmp/5yFSdOJh5B/stripY7gLSK debian/samtools/usr/bin/md5fa chmod --reference debian/samtools/usr/bin/md5fa /tmp/5yFSdOJh5B/stripY7gLSK cat '/tmp/5yFSdOJh5B/stripY7gLSK' > 'debian/samtools/usr/bin/md5fa' chmod --reference /tmp/5yFSdOJh5B/stripY7gLSK debian/samtools/usr/bin/md5fa objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/be/32849df02ebf065488439ee19d8a033c60de38.debug debian/samtools/usr/bin/md5fa /tmp/5yFSdOJh5B/objcopyj12497 chmod --reference debian/samtools/usr/bin/md5fa /tmp/5yFSdOJh5B/objcopyj12497 cat '/tmp/5yFSdOJh5B/objcopyj12497' > 'debian/samtools/usr/bin/md5fa' chmod --reference /tmp/5yFSdOJh5B/objcopyj12497 debian/samtools/usr/bin/md5fa 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 1edf063484ee91889e07bdf1c63f8c5c570ad6a4 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1e objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1e/df063484ee91889e07bdf1c63f8c5c570ad6a4.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1e/df063484ee91889e07bdf1c63f8c5c570ad6a4.debug strip --remove-section=.comment --remove-section=.note -o /tmp/5yFSdOJh5B/stripc7nA_6 debian/samtools/usr/bin/md5sum-lite chmod --reference debian/samtools/usr/bin/md5sum-lite /tmp/5yFSdOJh5B/stripc7nA_6 cat '/tmp/5yFSdOJh5B/stripc7nA_6' > 'debian/samtools/usr/bin/md5sum-lite' chmod --reference /tmp/5yFSdOJh5B/stripc7nA_6 debian/samtools/usr/bin/md5sum-lite objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/1e/df063484ee91889e07bdf1c63f8c5c570ad6a4.debug debian/samtools/usr/bin/md5sum-lite /tmp/5yFSdOJh5B/objcopyMnr0XI chmod --reference debian/samtools/usr/bin/md5sum-lite /tmp/5yFSdOJh5B/objcopyMnr0XI cat '/tmp/5yFSdOJh5B/objcopyMnr0XI' > 'debian/samtools/usr/bin/md5sum-lite' chmod --reference /tmp/5yFSdOJh5B/objcopyMnr0XI debian/samtools/usr/bin/md5sum-lite debugedit --build-id --build-id-seed=samtools/1.17-1 debian/samtools/usr/bin/samtools e7fef4f1c52b4f470cbe6f6f9387d780d93a8cf5 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/fef4f1c52b4f470cbe6f6f9387d780d93a8cf5.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/fef4f1c52b4f470cbe6f6f9387d780d93a8cf5.debug strip --remove-section=.comment --remove-section=.note -o /tmp/5yFSdOJh5B/strip733Is8 debian/samtools/usr/bin/samtools chmod --reference debian/samtools/usr/bin/samtools /tmp/5yFSdOJh5B/strip733Is8 cat '/tmp/5yFSdOJh5B/strip733Is8' > 'debian/samtools/usr/bin/samtools' chmod --reference /tmp/5yFSdOJh5B/strip733Is8 debian/samtools/usr/bin/samtools objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e7/fef4f1c52b4f470cbe6f6f9387d780d93a8cf5.debug debian/samtools/usr/bin/samtools /tmp/5yFSdOJh5B/objcopyWFcm1L chmod --reference debian/samtools/usr/bin/samtools /tmp/5yFSdOJh5B/objcopyWFcm1L cat '/tmp/5yFSdOJh5B/objcopyWFcm1L' > 'debian/samtools/usr/bin/samtools' chmod --reference /tmp/5yFSdOJh5B/objcopyWFcm1L 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 331a3a2445acaab61bd2ef8dce647365e0ffe332 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/33/1a3a2445acaab61bd2ef8dce647365e0ffe332.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/33/1a3a2445acaab61bd2ef8dce647365e0ffe332.debug strip --remove-section=.comment --remove-section=.note -o /tmp/5yFSdOJh5B/stripCP_3zM debian/samtools/usr/bin/wgsim chmod --reference debian/samtools/usr/bin/wgsim /tmp/5yFSdOJh5B/stripCP_3zM cat '/tmp/5yFSdOJh5B/stripCP_3zM' > 'debian/samtools/usr/bin/wgsim' chmod --reference /tmp/5yFSdOJh5B/stripCP_3zM debian/samtools/usr/bin/wgsim objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/33/1a3a2445acaab61bd2ef8dce647365e0ffe332.debug debian/samtools/usr/bin/wgsim /tmp/5yFSdOJh5B/objcopy484rzF chmod --reference debian/samtools/usr/bin/wgsim /tmp/5yFSdOJh5B/objcopy484rzF cat '/tmp/5yFSdOJh5B/objcopy484rzF' > 'debian/samtools/usr/bin/wgsim' chmod --reference /tmp/5yFSdOJh5B/objcopy484rzF debian/samtools/usr/bin/wgsim 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 9f142a3b80f7a3030f7f4c1fe7113596ec0072b3 install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9f objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9f/142a3b80f7a3030f7f4c1fe7113596ec0072b3.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9f/142a3b80f7a3030f7f4c1fe7113596ec0072b3.debug strip --remove-section=.comment --remove-section=.note -o /tmp/5yFSdOJh5B/stripGDcwWw debian/samtools/usr/bin/maq2sam-long chmod --reference debian/samtools/usr/bin/maq2sam-long /tmp/5yFSdOJh5B/stripGDcwWw cat '/tmp/5yFSdOJh5B/stripGDcwWw' > 'debian/samtools/usr/bin/maq2sam-long' chmod --reference /tmp/5yFSdOJh5B/stripGDcwWw debian/samtools/usr/bin/maq2sam-long objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9f/142a3b80f7a3030f7f4c1fe7113596ec0072b3.debug debian/samtools/usr/bin/maq2sam-long /tmp/5yFSdOJh5B/objcopyEDvUbV chmod --reference debian/samtools/usr/bin/maq2sam-long /tmp/5yFSdOJh5B/objcopyEDvUbV cat '/tmp/5yFSdOJh5B/objcopyEDvUbV' > 'debian/samtools/usr/bin/maq2sam-long' chmod --reference /tmp/5yFSdOJh5B/objcopyEDvUbV debian/samtools/usr/bin/maq2sam-long install -m0755 -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf 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/ace2sam 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 debian/samtools/usr/bin/maq2sam-long 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=1edf063484ee91889e07bdf1c63f8c5c570ad6a4 331a3a2445acaab61bd2ef8dce647365e0ffe332 3fdbc5b1d12572aee42c63535df84ff49c9da001 9f142a3b80f7a3030f7f4c1fe7113596ec0072b3 be32849df02ebf065488439ee19d8a033c60de38 c593c76bc62f0be2a5d126570a12e20e21498115 e7fef4f1c52b4f470cbe6f6f9387d780d93a8cf5" -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 " pkgstripfiles: processing control file: debian/samtools/DEBIAN/control, package samtools, directory debian/samtools .. removing usr/share/doc/samtools/changelog.gz pkgstripfiles: Running PNG optimization (using 4 cpus) for package samtools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'samtools' in '../samtools_1.17-1_armhf.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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_armhf.deb'. Renaming samtools-dbgsym_1.17-1_armhf.deb to samtools-dbgsym_1.17-1_armhf.ddeb mv debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.17-1_armhf.deb ../samtools-dbgsym_1.17-1_armhf.ddeb dpkg-genbuildinfo --build=any -O../samtools_1.17-1_armhf.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../samtools_1.17-1_armhf.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 2023-06-23T07:07:25Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ samtools_1.17-1_armhf.changes: ------------------------------ Format: 1.8 Date: Thu, 22 Jun 2023 22:31:55 +0200 Source: samtools Binary: samtools Built-For-Profiles: noudeb Architecture: armhf 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. Checksums-Sha1: 03f9b07e6b25c8e5619ca50e6d3f3473041deafa 911410 samtools-dbgsym_1.17-1_armhf.ddeb 43809ef6e7d13da507e4d5d2a8df810139166cc7 6588 samtools_1.17-1_armhf.buildinfo 967ee7ec727a99ff8b2c8f5316b868ed0cdfe0b4 588048 samtools_1.17-1_armhf.deb Checksums-Sha256: 2c463f4db6292fcca5453f399dd3ab23214d2eb68ee6c7f3bb56574f9210f14f 911410 samtools-dbgsym_1.17-1_armhf.ddeb 69db2872caea92a8dd9e32097736e37161c038133baf6d95263b2db558fd6642 6588 samtools_1.17-1_armhf.buildinfo 8dc1bfa072d2f90102807fc5120a3f7e651c16fa1c3b9036c946c95c84c3a276 588048 samtools_1.17-1_armhf.deb Files: a75ca45438ead0ed80bbd1a40b35d925 911410 debug optional samtools-dbgsym_1.17-1_armhf.ddeb b7590d61183ab9d5d9d6498a97a3901b 6588 science optional samtools_1.17-1_armhf.buildinfo a6db850b4a82d239032668803a9aa0a3 588048 science optional samtools_1.17-1_armhf.deb /<>/samtools_1.17-1_armhf.changes.new could not be renamed to /<>/samtools_1.17-1_armhf.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: samtools Binary: samtools samtools-dbgsym Architecture: armhf Version: 1.17-1 Checksums-Md5: a75ca45438ead0ed80bbd1a40b35d925 911410 samtools-dbgsym_1.17-1_armhf.ddeb a6db850b4a82d239032668803a9aa0a3 588048 samtools_1.17-1_armhf.deb Checksums-Sha1: 03f9b07e6b25c8e5619ca50e6d3f3473041deafa 911410 samtools-dbgsym_1.17-1_armhf.ddeb 967ee7ec727a99ff8b2c8f5316b868ed0cdfe0b4 588048 samtools_1.17-1_armhf.deb Checksums-Sha256: 2c463f4db6292fcca5453f399dd3ab23214d2eb68ee6c7f3bb56574f9210f14f 911410 samtools-dbgsym_1.17-1_armhf.ddeb 8dc1bfa072d2f90102807fc5120a3f7e651c16fa1c3b9036c946c95c84c3a276 588048 samtools_1.17-1_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Fri, 23 Jun 2023 07:07:25 +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-arm-linux-gnueabihf (= 2.40.50.20230622-1ubuntu1), binutils-common (= 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), 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), 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), 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), 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_armhf.deb ------------------------- new Debian package, version 2.0. size 588048 bytes: control archive=2920 bytes. 913 bytes, 18 lines control 5608 bytes, 82 lines md5sums Package: samtools Version: 1.17-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1101 Depends: libc6 (>= 2.34), libhts3 (>= 1.17), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.2.3.3) 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 13868 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 9772 2023-06-22 20:31 ./usr/bin/maq2sam-long -rwxr-xr-x root/root 9772 2023-06-22 20:31 ./usr/bin/maq2sam-short -rwxr-xr-x root/root 9772 2023-06-22 20:31 ./usr/bin/md5fa -rwxr-xr-x root/root 5676 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 504548 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 18004 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 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./usr/share/man/man1/samtools-stats.1.gz -rw-r--r-- root/root 1428 2023-06-22 20:31 ./usr/share/man/man1/samtools-targetcut.1.gz -rw-r--r-- root/root 2045 2023-06-22 20:31 ./usr/share/man/man1/samtools-tview.1.gz -rw-r--r-- root/root 7041 2023-06-22 20:31 ./usr/share/man/man1/samtools-view.1.gz -rw-r--r-- root/root 15923 2023-06-22 20:31 ./usr/share/man/man1/samtools.1.gz -rw-r--r-- root/root 410 2023-06-22 20:31 ./usr/share/man/man1/samtools.pl.1.gz -rw-r--r-- root/root 518 2023-06-22 20:31 ./usr/share/man/man1/wgsim.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 29140 Build-Time: 63 Distribution: mantic-proposed Host Architecture: armhf Install-Time: 10 Job: samtools_1.17-1.dsc Machine Architecture: arm64 Package: samtools Package-Time: 74 Source-Version: 1.17-1 Space: 29140 Status: successful Version: 1.17-1 -------------------------------------------------------------------------------- Finished at 2023-06-23T07:07:25Z Build needed 00:01:14, 29140k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=armhf PACKAGEBUILD-26332608 Scanning for processes to kill in build PACKAGEBUILD-26332608