https://launchpad.net/ubuntu/+source/samtools/1.10-4/+build/19481373 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-016 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 19 Jun 17:38:58 ntpdate[1876]: adjust time server 10.211.37.1 offset 0.010294 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19481373 --image-type chroot /home/buildd/filecache-default/a77e1afdcf3761e08e999e63510e3d2f5c5a8a8d Creating target for build PACKAGEBUILD-19481373 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19481373 Starting target for build PACKAGEBUILD-19481373 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19481373 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19481373 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19481373 Updating target for build PACKAGEBUILD-19481373 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf Packages [937 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe armhf Packages [8415 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5183 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf Packages [61.0 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [38.6 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf Packages [831 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [433 kB] Fetched 17.0 MB in 8s (2141 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files binutils binutils-arm-linux-gnueabihf binutils-common bsdutils bzip2 ca-certificates cpp-9 dash debconf debianutils dpkg dpkg-dev e2fsprogs fdisk g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan5 libassuan0 libatomic1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfdisk1 libgcc-9-dev libgcc-s1 libgmp10 libgnutls30 libgomp1 libgpg-error0 libidn2-0 libjson-c4 libkmod2 libmount1 libmpfr6 libncurses6 libncursesw6 libnpth0 libpcre3 libperl5.30 libprocps8 libseccomp2 libsmartcols1 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 libunistring2 libuuid1 libzstd1 linux-libc-dev login logsave make mount ncurses-base ncurses-bin passwd perl perl-base perl-modules-5.30 pkgbinarymangler procps systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata ubuntu-keyring util-linux 103 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 56.3 MB of archives. After this operation, 557 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libcrypt-dev armhf 1:4.4.16-1ubuntu1 [120 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libcrypt1 armhf 1:4.4.16-1ubuntu1 [93.4 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libc6-dev armhf 2.31-0ubuntu10 [1914 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libc-dev-bin armhf 2.31-0ubuntu10 [63.6 kB] Get:5 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf linux-libc-dev armhf 5.4.0-37.41 [1085 kB] Get:6 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libatomic1 armhf 10.1.0-4ubuntu2 [7208 B] Get:7 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libubsan1 armhf 10.1.0-4ubuntu2 [121 kB] Get:8 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libgomp1 armhf 10.1.0-4ubuntu2 [86.8 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf gcc-10-base armhf 10.1.0-4ubuntu2 [20.2 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libgcc-s1 armhf 10.1.0-4ubuntu2 [36.2 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libcc1-0 armhf 10.1.0-4ubuntu2 [34.6 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libstdc++6 armhf 10.1.0-4ubuntu2 [440 kB] Get:13 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libc6 armhf 2.31-0ubuntu10 [2133 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main armhf base-files armhf 11ubuntu7 [59.7 kB] Get:15 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf bsdutils armhf 1:2.35.1-5ubuntu2 [78.9 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main armhf debianutils armhf 4.11 [84.3 kB] Get:17 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf dpkg armhf 1.19.7ubuntu4 [1083 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf perl-modules-5.30 all 5.30.3-4 [2740 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libperl5.30 armhf 5.30.3-4 [3281 kB] Get:20 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf perl armhf 5.30.3-4 [223 kB] Get:21 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf perl-base armhf 5.30.3-4 [1410 kB] Get:22 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf bzip2 armhf 1.0.8-3ubuntu1 [31.8 kB] Get:23 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libbz2-1.0 armhf 1.0.8-3ubuntu1 [30.8 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main armhf debconf all 1.5.74 [121 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main armhf dash armhf 0.5.10.2-7 [79.2 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main armhf gzip armhf 1.10-2ubuntu1 [90.8 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main armhf login armhf 1:4.8.1-1ubuntu6 [217 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main armhf ncurses-bin armhf 6.2-1 [164 kB] Get:29 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libblkid1 armhf 2.35.1-5ubuntu2 [120 kB] Get:30 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libuuid1 armhf 2.35.1-5ubuntu2 [21.5 kB] Get:31 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libfdisk1 armhf 2.35.1-5ubuntu2 [159 kB] Get:32 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libmount1 armhf 2.35.1-5ubuntu2 [132 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main armhf libncurses6 armhf 6.2-1 [79.7 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main armhf libncursesw6 armhf 6.2-1 [106 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main armhf libtinfo6 armhf 6.2-1 [73.6 kB] Get:36 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libsmartcols1 armhf 2.35.1-5ubuntu2 [84.3 kB] Get:37 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf fdisk armhf 2.35.1-5ubuntu2 [113 kB] Get:38 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf util-linux armhf 2.35.1-5ubuntu2 [985 kB] Get:39 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libc-bin armhf 2.31-0ubuntu10 [492 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main armhf ncurses-base all 6.2-1 [18.7 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main armhf sysvinit-utils armhf 2.96-3ubuntu1 [19.1 kB] Get:42 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf systemd-sysv armhf 245.6-1ubuntu1 [10.3 kB] Get:43 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf systemd-timesyncd armhf 245.6-1ubuntu1 [27.9 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main armhf libacl1 armhf 2.2.53-8 [16.0 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main armhf libapparmor1 armhf 2.13.3-7ubuntu6 [29.2 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main armhf libcap2 armhf 1:2.34-2 [15.6 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main armhf libargon2-1 armhf 0~20171227-0.2build20.10.0 [20.0 kB] Get:48 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libudev1 armhf 245.6-1ubuntu1 [67.3 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main armhf libdevmapper1.02.1 armhf 2:1.02.167-1ubuntu3 [118 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main armhf libjson-c4 armhf 0.13.1+dfsg-9 [25.8 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main armhf libcryptsetup12 armhf 2:2.3.3-1ubuntu3 [173 kB] Get:52 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libgmp10 armhf 2:6.2.0+dfsg-6 [192 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main armhf libunistring2 armhf 0.9.10-4 [359 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main armhf libidn2-0 armhf 2.3.0-1 [49.9 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main armhf libgnutls30 armhf 3.6.13-4ubuntu2 [769 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main armhf libgpg-error0 armhf 1.38-1 [54.2 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main armhf libkmod2 armhf 27+20200310-2ubuntu1 [38.2 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main armhf libseccomp2 armhf 2.4.3-1ubuntu3 [32.5 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http://ftpmaster.internal/ubuntu groovy/main armhf e2fsprogs armhf 1.45.6-1ubuntu1 [510 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main armhf libcap-ng0 armhf 0.7.9-2.2 [9764 B] Get:71 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libdebconfclient0 armhf 0.252ubuntu1 [5716 B] Get:72 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libpcre3 armhf 2:8.39-13 [212 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main armhf passwd armhf 1:4.8.1-1ubuntu6 [749 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main armhf libcom-err2 armhf 1.45.6-1ubuntu1 [8708 B] Get:75 http://ftpmaster.internal/ubuntu groovy/main armhf libprocps8 armhf 2:3.3.16-5ubuntu1 [29.6 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/main armhf libss2 armhf 1.45.6-1ubuntu1 [9384 B] Get:77 http://ftpmaster.internal/ubuntu groovy/main armhf procps armhf 2:3.3.16-5ubuntu1 [222 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main armhf ca-certificates all 20190110ubuntu2 [145 kB] Get:79 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libsqlite3-0 armhf 3.32.2-2 [469 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main armhf tzdata all 2020a-0ubuntu1 [293 kB] Get:81 http://ftpmaster.internal/ubuntu groovy/main armhf libctf0 armhf 2.34-7ubuntu1 [37.1 kB] Get:82 http://ftpmaster.internal/ubuntu groovy/main armhf binutils-arm-linux-gnueabihf armhf 2.34-7ubuntu1 [2093 kB] Get:83 http://ftpmaster.internal/ubuntu groovy/main armhf libbinutils armhf 2.34-7ubuntu1 [317 kB] Get:84 http://ftpmaster.internal/ubuntu groovy/main armhf binutils armhf 2.34-7ubuntu1 [3364 B] Get:85 http://ftpmaster.internal/ubuntu groovy/main armhf binutils-common armhf 2.34-7ubuntu1 [207 kB] Get:86 http://ftpmaster.internal/ubuntu groovy/main armhf libctf-nobfd0 armhf 2.34-7ubuntu1 [38.0 kB] Get:87 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libasan5 armhf 9.3.0-14ubuntu2 [386 kB] Get:88 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf g++-9 armhf 9.3.0-14ubuntu2 [6694 kB] Get:89 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf gcc-9 armhf 9.3.0-14ubuntu2 [6556 kB] Get:90 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libstdc++-9-dev armhf 9.3.0-14ubuntu2 [1782 kB] Get:91 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libgcc-9-dev armhf 9.3.0-14ubuntu2 [688 kB] Get:92 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf cpp-9 armhf 9.3.0-14ubuntu2 [5878 kB] Get:93 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf gcc-9-base armhf 9.3.0-14ubuntu2 [19.5 kB] Get:94 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libmpfr6 armhf 4.0.2-1build1 [197 kB] Get:95 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf dpkg-dev all 1.19.7ubuntu4 [679 kB] Get:96 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libdpkg-perl all 1.19.7ubuntu4 [230 kB] Get:97 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf make armhf 4.3-3 [156 kB] Get:98 http://ftpmaster.internal/ubuntu groovy/main armhf libassuan0 armhf 2.5.3-7.1 [29.2 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/main armhf libnpth0 armhf 1.6-2 [6772 B] Get:100 http://ftpmaster.internal/ubuntu groovy/main armhf gpg armhf 2.2.20-1ubuntu1 [427 kB] Get:101 http://ftpmaster.internal/ubuntu groovy/main armhf gpgconf armhf 2.2.20-1ubuntu1 [107 kB] Get:102 http://ftpmaster.internal/ubuntu groovy/main armhf gpg-agent armhf 2.2.20-1ubuntu1 [195 kB] Get:103 http://ftpmaster.internal/ubuntu groovy/main armhf pkgbinarymangler all 146 [31.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 56.3 MB in 3s (20.8 MB/s) (Reading database ... 12562 files and directories currently installed.) 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19481373 armhf groovy-proposed -c chroot:build-PACKAGEBUILD-19481373 --arch=armhf --dist=groovy-proposed --nolog samtools_1.10-4.dsc Initiating build PACKAGEBUILD-19481373 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-016.buildd +==============================================================================+ | samtools 1.10-4 (armhf) 19 Jun 2020 17:40 | +==============================================================================+ Package: samtools Version: 1.10-4 Source Version: 1.10-4 Distribution: groovy-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/samtools-FVZviv/samtools-1.10' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-FVZviv' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19481373/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- samtools_1.10-4.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-mqbp79/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-mqbp79/apt_archive ./ InRelease Get:2 copy:/<>/resolver-mqbp79/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-mqbp79/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-mqbp79/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-mqbp79/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (57.9 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. 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Merged Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.10), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0), liblzma-dev, libbz2-dev Filtered Build-Depends: debhelper-compat (= 13), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.10), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0), liblzma-dev, libbz2-dev dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/<>/resolver-h8SQqm/apt_archive/sbuild-build-depends-samtools-dummy.deb'. Ign:1 copy:/<>/resolver-h8SQqm/apt_archive ./ InRelease Get:2 copy:/<>/resolver-h8SQqm/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-h8SQqm/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-h8SQqm/apt_archive ./ Sources [311 B] Get:5 copy:/<>/resolver-h8SQqm/apt_archive ./ Packages [622 B] Fetched 3052 B in 0s (74.8 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install samtools 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 bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db pkg-config po-debconf tabix zlib1g-dev Suggested packages: gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user 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 libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf autoconf-archive automake autopoint autotools-dev bash-completion bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libncurses-dev libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 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[43.4 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/universe armhf tabix armhf 1.10.2-3 [323 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 21.0 MB in 2s (10.6 MB/s) Selecting previously unselected package libbsd0:armhf. 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Unpacking liblzma-dev:armhf (5.2.4-1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../63-zlib1g-dev_1%3a1.2.11.dfsg-2ubuntu1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu1) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../64-libhts-dev_1.10.2-3_armhf.deb ... Unpacking libhts-dev:armhf (1.10.2-3) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../65-libio-pty-perl_1%3a1.12-1_armhf.deb ... Unpacking libio-pty-perl (1:1.12-1) ... Selecting previously unselected package libncurses-dev:armhf. Preparing to unpack .../66-libncurses-dev_6.2-1_armhf.deb ... Unpacking libncurses-dev:armhf (6.2-1) ... Selecting previously unselected package libncurses5-dev:armhf. Preparing to unpack .../67-libncurses5-dev_6.2-1_armhf.deb ... Unpacking libncurses5-dev:armhf (6.2-1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../68-pkg-config_0.29.2-1ubuntu1_armhf.deb ... Unpacking pkg-config (0.29.2-1ubuntu1) ... Selecting previously unselected package tabix. Preparing to unpack .../69-tabix_1.10.2-3_armhf.deb ... Unpacking tabix (1.10.2-3) ... Selecting previously unselected package sbuild-build-depends-samtools-dummy. Preparing to unpack .../70-sbuild-build-depends-samtools-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ... Setting up libpipeline1:armhf (1.5.2-2build1) ... Setting up libkeyutils1:armhf (1.6.1-2ubuntu1) ... Setting up libncurses-dev:armhf (6.2-1) ... Setting up libpsl5:armhf (0.21.0-1.1) ... Setting up libio-pty-perl (1:1.12-1) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.64.3-1) ... No schema files found: doing nothing. Setting up libicu66:armhf (66.1-2ubuntu2) ... Setting up libdebhelper-perl (13.1ubuntu1) ... Setting up libbrotli1:armhf (1.0.7-6.1) ... Setting up libnghttp2-14:armhf (1.41.0-2) ... Setting up libmagic1:armhf (1:5.38-5) ... Setting up libdeflate0:armhf (1.6-1) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up autoconf-archive (20190106-2.1ubuntu1) ... Setting up file (1:5.38-5) ... Setting up libldap-common (2.4.50+dfsg-1ubuntu2) ... Setting up libkrb5support0:armhf (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build1) ... Setting up bash-completion (1:2.10-1ubuntu1) ... Setting up libsigsegv2:armhf (2.12-2build1) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up pkg-config (0.29.2-1ubuntu1) ... Setting up libk5crypto3:armhf (1.17-6ubuntu4) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2) ... Setting up libroken18-heimdal:armhf (7.7.0+dfsg-2) ... Setting up liblzma-dev:armhf (5.2.4-1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libncurses5-dev:armhf (6.2-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:armhf (1.17-6ubuntu4) ... Setting up libbsd0:armhf (0.10.0-1) ... Setting up libelf1:armhf (0.176-1.1build1) ... Setting up libxml2:armhf (2.9.10+dfsg-5) ... Setting up libheimbase1-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libbz2-dev:armhf (1.0.8-3ubuntu1) ... Setting up libfile-stripnondeterminism-perl (1.8.1-1) ... Setting up libtool (2.4.6-14) ... Setting up libasn1-8-heimdal:armhf (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-4) ... Setting up libhcrypto4-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libwind0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-6ubuntu4) ... Setting up libcroco3:armhf (0.6.13-1) ... Setting up libssh-4:armhf (0.9.4-1ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.1-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up automake (1:1.16.2-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10build1) ... Setting up libhx509-5-heimdal:armhf (7.7.0+dfsg-2) ... Setting up man-db (2.9.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libkrb5-26-heimdal:armhf (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:armhf (2.4.50+dfsg-1ubuntu2) ... Setting up libcurl3-gnutls:armhf (7.68.0-1ubuntu2) ... Setting up tabix (1.10.2-3) ... Setting up libhts3:armhf (1.10.2-3) ... Setting up libhts-dev:armhf (1.10.2-3) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.1ubuntu1) ... Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-177-generic arm64 (armv7l) Toolchain package versions: binutils_2.34-7ubuntu1 dpkg-dev_1.19.7ubuntu4 g++-9_9.3.0-14ubuntu2 gcc-9_9.3.0-14ubuntu2 libc6-dev_2.31-0ubuntu10 libstdc++-9-dev_9.3.0-14ubuntu2 libstdc++6_10.1.0-4ubuntu2 linux-libc-dev_5.4.0-37.41 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.6 autoconf_2.69-11.1 autoconf-archive_20190106-2.1ubuntu1 automake_1:1.16.2-1ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu7 base-passwd_3.5.47 bash_5.0-6ubuntu1 bash-completion_1:2.10-1ubuntu1 binutils_2.34-7ubuntu1 binutils-arm-linux-gnueabihf_2.34-7ubuntu1 binutils-common_2.34-7ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.35.1-5ubuntu2 build-essential_12.8ubuntu1 bzip2_1.0.8-3ubuntu1 ca-certificates_20190110ubuntu2 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-14ubuntu2 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1ubuntu1 debianutils_4.11 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu4 dpkg-dev_1.19.7ubuntu4 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 fdisk_2.35.1-5ubuntu2 file_1:5.38-5 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-14ubuntu2 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-4ubuntu2 gcc-9_9.3.0-14ubuntu2 gcc-9-base_9.3.0-14ubuntu2 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.6 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan5_9.3.0-14ubuntu2 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4ubuntu2 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34-7ubuntu1 libblkid1_2.35.1-5ubuntu2 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-3ubuntu1 libbz2-dev_1.0.8-3ubuntu1 libc-bin_2.31-0ubuntu10 libc-dev-bin_2.31-0ubuntu10 libc6_2.31-0ubuntu10 libc6-dev_2.31-0ubuntu10 libcap-ng0_0.7.9-2.2 libcap2_1:2.34-2 libcc1-0_10.1.0-4ubuntu2 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1ubuntu1 libcrypt1_1:4.4.16-1ubuntu1 libcryptsetup12_2:2.3.3-1ubuntu3 libctf-nobfd0_2.34-7ubuntu1 libctf0_2.34-7ubuntu1 libcurl3-gnutls_7.68.0-1ubuntu2 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.252ubuntu1 libdebhelper-perl_13.1ubuntu1 libdeflate0_1.6-1 libdevmapper1.02.1_2:1.02.167-1ubuntu3 libdpkg-perl_1.19.7ubuntu4 libelf1_0.176-1.1build1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libfdisk1_2.35.1-5ubuntu2 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.1-1 libgcc-9-dev_9.3.0-14ubuntu2 libgcc-s1_10.1.0-4ubuntu2 libgcrypt20_1.8.5-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.3-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.13-4ubuntu2 libgomp1_10.1.0-4ubuntu2 libgpg-error0_1.38-1 libgssapi-krb5-2_1.17-6ubuntu4 libgssapi3-heimdal_7.7.0+dfsg-2 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libhx509-5-heimdal_7.7.0+dfsg-2 libicu66_66.1-2ubuntu2 libidn2-0_2.3.0-1 libio-pty-perl_1:1.12-1 libip4tc2_1.8.4-3ubuntu2 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libk5crypto3_1.17-6ubuntu4 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-6ubuntu4 libkrb5support0_1.17-6ubuntu4 libldap-2.4-2_2.4.50+dfsg-1ubuntu2 libldap-common_2.4.50+dfsg-1ubuntu2 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.1-5ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1build1 libncurses-dev_6.2-1 libncurses5-dev_6.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.41.0-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-5ubuntu1 libpsl5_0.21.0-1.1 libreadline8_8.0-4 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1ubuntu3 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2build1 libsmartcols1_2.35.1-5ubuntu2 libsqlite3-0_3.32.2-2 libss2_1.45.6-1ubuntu1 libssh-4_0.9.4-1ubuntu1 libssl1.1_1.1.1f-1ubuntu2 libstdc++-9-dev_9.3.0-14ubuntu2 libstdc++6_10.1.0-4ubuntu2 libsub-override-perl_0.09-2 libsystemd0_245.6-1ubuntu1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-4ubuntu2 libuchardet0_0.0.7-1 libudev1_245.6-1ubuntu1 libunistring2_0.9.10-4 libuuid1_2.35.1-5ubuntu2 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-5 libzstd1_1.4.5+dfsg-2 linux-libc-dev_5.4.0-37.41 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-3 man-db_2.9.2-1 mawk_1.3.4.20200120-2 mount_2.35.1-5ubuntu2 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1f-1ubuntu2 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-3build1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu1 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_245.6-1ubuntu1 systemd-sysv_245.6-1ubuntu1 systemd-timesyncd_245.6-1ubuntu1 sysvinit-utils_2.96-3ubuntu1 tabix_1.10.2-3 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.35.1-5ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Jun 19 11:26:24 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./samtools_1.10-4.dsc dpkg-source: info: extracting samtools in samtools-1.10 dpkg-source: info: unpacking samtools_1.10.orig.tar.gz dpkg-source: info: unpacking samtools_1.10-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19481373 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19481373 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19481373 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.10-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from samtools-1.10/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 -- install -d /<>/debian/.debhelper/generated/_source/home /<>/debian/.debhelper/generated/_source/xdg-runtime-dir 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 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* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a 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:63: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:63: the top level configure.ac:63: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:63: the top level configure.ac:63: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:63: the top level configure.ac:63: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:63: 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 configure.ac:63: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:63: the top level autoconf configure.ac:63: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:63: the top level dh_auto_configure -- --with-htslib=system install -d /<>/debian/.debhelper/generated/_source/home /<>/debian/.debhelper/generated/_source/xdg-runtime-dir ./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 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /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 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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" "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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.10"' > version.h gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c ar -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o ar: `u' modifier ignored since `D' is the default (see `U') ar -rcs libst.a sam_opts.o sam_utils.o gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -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_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.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 ./lz4/lz4.o libbam.a 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_trans_tbl_init test/merge/test_trans_tbl_init.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 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 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:-} /usr/bin/bgzip -c -b 65272 -s 5 /tmp/q48Qg2JNvO/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 979200 -s 6 /tmp/q48Qg2JNvO/bgzip.dat.gz .. ok /usr/bin/bgzip -c -b 652804 -s 6 /tmp/q48Qg2JNvO/bgzip.dat.gz .. ok /<>/samtools faidx /tmp/q48Qg2JNvO/faidx.fa 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/q48Qg2JNvO/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /<>/samtools faidx /tmp/q48Qg2JNvO/faidx.fa 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/q48Qg2JNvO/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /<>/samtools faidx /tmp/q48Qg2JNvO/faidx.fa 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/q48Qg2JNvO/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /<>/samtools faidx /tmp/q48Qg2JNvO/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /<>/samtools faidx /tmp/q48Qg2JNvO/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /<>/samtools fqidx /tmp/q48Qg2JNvO/fqidx.fq 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/q48Qg2JNvO/fqidx.fq.gz 3:11-13 .. ok .. ok /<>/samtools fqidx /tmp/q48Qg2JNvO/fqidx.fq 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/q48Qg2JNvO/fqidx.fq.gz 2:998-1003 .. ok .. ok /<>/samtools fqidx /tmp/q48Qg2JNvO/fqidx.fq 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/q48Qg2JNvO/fqidx.fq.gz 1:100-104 .. ok .. ok /<>/samtools fqidx /tmp/q48Qg2JNvO/fqidx.fq 1:99998-100007 .. ok .. ok /<>/samtools fqidx /tmp/q48Qg2JNvO/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/q48Qg2JNvO/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_index: /<>/samtools view /tmp/q48Qg2JNvO/large_chrom.bam ref2 .. ok test_index: /<>/samtools view /tmp/q48Qg2JNvO/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/q48Qg2JNvO/test_input_1_b.bam.bai ref2 .. 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/q48Qg2JNvO/test_input_1_b.bam.bai .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.bam /tmp/q48Qg2JNvO/auto_indexed.csi && cat /tmp/q48Qg2JNvO/auto_indexed.csi .. ok test_index: /<>/samtools index /<>/test/dat/auto_indexed.tmp.cram /tmp/q48Qg2JNvO/auto_indexed.crai && cat /tmp/q48Qg2JNvO/auto_indexed.crai .. ok test_index: /<>/samtools index -c /<>/test/dat/auto_indexed.tmp.sam /tmp/q48Qg2JNvO/auto_indexed.csi && cat /tmp/q48Qg2JNvO/auto_indexed.csi .. ok test_index: /<>/samtools view -@ 2 /tmp/q48Qg2JNvO/large_chrom.bam ref2 .. ok test_index: /<>/samtools view -@ 2 /tmp/q48Qg2JNvO/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/q48Qg2JNvO/test_input_1_b.bam.bai ref2 .. 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/q48Qg2JNvO/test_input_1_b.bam.bai .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.bam /tmp/q48Qg2JNvO/auto_indexed.csi && cat /tmp/q48Qg2JNvO/auto_indexed.csi .. ok test_index: /<>/samtools index -@ 2 /<>/test/dat/auto_indexed.tmp.cram /tmp/q48Qg2JNvO/auto_indexed.crai && cat /tmp/q48Qg2JNvO/auto_indexed.crai .. ok test_index: /<>/samtools index -@ 2 -c /<>/test/dat/auto_indexed.tmp.sam /tmp/q48Qg2JNvO/auto_indexed.csi && cat /tmp/q48Qg2JNvO/auto_indexed.csi .. ok test_mpileup: /<>/samtools mpileup -b /tmp/q48Qg2JNvO/mpileup.bam.list -f /tmp/q48Qg2JNvO/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/q48Qg2JNvO/mpileup.cram.list -f /tmp/q48Qg2JNvO/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/q48Qg2JNvO/mpileup.bam.urllist -f /tmp/q48Qg2JNvO/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -b /tmp/q48Qg2JNvO/mpileup.cram.urllist -f /tmp/q48Qg2JNvO/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /<>/samtools mpileup -uvDV -b /tmp/q48Qg2JNvO/mpileup.bam.list -f /tmp/q48Qg2JNvO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uvDV -b /tmp/q48Qg2JNvO/mpileup.cram.list -f /tmp/q48Qg2JNvO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/q48Qg2JNvO/mpileup.cram.list -f /tmp/q48Qg2JNvO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/q48Qg2JNvO/mpileup.cram.list -f /tmp/q48Qg2JNvO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/q48Qg2JNvO/mpileup.ref.fa.gz -r17:1050-1060 /tmp/q48Qg2JNvO/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /<>/samtools mpileup -B --ff 0x14 -f /tmp/q48Qg2JNvO/mpileup.ref.fa.gz -r17:1050-1060 /tmp/q48Qg2JNvO/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, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, coverage, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad .. 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 collate Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools cat Usage on stderr rather than stdout .. expected failure 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 bedcov Usage on stderr rather than stdout .. expected failure test_usage_subcommand: samtools coverage .. ok test_usage_subcommand: samtools depth Usage on stderr rather than stdout .. expected failure 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 flags Usage on stderr rather than stdout .. expected failure 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_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/q48Qg2JNvO/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/q48Qg2JNvO/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/q48Qg2JNvO/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/q48Qg2JNvO/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/q48Qg2JNvO/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/q48Qg2JNvO/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/q48Qg2JNvO/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/q48Qg2JNvO/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/q48Qg2JNvO/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/q48Qg2JNvO/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/q48Qg2JNvO/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/q48Qg2JNvO/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/q48Qg2JNvO/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/q48Qg2JNvO/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/q48Qg2JNvO/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/q48Qg2JNvO/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/q48Qg2JNvO/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/q48Qg2JNvO/view.001.fogn (CRAM input).. ok 67: Filter -d BC:TGCA (SAM input) .. ok 68: Count -d BC:TGCA (SAM input) .. ok 69: Filter -d BC:TGCA (BAM input) .. ok 70: Count -d BC:TGCA (BAM input) .. ok 71: Filter -d BC:TGCA (CRAM input) .. ok 72: Count -d BC:TGCA (CRAM input) .. ok 73: Filter -D BC:/tmp/q48Qg2JNvO/view.001.fobc (SAM input) .. ok 74: Count -D BC:/tmp/q48Qg2JNvO/view.001.fobc (SAM input) .. ok 75: Filter -D BC:/tmp/q48Qg2JNvO/view.001.fobc (BAM input) .. ok 76: Count -D BC:/tmp/q48Qg2JNvO/view.001.fobc (BAM input) .. ok 77: Filter -D BC:/tmp/q48Qg2JNvO/view.001.fobc (CRAM input) .. ok 78: Count -D BC:/tmp/q48Qg2JNvO/view.001.fobc (CRAM input) .. ok 79: Filter -D BC:/tmp/q48Qg2JNvO/view.001.fobc -d BC:TGCA (SAM input).. ok 80: Count -D BC:/tmp/q48Qg2JNvO/view.001.fobc -d BC:TGCA (SAM input).. ok 81: Filter -D BC:/tmp/q48Qg2JNvO/view.001.fobc -d BC:TGCA (BAM input).. ok 82: Count -D BC:/tmp/q48Qg2JNvO/view.001.fobc -d BC:TGCA (BAM input).. ok 83: Filter -D BC:/tmp/q48Qg2JNvO/view.001.fobc -d BC:TGCA (CRAM input).. ok 84: Count -D BC:/tmp/q48Qg2JNvO/view.001.fobc -d BC:TGCA (CRAM input).. ok 85: Filter -d BC:TGCA -D BC:/tmp/q48Qg2JNvO/view.001.fobc (SAM input).. ok 86: Count -d BC:TGCA -D BC:/tmp/q48Qg2JNvO/view.001.fobc (SAM input).. ok 87: Filter -d BC:TGCA -D BC:/tmp/q48Qg2JNvO/view.001.fobc (BAM input).. ok 88: Count -d BC:TGCA -D BC:/tmp/q48Qg2JNvO/view.001.fobc (BAM input).. ok 89: Filter -d BC:TGCA -D BC:/tmp/q48Qg2JNvO/view.001.fobc (CRAM input).. ok 90: Count -d BC:TGCA -D BC:/tmp/q48Qg2JNvO/view.001.fobc (CRAM input).. ok 91: Filter -D RG:/tmp/q48Qg2JNvO/view.001.fogn (SAM input) .. ok 92: Count -D RG:/tmp/q48Qg2JNvO/view.001.fogn (SAM input) .. ok 93: Filter -D RG:/tmp/q48Qg2JNvO/view.001.fogn (BAM input) .. ok 94: Count -D RG:/tmp/q48Qg2JNvO/view.001.fogn (BAM input) .. ok 95: Filter -D RG:/tmp/q48Qg2JNvO/view.001.fogn (CRAM input) .. ok 96: Count -D RG:/tmp/q48Qg2JNvO/view.001.fogn (CRAM input) .. ok 97: Filter -d NE:TGCA (SAM input) .. ok 98: Count -d NE:TGCA (SAM input) .. ok 99: Filter -d NE:TGCA (BAM input) .. ok 100: Count -d NE:TGCA (BAM input) .. ok 101: Filter -d NE:TGCA (CRAM input) .. ok 102: Count -d NE:TGCA (CRAM input) .. ok 103: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /<>/samtools view -o /tmp/q48Qg2JNvO/view.test103.sam -h -d TGCA /tmp/q48Qg2JNvO/view.001.sam --no-PG .. expected failure 104: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /<>/samtools view -c -d TGCA /tmp/q48Qg2JNvO/view.001.sam --no-PG .. expected failure 105: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /<>/samtools view -o /tmp/q48Qg2JNvO/view.test105.sam -h -d TGCA /tmp/q48Qg2JNvO/view.test001.bam --no-PG .. expected failure 106: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /<>/samtools view -c -d TGCA /tmp/q48Qg2JNvO/view.test001.bam --no-PG .. expected failure 107: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /<>/samtools view -o /tmp/q48Qg2JNvO/view.test107.sam -h -d TGCA /tmp/q48Qg2JNvO/view.test006.cram --no-PG .. expected failure 108: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA": No such file or directory Failed command: /<>/samtools view -c -d TGCA /tmp/q48Qg2JNvO/view.test006.cram --no-PG .. expected failure 109: Filter -D BClong:/tmp/q48Qg2JNvO/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/q48Qg2JNvO/view.001.fobc": No such file or directory Failed command: /<>/samtools view -o /tmp/q48Qg2JNvO/view.test109.sam -h -D BClong:/tmp/q48Qg2JNvO/view.001.fobc /tmp/q48Qg2JNvO/view.001.sam --no-PG .. expected failure 110: Count -D BClong:/tmp/q48Qg2JNvO/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/q48Qg2JNvO/view.001.fobc": No such file or directory Failed command: /<>/samtools view -c -D BClong:/tmp/q48Qg2JNvO/view.001.fobc /tmp/q48Qg2JNvO/view.001.sam --no-PG .. expected failure 111: Filter -D BClong:/tmp/q48Qg2JNvO/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/q48Qg2JNvO/view.001.fobc": No such file or directory Failed command: /<>/samtools view -o /tmp/q48Qg2JNvO/view.test111.sam -h -D BClong:/tmp/q48Qg2JNvO/view.001.fobc /tmp/q48Qg2JNvO/view.test001.bam --no-PG .. expected failure 112: Count -D BClong:/tmp/q48Qg2JNvO/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/q48Qg2JNvO/view.001.fobc": No such file or directory Failed command: /<>/samtools view -c -D BClong:/tmp/q48Qg2JNvO/view.001.fobc /tmp/q48Qg2JNvO/view.test001.bam --no-PG .. expected failure 113: Filter -D BClong:/tmp/q48Qg2JNvO/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/q48Qg2JNvO/view.001.fobc": No such file or directory Failed command: /<>/samtools view -o /tmp/q48Qg2JNvO/view.test113.sam -h -D BClong:/tmp/q48Qg2JNvO/view.001.fobc /tmp/q48Qg2JNvO/view.test006.cram --no-PG .. expected failure 114: Count -D BClong:/tmp/q48Qg2JNvO/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/q48Qg2JNvO/view.001.fobc": No such file or directory Failed command: /<>/samtools view -c -D BClong:/tmp/q48Qg2JNvO/view.001.fobc /tmp/q48Qg2JNvO/view.test006.cram --no-PG .. expected failure 115: 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/q48Qg2JNvO/view.test115.sam -h -d BC:ACGT -d RG:grp2 /tmp/q48Qg2JNvO/view.001.sam --no-PG .. expected failure 116: 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/q48Qg2JNvO/view.001.sam --no-PG .. expected failure 117: 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/q48Qg2JNvO/view.test117.sam -h -d BC:ACGT -d RG:grp2 /tmp/q48Qg2JNvO/view.test001.bam --no-PG .. expected failure 118: 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/q48Qg2JNvO/view.test001.bam --no-PG .. expected failure 119: 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/q48Qg2JNvO/view.test119.sam -h -d BC:ACGT -d RG:grp2 /tmp/q48Qg2JNvO/view.test006.cram --no-PG .. expected failure 120: 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/q48Qg2JNvO/view.test006.cram --no-PG .. expected failure 121: Filter -l Library 2 (SAM input) .. ok 122: Count -l Library 2 (SAM input) .. ok 123: Filter -l Library 2 (BAM input) .. ok 124: Count -l Library 2 (BAM input) .. ok 125: Filter -l Library 2 (CRAM input) .. ok 126: Count -l Library 2 (CRAM input) .. ok 127: Filter -l Library 3 (SAM input) .. ok 128: Count -l Library 3 (SAM input) .. ok 129: Filter -l Library 3 (BAM input) .. ok 130: Count -l Library 3 (BAM input) .. ok 131: Filter -l Library 3 (CRAM input) .. ok 132: Count -l Library 3 (CRAM input) .. ok 133: Filter -q 50 (SAM input) .. ok 134: Count -q 50 (SAM input) .. ok 135: Filter -q 50 (BAM input) .. ok 136: Count -q 50 (BAM input) .. ok 137: Filter -q 50 (CRAM input) .. ok 138: Count -q 50 (CRAM input) .. ok 139: Filter -q 99 (SAM input) .. ok 140: Count -q 99 (SAM input) .. ok 141: Filter -q 99 (BAM input) .. ok 142: Count -q 99 (BAM input) .. ok 143: Filter -q 99 (CRAM input) .. ok 144: Count -q 99 (CRAM input) .. ok 145: Filter -q 100 (SAM input) .. ok 146: Count -q 100 (SAM input) .. ok 147: Filter -q 100 (BAM input) .. ok 148: Count -q 100 (BAM input) .. ok 149: Filter -q 100 (CRAM input) .. ok 150: Count -q 100 (CRAM input) .. ok 151: Filter -x fa (SAM input) .. ok 152: Count -x fa (SAM input) .. ok 153: Filter -x fa (BAM input) .. ok 154: Count -x fa (BAM input) .. ok 155: Filter -x fa (CRAM input) .. ok 156: Count -x fa (CRAM input) .. ok 157: Filter -x fa -x ha (SAM input) .. ok 158: Count -x fa -x ha (SAM input) .. ok 159: Filter -x fa -x ha (BAM input) .. ok 160: Count -x fa -x ha (BAM input) .. ok 161: Filter -x fa -x ha (CRAM input) .. ok 162: Count -x fa -x ha (CRAM input) .. ok 163: Filter -x fa -r grp2 (SAM input) .. ok 164: Count -x fa -r grp2 (SAM input) .. ok 165: Filter -x fa -r grp2 (BAM input) .. ok 166: Count -x fa -r grp2 (BAM input) .. ok 167: Filter -x fa -r grp2 (CRAM input) .. ok 168: Count -x fa -r grp2 (CRAM input) .. ok 169: Filter -x RG -r grp2 (SAM input) .. ok 170: Count -x RG -r grp2 (SAM input) .. ok 171: Filter -x RG -r grp2 (BAM input) .. ok 172: Count -x RG -r grp2 (BAM input) .. ok 173: Filter -x RG -r grp2 (CRAM input) .. ok 174: Count -x RG -r grp2 (CRAM input) .. ok 175: Filter -m 10 (SAM input) .. ok 176: Count -m 10 (SAM input) .. ok 177: Filter -m 10 (BAM input) .. ok 178: Count -m 10 (BAM input) .. ok 179: Filter -m 10 (CRAM input) .. ok 180: Count -m 10 (CRAM input) .. ok 181: Filter -m 11 (SAM input) .. ok 182: Count -m 11 (SAM input) .. ok 183: Filter -m 11 (BAM input) .. ok 184: Count -m 11 (BAM input) .. ok 185: Filter -m 11 (CRAM input) .. ok 186: Count -m 11 (CRAM input) .. ok 187: Filter -m 15 (SAM input) .. ok 188: Count -m 15 (SAM input) .. ok 189: Filter -m 15 (BAM input) .. ok 190: Count -m 15 (BAM input) .. ok 191: Filter -m 15 (CRAM input) .. ok 192: Count -m 15 (CRAM input) .. ok 193: Filter -m 16 (SAM input) .. ok 194: Count -m 16 (SAM input) .. ok 195: Filter -m 16 (BAM input) .. ok 196: Count -m 16 (BAM input) .. ok 197: Filter -m 16 (CRAM input) .. ok 198: Count -m 16 (CRAM input) .. ok 199: 1bp reads file SAM -> BAM -> SAM .. ok 200: 1bp reads file SAM -> CRAM -> SAM .. ok 200: Region Z (BAM input) .. ok 201: Count Z (BAM input) .. ok 202: Region Z (CRAM input) .. ok 203: Count Z (CRAM input) .. ok 204: Region Z:30 (BAM input) .. ok 205: Count Z:30 (BAM input) .. ok 206: Region Z:30 (CRAM input) .. ok 207: Count Z:30 (CRAM input) .. ok 208: Region Z:20-40 (BAM input) .. ok 209: Count Z:20-40 (BAM input) .. ok 210: Region Z:20-40 (CRAM input) .. ok 211: Count Z:20-40 (CRAM input) .. ok 212: Region ref1 (BAM input) .. ok 213: Count ref1 (BAM input) .. ok 214: Region ref1 (CRAM input) .. ok 215: Count ref1 (CRAM input) .. ok 216: Region ref1:15 (BAM input) .. ok 217: Count ref1:15 (BAM input) .. ok 218: Region ref1:15 (CRAM input) .. ok 219: Count ref1:15 (CRAM input) .. ok 220: Region ref1:15-45 (BAM input) .. ok 221: Count ref1:15-45 (BAM input) .. ok 222: Region ref1:15-45 (CRAM input) .. ok 223: Count ref1:15-45 (CRAM input) .. ok 224: Region ref1:15-45 ref2 (BAM input) .. ok 225: Count ref1:15-45 ref2 (BAM input) .. ok 226: Region ref1:15-45 ref2 (CRAM input) .. ok 227: Count ref1:15-45 ref2 (CRAM input) .. ok 228: Region ref1:15-45 ref2:16 (BAM input) .. ok 229: Count ref1:15-45 ref2:16 (BAM input) .. ok 230: Region ref1:15-45 ref2:16 (CRAM input) .. ok 231: Count ref1:15-45 ref2:16 (CRAM input) .. ok 232: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 233: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 234: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 235: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 236: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 237: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 238: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 239: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 240: Region -f 128 ref1 (BAM input) .. ok 241: Count -f 128 ref1 (BAM input) .. ok 242: Region -f 128 ref1 (CRAM input) .. ok 243: Count -f 128 ref1 (CRAM input) .. ok 244: Region -q 50 ref1:15-45 (BAM input) .. ok 245: Count -q 50 ref1:15-45 (BAM input) .. ok 246: Region -q 50 ref1:15-45 (CRAM input) .. ok 247: Count -q 50 ref1:15-45 (CRAM input) .. ok 248: Region -r grp2 ref1:15-45 (BAM input) .. ok 249: Count -r grp2 ref1:15-45 (BAM input) .. ok 250: Region -r grp2 ref1:15-45 (CRAM input) .. ok 251: Count -r grp2 ref1:15-45 (CRAM input) .. ok 252: Region * (BAM input) .. ok 253: Count * (BAM input) .. ok 254: Region * (CRAM input) .. ok 255: Count * (CRAM input) .. ok 256: Region -L /<>/test/dat/view.002.01.bed (BAM input).. ok 257: Count -L /<>/test/dat/view.002.01.bed (BAM input).. ok 258: Region -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 259: Count -L /<>/test/dat/view.002.01.bed (CRAM input).. ok 260: Region -L /<>/test/dat/view.002.02.bed (BAM input).. ok 261: Count -L /<>/test/dat/view.002.02.bed (BAM input).. ok 262: Region -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 263: Count -L /<>/test/dat/view.002.02.bed (CRAM input).. ok 264: Region -L /<>/test/dat/view.001.01.bed (BAM input).. ok 265: Count -L /<>/test/dat/view.001.01.bed (BAM input).. ok 266: Region -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 267: Count -L /<>/test/dat/view.001.01.bed (CRAM input).. ok 268: Region -L /<>/test/dat/view.001.02.bed (BAM input).. ok 269: Count -L /<>/test/dat/view.001.02.bed (BAM input).. ok 270: Region -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 271: Count -L /<>/test/dat/view.001.02.bed (CRAM input).. ok 272: Region -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 273: Count -L /<>/test/dat/view.002.01.bed Z (BAM input).. ok 274: Region -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 275: Count -L /<>/test/dat/view.002.01.bed Z (CRAM input).. ok 276: Region -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 277: Count -L /<>/test/dat/view.002.01.bed Z:30 (BAM input).. ok 278: Region -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 279: Count -L /<>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 280: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 281: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 282: Region -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 283: Count -L /<>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 284: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 285: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 286: Region -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 287: Count -L /<>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 288: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 289: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 290: Region -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 291: Count -L /<>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 292: Region -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 293: Count -L /<>/test/dat/view.001.01.bed ref2 (BAM input).. ok 294: Region -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 295: Count -L /<>/test/dat/view.001.01.bed ref2 (CRAM input).. ok 296: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 297: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 298: Region -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 299: Count -L /<>/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 300: Region -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 301: Count -L /<>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 302: Region -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 303: Count -L /<>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 304: Region -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 305: Count -L /<>/test/dat/view.001.01.bed -f 128 (BAM input).. ok 306: Region -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 307: Count -L /<>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 308: Region -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 309: Count -L /<>/test/dat/view.001.01.bed -q 5 (BAM input).. ok 310: Region -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 311: Count -L /<>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 312: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 313: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 314: Region -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 315: Count -L /<>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 316: Make BAM with no M5/UR tags .. ok 317: Add @SQ with -t (SAM -> SAM) .. ok 318: Add @SQ with -T (SAM -> SAM) .. ok 319: Add @SQ with -t (BAM -> SAM) .. ok 320: Add @SQ with -T (BAM -> SAM) .. ok 321: Add @SQ with -t (SAM -> BAM) .. ok 322: Add @SQ with -T (SAM -> BAM) .. ok 323: Add @SQ with -t (BAM -> BAM) .. ok 324: Add @SQ with -T (BAM -> BAM) .. ok 325: Add @SQ with -t (SAM -> CRAM) .. ok 326: Add @SQ with -T (SAM -> CRAM) .. ok 327: Add @SQ with -t (BAM -> CRAM) .. ok 328: Add @SQ with -T (BAM -> CRAM) .. ok 329: Make CRAM with no UR field .. ok 330: Decoding CRAM with no UR field via -T .. ok 331: CIGAR B-operator removal .. ok 332: Big SAM -> BAM .. ok 333: Big SAM -> BAM (2 threads) .. ok 334: Big SAM -> BAM (4 threads) .. ok 335: Big SAM -> CRAM .. ok 336: Big SAM -> CRAM (2 threads) .. ok 337: Big SAM -> CRAM (4 threads) .. ok 338: Subsample 0.2 (SAM input) ............ ok 339: Subsample 0.5 (SAM input) ............ ok 340: Subsample 0.8 (SAM input) ............ ok 341: Subsample 0.2 (BAM input) ............ ok 342: Subsample 0.5 (BAM input) ............ ok 343: Subsample 0.8 (BAM input) ............ ok 344: Subsample 0.2 (CRAM input) ............ ok 345: Subsample 0.5 (CRAM input) ............ ok 346: Subsample 0.8 (CRAM input) ............ ok 347: SAM add PG .. 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_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 fastq -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -N -s /tmp/q48Qg2JNvO/bam2fq.discard.s.fq -0 /tmp/q48Qg2JNvO/bam2fq.discard.0.fq /<>/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 fastq -@ 2 -N -o /<>/test/o.fq /<>/test/dat/bam2fq.001.sam .. ok test_bam2fq: /<>/samtools fastq -@ 2 -N -s /tmp/q48Qg2JNvO/bam2fq.discard.s.fq -0 /tmp/q48Qg2JNvO/bam2fq.discard.0.fq /<>/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_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/iJRlsiSMwx - /<>/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 -s 1 -p -c -t PG -O SAM - /tmp/q48Qg2JNvO/merge.tag.1.bam /tmp/q48Qg2JNvO/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/q48Qg2JNvO/merge.tag.3.bam /tmp/q48Qg2JNvO/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 -@ 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/whXsbZLwOk - /<>/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 -s 1 -p -c -t PG -O SAM - /tmp/q48Qg2JNvO/merge.tag.1.bam /tmp/q48Qg2JNvO/merge.tag.2.bam .. ok test_merge: /<>/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/q48Qg2JNvO/merge.tag.3.bam /tmp/q48Qg2JNvO/merge.tag.4.bam .. ok test_merge: /<>/samtools merge -@ 2 --no-PG -O SAM - /<>/test/merge/test_no_pg_rg_co.sam .. ok test_sort: /<>/samtools sort /<>/test/dat/test_input_1_a.bam /tmp/q48Qg2JNvO/sortout .. ok test_sort: /<>/samtools sort -f /<>/test/dat/test_input_1_a.bam /tmp/q48Qg2JNvO/sortout.bam .. ok test_sort: /<>/samtools sort -o /<>/test/dat/test_input_1_a.bam /tmp/q48Qg2JNvO/sorttmp .. ok test_sort: /<>/samtools sort /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -n /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -t RG /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -n -t RG /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -t AS /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -t FI /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 /<>/test/dat/test_input_1_a.bam /tmp/q48Qg2JNvO/sortout .. ok test_sort: /<>/samtools sort -@ 2 -f /<>/test/dat/test_input_1_a.bam /tmp/q48Qg2JNvO/sortout.bam .. ok test_sort: /<>/samtools sort -@ 2 -o /<>/test/dat/test_input_1_a.bam /tmp/q48Qg2JNvO/sorttmp .. ok test_sort: /<>/samtools sort -@ 2 /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -n /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t RG /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -n -t RG /<>/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t AS /<>/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /<>/samtools sort -@ 2 -t FI /<>/test/dat/test_input_1_d.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 -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 -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -O sam /<>/test/fixmate/8_isize_overflow_64bit.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 -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 -O sam /<>/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /<>/samtools fixmate -@ 2 -O sam /<>/test/fixmate/8_isize_overflow_64bit.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 -@ 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_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: [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: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /<>/samtools markdup -O sam --no-PG /<>/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [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: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [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 -@ 2 -O sam --no-PG /<>/test/markdup/1_name_sort.sam - ERR: [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: [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: [markdup] error: no MC tag. Please run samtools fixmate on file first. [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: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [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_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_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/q48Qg2JNvO/longref.sam.gz .. ok test_large_positions: /<>/samtools view -h --no-PG /tmp/q48Qg2JNvO/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /<>/samtools view -h --no-PG -L /<>/test/large_pos/test.bed /tmp/q48Qg2JNvO/longref.sam.gz .. ok test_large_positions: /<>/samtools sort -O sam --no-PG /<>/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/q48Qg2JNvO/longref.sam.gz .. ok test_large_positions: /<>/samtools sort -O sam --no-PG -n test/large_pos/longref3.sam | /<>/samtools fixmate -O sam --no-PG - - | /<>/samtools sort -O sam --no-PG .. ok Number of tests: total .. 671 passed .. 626 failed .. 0 expected failure .. 45 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 && ./regression.sh mpileup.reg === Testing mpileup.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 163 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && ./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: 43 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a 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 -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/interpolate_sam.pl misc/novo2sam.pl 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 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* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a 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 -d debian/samtools//usr cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/ install -d debian/samtools//usr/share/man cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/ install -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// cp --reflink=auto -a ./debian/mans/ace2sam.1 ./debian/mans/samtools.pl.1 ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/ install -d debian/.debhelper/generated/samtools install -d debian/.debhelper/generated/samtools-test # 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 make[1]: Leaving directory '/<>' dh_installdocs -a install -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 -p -m0644 debian/changelog 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 -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 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-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-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.1 man-recode --to-code UTF-8 --suffix .dh-new 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-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.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 man-recode --to-code UTF-8 --suffix .dh-new 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 man-recode --to-code UTF-8 --suffix .dh-new 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-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.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-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-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-idxstats.1.dh-new debian/samtools/usr/share/man/man1/samtools-idxstats.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 chmod 0644 -- 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-idxstats.1 debian/samtools/usr/share/man/man1/samtools-index.1 debian/samtools/usr/share/man/man1/samtools-markdup.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-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-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 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-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-depad.1 debian/samtools/usr/share/man/man1/samtools-depth.1 debian/samtools/usr/share/man/man1/samtools-dict.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-reheader.1.dh-new debian/samtools/usr/share/man/man1/samtools-reheader.1 mv debian/samtools/usr/share/man/man1/samtools-rmdup.1.dh-new debian/samtools/usr/share/man/man1/samtools-rmdup.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 chmod 0644 -- 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-reheader.1 debian/samtools/usr/share/man/man1/samtools-rmdup.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 dh_lintian -a install -d debian/samtools/usr/share/lintian/overrides install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools dh_perl -a (grep -a -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl:any) > debian/samtools.substvars.new 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 1592559700 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/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-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-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-idxstats.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-reheader.1 usr/share/man/man1/samtools-rmdup.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/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-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-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-idxstats.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-reheader.1 usr/share/man/man1/samtools-rmdup.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 -a install -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 560917 new size 581097 objcopy --compress-debug-sections debian/samtools/usr/lib/debug/.dwz/arm-linux-gnueabihf/samtools.debug dh_strip -a -a install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7a objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7a/eb67a84eee610529449175c1072f04eaf80ef9.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7a/eb67a84eee610529449175c1072f04eaf80ef9.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7a/eb67a84eee610529449175c1072f04eaf80ef9.debug debian/samtools/usr/bin/md5sum-lite install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/49 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/49/4192126eaffaa3a7f07c20588dd0a189f0487d.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/49/4192126eaffaa3a7f07c20588dd0a189f0487d.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/49/4192126eaffaa3a7f07c20588dd0a189f0487d.debug debian/samtools/usr/bin/maq2sam-short install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7c objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7c/c27665b27447e18c9b73adabe6d98ae36378f6.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7c/c27665b27447e18c9b73adabe6d98ae36378f6.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7c/c27665b27447e18c9b73adabe6d98ae36378f6.debug debian/samtools/usr/bin/maq2sam-long install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/62 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/62/044a26871c1cd09e4d1d88a32ed979b2a7bf3d.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/62/044a26871c1cd09e4d1d88a32ed979b2a7bf3d.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/62/044a26871c1cd09e4d1d88a32ed979b2a7bf3d.debug debian/samtools/usr/bin/samtools install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/0cf68ed72796e517695edd0b6b2bc1de235aa5.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/0cf68ed72796e517695edd0b6b2bc1de235aa5.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/0cf68ed72796e517695edd0b6b2bc1de235aa5.debug debian/samtools/usr/bin/md5fa objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/be891611bcfe348613f4eec63ab7ea6625e4df.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/be891611bcfe348613f4eec63ab7ea6625e4df.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ad/be891611bcfe348613f4eec63ab7ea6625e4df.debug debian/samtools/usr/bin/ace2sam install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1 objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/a1e3dad9f01722846b0e20dece854c45362d35.debug chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/a1e3dad9f01722846b0e20dece854c45362d35.debug strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/a1e3dad9f01722846b0e20dece854c45362d35.debug debian/samtools/usr/bin/wgsim install -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 -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym dh_makeshlibs -a -a rm -f debian/samtools/DEBIAN/shlibs dh_shlibdeps -a -a install -d debian/samtools/DEBIAN dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/samtools.substvars echo misc:Pre-Depends= >> debian/samtools.substvars install -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 -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=debug symbols for samtools" "-DBuild-Ids=494192126eaffaa3a7f07c20588dd0a189f0487d 62044a26871c1cd09e4d1d88a32ed979b2a7bf3d 7aeb67a84eee610529449175c1072f04eaf80ef9 7cc27665b27447e18c9b73adabe6d98ae36378f6 ad0cf68ed72796e517695edd0b6b2bc1de235aa5 adbe891611bcfe348613f4eec63ab7ea6625e4df d1a1e3dad9f01722846b0e20dece854c45362d35" -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 cd debian/samtools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools/DEBIAN/md5sums 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 .. install -d debian/.debhelper/scratch-space/build-samtools dpkg-deb --root-owner-group --build debian/.debhelper/samtools/dbgsym-root debian/.debhelper/scratch-space/build-samtools INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing samtools-dbgsym (in debian/.debhelper/samtools/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing samtools (in debian/samtools); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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_1.10-4_armhf.deb'. pkgstripfiles: processing control file: debian/samtools/DEBIAN/control, package samtools, directory debian/samtools .. removing usr/share/doc/samtools/changelog.gz pkgstripfiles: Truncating usr/share/doc/samtools/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package samtools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'samtools' in '../samtools_1.10-4_armhf.deb'. Renaming samtools-dbgsym_1.10-4_armhf.deb to samtools-dbgsym_1.10-4_armhf.ddeb mv debian/.debhelper/scratch-space/build-samtools/samtools-dbgsym_1.10-4_armhf.deb ../samtools-dbgsym_1.10-4_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../samtools_1.10-4_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-1.10/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200619-1746 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ samtools_1.10-4_armhf.changes: ------------------------------ Format: 1.8 Date: Fri, 19 Jun 2020 11:41:40 +0200 Source: samtools Binary: samtools Architecture: armhf Version: 1.10-4 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: samtools - processing sequence alignments in SAM, BAM and CRAM formats Closes: 963093 Changes: samtools (1.10-4) unstable; urgency=medium . * cwltools only "Suggests" not "Recommends" * There are no Python scripts provided in samtools any more Closes: #963093 * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) Checksums-Sha1: fd0cf2255bd760f03addd0a9d5f1bda285efef4b 771360 samtools-dbgsym_1.10-4_armhf.ddeb 497c35e71a460b80346a2bf0e5146294d5c09968 6559 samtools_1.10-4_armhf.buildinfo fae61467b9903de4c11b54c5090c2e2a77083fdf 467996 samtools_1.10-4_armhf.deb Checksums-Sha256: 69ce6a7a84ad998b85341c17d9adb4fabc812ebdf3daff21c4df447bd3b778af 771360 samtools-dbgsym_1.10-4_armhf.ddeb 2cdbc43f41fda7594316d70884721cf07e132d28457eb92088b576a818a09b93 6559 samtools_1.10-4_armhf.buildinfo b637f74ed403a276cf741a36e9cdc19d9a2c26b3846fedc766a68e408342324c 467996 samtools_1.10-4_armhf.deb Files: efb5032315619d083599080aa3154a77 771360 debug optional samtools-dbgsym_1.10-4_armhf.ddeb 73d5612e86968e71bf95b0f6cdc2daae 6559 science optional samtools_1.10-4_armhf.buildinfo 5edb88da5ac59625ec1142cdfdb322f7 467996 science optional samtools_1.10-4_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ samtools_1.10-4_armhf.deb ------------------------- new debian package, version 2.0. size 467996 bytes: control archive=2700 bytes. 969 bytes, 19 lines control 4722 bytes, 70 lines md5sums Package: samtools Version: 1.10-4 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 911 Depends: libc6 (>= 2.29), libhts3 (>= 1.10), libncurses6 (>= 6), libtinfo6 (>= 6), zlib1g (>= 1:1.2.3.3) Suggests: cwltool Breaks: bio-tradis (<= 1.4.5+dfsg-1), iva (<= 1.0.9+ds-6) Section: science Priority: optional Homepage: http://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 2020-06-19 09:41 ./ drwxr-xr-x root/root 0 2020-06-19 09:41 ./usr/ drwxr-xr-x root/root 0 2020-06-19 09:41 ./usr/bin/ -rwxr-xr-x root/root 13868 2020-06-19 09:41 ./usr/bin/ace2sam -rwxr-xr-x root/root 5437 2020-06-19 09:41 ./usr/bin/blast2sam.pl -rwxr-xr-x root/root 3360 2020-06-19 09:41 ./usr/bin/bowtie2sam.pl -rwxr-xr-x root/root 17996 2020-06-19 09:41 ./usr/bin/export2sam.pl -rwxr-xr-x root/root 6121 2020-06-19 09:41 ./usr/bin/interpolate_sam.pl -rwxr-xr-x root/root 9772 2020-06-19 09:41 ./usr/bin/maq2sam-long -rwxr-xr-x root/root 9772 2020-06-19 09:41 ./usr/bin/maq2sam-short -rwxr-xr-x root/root 9772 2020-06-19 09:41 ./usr/bin/md5fa -rwxr-xr-x root/root 5676 2020-06-19 09:41 ./usr/bin/md5sum-lite -rwxr-xr-x root/root 7969 2020-06-19 09:41 ./usr/bin/novo2sam.pl -rwxr-xr-x root/root 50473 2020-06-19 09:41 ./usr/bin/plot-bamstats -rwxr-xr-x 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+------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 23508 Build-Time: 299 Distribution: groovy-proposed Host Architecture: armhf Install-Time: 43 Job: samtools_1.10-4.dsc Machine Architecture: arm64 Package: samtools Package-Time: 345 Source-Version: 1.10-4 Space: 23508 Status: successful Version: 1.10-4 -------------------------------------------------------------------------------- Finished at 20200619-1746 Build needed 00:05:45, 23508k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19481373 Scanning for processes to kill in build PACKAGEBUILD-19481373