https://launchpad.net/ubuntu/+archive/test-rebuild-20191220-focal/+build/18309792 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-061 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:56:55 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_186 python-lpbuildd_186 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... 12 Feb 18:28:32 ntpdate[1928]: adjust time server 10.211.37.1 offset 0.024125 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-18309792 --image-type chroot /home/buildd/filecache-default/f005b6164729459c78307140747b338a2f357aa2 Creating target for build PACKAGEBUILD-18309792 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-18309792 Starting target for build PACKAGEBUILD-18309792 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-18309792 'deb http://ftpmaster.internal/ubuntu focal main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-18309792 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-18309792 Updating target for build PACKAGEBUILD-18309792 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main armhf Packages [941 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main Translation-en [505 kB] Get:4 http://ftpmaster.internal/ubuntu focal/restricted armhf Packages [7060 B] Get:5 http://ftpmaster.internal/ubuntu focal/restricted Translation-en [6132 B] Get:6 http://ftpmaster.internal/ubuntu focal/universe armhf Packages [8360 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5147 kB] Get:8 http://ftpmaster.internal/ubuntu focal/multiverse armhf Packages [117 kB] Get:9 http://ftpmaster.internal/ubuntu focal/multiverse Translation-en [106 kB] Fetched 15.4 MB in 8s (2011 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-10-base libctf-nobfd0 libctf0 libffi7 libgcc-s1 libhogweed5 libisl22 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils bzip2 cpp-9 debianutils e2fsprogs fdisk g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv grep gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libext2fs2 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave lsb-base mount ncurses-base ncurses-bin openssl passwd perl perl-base sensible-utils systemd systemd-sysv sysvinit-utils ubuntu-keyring util-linux 103 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 56.5 MB of archives. After this operation, 37.8 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main armhf libc6-dev armhf 2.30-0ubuntu3 [1943 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main armhf libc-dev-bin armhf 2.30-0ubuntu3 [63.6 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main armhf linux-libc-dev armhf 5.4.0-12.15 [1085 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main armhf gcc-10-base armhf 10-20200211-1ubuntu1 [18.8 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main armhf libgcc-s1 armhf 10-20200211-1ubuntu1 [36.5 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main armhf libgcc1 armhf 1:10-20200211-1ubuntu1 [36.4 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main armhf libc6 armhf 2.30-0ubuntu3 [2144 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main armhf base-files armhf 11ubuntu2 [59.8 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main armhf debianutils armhf 4.9.1 [84.6 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main armhf bash armhf 5.0-5ubuntu1 [576 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main armhf bsdutils armhf 1:2.34-0.1ubuntu5 [58.3 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main armhf grep armhf 3.4-1 [141 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main armhf gzip armhf 1.10-0ubuntu4 [91.1 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main armhf hostname armhf 3.23 [10.4 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main armhf login armhf 1:4.8-1ubuntu1 [217 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main armhf ncurses-bin armhf 6.1+20191019-1ubuntu1 [163 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main armhf perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main armhf libperl5.30 armhf 5.30.0-9 [3286 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main armhf perl armhf 5.30.0-9 [224 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main armhf perl-base armhf 5.30.0-9 [1408 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main armhf bzip2 armhf 1.0.8-2 [32.4 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main armhf libbz2-1.0 armhf 1.0.8-2 [31.0 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main armhf libblkid1 armhf 2.34-0.1ubuntu5 [125 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main armhf libuuid1 armhf 2.34-0.1ubuntu5 [19.7 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main armhf libfdisk1 armhf 2.34-0.1ubuntu5 [163 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main armhf libpcre2-8-0 armhf 10.34-7 [172 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main armhf libselinux1 armhf 3.0-1 [60.1 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main armhf libmount1 armhf 2.34-0.1ubuntu5 [135 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main armhf libncurses6 armhf 6.1+20191019-1ubuntu1 [79.7 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main armhf libtinfo6 armhf 6.1+20191019-1ubuntu1 [72.8 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main armhf libncursesw6 armhf 6.1+20191019-1ubuntu1 [106 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main armhf libsmartcols1 armhf 2.34-0.1ubuntu5 [89.1 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main armhf fdisk armhf 2.34-0.1ubuntu5 [109 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main armhf util-linux armhf 2.34-0.1ubuntu5 [957 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main armhf libdebconfclient0 armhf 0.251ubuntu1 [5592 B] Get:36 http://ftpmaster.internal/ubuntu focal/main armhf base-passwd armhf 3.5.47 [46.4 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main armhf libc-bin armhf 2.30-0ubuntu3 [496 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main armhf ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main armhf lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main armhf sysvinit-utils armhf 2.96-1ubuntu1 [19.2 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main armhf libgpg-error0 armhf 1.36-7ubuntu1 [49.8 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main armhf libgcrypt20 armhf 1.8.5-3ubuntu1 [364 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main armhf liblz4-1 armhf 1.9.2-2 [51.7 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main armhf libstdc++6 armhf 10-20200211-1ubuntu1 [440 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main armhf systemd-sysv armhf 244.1-0ubuntu3 [9372 B] Get:46 http://ftpmaster.internal/ubuntu focal/main armhf libacl1 armhf 2.2.53-5ubuntu1 [15.8 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main armhf libapparmor1 armhf 2.13.3-7ubuntu1 [29.4 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main armhf libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:49 http://ftpmaster.internal/ubuntu focal/main armhf libcap-ng0 armhf 0.7.9-2.1 [9692 B] Get:50 http://ftpmaster.internal/ubuntu focal/main armhf libaudit1 armhf 1:2.8.5-2ubuntu5 [35.9 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main armhf libcap2 armhf 1:2.27-1 [12.7 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main armhf libudev1 armhf 244.1-0ubuntu3 [69.5 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main armhf libdevmapper1.02.1 armhf 2:1.02.155-2ubuntu8 [118 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main armhf libjson-c4 armhf 0.13.1+dfsg-6 [25.6 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main armhf libssl1.1 armhf 1.1.1d-2ubuntu3 [1080 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main armhf libcryptsetup12 armhf 2:2.2.2-3ubuntu1 [163 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main armhf libnettle7 armhf 3.5.1+really3.5.1-2 [126 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main armhf libhogweed5 armhf 3.5.1+really3.5.1-2 [127 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main armhf libffi7 armhf 3.3-3 [16.5 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main armhf libp11-kit0 armhf 0.23.20-1build1 [167 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main armhf libtasn1-6 armhf 4.15.0-2 [33.0 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main armhf libgnutls30 armhf 3.6.11.1-2ubuntu2 [733 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main armhf libkmod2 armhf 26-3ubuntu1 [37.0 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main armhf libpam0g armhf 1.3.1-5ubuntu4 [49.6 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main armhf libseccomp2 armhf 2.4.2-2ubuntu2 [32.5 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main armhf mount armhf 2.34-0.1ubuntu5 [108 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main armhf systemd armhf 244.1-0ubuntu3 [3533 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main armhf libsystemd0 armhf 244.1-0ubuntu3 [241 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main armhf libzstd1 armhf 1.4.4+dfsg-1 [207 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main armhf libapt-pkg5.90 armhf 1.9.9 [776 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main armhf gpgv armhf 2.2.17-3ubuntu1 [170 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main armhf ubuntu-keyring all 2020.02.11.1 [22.3 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main armhf apt armhf 1.9.9 [1236 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main armhf libpam-modules-bin armhf 1.3.1-5ubuntu4 [33.8 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main armhf libpam-modules armhf 1.3.1-5ubuntu4 [232 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main armhf logsave armhf 1.45.3-4ubuntu3 [9172 B] Get:77 http://ftpmaster.internal/ubuntu focal/main armhf libext2fs2 armhf 1.45.3-4ubuntu3 [168 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main armhf e2fsprogs armhf 1.45.3-4ubuntu3 [506 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main armhf libattr1 armhf 1:2.4.48-5 [11.5 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main armhf libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main armhf libsepol1 armhf 3.0-1 [220 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main armhf libsemanage-common all 3.0-1 [9880 B] Get:83 http://ftpmaster.internal/ubuntu focal/main armhf libsemanage1 armhf 3.0-1 [73.9 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main armhf passwd armhf 1:4.8-1ubuntu1 [748 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main armhf libgomp1 armhf 10-20200211-1ubuntu1 [86.5 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main armhf libatomic1 armhf 10-20200211-1ubuntu1 [7244 B] Get:87 http://ftpmaster.internal/ubuntu focal/main armhf libasan5 armhf 9.2.1-28ubuntu1 [387 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main armhf libubsan1 armhf 10-20200211-1ubuntu1 [121 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main armhf g++-9 armhf 9.2.1-28ubuntu1 [6681 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main armhf gcc-9 armhf 9.2.1-28ubuntu1 [6537 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main armhf libstdc++-9-dev armhf 9.2.1-28ubuntu1 [1779 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main armhf libgcc-9-dev armhf 9.2.1-28ubuntu1 [690 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main armhf libisl22 armhf 0.22-2 [460 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main armhf libcc1-0 armhf 10-20200211-1ubuntu1 [34.3 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main armhf binutils-arm-linux-gnueabihf armhf 2.34-1ubuntu1 [2093 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main armhf libbinutils armhf 2.34-1ubuntu1 [319 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main armhf binutils armhf 2.34-1ubuntu1 [3368 B] Get:98 http://ftpmaster.internal/ubuntu focal/main armhf binutils-common armhf 2.34-1ubuntu1 [206 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main armhf libctf-nobfd0 armhf 2.34-1ubuntu1 [37.3 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main armhf libctf0 armhf 2.34-1ubuntu1 [37.0 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main armhf cpp-9 armhf 9.2.1-28ubuntu1 [5874 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main armhf gcc-9-base armhf 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[10.5 kB] Get:113 http://ftpmaster.internal/ubuntu focal/main armhf liblockfile1 armhf 1.16-1.1 [5620 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 56.5 MB in 2s (24.0 MB/s) (Reading database ... 12487 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.30-0ubuntu3_armhf.deb ... Unpacking libc6-dev:armhf (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../libc-dev-bin_2.30-0ubuntu3_armhf.deb ... Unpacking libc-dev-bin (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../linux-libc-dev_5.4.0-12.15_armhf.deb ... Unpacking linux-libc-dev:armhf (5.4.0-12.15) over (5.3.0-18.19) ... Selecting previously unselected package gcc-10-base:armhf. Preparing to unpack .../gcc-10-base_10-20200211-1ubuntu1_armhf.deb ... Unpacking gcc-10-base:armhf (10-20200211-1ubuntu1) ... Setting up gcc-10-base:armhf (10-20200211-1ubuntu1) ... Selecting previously unselected package libgcc-s1:armhf. (Reading database ... 12498 files and directories currently installed.) Preparing to unpack .../libgcc-s1_10-20200211-1ubuntu1_armhf.deb ... Unpacking libgcc-s1:armhf (10-20200211-1ubuntu1) ... Replacing files in old package libgcc1:armhf (1:9.2.1-9ubuntu2) ... 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Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket. Setting up e2fsprogs (1.45.3-4ubuntu3) ... Setting up libasan5:armhf (9.2.1-28ubuntu1) ... Setting up perl (5.30.0-9) ... Setting up cpp-9 (9.2.1-28ubuntu1) ... Setting up libc6-dev:armhf (2.30-0ubuntu3) ... Setting up libcryptsetup12:armhf (2:2.2.2-3ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (2.34-1ubuntu1) ... Setting up systemd (244.1-0ubuntu3) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from KVM UUID. Setting up binutils (2.34-1ubuntu1) ... Setting up libgcc-9-dev:armhf (9.2.1-28ubuntu1) ... Setting up gcc-9 (9.2.1-28ubuntu1) ... Setting up systemd-sysv (244.1-0ubuntu3) ... Setting up libstdc++-9-dev:armhf (9.2.1-28ubuntu1) ... Setting up g++-9 (9.2.1-28ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18309792 armhf focal -c chroot:build-PACKAGEBUILD-18309792 --arch=armhf --dist=focal --nolog iva_1.0.9+ds-6.dsc Initiating build PACKAGEBUILD-18309792 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-173-generic #203-Ubuntu SMP Wed Jan 15 02:56:55 UTC 2020 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-061.buildd +==============================================================================+ | iva 1.0.9+ds-6 (armhf) 12 Feb 2020 18:29 | +==============================================================================+ Package: iva Version: 1.0.9+ds-6 Source Version: 1.0.9+ds-6 Distribution: focal Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/iva-jaVNhl/iva-1.0.9+ds' with '<>' I: NOTICE: Log filtering will replace 'build/iva-jaVNhl' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18309792/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- iva_1.0.9+ds-6.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-lL2G9X/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-lL2G9X/apt_archive ./ InRelease Get:2 copy:/<>/resolver-lL2G9X/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-lL2G9X/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-lL2G9X/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-lL2G9X/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (86.5 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 packages were automatically installed and are no longer required: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-lL2G9X/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (67.6 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14411 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless Filtered Build-Depends: debhelper (>= 11~), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless dpkg-deb: building package 'sbuild-build-depends-iva-dummy' in '/<>/resolver-WHHrPo/apt_archive/sbuild-build-depends-iva-dummy.deb'. Ign:1 copy:/<>/resolver-WHHrPo/apt_archive ./ InRelease Get:2 copy:/<>/resolver-WHHrPo/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-WHHrPo/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-WHHrPo/apt_archive ./ Sources [310 B] Get:5 copy:/<>/resolver-WHHrPo/apt_archive ./ Packages [630 B] Fetched 3059 B in 0s (84.7 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install iva build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdmainutils ca-certificates-java debhelper default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasn1-8-heimdal libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libbrotli1 libbsd0 libcapture-tiny-perl libclass-data-inheritable-perl libcroco3 libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libelf1 libexception-class-perl libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libicu63 libio-string-perl libjpeg-turbo8 libjpeg8 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mime-support mummer openjdk-11-jdk-headless openjdk-11-jre-headless po-debconf python3 python3-decorator python3-distutils python3-lib2to3 python3-minimal python3-networkx python3-nose python3-numpy python3-pkg-resources python3-pysam python3-setuptools python3.7 python3.7-minimal python3.8 python3.8-minimal samtools smalt ucf x11-common Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make default-jre gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff libasound2-plugins alsa-utils libxml-sax-expatxs-perl cups-common krb5-doc krb5-user liblcms2-utils pcscd libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser openjdk-11-demo openjdk-11-source libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl python3-doc python3-tk python3-venv python-networkx-doc python3-gdal python3-matplotlib python3-pygraphviz | python3-pydot python3-scipy python-nose-doc gfortran python-numpy-doc python3-dev python3-pytest python3-numpy-dbg python-setuptools-doc python3.7-venv python3.7-doc binfmt-support python3.8-venv python3.8-doc Recommended packages: bioperl-run perl-doc libhttp-message-perl libwww-perl libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl liburi-perl libxml-simple-perl libyaml-perl libace-perl liblist-moreutils-perl libxml-twig-perl libset-scalar-perl curl | wget | lynx libalgorithm-diff-xs-perl alsa-ucm-conf alsa-topology-conf bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python3-yaml cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdmainutils ca-certificates-java debhelper default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasn1-8-heimdal libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libbrotli1 libbsd0 libcapture-tiny-perl libclass-data-inheritable-perl libcroco3 libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libelf1 libexception-class-perl libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libicu63 libio-string-perl libjpeg-turbo8 libjpeg8 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mime-support mummer openjdk-11-jdk-headless openjdk-11-jre-headless po-debconf python3 python3-decorator python3-distutils python3-lib2to3 python3-minimal python3-networkx python3-nose python3-numpy python3-pkg-resources python3-pysam python3-setuptools python3.7 python3.7-minimal python3.8 python3.8-minimal samtools sbuild-build-depends-iva-dummy smalt ucf x11-common 0 upgraded, 147 newly installed, 0 to remove and 0 not upgraded. Need to get 266 MB of archives. After this operation, 521 MB of additional disk space will be used. Get:1 copy:/<>/resolver-WHHrPo/apt_archive ./ sbuild-build-depends-iva-dummy 0.invalid.0 [964 B] Get:2 http://ftpmaster.internal/ubuntu focal/main armhf liblocale-gettext-perl armhf 1.07-4 [16.2 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main armhf libpython3.7-minimal armhf 3.7.6-1ubuntu2 [541 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main armhf libexpat1 armhf 2.2.9-1 [53.2 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main armhf python3.7-minimal armhf 3.7.6-1ubuntu2 [1350 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main armhf python3-minimal armhf 3.7.5-1ubuntu1 [23.3 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main armhf mime-support all 3.64ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main armhf libmpdec2 armhf 2.4.2-2 [66.4 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main armhf libpython3.7-stdlib armhf 3.7.6-1ubuntu2 [1688 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main armhf python3.7 armhf 3.7.6-1ubuntu2 [304 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main armhf libpython3-stdlib armhf 3.7.5-1ubuntu1 [6844 B] Get:12 http://ftpmaster.internal/ubuntu focal/main armhf python3 armhf 3.7.5-1ubuntu1 [47.2 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main armhf libbsd0 armhf 0.10.0-1 [49.8 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main armhf bsdmainutils armhf 11.1.2ubuntu2 [176 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main armhf libuchardet0 armhf 0.0.6-3 [62.1 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main armhf groff-base armhf 1.22.4-4 [777 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main armhf libpipeline1 armhf 1.5.2-2build1 [23.5 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main armhf man-db armhf 2.9.0-2 [1079 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main armhf libsigsegv2 armhf 2.12-2 [13.1 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main armhf gawk armhf 1:5.0.1+dfsg-1 [382 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main armhf libpython3.8-minimal armhf 3.8.1-2ubuntu3 [697 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main armhf python3.8-minimal armhf 3.8.1-2ubuntu3 [1577 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main armhf libmagic-mgc armhf 1:5.38-4 [218 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main armhf libmagic1 armhf 1:5.38-4 [68.3 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main armhf file armhf 1:5.38-4 [22.4 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main armhf libdbus-1-3 armhf 1.12.16-2ubuntu2 [156 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main armhf libelf1 armhf 0.176-1.1build1 [41.3 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main armhf libglib2.0-0 armhf 2.63.3-3 [1117 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main armhf libicu63 armhf 63.2-2 [8002 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main armhf libxml2 armhf 2.9.4+dfsg1-8ubuntu3 [554 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main armhf python3-pkg-resources all 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http://ftpmaster.internal/ubuntu focal/main armhf libxcb1 armhf 1.13.1-5build1 [41.3 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main armhf libx11-data all 2:1.6.8-1 [113 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main armhf libx11-6 armhf 2:1.6.8-1 [517 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main armhf libxext6 armhf 2:1.3.4-0ubuntu1 [24.2 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main armhf m4 armhf 1.4.18-4 [187 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main armhf autoconf all 2.69-11.1 [321 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main armhf automake all 1:1.16.1-4ubuntu6 [522 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main armhf autopoint all 0.19.8.1-10 [412 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main armhf libio-string-perl all 1.08-3 [11.1 kB] Get:52 http://ftpmaster.internal/ubuntu focal/universe armhf libdata-stag-perl all 0.14-2 [369 kB] Get:53 http://ftpmaster.internal/ubuntu focal/universe armhf libbio-perl-perl all 1.7.6-3 [2568 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main armhf libclass-data-inheritable-perl all 0.08-3 [8084 B] Get:55 http://ftpmaster.internal/ubuntu focal/main armhf libdevel-stacktrace-perl all 2.0400-1 [22.7 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main armhf libexception-class-perl all 1.44-1 [25.9 kB] Get:57 http://ftpmaster.internal/ubuntu focal/universe armhf libtest-deep-perl all 1.128-1 [41.3 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main armhf libcapture-tiny-perl all 0.48-1 [20.4 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main armhf libalgorithm-diff-perl all 1.19.03-2 [46.6 kB] Get:60 http://ftpmaster.internal/ubuntu focal/universe armhf libtext-diff-perl all 1.45-1 [25.7 kB] Get:61 http://ftpmaster.internal/ubuntu focal/universe armhf libtest-differences-perl all 0.67-1 [16.3 kB] Get:62 http://ftpmaster.internal/ubuntu focal/universe armhf libsub-uplevel-perl all 0.2800-1 [13.5 kB] Get:63 http://ftpmaster.internal/ubuntu focal/universe armhf libtest-exception-perl all 0.43-1 [14.7 kB] Get:64 http://ftpmaster.internal/ubuntu focal/universe armhf libtest-warn-perl all 0.36-1 [14.0 kB] Get:65 http://ftpmaster.internal/ubuntu focal/universe armhf libtest-most-perl all 0.35-1 [22.1 kB] Get:66 http://ftpmaster.internal/ubuntu focal/universe armhf bioperl all 1.7.6-3 [211 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main armhf java-common all 0.72 [6816 B] Get:68 http://ftpmaster.internal/ubuntu focal/main armhf libavahi-common-data armhf 0.7-4ubuntu6 [21.3 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main armhf libavahi-common3 armhf 0.7-4ubuntu6 [18.3 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main armhf libavahi-client3 armhf 0.7-4ubuntu6 [22.0 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main armhf libcups2 armhf 2.3.1-4 [199 kB] Get:72 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armhf python3-networkx all 2.4-3ubuntu1 [855 kB] Get:142 http://ftpmaster.internal/ubuntu focal/universe armhf python3-nose all 1.3.7-5 [116 kB] Get:143 http://ftpmaster.internal/ubuntu focal/main armhf python3.8 armhf 3.8.1-2ubuntu3 [360 kB] Get:144 http://ftpmaster.internal/ubuntu focal/main armhf python3-numpy armhf 1:1.17.4-5ubuntu2 [4211 kB] Get:145 http://ftpmaster.internal/ubuntu focal/universe armhf python3-pysam armhf 0.15.4+ds-1 [2451 kB] Get:146 http://ftpmaster.internal/ubuntu focal/main armhf python3-setuptools all 44.0.0-1 [257 kB] Get:147 http://ftpmaster.internal/ubuntu focal/universe armhf smalt armhf 0.7.6-9 [98.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 266 MB in 11s (23.3 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 14411 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-4) ... Selecting previously unselected package libpython3.7-minimal:armhf. Preparing to unpack .../libpython3.7-minimal_3.7.6-1ubuntu2_armhf.deb ... Unpacking libpython3.7-minimal:armhf (3.7.6-1ubuntu2) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.2.9-1_armhf.deb ... Unpacking libexpat1:armhf (2.2.9-1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.6-1ubuntu2_armhf.deb ... Unpacking python3.7-minimal (3.7.6-1ubuntu2) ... Setting up libpython3.7-minimal:armhf (3.7.6-1ubuntu2) ... Setting up libexpat1:armhf (2.2.9-1) ... Setting up python3.7-minimal (3.7.6-1ubuntu2) ... Selecting previously unselected package python3-minimal. (Reading database ... 14674 files and directories currently installed.) 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Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../103-libnghttp2-14_1.40.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.40.0-1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../104-librtmp1_2.4+20151223.gitfa8646d.1-2build1_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build1) ... Selecting previously unselected package libssh-4:armhf. Preparing to unpack .../105-libssh-4_0.9.3-2ubuntu1_armhf.deb ... Unpacking libssh-4:armhf (0.9.3-2ubuntu1) ... Selecting previously unselected package libcurl3-gnutls:armhf. Preparing to unpack .../106-libcurl3-gnutls_7.66.0-1ubuntu1_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.66.0-1ubuntu1) ... Selecting previously unselected package libdeflate0. Preparing to unpack .../107-libdeflate0_1.5-2_armhf.deb ... Unpacking libdeflate0 (1.5-2) ... Selecting previously unselected package libhts3:armhf. 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Setting up gawk (1:5.0.1+dfsg-1) ... Setting up libalgorithm-diff-perl (1.19.03-2) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:armhf (2.63.3-3) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.7.3ubuntu1) ... Setting up libbrotli1:armhf (1.0.7-6) ... Setting up x11-common (1:7.7+19ubuntu14) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:armhf (1.40.0-1) ... Setting up libmagic1:armhf (1:5.38-4) ... Setting up libdeflate0 (1.5-2) ... Setting up gettext-base (0.19.8.1-10) ... Setting up m4 (1.4.18-4) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.49+dfsg-1ubuntu1) ... Setting up libicu63:armhf (63.2-2) ... Setting up libkrb5support0:armhf (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2) ... Setting up libasound2-data (1.2.1.2-2ubuntu2) ... Setting up libio-string-perl (1.08-3) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:armhf (3.9.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libfreetype6:armhf (2.10.1-2) ... Setting up libx11-data (2:1.6.8-1) ... Setting up libnspr4:armhf (2:4.24-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libavahi-common-data:armhf (0.7-4ubuntu6) ... Setting up libdbus-1-3:armhf (1.12.16-2ubuntu2) ... Setting up libbambamc0 (0.0.50-3) ... Setting up libssl-dev:armhf (1.1.1d-2ubuntu3) ... Setting up autopoint (0.19.8.1-10) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libpcsclite1:armhf (1.8.26-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libk5crypto3:armhf (1.17-6ubuntu4) ... Setting up libjpeg-turbo8:armhf (2.0.3-0ubuntu1) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2) ... Setting up libgfortran5:armhf (10-20200211-1ubuntu1) ... Setting up libroken18-heimdal:armhf (7.7.0+dfsg-1) ... Setting up autoconf (2.69-11.1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libdata-stag-perl (0.14-2) ... Setting up python3.8-minimal (3.8.1-2ubuntu3) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libasound2:armhf (1.2.1.2-2ubuntu2) ... Setting up mummer (3.23+dfsg-4) ... Setting up libsub-uplevel-perl (0.2800-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libkrb5-3:armhf (1.17-6ubuntu4) ... Setting up libbio-perl-perl (1.7.6-3) ... Setting up libmpdec2:armhf (2.4.2-2) ... Setting up libpython3.8-stdlib:armhf (3.8.1-2ubuntu3) ... Setting up python3.8 (3.8.1-2ubuntu3) ... Setting up libbsd0:armhf (0.10.0-1) ... Setting up libelf1:armhf (0.176-1.1build1) ... Setting up kmc (2.3+dfsg-7) ... Setting up libxml2:armhf (2.9.4+dfsg1-8ubuntu3) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up libheimbase1-heimdal:armhf (7.7.0+dfsg-1) ... Setting up libjpeg8:armhf (8c-2ubuntu8) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up smalt (0.7.6-9) ... Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu1) ... Setting up libpython3.7-stdlib:armhf (3.7.6-1ubuntu2) ... Setting up liblapack3:armhf (3.9.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libxcb1:armhf (1.13.1-5build1) ... Setting up libtool (2.4.6-12) ... Setting up fontconfig-config (2.13.1-2ubuntu2) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libasn1-8-heimdal:armhf (7.7.0+dfsg-1) ... Setting up libavahi-common3:armhf (0.7-4ubuntu6) ... Setting up libtest-differences-perl (0.67-1) ... Setting up libnss3:armhf (2:3.49.1-1ubuntu1) ... Setting up libexception-class-perl (1.44-1) ... Setting up libhcrypto4-heimdal:armhf (7.7.0+dfsg-1) ... Setting up help2man (1.47.12) ... Setting up libwind0-heimdal:armhf (7.7.0+dfsg-1) ... Setting up libtest-exception-perl (0.43-1) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-6ubuntu4) ... Setting up libcroco3:armhf (0.6.13-1) ... Setting up libssh-4:armhf (0.9.3-2ubuntu1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up libx11-6:armhf (2:1.6.8-1) ... Setting up libfontconfig1:armhf (2.13.1-2ubuntu2) ... Setting up libavahi-client3:armhf (0.7-4ubuntu6) ... Setting up libpython3-stdlib:armhf (3.7.5-1ubuntu1) ... Setting up python3.7 (3.7.6-1ubuntu2) ... Setting up gettext (0.19.8.1-10) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libtest-most-perl (0.35-1) ... Setting up libhx509-5-heimdal:armhf (7.7.0+dfsg-1) ... Setting up libxext6:armhf (2:1.3.4-0ubuntu1) ... Setting up python3 (3.7.5-1ubuntu1) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-decorator (4.3.0-1.1build1) ... Setting up libcups2:armhf (2.3.1-4) ... Setting up python3-lib2to3 (3.8.0-1) ... Setting up libkrb5-26-heimdal:armhf (7.7.0+dfsg-1) ... Setting up python3-pkg-resources (44.0.0-1) ... Setting up python3-distutils (3.8.0-1) ... Setting up dh-python (4.20191017ubuntu5) ... Setting up bioperl (1.7.6-3) ... Setting up python3-setuptools (44.0.0-1) ... Setting up libxi6:armhf (2:1.7.10-0ubuntu1) ... Setting up libxtst6:armhf (2:1.2.3-1) ... Setting up po-debconf (1.0.21) ... Setting up python3-networkx (2.4-3ubuntu1) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.nodes['n1']['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.edges['n0','n1',1]['special'] is 0 Setting up python3-nose (1.3.7-5) ... Setting up libheimntlm0-heimdal:armhf (7.7.0+dfsg-1) ... Setting up libgssapi3-heimdal:armhf (7.7.0+dfsg-1) ... Setting up python3-numpy (1:1.17.4-5ubuntu2) ... Setting up libldap-2.4-2:armhf (2.4.49+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:armhf (7.66.0-1ubuntu1) ... Setting up libhts3:armhf (1.10.2-2ubuntu1) ... Setting up python3-pysam (0.15.4+ds-1) ... Setting up samtools (1.10-3) ... Setting up fastaq (3.17.0-2) ... Setting up dh-autoreconf (19) ... Setting up default-jre-headless (2:1.11-72) ... Setting up openjdk-11-jre-headless:armhf (11.0.6+10-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up debhelper (12.7.3ubuntu1) ... Setting up openjdk-11-jdk-headless:armhf (11.0.6+10-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jdk-headless (2:1.11-72) ... Setting up ca-certificates-java (20190405ubuntu1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:AffirmTrust_Commercial.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:EC-ACC.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:DST_Root_CA_X3.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AddTrust_External_Root.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:SecureTrust_CA.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:AffirmTrust_Networking.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:Izenpe.com.pem Adding debian:ACCVRAIZ1.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Certigna.pem Adding debian:Secure_Global_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Taiwan_GRCA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:ISRG_Root_X1.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:USERTrust_RSA_Certification_Authority.pem done. Setting up sbuild-build-depends-iva-dummy (0.invalid.0) ... Processing triggers for systemd (244.1-0ubuntu3) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Processing triggers for libc-bin (2.30-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-173-generic arm64 (armv7l) Toolchain package versions: binutils_2.34-1ubuntu1 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-28ubuntu1 gcc-9_9.2.1-28ubuntu1 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-28ubuntu1 libstdc++6_10-20200211-1ubuntu1 linux-libc-dev_5.4.0-12.15 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.9 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 binutils_2.34-1ubuntu1 binutils-arm-linux-gnueabihf_2.34-1ubuntu1 binutils-common_2.34-1ubuntu1 bioperl_1.7.6-3 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu5 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 ca-certificates-java_20190405ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-28ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.3ubuntu1 debianutils_4.9.1 default-jdk-headless_2:1.11-72 default-jre-headless_2:1.11-72 dh-autoreconf_19 dh-python_4.20191017ubuntu5 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-5 e2fsprogs_1.45.3-4ubuntu3 fakeroot_1.24-1 fastaq_3.17.0-2 fdisk_2.34-0.1ubuntu5 file_1:5.38-4 findutils_4.6.0+git+20190209-2ubuntu1 fontconfig-config_2.13.1-2ubuntu2 fonts-dejavu-core_2.37-1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-28ubuntu1 gawk_1:5.0.1+dfsg-1 gcc_4:9.2.1-3.1ubuntu1 gcc-10-base_10-20200211-1ubuntu1 gcc-9_9.2.1-28ubuntu1 gcc-9-base_9.2.1-28ubuntu1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpg_2.2.17-3ubuntu1 gpg-agent_2.2.17-3ubuntu1 gpgconf_2.2.17-3ubuntu1 gpgv_2.2.17-3ubuntu1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-0ubuntu4 help2man_1.47.12 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 java-common_0.72 kmc_2.3+dfsg-7 libacl1_2.2.53-5ubuntu1 libalgorithm-diff-perl_1.19.03-2 libapparmor1_2.13.3-7ubuntu1 libapt-pkg5.90_1.9.9 libarchive-zip-perl_1.67-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-28ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-1 libasound2_1.2.1.2-2ubuntu2 libasound2-data_1.2.1.2-2ubuntu2 libassuan0_2.5.3-7ubuntu2 libatomic1_10-20200211-1ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu5 libaudit1_1:2.8.5-2ubuntu5 libavahi-client3_0.7-4ubuntu6 libavahi-common-data_0.7-4ubuntu6 libavahi-common3_0.7-4ubuntu6 libbambamc0_0.0.50-3 libbinutils_2.34-1ubuntu1 libbio-perl-perl_1.7.6-3 libblas3_3.9.0-1 libblkid1_2.34-0.1ubuntu5 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-0ubuntu3 libc-dev-bin_2.30-0ubuntu3 libc6_2.30-0ubuntu3 libc6-dev_2.30-0ubuntu3 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcapture-tiny-perl_0.48-1 libcc1-0_10-20200211-1ubuntu1 libclass-data-inheritable-perl_0.08-3 libcom-err2_1.45.3-4ubuntu3 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.2-3ubuntu1 libctf-nobfd0_2.34-1ubuntu1 libctf0_2.34-1ubuntu1 libcups2_2.3.1-4 libcurl3-gnutls_7.66.0-1ubuntu1 libdata-stag-perl_0.14-2 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdbus-1-3_1.12.16-2ubuntu2 libdebconfclient0_0.251ubuntu1 libdebhelper-perl_12.7.3ubuntu1 libdeflate0_1.5-2 libdevel-stacktrace-perl_2.0400-1 libdevmapper1.02.1_2:1.02.155-2ubuntu8 libdpkg-perl_1.19.7ubuntu2 libelf1_0.176-1.1build1 libexception-class-perl_1.44-1 libexpat1_2.2.9-1 libext2fs2_1.45.3-4ubuntu3 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu5 libffi6_3.2.1-9 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libfontconfig1_2.13.1-2ubuntu2 libfreetype6_2.10.1-2 libgcc-9-dev_9.2.1-28ubuntu1 libgcc-s1_10-20200211-1ubuntu1 libgcc1_1:10-20200211-1ubuntu1 libgcrypt20_1.8.5-3ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10-20200211-1ubuntu1 libglib2.0-0_2.63.3-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2ubuntu2 libgomp1_10-20200211-1ubuntu1 libgpg-error0_1.36-7ubuntu1 libgssapi-krb5-2_1.17-6ubuntu4 libgssapi3-heimdal_7.7.0+dfsg-1 libhcrypto4-heimdal_7.7.0+dfsg-1 libheimbase1-heimdal_7.7.0+dfsg-1 libheimntlm0-heimdal_7.7.0+dfsg-1 libhogweed4_3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhts3_1.10.2-2ubuntu1 libhx509-5-heimdal_7.7.0+dfsg-1 libicu63_63.2-2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libip4tc2_1.8.3-2ubuntu5 libisl21_0.21-2 libisl22_0.22-2 libjpeg-turbo8_2.0.3-0ubuntu1 libjpeg8_8c-2ubuntu8 libjson-c4_0.13.1+dfsg-6 libk5crypto3_1.17-6ubuntu4 libkeyutils1_1.6-6ubuntu1 libkmod2_26-3ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-1 libkrb5-3_1.17-6ubuntu4 libkrb5support0_1.17-6ubuntu4 liblapack3_3.9.0-1 liblcms2-2_2.9-4 libldap-2.4-2_2.4.49+dfsg-1ubuntu1 libldap-common_2.4.49+dfsg-1ubuntu1 liblocale-gettext-perl_1.07-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1ubuntu5 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1ubuntu1 libncursesw6_6.1+20191019-1ubuntu1 libnettle6_3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnpth0_1.6-1 libnspr4_2:4.24-1 libnss3_2:3.49.1-1ubuntu1 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_2:8.39-12 libpcsclite1_1.8.26-3 libperl5.28_5.28.1-6build1 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libpsl5_0.20.2-2 libpython3-stdlib_3.7.5-1ubuntu1 libpython3.7-minimal_3.7.6-1ubuntu2 libpython3.7-stdlib_3.7.6-1ubuntu2 libpython3.8-minimal_3.8.1-2ubuntu3 libpython3.8-stdlib_3.8.1-2ubuntu3 libreadline8_8.0-3 libroken18-heimdal_7.7.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2ubuntu2 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu5 libsqlite3-0_3.30.1-1ubuntu1 libss2_1.45.3-4ubuntu3 libssh-4_0.9.3-2ubuntu1 libssl-dev_1.1.1d-2ubuntu3 libssl1.1_1.1.1d-2ubuntu3 libstdc++-9-dev_9.2.1-28ubuntu1 libstdc++6_10-20200211-1ubuntu1 libsub-override-perl_0.09-2 libsub-uplevel-perl_0.2800-1 libsystemd0_244.1-0ubuntu3 libtasn1-6_4.15.0-2 libtest-deep-perl_1.128-1 libtest-differences-perl_0.67-1 libtest-exception-perl_0.43-1 libtest-most-perl_0.35-1 libtest-warn-perl_0.36-1 libtext-diff-perl_1.45-1 libtinfo6_6.1+20191019-1ubuntu1 libtool_2.4.6-12 libubsan1_10-20200211-1ubuntu1 libuchardet0_0.0.6-3 libudev1_244.1-0ubuntu3 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu5 libwind0-heimdal_7.7.0+dfsg-1 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.9-0ubuntu1 libxcb1_1.13.1-5build1 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxi6_2:1.7.10-0ubuntu1 libxml2_2.9.4+dfsg1-8ubuntu3 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.4.0-12.15 lockfile-progs_0.1.18 login_1:4.8-1ubuntu1 logsave_1.45.3-4ubuntu3 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17ubuntu3 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu5 mummer_3.23+dfsg-4 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 openjdk-11-jdk-headless_11.0.6+10-1ubuntu1 openjdk-11-jre-headless_11.0.6+10-1ubuntu1 openssl_1.1.1d-2ubuntu3 optipng_0.7.7-1 passwd_1:4.8-1ubuntu1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 python3_3.7.5-1ubuntu1 python3-decorator_4.3.0-1.1build1 python3-distutils_3.8.0-1 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-1ubuntu1 python3-networkx_2.4-3ubuntu1 python3-nose_1.3.7-5 python3-numpy_1:1.17.4-5ubuntu2 python3-pkg-resources_44.0.0-1 python3-pysam_0.15.4+ds-1 python3-setuptools_44.0.0-1 python3.7_3.7.6-1ubuntu2 python3.7-minimal_3.7.6-1ubuntu2 python3.8_3.8.1-2ubuntu3 python3.8-minimal_3.8.1-2ubuntu3 readline-common_8.0-3 samtools_1.10-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-iva-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 smalt_0.7.6-9 systemd_244.1-0ubuntu3 systemd-sysv_244.1-0ubuntu3 sysvinit-utils_2.96-1ubuntu1 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2020.02.11.1 ucf_3.0038+nmu1 util-linux_2.34-0.1ubuntu5 x11-common_1:7.7+19ubuntu14 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Aug 1 19:53:01 2018 UTC gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: issuer "satta@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./iva_1.0.9+ds-6.dsc dpkg-source: info: extracting iva in iva-1.0.9+ds dpkg-source: info: unpacking iva_1.0.9+ds.orig.tar.xz dpkg-source: info: unpacking iva_1.0.9+ds-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-multithreaded-test.patch dpkg-source: info: applying perl-shebang.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-18309792 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18309792 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18309792 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.9+ds-6 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/iva-1.0.9+ds' rm -rf .pybuild rm -f iva/gage/*.class rm -rf /<>/iva-1.0.9+ds/debian/man find . -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/<>/iva-1.0.9+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:217: python3.7 setup.py config Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>/iva-1.0.9+ds' chmod a-x /<>/iva-1.0.9+ds/iva/read_trim/adapters.fasta chmod a+x /<>/iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh chmod a+x /<>/iva-1.0.9+ds/iva/ratt/main.ratt.pl chmod a+x scripts/* javac -verbose /<>/iva-1.0.9+ds/iva/gage/*.java [parsing started SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/GetFastaStats.java]] [parsing completed 147ms] [parsing started SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/SizeFasta.java]] [parsing completed 12ms] [parsing started SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 8ms] [parsing started SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/Utils.java]] [parsing completed 45ms] [parsing started SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/getScaffoldStats.java]] [parsing completed 121ms] [loading /modules/jdk.scripting.nashorn.shell/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/jdk.compiler/module-info.class] [loading /modules/java.instrument/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/jdk.javadoc/module-info.class] [loading /modules/jdk.management.jfr/module-info.class] [loading /modules/java.smartcardio/module-info.class] [loading /modules/jdk.accessibility/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/java.net.http/module-info.class] [loading /modules/java.prefs/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/java.logging/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/java.desktop/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/jdk.jstatd/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/java.xml/module-info.class] [loading /modules/jdk.management.agent/module-info.class] [loading /modules/java.security.sasl/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/jdk.net/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/java.rmi/module-info.class] [loading /modules/java.security.jgss/module-info.class] [loading /modules/java.transaction.xa/module-info.class] [loading /modules/jdk.sctp/module-info.class] [loading /modules/jdk.hotspot.agent/module-info.class] [loading /modules/java.base/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [loading /modules/jdk.jshell/module-info.class] [loading /modules/java.management.rmi/module-info.class] [loading /modules/jdk.internal.ed/module-info.class] [loading /modules/jdk.internal.jvmstat/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/jdk.security.auth/module-info.class] [loading /modules/jdk.jfr/module-info.class] [loading /modules/jdk.rmic/module-info.class] [loading /modules/jdk.dynalink/module-info.class] [loading /modules/jdk.jcmd/module-info.class] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/jdk.pack/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/java.scripting/module-info.class] [loading /modules/jdk.internal.le/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/jdk.scripting.nashorn/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/jdk.localedata/module-info.class] [loading /modules/jdk.jsobject/module-info.class] [loading /modules/java.management/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-11-openjdk-armhf/lib/modules,.] [loading /modules/java.base/java/io/BufferedReader.class] [loading /modules/java.base/java/io/FileInputStream.class] [loading /modules/java.base/java/io/InputStreamReader.class] [loading /modules/java.base/java/text/DecimalFormat.class] [loading /modules/java.base/java/text/NumberFormat.class] [loading /modules/java.base/java/util/ArrayList.class] [loading /modules/java.base/java/util/Arrays.class] [loading /modules/java.base/java/util/HashMap.class] [loading /modules/java.base/java/lang/Object.class] [loading /modules/java.base/java/lang/String.class] [loading /modules/java.base/java/lang/Integer.class] [loading /modules/java.base/java/lang/Exception.class] [loading /modules/java.base/java/lang/StringBuffer.class] [loading /modules/java.management/java/lang/management/ManagementFactory.class] [loading /modules/java.management/java/lang/management/MemoryMXBean.class] [loading /modules/java.base/java/io/File.class] [loading /modules/java.base/java/io/FileReader.class] [loading /modules/java.base/java/lang/Boolean.class] [loading /modules/java.base/java/lang/Enum.class] [loading /modules/java.base/java/lang/Comparable.class] [loading /modules/java.base/java/io/Serializable.class] [loading /modules/java.base/java/util/Collections.class] [loading /modules/java.base/java/lang/Deprecated.class] [loading /modules/java.base/java/lang/annotation/Retention.class] [loading /modules/java.base/java/lang/annotation/RetentionPolicy.class] [loading /modules/java.base/java/lang/annotation/Target.class] [loading /modules/java.base/java/lang/annotation/ElementType.class] [checking GetFastaStats] [loading /modules/java.base/java/lang/AutoCloseable.class] [loading /modules/java.base/java/util/Map.class] [loading /modules/java.base/java/lang/Throwable.class] [loading /modules/java.base/java/lang/CharSequence.class] [loading /modules/java.base/java/io/Reader.class] [loading /modules/java.base/java/lang/Readable.class] [loading /modules/java.base/java/io/Closeable.class] [loading /modules/java.base/java/lang/Number.class] [loading /modules/java.base/java/lang/Cloneable.class] [loading /modules/java.base/java/util/AbstractMap.class] [loading /modules/java.base/java/lang/AbstractStringBuilder.class] [loading /modules/java.base/java/lang/Appendable.class] [loading /modules/java.base/java/lang/Byte.class] [loading /modules/java.base/java/lang/Character.class] [loading /modules/java.base/java/lang/Short.class] [loading /modules/java.base/java/lang/Long.class] [loading /modules/java.base/java/lang/Float.class] [loading /modules/java.base/java/lang/Double.class] [loading /modules/java.base/java/lang/Void.class] [loading /modules/java.base/java/io/FileDescriptor.class] [loading /modules/java.base/java/lang/System.class] [loading /modules/java.base/java/io/PrintStream.class] [loading /modules/java.base/java/io/FilterOutputStream.class] [loading /modules/java.base/java/io/OutputStream.class] [loading /modules/java.base/java/io/Flushable.class] [loading /modules/java.base/java/util/Set.class] [loading /modules/java.base/java/lang/Iterable.class] [loading /modules/java.base/java/util/Collection.class] [loading /modules/java.base/java/lang/Math.class] [loading /modules/java.base/java/util/List.class] [loading /modules/java.base/java/util/RandomAccess.class] [loading /modules/java.base/java/util/AbstractList.class] [loading /modules/java.base/java/util/AbstractCollection.class] [loading /modules/java.base/java/util/function/IntFunction.class] [loading /modules/java.base/java/util/Comparator.class] [loading /modules/java.base/java/text/Format.class] [loading /modules/java.base/java/lang/Error.class] [loading /modules/java.base/java/lang/RuntimeException.class] [loading /modules/java.base/java/io/IOException.class] [loading /modules/java.base/java/lang/NumberFormatException.class] [loading /modules/java.base/java/lang/IllegalArgumentException.class] [loading /modules/java.base/java/io/FileNotFoundException.class] [loading /modules/java.base/java/util/Iterator.class] [wrote /<>/iva-1.0.9+ds/iva/gage/GetFastaStats$ContigAt.class] [loading /modules/java.base/java/lang/invoke/StringConcatFactory.class] [loading /modules/java.base/java/lang/invoke/MethodHandles.class] [loading /modules/java.base/java/lang/invoke/MethodHandles$Lookup.class] [loading /modules/java.base/java/lang/invoke/MethodType.class] [loading /modules/java.base/java/io/InputStream.class] [loading /modules/java.base/java/lang/invoke/CallSite.class] [wrote /<>/iva-1.0.9+ds/iva/gage/GetFastaStats.class] [checking SizeFasta] [wrote /<>/iva-1.0.9+ds/iva/gage/SizeFasta.class] [checking SplitFastaByLetter] [wrote /<>/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.class] [checking Utils] [loading /modules/java.base/java/lang/CloneNotSupportedException.class] [loading /modules/java.base/java/lang/Class.class] [loading /modules/java.base/java/net/URI.class] [loading /modules/java.base/java/lang/Process.class] [loading /modules/java.base/java/lang/Runtime.class] [loading /modules/java.base/java/lang/StringBuilder.class] [loading /modules/java.base/java/lang/reflect/GenericDeclaration.class] [loading /modules/java.base/java/lang/reflect/AnnotatedElement.class] [loading /modules/java.base/java/lang/reflect/Type.class] [loading /modules/java.base/java/lang/AssertionError.class] [wrote /<>/iva-1.0.9+ds/iva/gage/Utils$Pair.class] [wrote /<>/iva-1.0.9+ds/iva/gage/Utils$Translate.class] [wrote /<>/iva-1.0.9+ds/iva/gage/Utils$ToProtein.class] [wrote /<>/iva-1.0.9+ds/iva/gage/Utils.class] [checking getScaffoldStats] [wrote /<>/iva-1.0.9+ds/iva/gage/getScaffoldStats$Scaffold.class] [wrote /<>/iva-1.0.9+ds/iva/gage/getScaffoldStats.class] [total 3963ms] dh_auto_build -- I: pybuild base:217: /usr/bin/python3 setup.py build Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running build running build_py creating /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/__init__.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/seed.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/contig_trim.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/common.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/external_progs.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/qc.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/egg_extract.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/kmers.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/edge.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/qc_external.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/graph.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/mapping.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/test_data_runner.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/assembly.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/read_trim.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/seed_processor.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/kraken.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/kcount.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/mummer.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/contig.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva creating /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/Utils.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/SizeFasta.java -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/Utils.java -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/getScaffoldStats.java -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/GetFastaStats.java -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/colsum.pl -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage creating /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/ratt.config -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt creating /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/read_trim creating /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/reads_1.fq.gz -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.7 copying and adjusting scripts/iva_qc -> build/scripts-3.7 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.7 copying and adjusting scripts/iva -> build/scripts-3.7 changing mode of build/scripts-3.7/iva_qc from 664 to 775 changing mode of build/scripts-3.7/iva_qc_make_db from 664 to 775 changing mode of build/scripts-3.7/iva from 664 to 775 make[1]: Leaving directory '/<>/iva-1.0.9+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/iva-1.0.9+ds' python3 setup.py test Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running test WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox. running egg_info creating iva.egg-info writing iva.egg-info/PKG-INFO writing dependency_links to iva.egg-info/dependency_links.txt writing requirements to iva.egg-info/requires.txt writing top-level names to iva.egg-info/top_level.txt writing manifest file 'iva.egg-info/SOURCES.txt' reading manifest file 'iva.egg-info/SOURCES.txt' writing manifest file 'iva.egg-info/SOURCES.txt' running build_ext /<>/iva-1.0.9+ds/iva/mapping.py:157: DeprecationWarning: invalid escape sequence \^ s = re.sub('\^.', '', s) /<>/iva-1.0.9+ds/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence \( 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), /<>/iva-1.0.9+ds/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence \( 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), /<>/iva-1.0.9+ds/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence \( 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), /<>/iva-1.0.9+ds/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence \( 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), /<>/iva-1.0.9+ds/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence \d 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), /<>/iva-1.0.9+ds/iva/kraken.py:360: DeprecationWarning: invalid escape sequence \. self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') /<>/iva-1.0.9+ds/iva/kraken.py:415: DeprecationWarning: invalid escape sequence \W return re.sub('\W', '_', s).strip('_') test_add_new_seed_contig (assembly_test.TestAssembly) Test add_new_seed_contig ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/tmp.make_seed.3q3ysg66/out.bam' The following command failed with exit code 134 bash run_kmc.sh The output was: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc run_kmc.sh: line 2: 7111 Aborted (core dumped) kmc -fa -m4 -k10 -sf1 -ci1 -cs1000000000 -cx1000000000 /<>/iva-1.0.9+ds/tmp.common_kmers.ao0gcg0v/reads.fa kmc_out $PWD ERROR test_contig_contained_in_nucmer_hits (assembly_test.TestAssembly) Test _contig_contained_in_nucmer_hits ... ok test_contig_names_size_order (assembly_test.TestAssembly) Test _contig_names_size_order ... ok test_contig_worth_extending (assembly_test.TestAssembly) Test _contig_worth_extending ... ok test_coords_to_new_contig (assembly_test.TestAssembly) Test _coords_to_new_contig ... ok test_extend_contigs_with_bam (assembly_test.TestAssembly) test _extend_contigs_with_bam ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_get_contig_order_by_orfs (assembly_test.TestAssembly) Test get_contig_order_by_orfs ... ok test_get_ref_length (assembly_test.TestAssembly) Test _get_ref_length ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/assembly_test.mapped.bam' ok test_get_ref_length_sam_pair (assembly_test.TestAssembly) Test _get_ref_length_sam_pair ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/assembly_test.mapped.bam' ok test_get_unmapped_pairs (assembly_test.TestAssembly) Test _get_unmapped_pairs ... [E::idx_find_and_load] Could not retrieve index file for 'tmp.bam' ok test_good_intervals_from_strand_coverage (assembly_test.TestAssembly) Test good_intervals_from_strand_coverage ... ok test_init_and_write (assembly_test.TestAssembly) test assembly initialise and write to file ... ok test_map_reads (assembly_test.TestAssembly) test _map_reads ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/assembly_test.mapped.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.assembly_test.out.bam' ok test_merge_overlapping_contigs (assembly_test.TestAssembly) Test _merge_overlapping_contigs ... ok test_read_pair_extend (assembly_test.TestAssembly) Test read_pair_extend ... [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.2.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.3.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.4.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.5.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.2.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.3.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.4.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.5.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.2.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.3.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.4.1.map.bam' The following command failed with exit code 1 samtools sort -@1 -m 500M /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.trim_strand_biased_ends.ojf935y1/out.unsorted.bam /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.trim_strand_biased_ends.ojf935y1/out The output was: [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set) -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam --no-PG do not add a PG line --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] --verbosity INT Set level of verbosity ERROR test_remove_contained_contigs (assembly_test.TestAssembly) Test _remove_contained_contigs ... ok test_remove_contig (assembly_test.TestAssembly) Test _remove_contig ... ok test_remove_contig_from_nucmer_hits (assembly_test.TestAssembly) Test _remove_contig_from_nucmer_hits ... ok test_subcontigs_from_strand_bias (assembly_test.TestAssembly) Test _subcontigs_from_strand_bias ... ok test_trim_contig_for_strand_bias (assembly_test.TestAssembly) Test _trim_contig_for_strand_bias ... ok test_trim_contigs (assembly_test.TestAssembly) Test trim_contigs ... ok test_trim_strand_biased_ends (assembly_test.TestAssembly) Test _trim_strand_biased_ends ... ok test_worth_extending (assembly_test.TestAssembly) Test worth_extending ... ok test_add_left_kmer (contig_test.TestContig) Test add_left_kmer ... ok test_add_right_kmer (contig_test.TestContig) Test add_right_kmer ... ok test_extend (contig_test.TestContig) Test extend ... ok test_init (contig_test.TestContig) Test init ... ok test_len (contig_test.TestContig) Test len ... ok test_coverage_to_trimmed_coords (contig_trim_test.TestContigTrim) Test _coverage_to_trimmed_coords ... ok test_trim_ends (contig_trim_test.TestContigTrim) Test _trim_ends ... The following command failed with exit code 1 samtools sort -@1 -m 500M /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.adapter_trim.9h6vq580/out.unsorted.bam /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.adapter_trim.9h6vq580/out The output was: [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set) -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam --no-PG do not add a PG line --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] --verbosity INT Set level of verbosity ERROR test_trim_primers_and_adapters (contig_trim_test.TestContigTrim) Test trim_primers_and_adapters ... The following command failed with exit code 1 samtools sort -@1 -m 500M /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.adapter_trim.m1el5x94/out.unsorted.bam /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.adapter_trim.m1el5x94/out The output was: [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set) -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam --no-PG do not add a PG line --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] --verbosity INT Set level of verbosity ERROR test_change_hit_coords_with_intersection (edge_test.TestEdge) test test_change_hit_coords_with_intersection ... ok test_make_contig_first (edge_test.TestEdge) test make_contig_first ... ok test_make_contig_forwards (edge_test.TestEdge) test make_contig_forwards ... ok test_merge_into (edge_test.TestEdge) test merge_into ... ok test_open_end (edge_test.TestEdge) test open_end ... ok test_reverse (edge_test.TestEdge) test reverse ... ok test_copy_dir (egg_extract_test.TestEggExtract) test copy_dir ... ok test_copy_dir_unzipped (egg_extract_test.TestEggExtract) test copy_dir_unzipped ... ok test_copy_dir_zipped (egg_extract_test.TestEggExtract) test copy_dir_zipped ... ok test_copy_file (egg_extract_test.TestEggExtract) test copy_file ... ok test_copy_file_unzipped (egg_extract_test.TestEggExtract) test _copy_file_unzipped ... ok test_copy_file_zipped (egg_extract_test.TestEggExtract) test _copy_file_zipped ... ok test_init_and_write (egg_extract_test.TestEggExtract) test __init__ ... ok test_blastn_version (external_progs_test.TestExternalProgs) Test blastn version ... ok test_delta_filter_in_path (external_progs_test.TestExternalProgs) Test delta-filter in path ... ok test_kmc_dump_in_path (external_progs_test.TestExternalProgs) Test kmc_dump in path ... ok test_kmc_dump_version (external_progs_test.TestExternalProgs) Test kmc_dump version ... ok test_kmc_in_path (external_progs_test.TestExternalProgs) Test kmc in path ... ok test_kmc_version (external_progs_test.TestExternalProgs) Test kmc version ... ok test_makeblastdb_version (external_progs_test.TestExternalProgs) Test makeblastdb version ... ok test_nucmer_in_path (external_progs_test.TestExternalProgs) Test nucmer in path ... ok test_nucmer_version (external_progs_test.TestExternalProgs) Test nucmer version ... ok test_r_version (external_progs_test.TestExternalProgs) Test R versions ... ok test_samtools_in_path (external_progs_test.TestExternalProgs) Test samtools in path ... ok test_samtools_original_version (external_progs_test.TestExternalProgs) Test samtools original version ... ok test_samtools_version (external_progs_test.TestExternalProgs) Test samtools version ... ok test_show_coords_in_path (external_progs_test.TestExternalProgs) Test show-coords in path ... ok test_smalt_in_path (external_progs_test.TestExternalProgs) Test smalt in path ... ok test_smalt_version (external_progs_test.TestExternalProgs) Test smalt version ... ok test_add_and_get_edges (graph_test.TestGraph) test adding and getting edges ... ok test_connected_components (graph_test.TestGraph) test connected_components ... ok test_degree (graph_test.TestGraph) test degree ... ok test_edges_are_consistent (graph_test.TestGraph) test edges_are_consistent ... ok test_find_simple_path (graph_test.TestGraph) test find_simple_path ... ok test_get_nodes (graph_test.TestGraph) test get_nodes ... ok test_merged_coords_from_simple_nonredundant_path (graph_test.TestGraph) test merged_coords_from_simple_nonredundant_path ... ok test_node_to_coords (graph_test.TestGraph) test _node_to_coords ... ok test_remove_middle_node (graph_test.TestGraph) test remove_middle_node ... ok test_remove_node (graph_test.TestGraph) test remove_node ... ok test_remove_redundant_nodes_from_simple_path (graph_test.TestGraph) test remove_redundant_nodes_from_simple_path ... ok test_simple_path_is_consistent (graph_test.TestGraph) test simple_path_is_consistent ... ok test_counts_file_to_fasta (kcount_test.TestKcount) Test _counts_file_to_fasta ... ok test_get_most_common_kmers (kcount_test.TestKcount) Test get_most_common_kmers ... The following command failed with exit code 134 bash run_kmc.sh The output was: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc run_kmc.sh: line 2: 7238 Aborted (core dumped) kmc -fa -m4 -k10 -sf1 -ci2 -cs4 -cx4 /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.common_kmers.o792qocf/reads.fa kmc_out $PWD > /dev/null ERROR test_head_fastaq_fa (kcount_test.TestKcount) Test head_fastaq with FASTA input ... ok test_head_fastaq_fq (kcount_test.TestKcount) Test head_fastaq with FASTQ input ... ok test_kmc_to_kmer_counts (kcount_test.TestKcount) Test _kmc_to_kmer_counts ... ok test_median (kcount_test.TestKcount) Test _median() ... ok test_run_kmc (kcount_test.TestKcount) Test test_run_kmc ... The following command failed with exit code 134 bash run_kmc.sh The output was: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc run_kmc.sh: line 2: 7246 Aborted (core dumped) kmc -fa -m4 -k10 -sf1 -ci2 -cs4 -cx4 /<>/iva-1.0.9+ds/iva/tests/data/kcount_test.run_kmc.fa kmc_out $PWD > /dev/null ERROR test_run_kmc_two_threads (kcount_test.TestKcount) Test test_run_kmc with two threads ... The following command failed with exit code 134 bash run_kmc.sh The output was: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc run_kmc.sh: line 2: 7254 Aborted (core dumped) kmc -fa -m4 -k10 -sf2 -ci2 -cs4 -cx4 /<>/iva-1.0.9+ds/iva/tests/data/kcount_test.run_kmc.fa kmc_out $PWD > /dev/null ERROR test_append (kmers_test.TestKmers) Test append ... ok test_commonest_kmers (kmers_test.TestKmers) ... ok test_extend (kmers_test.TestKmers) Test extend ... ok test_extension (kmers_test.TestKmers) Test extension ... ok test_init (kmers_test.TestKmers) Test __init__ ... ok test_kmer_dict (kmers_test.TestKmers) Test kmer_dict ... ok test_append_to_file (kraken_test.TestKraken) test _append_to_file ... ok test_count_cds_from_embl (kraken_test.TestKraken) test count_cds_from_embl ... ok test_genbank_to_taxon_and_gi (kraken_test.TestKraken) test _genbank_to_taxon_and_gi ... ok test_get_most_common_species_dir (kraken_test.TestKraken) Test get_most_common_species ... ok test_get_parent_taxons (kraken_test.TestKraken) test _get_parent_taxons ... ok test_load_extra_ref_info (kraken_test.TestKraken) test _load_extra_ref_info ... ok test_replace_fasta_header (kraken_test.TestKraken) test _replace_fasta_header ... ok test_species_to_dir (kraken_test.TestKraken) test species_to_dir ... ok test_bam_file_to_fasta_pair_files (mapping_test.TestMapping) Test bam_file_to_fasta_pair_files ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_bam_file_to_fasta_pair_files_region (mapping_test.TestMapping) Test bam_file_to_fasta_pair_files with a region ... ok test_bam_file_to_region_fasta (mapping_test.TestMapping) Test bam_file_to_region_fasta ... ok test_bam_to_fasta (mapping_test.TestMapping) Test bam_to_fasta ... ok test_can_extend (mapping_test.TestMapping) Test can_extend ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_consensus_base (mapping_test.TestMapping) Test consensus_base ... ok test_consensus_base_both_strands (mapping_test.TestMapping) Test consensus_base_both_strands ... ok test_find_incorrect_ref_bases (mapping_test.TestMapping) Test find_incorrect_ref_bases ... ok test_get_bam_region_coverage_fwd (mapping_test.TestMapping) Test get_bam_region_coverage forward strand ... ok test_get_bam_region_coverage_fwd_And_rev (mapping_test.TestMapping) Test get_bam_region_coverage both strands ... ok test_get_bam_region_coverage_rev (mapping_test.TestMapping) Test get_bam_region_coverage reverse strand ... ok test_get_pair_type (mapping_test.TestMapping) Test get_pair_type ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_get_ref_name (mapping_test.TestMapping) Test get_ref_name ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_map_reads (mapping_test.TestMapping) Test mapping reads ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bam' ok test_map_reads_and_sort (mapping_test.TestMapping) Test mapping reads and sort BAM ... The following command failed with exit code 1 samtools sort -@1 -m 500M tmp.out.unsorted.bam tmp.out The output was: [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set) -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam --no-PG do not add a PG line --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] --verbosity INT Set level of verbosity ERROR test_map_reads_wth_flag (mapping_test.TestMapping) Test map_reads with required flag ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.flag12.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bam' ok test_remove_indels (mapping_test.TestMapping) Test _remove_indels ... ok test_sam_to_fasta (mapping_test.TestMapping) Test sam_to_fasta ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_smalt_in_path (mapping_test.TestMapping) Test that samtools is in the user's path ... ok test_soft_clipped (mapping_test.TestMapping) Test soft_clipped ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/mapping_test.smalt.out.bam' ok test_strip_mpileup_coverage_string (mapping_test.TestMapping) Test strip_mpileup_coverage_string ... ok test_total_ref_length_from_bam (mapping_test.TestMapping) Test _total_ref_length_from_bam ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva-1.0.9+ds/iva/tests/data/mapping_test.total_ref_length_from_bam.bam' ok test_file_read (mummer_test.TestMummer) test file_read ... ok test_is_at_ends (mummer_test.TestMummer) Test is_at_ends ... ok test_is_self_hit (mummer_test.TestMummer) Test is_self_hit ... ok test_on_same_strand (mummer_test.TestMummer) test on_same_strand ... ok test_qry_coords (mummer_test.TestMummer) Test qry_coords ... ok test_ref_coords (mummer_test.TestMummer) Test ref_coords ... ok test_run_nucmer (mummer_test.TestMummer) test run_nucmer ... ok test_sort (mummer_test.TestMummer) test sort ... ok test_swap (mummer_test.TestMummer) test swap ... ok test_to_graph_edge (mummer_test.TestMummer) Test to_graph_edge ... ok test_run_gage (qc_external_test.TestQcExternal) test run_gage ... ok test_run_ratt (qc_external_test.TestQcExternal) test run_ratt ... ok test_calculate_cds_assembly_stats (qc_test.TestQc) test _calculate_cds_assembly_stats ... ok test_calculate_contig_placement (qc_test.TestQc) test calculate_contig_placement ... ok test_calculate_ref_positions_covered_by_contigs (qc_test.TestQc) test _calculate_ref_positions_covered_by_contigs ... ok test_calculate_ref_read_coverage (qc_test.TestQc) test _calculate_ref_read_coverage ... The following command failed with exit code 1 samtools sort -@1 -m 500M tmp.qc.reads_mapped_to_ref.unsorted.bam tmp.qc.reads_mapped_to_ref The output was: [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set) -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam --no-PG do not add a PG line --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] --verbosity INT Set level of verbosity ERROR test_calculate_ref_read_region_coverage (qc_test.TestQc) test _calculate_ref_read_region_coverage ... ok test_calculate_refseq_assembly_stats (qc_test.TestQc) test _calculate_refseq_assembly_stats ... ok test_calculate_should_have_assembled (qc_test.TestQc) test _calculate_should_have_assembled ... ok test_contig_placement_in_reference (qc_test.TestQc) test _contig_placement_in_reference ... ok test_contigs_and_bases_that_hit_ref (qc_test.TestQc) test _contigs_and_bases_that_hit_ref ... ok test_cov_to_R_string (qc_test.TestQc) test _cov_to_R_string ... ok test_coverage_list_to_low_cov_intervals (qc_test.TestQc) test _coverage_list_to_low_cov_intervals ... ok test_get_R_plot_contig_order_from_contig_placement (qc_test.TestQc) test _get_R_plot_contig_order_from_contig_placement ... ok test_get_contig_hits_to_reference (qc_test.TestQc) test _get_contig_hits_to_reference ... ok test_get_overlapping_qry_hits (qc_test.TestQc) test _get_overlapping_qry_hits ... ok test_get_ref_cds_from_gff (qc_test.TestQc) test _get_ref_cds_from_gff ... ok test_get_unique_and_repetitive_from_contig_hits (qc_test.TestQc) test _get_unique_and_repetitive_from_contig_hits ... ok test_gff_and_fasta_to_cds (qc_test.TestQc) test _gff_and_fasta_to_cds ... ok test_has_orf (qc_test.TestQc) test _has_orf ... ok test_hash_nucmer_hits_by_ref (qc_test.TestQc) test _hash_nucmer_hits_by_ref ... ok test_ids_in_order_from_fai (qc_test.TestQc) test _ids_in_order_from_fai ... ok test_invert_list (qc_test.TestQc) test _invert_list ... ok test_map_cds_to_assembly (qc_test.TestQc) test _map_cds_to_assembly ... ok test_mummer_coords_file_to_dict (qc_test.TestQc) test _mummer_coords_file_to_dict ... ok test_write_cds_seqs (qc_test.TestQc) test _write_cds_seqs ... ok test_write_fasta_contigs_hit_ref (qc_test.TestQc) test _write_fasta_contigs_hit_ref ... ok test_write_fasta_contigs_not_hit_ref (qc_test.TestQc) test _write_fasta_contigs_not_hit_ref ... ok test_write_ref_coverage_to_files_for_R (qc_test.TestQc) test _write_ref_coverage_to_files_for_R ... ok test_run_trimmomatic (read_trim_test.TestReadTrim) Test run_trimmomatic ... ok test_extend (seed_test.TestSeed) Test extend ... ok test_extend_with_reads_as_single_end (seed_test.TestSeed) Test _extend_with_reads_as_single_end ... ok test_extension_from_read (seed_test.TestSeed) Test _test_extension_from_read ... ok test_extensions_from_reads_file (seed_test.TestSeed) Test _extensions_from_reads_file ... ok test_init (seed_test.TestSeed) test init ... ok test_kmc_in_path (seed_test.TestSeed) Test that kmc is in the user's path ... ok test_len (seed_test.TestSeed) Test len ... ok test_write_fasta (seed_test.TestSeed) Test write_fasta ... ok ====================================================================== ERROR: test_add_new_seed_contig (assembly_test.TestAssembly) Test add_new_seed_contig ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/iva-1.0.9+ds/iva/tests/assembly_test.py", line 166, in test_add_new_seed_contig new_contig_name = a.add_new_seed_contig(reads1, reads2) File "/<>/iva-1.0.9+ds/iva/assembly.py", line 601, in add_new_seed_contig s = seed.Seed(reads1=seed_reads1, reads2=seed_reads2, extend_length=self.seed_ext_max_bases, seed_length=self.seed_start_length, seed_min_count=self.seed_min_kmer_count, seed_max_count=self.seed_max_kmer_count, ext_min_cov=self.seed_min_cov, ext_min_ratio=self.seed_min_ratio, verbose=self.verbose, kmc_threads=self.kmc_threads, map_threads=self.threads, sequences_to_ignore=self.used_seeds, contigs_to_check=self.contigs) File "/<>/iva-1.0.9+ds/iva/seed.py", line 41, in __init__ kmer_counts = kcount.get_most_common_kmers(reads1, reads2, most_common=1, min_count=seed_min_count, max_count=seed_max_count, kmer_length=seed_length, verbose=self.verbose, ignore_seqs=sequences_to_ignore, contigs_to_check=contigs_to_check, kmc_threads=self.kmc_threads, map_threads=self.map_threads) File "/<>/iva-1.0.9+ds/iva/kcount.py", line 234, in get_most_common_kmers counts_file = _run_kmc(reads, os.path.join(tmpdir, 'out'), kmer_length, min_count, max_count, verbose=verbose, threads=kmc_threads) File "/<>/iva-1.0.9+ds/iva/kcount.py", line 113, in _run_kmc ran_ok = _run_kmc_with_script('run_kmc.sh', reads, kmer_counts_file, kmer, min_count, max_count, 4, verbose, False, threads=threads) File "/<>/iva-1.0.9+ds/iva/kcount.py", line 94, in _run_kmc_with_script return common.syscall('bash ' + script, allow_fail=allow_fail) File "/<>/iva-1.0.9+ds/iva/common.py", line 44, in syscall sys.exit(1) SystemExit: 1 -------------------- >> begin captured stdout << --------------------- map reads /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_add_new_seed_contig.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_add_new_seed_contig.reads_2.fa map reads. Index: smalt index -k 15 -s 3 /<>/iva-1.0.9+ds/tmp.make_seed.3q3ysg66/out.map_index /<>/iva-1.0.9+ds/tmp.make_seed.3q3ysg66/out.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 /<>/iva-1.0.9+ds/tmp.make_seed.3q3ysg66/out.map_index /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_add_new_seed_contig.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_add_new_seed_contig.reads_2.fa | samtools view -f 12 -bS -T /<>/iva-1.0.9+ds/tmp.make_seed.3q3ysg66/out.ref.fa - > /<>/iva-1.0.9+ds/tmp.make_seed.3q3ysg66/out.bam run kmc: /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc kmc -fa -m32 -k10 -sf1 -ci1 -cs1000000000 -cx1000000000 /<>/iva-1.0.9+ds/tmp.common_kmers.ao0gcg0v/reads.fa kmc_out $PWD First try of running kmc failed. Trying again with -m4 instead of -m32... run kmc: /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc kmc -fa -m4 -k10 -sf1 -ci1 -cs1000000000 -cx1000000000 /<>/iva-1.0.9+ds/tmp.common_kmers.ao0gcg0v/reads.fa kmc_out $PWD --------------------- >> end captured stdout << ---------------------- ====================================================================== ERROR: test_read_pair_extend (assembly_test.TestAssembly) Test read_pair_extend ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/iva-1.0.9+ds/iva/tests/assembly_test.py", line 118, in test_read_pair_extend a.read_pair_extend(reads_prefix, 'tmp.extend') File "/<>/iva-1.0.9+ds/iva/assembly.py", line 423, in read_pair_extend self._read_pair_extension_iterations(current_reads_prefix, out_prefix + '.' + str(i)) File "/<>/iva-1.0.9+ds/iva/assembly.py", line 394, in _read_pair_extension_iterations self._trim_strand_biased_ends(reads_prefix, tag_as_trimmed=False) File "/<>/iva-1.0.9+ds/iva/assembly.py", line 277, in _trim_strand_biased_ends self._map_reads(reads_prefix + '_1.fa', reads_prefix + '_2.fa', tmp_prefix, sort_reads=True) File "/<>/iva-1.0.9+ds/iva/assembly.py", line 147, in _map_reads mapping.map_reads(fwd_reads, rev_reads, reference, out_prefix, index_k=self.map_index_k, index_s=self.map_index_s, threads=self.threads, max_insert=self.max_insert, minid=self.map_minid, verbose=self.verbose, required_flag=required_flag, sort=sort_reads, exclude_flag=exclude_flag) File "/<>/iva-1.0.9+ds/iva/mapping.py", line 103, in map_reads common.syscall(sort_cmd) File "/<>/iva-1.0.9+ds/iva/common.py", line 44, in syscall sys.exit(1) SystemExit: 1 -------------------- >> begin captured stdout << --------------------- ______________________________ START ITERATION 1 ______________________________ --------------- tmp.extend.1 start extension subiteration 0001 ---------------- map reads /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.1.1.map.map_index tmp.extend.1.1.1.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.1.1.map.map_index /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_2.fa | samtools view -bS -T tmp.extend.1.1.1.map.ref.fa - > tmp.extend.1.1.1.map.bam trying to extend left end ... all kmers: GCATGA GCATGAGAATGACACGGGCGGATTG GCATGAG GCATGA GCATGAG GCATGAGAATG GCATGAGAATGACACGGGCG GCATG GCATGAGAATGACACGGG GCATGAGAATGACACGGGCG GCATG GCA GCA GCATGAGAAT GCATGAGAATGACACGGGCG GCATGAGAATGACACGGGCGGA GCATGAGAATGACACGGGCGGATT k = 25 commonest two kmers: (None, 'GCATGAGAATGACACGGGCGGATTG') have frequency: (None, 1) k = 24 commonest two kmers: (None, 'GCATGAGAATGACACGGGCGGATT') have frequency: (None, 2) k = 23 commonest two kmers: (None, 'GCATGAGAATGACACGGGCGGAT') have frequency: (None, 2) k = 22 commonest two kmers: (None, 'GCATGAGAATGACACGGGCGGA') have frequency: (None, 3) k = 21 commonest two kmers: (None, 'GCATGAGAATGACACGGGCGG') have frequency: (None, 3) k = 20 commonest two kmers: (None, 'GCATGAGAATGACACGGGCG') have frequency: (None, 6) trying to extend right end ... all kmers: ATCTAACACAACTAAG ATCTA ATCTAACACAACTAAGACCAAT ATCTAACACAACTAAGACCAATCA ATCTAACACAACTAAGACCAATC ATCTAACACAA ATCTAACACAACTAAGACCA ATCTAAC ATCTAACACAACTAAGACCA ATCTAACACAACTA ATCTAAC ATCTAACACAACTAAGACCA ATC ATC ATCTA ATCTAACACAACTAAGACC ATCTAACAC ATCTAACACAACTAAGACCAATCAG k = 25 commonest two kmers: (None, 'ATCTAACACAACTAAGACCAATCAG') have frequency: (None, 1) k = 24 commonest two kmers: (None, 'ATCTAACACAACTAAGACCAATCA') have frequency: (None, 2) k = 23 commonest two kmers: (None, 'ATCTAACACAACTAAGACCAATC') have frequency: (None, 3) k = 22 commonest two kmers: (None, 'ATCTAACACAACTAAGACCAAT') have frequency: (None, 4) k = 21 commonest two kmers: (None, 'ATCTAACACAACTAAGACCAA') have frequency: (None, 4) k = 20 commonest two kmers: (None, 'ATCTAACACAACTAAGACCA') have frequency: (None, 7) new left sequence: GCGGGCACAGTAAGAGTACG new right sequence: ATCTAACACAACTAAGACCA extend contig 1 new_length:640 added_left:20 added_right:20 map reads /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.0_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.0_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.1.2.map.map_index tmp.extend.1.1.2.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.1.2.map.map_index /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.0_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.0_2.fa | samtools view -bS -T tmp.extend.1.1.2.map.ref.fa - > tmp.extend.1.1.2.map.bam trying to extend left end ... all kmers: GATTG GATTGATT GATTGA GATTGATTGCATGAGA GATTGATTGCATGAGAGCATGTT GATTGATTGCAT GATTGATT GATTGATT GATTGATTGCA GATTGAT GATTGATTGCATGAGAGCAT GATTGATTGCA GATTGATTGCATGAGAGC GATT k = 23 commonest two kmers: (None, 'GATTGATTGCATGAGAGCATGTT') have frequency: (None, 1) k = 22 commonest two kmers: (None, 'GATTGATTGCATGAGAGCATGT') have frequency: (None, 1) k = 21 commonest two kmers: (None, 'GATTGATTGCATGAGAGCATG') have frequency: (None, 1) k = 20 commonest two kmers: (None, 'GATTGATTGCATGAGAGCAT') have frequency: (None, 2) k = 19 commonest two kmers: (None, 'GATTGATTGCATGAGAGCA') have frequency: (None, 2) k = 18 commonest two kmers: (None, 'GATTGATTGCATGAGAGC') have frequency: (None, 3) k = 17 commonest two kmers: (None, 'GATTGATTGCATGAGAG') have frequency: (None, 3) k = 16 commonest two kmers: (None, 'GATTGATTGCATGAGA') have frequency: (None, 4) k = 15 commonest two kmers: (None, 'GATTGATTGCATGAG') have frequency: (None, 4) k = 14 commonest two kmers: (None, 'GATTGATTGCATGA') have frequency: (None, 4) k = 13 commonest two kmers: (None, 'GATTGATTGCATG') have frequency: (None, 4) k = 12 commonest two kmers: (None, 'GATTGATTGCAT') have frequency: (None, 5) trying to extend right end ... all kmers: ATCAGGGTATTAAA ATCAGGGTAT ATCAGGGT ATCAGGGTATTAAAA ATCA ATC ATCAGGGTATTAAAAGTCTGCTA ATCAGGGTATTA ATCAGGGTATTAAAAGTCT ATCAGGGTATTAAAAG ATCAGGGTATTA ATCAGGGTATTAAAAGTCTGCTAA ATCAGGGTAT ATCAG k = 24 commonest two kmers: (None, 'ATCAGGGTATTAAAAGTCTGCTAA') have frequency: (None, 1) k = 23 commonest two kmers: (None, 'ATCAGGGTATTAAAAGTCTGCTA') have frequency: (None, 2) k = 22 commonest two kmers: (None, 'ATCAGGGTATTAAAAGTCTGCT') have frequency: (None, 2) k = 21 commonest two kmers: (None, 'ATCAGGGTATTAAAAGTCTGC') have frequency: (None, 2) k = 20 commonest two kmers: (None, 'ATCAGGGTATTAAAAGTCTG') have frequency: (None, 2) k = 19 commonest two kmers: (None, 'ATCAGGGTATTAAAAGTCT') have frequency: (None, 3) k = 18 commonest two kmers: (None, 'ATCAGGGTATTAAAAGTC') have frequency: (None, 3) k = 17 commonest two kmers: (None, 'ATCAGGGTATTAAAAGT') have frequency: (None, 3) k = 16 commonest two kmers: (None, 'ATCAGGGTATTAAAAG') have frequency: (None, 4) k = 15 commonest two kmers: (None, 'ATCAGGGTATTAAAA') have frequency: (None, 5) new left sequence: TACGTTAGTTAG new right sequence: ATCAGGGTATTAAAA extend contig 1 new_length:667 added_left:12 added_right:15 map reads /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.1_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.1_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.1.3.map.map_index tmp.extend.1.1.3.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.1.3.map.map_index /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.1_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.1_2.fa | samtools view -bS -T tmp.extend.1.1.3.map.ref.fa - > tmp.extend.1.1.3.map.bam trying to extend left end ... all kmers: GAGAGCATGTTGACAGCTTAGA GAGA GAGAGCATGTT GAGAGCAT GAGAGCATGTTGACAGCTTAGAT GAGAGC k = 23 commonest two kmers: (None, 'GAGAGCATGTTGACAGCTTAGAT') have frequency: (None, 1) k = 22 commonest two kmers: (None, 'GAGAGCATGTTGACAGCTTAGA') have frequency: (None, 2) k = 21 commonest two kmers: (None, 'GAGAGCATGTTGACAGCTTAG') have frequency: (None, 2) k = 20 commonest two kmers: (None, 'GAGAGCATGTTGACAGCTTA') have frequency: (None, 2) k = 19 commonest two kmers: (None, 'GAGAGCATGTTGACAGCTT') have frequency: (None, 2) k = 18 commonest two kmers: (None, 'GAGAGCATGTTGACAGCT') have frequency: (None, 2) k = 17 commonest two kmers: (None, 'GAGAGCATGTTGACAGC') have frequency: (None, 2) k = 16 commonest two kmers: (None, 'GAGAGCATGTTGACAG') have frequency: (None, 2) k = 15 commonest two kmers: (None, 'GAGAGCATGTTGACA') have frequency: (None, 2) k = 14 commonest two kmers: (None, 'GAGAGCATGTTGAC') have frequency: (None, 2) k = 13 commonest two kmers: (None, 'GAGAGCATGTTGA') have frequency: (None, 2) k = 12 commonest two kmers: (None, 'GAGAGCATGTTG') have frequency: (None, 2) k = 11 commonest two kmers: (None, 'GAGAGCATGTT') have frequency: (None, 3) k = 10 commonest two kmers: (None, 'GAGAGCATGT') have frequency: (None, 3) k = 9 commonest two kmers: (None, 'GAGAGCATG') have frequency: (None, 3) k = 8 commonest two kmers: (None, 'GAGAGCAT') have frequency: (None, 4) k = 7 commonest two kmers: (None, 'GAGAGCA') have frequency: (None, 4) k = 6 commonest two kmers: (None, 'GAGAGC') have frequency: (None, 5) trying to extend right end ... all kmers: GTCTGCTAAGCT GTCTGCTAAGCT GTCTGCTAAGCTGAGCGCACCAGGC GTCTGCTAAGCTGA GTCTGCTAAGC GTCTGCTAAGCT GTCTGCTA GTCTGCTAAGCTGAGCGC GTCT GTCTGCTAAGCTGAGCG GTCTGCTAAGCTGAG GTCTGCTAAGCTGAGCGCACCA GTCTGCTAAGCTGAG GTCTGCTAAGCTGAGCGCACCAGG GTCTGCTAAGCTGAG GTCTGCTAA GTCTGCTAAGCTGAGC k = 25 commonest two kmers: (None, 'GTCTGCTAAGCTGAGCGCACCAGGC') have frequency: (None, 1) k = 24 commonest two kmers: (None, 'GTCTGCTAAGCTGAGCGCACCAGG') have frequency: (None, 2) k = 23 commonest two kmers: (None, 'GTCTGCTAAGCTGAGCGCACCAG') have frequency: (None, 2) k = 22 commonest two kmers: (None, 'GTCTGCTAAGCTGAGCGCACCA') have frequency: (None, 3) k = 21 commonest two kmers: (None, 'GTCTGCTAAGCTGAGCGCACC') have frequency: (None, 3) k = 20 commonest two kmers: (None, 'GTCTGCTAAGCTGAGCGCAC') have frequency: (None, 3) k = 19 commonest two kmers: (None, 'GTCTGCTAAGCTGAGCGCA') have frequency: (None, 3) k = 18 commonest two kmers: (None, 'GTCTGCTAAGCTGAGCGC') have frequency: (None, 4) k = 17 commonest two kmers: (None, 'GTCTGCTAAGCTGAGCG') have frequency: (None, 5) new left sequence: CGAGAG new right sequence: GTCTGCTAAGCTGAGCG extend contig 1 new_length:690 added_left:6 added_right:17 map reads /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.2_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.2_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.1.4.map.map_index tmp.extend.1.1.4.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.1.4.map.map_index /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.2_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.2_2.fa | samtools view -bS -T tmp.extend.1.1.4.map.ref.fa - > tmp.extend.1.1.4.map.bam trying to extend left end ... all kmers: ATGTTGACAGCTTAG ATGTTGACAGCTTAGA ATGTT ATGTTGACAGCTTAGAT ATGTTGACA ATGTTGACAGCTTAGATTTGGTTC ATGTTGACAGCTTAGAT ATGTTGACAGCTTAGATTTG ATGTTGACAGCTTAGATTT k = 24 commonest two kmers: (None, 'ATGTTGACAGCTTAGATTTGGTTC') have frequency: (None, 1) k = 23 commonest two kmers: (None, 'ATGTTGACAGCTTAGATTTGGTT') have frequency: (None, 1) k = 22 commonest two kmers: (None, 'ATGTTGACAGCTTAGATTTGGT') have frequency: (None, 1) k = 21 commonest two kmers: (None, 'ATGTTGACAGCTTAGATTTGG') have frequency: (None, 1) k = 20 commonest two kmers: (None, 'ATGTTGACAGCTTAGATTTG') have frequency: (None, 2) k = 19 commonest two kmers: (None, 'ATGTTGACAGCTTAGATTT') have frequency: (None, 3) k = 18 commonest two kmers: (None, 'ATGTTGACAGCTTAGATT') have frequency: (None, 3) k = 17 commonest two kmers: (None, 'ATGTTGACAGCTTAGAT') have frequency: (None, 5) trying to extend right end ... all kmers: CACCAGGCACCGAA CACCAGGCAC CACCAGGCACCGA CACCAGGCACCGAA CACCAGGCACCGAA CACCAGGC CACCAGGCACCGAACCCTTA CACCAGGCACCGA CACCAGGCACCGAACCCTTAATA CACCAGGCACCGAACCC CACCA CACCAGG CACCAGGCACCGAACCCTT CACCAGGCAC CACCAGGCA k = 23 commonest two kmers: (None, 'CACCAGGCACCGAACCCTTAATA') have frequency: (None, 1) k = 22 commonest two kmers: (None, 'CACCAGGCACCGAACCCTTAAT') have frequency: (None, 1) k = 21 commonest two kmers: (None, 'CACCAGGCACCGAACCCTTAA') have frequency: (None, 1) k = 20 commonest two kmers: (None, 'CACCAGGCACCGAACCCTTA') have frequency: (None, 2) k = 19 commonest two kmers: (None, 'CACCAGGCACCGAACCCTT') have frequency: (None, 3) k = 18 commonest two kmers: (None, 'CACCAGGCACCGAACCCT') have frequency: (None, 3) k = 17 commonest two kmers: (None, 'CACCAGGCACCGAACCC') have frequency: (None, 4) k = 16 commonest two kmers: (None, 'CACCAGGCACCGAACC') have frequency: (None, 4) k = 15 commonest two kmers: (None, 'CACCAGGCACCGAAC') have frequency: (None, 4) k = 14 commonest two kmers: (None, 'CACCAGGCACCGAA') have frequency: (None, 7) new left sequence: TAGATTCGACAGTTGTA new right sequence: CACCAGGCACCGAA extend contig 1 new_length:721 added_left:17 added_right:14 map reads /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.3_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.3_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.1.5.map.map_index tmp.extend.1.1.5.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.1.5.map.map_index /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.3_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.ttfqfxeb/reads.3_2.fa | samtools view -bS -T tmp.extend.1.1.5.map.ref.fa - > tmp.extend.1.1.5.map.bam trying to extend left end ... all kmers: TTGGTTCTTAGCCC TTGGTTCTTAGCCCCAGGC TTGGTTCTTAGCCCCAGGC TTGGTTCTTAGCCCCAGGCAGGA TTGGTTCTTAGC TTGGTTC TTGGTTCTTAGCCC TTG k = 23 commonest two kmers: (None, 'TTGGTTCTTAGCCCCAGGCAGGA') have frequency: (None, 1) k = 22 commonest two kmers: (None, 'TTGGTTCTTAGCCCCAGGCAGG') have frequency: (None, 1) k = 21 commonest two kmers: (None, 'TTGGTTCTTAGCCCCAGGCAG') have frequency: (None, 1) k = 20 commonest two kmers: (None, 'TTGGTTCTTAGCCCCAGGCA') have frequency: (None, 1) k = 19 commonest two kmers: (None, 'TTGGTTCTTAGCCCCAGGC') have frequency: (None, 3) k = 18 commonest two kmers: (None, 'TTGGTTCTTAGCCCCAGG') have frequency: (None, 3) k = 17 commonest two kmers: (None, 'TTGGTTCTTAGCCCCAG') have frequency: (None, 3) k = 16 commonest two kmers: (None, 'TTGGTTCTTAGCCCCA') have frequency: (None, 3) k = 15 commonest two kmers: (None, 'TTGGTTCTTAGCCCC') have frequency: (None, 3) k = 14 commonest two kmers: (None, 'TTGGTTCTTAGCCC') have frequency: (None, 5) trying to extend right end ... all kmers: CCCTTAATAGGTTTAAGAAC CCCTTAATAGGTTTAAGAA CCCTTAATAGGT CCCTTAATAGGT CCCTTA CCCTTAATAGGT CCCTTAATA CCC CCCTTAATAGGTTTAAG CCCTTAATAGGTTTAAGAA CCCTTAATAGGT CCCTT CCCTTAATAGGTTTAAGA CCCTTAATAGGTTTAAGAAC CCCTTAATAGGTTT CCCTTAATAGGTTT k = 20 commonest two kmers: (None, 'CCCTTAATAGGTTTAAGAAC') have frequency: (None, 2) k = 19 commonest two kmers: (None, 'CCCTTAATAGGTTTAAGAA') have frequency: (None, 4) k = 18 commonest two kmers: (None, 'CCCTTAATAGGTTTAAGA') have frequency: (None, 5) new left sequence: CCCGATTCTTGGTT new right sequence: CCCTTAATAGGTTTAAGA extend contig 1 new_length:753 added_left:14 added_right:18 --------------- tmp.extend.1 start extension subiteration 0002 ---------------- map reads /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.2.1.map.map_index tmp.extend.1.2.1.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.2.1.map.map_index /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_2.fa | samtools view -bS -T tmp.extend.1.2.1.map.ref.fa - > tmp.extend.1.2.1.map.bam trying to extend left end ... all kmers: CAGGCAGGATAGCTA CAGGC CAGGCAGGATAG CAGGC CAGGCAGGA CAGGCAGGATAGCTATAGCAAATTC CAGGCAGGATAGCTAT k = 25 commonest two kmers: (None, 'CAGGCAGGATAGCTATAGCAAATTC') have frequency: (None, 1) k = 24 commonest two kmers: (None, 'CAGGCAGGATAGCTATAGCAAATT') have frequency: (None, 1) k = 23 commonest two kmers: (None, 'CAGGCAGGATAGCTATAGCAAAT') have frequency: (None, 1) k = 22 commonest two kmers: (None, 'CAGGCAGGATAGCTATAGCAAA') have frequency: (None, 1) k = 21 commonest two kmers: (None, 'CAGGCAGGATAGCTATAGCAA') have frequency: (None, 1) k = 20 commonest two kmers: (None, 'CAGGCAGGATAGCTATAGCA') have frequency: (None, 1) k = 19 commonest two kmers: (None, 'CAGGCAGGATAGCTATAGC') have frequency: (None, 1) k = 18 commonest two kmers: (None, 'CAGGCAGGATAGCTATAG') have frequency: (None, 1) k = 17 commonest two kmers: (None, 'CAGGCAGGATAGCTATA') have frequency: (None, 1) k = 16 commonest two kmers: (None, 'CAGGCAGGATAGCTAT') have frequency: (None, 2) k = 15 commonest two kmers: (None, 'CAGGCAGGATAGCTA') have frequency: (None, 3) k = 14 commonest two kmers: (None, 'CAGGCAGGATAGCT') have frequency: (None, 3) k = 13 commonest two kmers: (None, 'CAGGCAGGATAGC') have frequency: (None, 3) k = 12 commonest two kmers: (None, 'CAGGCAGGATAG') have frequency: (None, 4) k = 11 commonest two kmers: (None, 'CAGGCAGGATA') have frequency: (None, 4) k = 10 commonest two kmers: (None, 'CAGGCAGGAT') have frequency: (None, 4) k = 9 commonest two kmers: (None, 'CAGGCAGGA') have frequency: (None, 5) trying to extend right end ... all kmers: ACCAAACCAGGAGAGTTTCCTC ACCAAACCAGGA ACCAAACCAGGAGAGTTTCCTCACG ACCAAACCAGGAGAGTTT ACCAAACCAGGAGAGTTTCCTCACG ACCAAACCAGGAGAGTTTCCTCACG ACCAAACCAGGA ACCAAACCAGGAGAGTTTCCTC ACCAAACCAGGAGAGTTTCC ACCAAACCAGGAG k = 25 commonest two kmers: (None, 'ACCAAACCAGGAGAGTTTCCTCACG') have frequency: (None, 3) k = 24 commonest two kmers: (None, 'ACCAAACCAGGAGAGTTTCCTCAC') have frequency: (None, 3) k = 23 commonest two kmers: (None, 'ACCAAACCAGGAGAGTTTCCTCA') have frequency: (None, 3) k = 22 commonest two kmers: (None, 'ACCAAACCAGGAGAGTTTCCTC') have frequency: (None, 5) new left sequence: AGGACGGAC new right sequence: ACCAAACCAGGAGAGTTTCCTC extend contig 1 new_length:784 added_left:9 added_right:22 map reads /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.0_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.0_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.2.2.map.map_index tmp.extend.1.2.2.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.2.2.map.map_index /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.0_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.0_2.fa | samtools view -bS -T tmp.extend.1.2.2.map.ref.fa - > tmp.extend.1.2.2.map.bam trying to extend left end ... all kmers: TAGCTATAGCAAATTCCTTATCAGA TAGCTA TAGCTATAGCAAATTCCTTATCAG TAGCTATAGCAAATTCCTTATCAG TAGCTATAGCAAATTCCTTATC TAG TAGCTATAGCAAATTCC TAGCTATAGCAAATTC TAGCTATAGCAAATTCCTTATCAGA TAGCTATAGCAAATTCCTTATC TAGCTATAGCAAATTCC TAGCTATAGCAAATTCCTTA TAGCTATAGCAAATTCCTT TAGCTATAGCAAATTCCT TAGCTATAGCAAATTCCT TAGCTAT TAGCTATAGCAAATTCC k = 25 commonest two kmers: (None, 'TAGCTATAGCAAATTCCTTATCAGA') have frequency: (None, 2) k = 24 commonest two kmers: (None, 'TAGCTATAGCAAATTCCTTATCAG') have frequency: (None, 4) k = 23 commonest two kmers: (None, 'TAGCTATAGCAAATTCCTTATCA') have frequency: (None, 4) k = 22 commonest two kmers: (None, 'TAGCTATAGCAAATTCCTTATC') have frequency: (None, 6) trying to extend right end ... all kmers: ACGACAA ACGACAAATTG ACGACAAAT ACGACAAATTGAACATGT ACGACAAATTGAACATGTTCGT ACGACAAATTGAACATG ACGACAAATTGA ACG ACGA ACGACAAATTGAACATGTTCGTG ACG ACG ACGACAAATTGAAC ACGAC ACGACAAATTGAACATGTTC k = 23 commonest two kmers: (None, 'ACGACAAATTGAACATGTTCGTG') have frequency: (None, 1) k = 22 commonest two kmers: (None, 'ACGACAAATTGAACATGTTCGT') have frequency: (None, 2) k = 21 commonest two kmers: (None, 'ACGACAAATTGAACATGTTCG') have frequency: (None, 2) k = 20 commonest two kmers: (None, 'ACGACAAATTGAACATGTTC') have frequency: (None, 3) k = 19 commonest two kmers: (None, 'ACGACAAATTGAACATGTT') have frequency: (None, 3) k = 18 commonest two kmers: (None, 'ACGACAAATTGAACATGT') have frequency: (None, 4) k = 17 commonest two kmers: (None, 'ACGACAAATTGAACATG') have frequency: (None, 5) new left sequence: CTATTCCTTAAACGATATCGAT new right sequence: ACGACAAATTGAACATG extend contig 1 new_length:823 added_left:22 added_right:17 map reads /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.1_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.1_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.2.3.map.map_index tmp.extend.1.2.3.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.2.3.map.map_index /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.1_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.1_2.fa | samtools view -bS -T tmp.extend.1.2.3.map.ref.fa - > tmp.extend.1.2.3.map.bam trying to extend left end ... all kmers: AGA AGAGGTATCGCGACCTCCCGGTAC AGAGGTATCGCGACCTCCCGGT AGAGGTAT AGAGGTATCGCGACCT AGAGGTATCGCGA AGAGGT AGAGGTA AGAGGTATCGCG AGA AGAGGTATCGC AGAGGTAT AGAGGTATC AGAGGTATCGCGACCTCCCG AGAGG AGAGGTATCGCGAC k = 24 commonest two kmers: (None, 'AGAGGTATCGCGACCTCCCGGTAC') have frequency: (None, 1) k = 23 commonest two kmers: (None, 'AGAGGTATCGCGACCTCCCGGTA') have frequency: (None, 1) k = 22 commonest two kmers: (None, 'AGAGGTATCGCGACCTCCCGGT') have frequency: (None, 2) k = 21 commonest two kmers: (None, 'AGAGGTATCGCGACCTCCCGG') have frequency: (None, 2) k = 20 commonest two kmers: (None, 'AGAGGTATCGCGACCTCCCG') have frequency: (None, 3) k = 19 commonest two kmers: (None, 'AGAGGTATCGCGACCTCCC') have frequency: (None, 3) k = 18 commonest two kmers: (None, 'AGAGGTATCGCGACCTCC') have frequency: (None, 3) k = 17 commonest two kmers: (None, 'AGAGGTATCGCGACCTC') have frequency: (None, 3) k = 16 commonest two kmers: (None, 'AGAGGTATCGCGACCT') have frequency: (None, 4) k = 15 commonest two kmers: (None, 'AGAGGTATCGCGACC') have frequency: (None, 4) k = 14 commonest two kmers: (None, 'AGAGGTATCGCGAC') have frequency: (None, 5) trying to extend right end ... all kmers: TTCGTGGTACTGGCTTCTAG TTCGTGGTACTGGCTTCTAGT TTCGTGGTACTGGCTTCTAGTC TTCGTGGTACTGGCTT TTCGTGGTACTGGCTTCTAGTCA TTCGTGGTA TTCGT TTCGTGGTACTGGCTTCTAGTCATC TTCGTG TTCGTGGTACTGGCTTCT TTCGTGGTACTGGCTTCTAGT TTCGTGGTAC TTCGTGGTACTGGCTTCTAGTC TTCGTGGTACTGGCTTCTAGTCATC TTCGTGGTA TTCGTGGTACTGGCTTCTAG TTC TTCGTGGTACTGGCTT k = 25 commonest two kmers: (None, 'TTCGTGGTACTGGCTTCTAGTCATC') have frequency: (None, 2) k = 24 commonest two kmers: (None, 'TTCGTGGTACTGGCTTCTAGTCAT') have frequency: (None, 2) k = 23 commonest two kmers: (None, 'TTCGTGGTACTGGCTTCTAGTCA') have frequency: (None, 3) k = 22 commonest two kmers: (None, 'TTCGTGGTACTGGCTTCTAGTC') have frequency: (None, 5) new left sequence: CAGCGCTATGGAGA new right sequence: TTCGTGGTACTGGCTTCTAGTC extend contig 1 new_length:859 added_left:14 added_right:22 map reads /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.2_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.2_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.2.4.map.map_index tmp.extend.1.2.4.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.2.4.map.map_index /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.2_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.2_2.fa | samtools view -bS -T tmp.extend.1.2.4.map.ref.fa - > tmp.extend.1.2.4.map.bam trying to extend left end ... all kmers: CTCCCGGTACGGATGGTA CTCCCGGTACGGATGGTACCG CTCCCGGTAC CTCCCGGT CTCCCGGTACGGAT CTCCCGGTACGGATG CTCCCGGTACG CTCCCGGTACGGATGGTACCG CTCCCGGTACGG CTCCCGGTACGGATGGTA CTCCCG CTCCCGGTACGGATGGTACCGAA CTCCCGGTACGG k = 23 commonest two kmers: (None, 'CTCCCGGTACGGATGGTACCGAA') have frequency: (None, 1) k = 22 commonest two kmers: (None, 'CTCCCGGTACGGATGGTACCGA') have frequency: (None, 1) k = 21 commonest two kmers: (None, 'CTCCCGGTACGGATGGTACCG') have frequency: (None, 3) k = 20 commonest two kmers: (None, 'CTCCCGGTACGGATGGTACC') have frequency: (None, 3) k = 19 commonest two kmers: (None, 'CTCCCGGTACGGATGGTAC') have frequency: (None, 3) k = 18 commonest two kmers: (None, 'CTCCCGGTACGGATGGTA') have frequency: (None, 5) trying to extend right end ... all kmers: ATCGGAGTTGAGAGTAAGGT ATCGGAGTTGAGA ATCGGAGTTGAGAGTAAGGTGTAGG ATCGGAGT ATCGGAGTTGAG ATC ATCGGAGTTGAGAGTAAGGTGTAGG ATCGGAGTTGAGAG ATC ATCGGAGTTGAGAGTAAGG k = 25 commonest two kmers: (None, 'ATCGGAGTTGAGAGTAAGGTGTAGG') have frequency: (None, 2) k = 24 commonest two kmers: (None, 'ATCGGAGTTGAGAGTAAGGTGTAG') have frequency: (None, 2) k = 23 commonest two kmers: (None, 'ATCGGAGTTGAGAGTAAGGTGTA') have frequency: (None, 2) k = 22 commonest two kmers: (None, 'ATCGGAGTTGAGAGTAAGGTGT') have frequency: (None, 2) k = 21 commonest two kmers: (None, 'ATCGGAGTTGAGAGTAAGGTG') have frequency: (None, 2) k = 20 commonest two kmers: (None, 'ATCGGAGTTGAGAGTAAGGT') have frequency: (None, 3) k = 19 commonest two kmers: (None, 'ATCGGAGTTGAGAGTAAGG') have frequency: (None, 4) k = 18 commonest two kmers: (None, 'ATCGGAGTTGAGAGTAAG') have frequency: (None, 4) k = 17 commonest two kmers: (None, 'ATCGGAGTTGAGAGTAA') have frequency: (None, 4) k = 16 commonest two kmers: (None, 'ATCGGAGTTGAGAGTA') have frequency: (None, 4) k = 15 commonest two kmers: (None, 'ATCGGAGTTGAGAGT') have frequency: (None, 4) k = 14 commonest two kmers: (None, 'ATCGGAGTTGAGAG') have frequency: (None, 5) new left sequence: ATGGTAGGCATGGCCCTC new right sequence: ATCGGAGTTGAGAG extend contig 1 new_length:891 added_left:18 added_right:14 map reads /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.3_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.3_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.2.5.map.map_index tmp.extend.1.2.5.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.2.5.map.map_index /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.3_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.k4hspeku/reads.3_2.fa | samtools view -bS -T tmp.extend.1.2.5.map.ref.fa - > tmp.extend.1.2.5.map.bam trying to extend left end ... all kmers: CCGAAAAG CCGAAAAGAGA CCGAAAAGAGAAGTGT CCGAAAAGAGAA CCG CCGAAAAGAGAAGTGT CCGAAAAGAGAAGTGT CCGAAAAGAGAAGTGTC CCGAAAAGAGAAGTGTCA CCGAAAAGAGAAGTGTCAGTTGA CCGAAAAGAGA CCGAAAAGAGAA CCGAAAAGAGAAG CCGAAAAGA CCGAAAAGAGAAGTGTCAG CCGAAAAGAGAAG CCG CCGAAAAGAGA CCGAAAAGAGAAGTGTCAGTT CCGAA k = 23 commonest two kmers: (None, 'CCGAAAAGAGAAGTGTCAGTTGA') have frequency: (None, 1) k = 22 commonest two kmers: (None, 'CCGAAAAGAGAAGTGTCAGTTG') have frequency: (None, 1) k = 21 commonest two kmers: (None, 'CCGAAAAGAGAAGTGTCAGTT') have frequency: (None, 2) k = 20 commonest two kmers: (None, 'CCGAAAAGAGAAGTGTCAGT') have frequency: (None, 2) k = 19 commonest two kmers: (None, 'CCGAAAAGAGAAGTGTCAG') have frequency: (None, 3) k = 18 commonest two kmers: (None, 'CCGAAAAGAGAAGTGTCA') have frequency: (None, 4) k = 17 commonest two kmers: (None, 'CCGAAAAGAGAAGTGTC') have frequency: (None, 5) trying to extend right end ... all kmers: TAAGGTGTAGGG TAAGGT TAAGGTGTAGGGACACTTG TAAGGTGTAGG TAAGGTGTAGGGACACTTGC TAAGGTGTAGGGACAC TAAGGTGTAGG TAAGGTGTAGGGACACTTGCCAG TAAGGTGTAGGGAC TAAGGTGTAGGGACACTTGCCAGT TAAGG k = 24 commonest two kmers: (None, 'TAAGGTGTAGGGACACTTGCCAGT') have frequency: (None, 1) k = 23 commonest two kmers: (None, 'TAAGGTGTAGGGACACTTGCCAG') have frequency: (None, 2) k = 22 commonest two kmers: (None, 'TAAGGTGTAGGGACACTTGCCA') have frequency: (None, 2) k = 21 commonest two kmers: (None, 'TAAGGTGTAGGGACACTTGCC') have frequency: (None, 2) k = 20 commonest two kmers: (None, 'TAAGGTGTAGGGACACTTGC') have frequency: (None, 3) k = 19 commonest two kmers: (None, 'TAAGGTGTAGGGACACTTG') have frequency: (None, 4) k = 18 commonest two kmers: (None, 'TAAGGTGTAGGGACACTT') have frequency: (None, 4) k = 17 commonest two kmers: (None, 'TAAGGTGTAGGGACACT') have frequency: (None, 4) k = 16 commonest two kmers: (None, 'TAAGGTGTAGGGACAC') have frequency: (None, 5) new left sequence: CTGTGAAGAGAAAAGCC new right sequence: TAAGGTGTAGGGACAC extend contig 1 new_length:924 added_left:17 added_right:16 --------------- tmp.extend.1 start extension subiteration 0003 ---------------- map reads /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.3.1.map.map_index tmp.extend.1.3.1.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.3.1.map.map_index /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_2.fa | samtools view -bS -T tmp.extend.1.3.1.map.ref.fa - > tmp.extend.1.3.1.map.bam trying to extend left end ... all kmers: AGTTGAGTTCACTG AGTTGAGTTCACTGCCCCCCGT AGTTGAGTTC AGTTGA AGTTGAGTTCA AGTTGAGTTCACTGCCCCC AGTTGAGTTCACT AGTTGAGTTCACTGCCCCCCGTGA AGTTGAGTTCACTGCCCCCC AGTTGAGTTCAC AGTT AGTTGAGTTCACTGCCCCCCGTGAA AGTTGAGTTCACTGCCCCC AGTTGAGTTCACTGCCCCCCGT k = 25 commonest two kmers: (None, 'AGTTGAGTTCACTGCCCCCCGTGAA') have frequency: (None, 1) k = 24 commonest two kmers: (None, 'AGTTGAGTTCACTGCCCCCCGTGA') have frequency: (None, 2) k = 23 commonest two kmers: (None, 'AGTTGAGTTCACTGCCCCCCGTG') have frequency: (None, 2) k = 22 commonest two kmers: (None, 'AGTTGAGTTCACTGCCCCCCGT') have frequency: (None, 4) k = 21 commonest two kmers: (None, 'AGTTGAGTTCACTGCCCCCCG') have frequency: (None, 4) k = 20 commonest two kmers: (None, 'AGTTGAGTTCACTGCCCCCC') have frequency: (None, 5) trying to extend right end ... all kmers: TTGCCAGTCAAATAAATG TTGCCAGTCAAATAAA TTG TTGCCAGTCAAAT TTGCCAGTCAAAT TTGCCAGTCAAATA TTGC TTGCCAG TTGCCAGTCAAATAAATGCAT TTGCCAGT k = 21 commonest two kmers: (None, 'TTGCCAGTCAAATAAATGCAT') have frequency: (None, 1) k = 20 commonest two kmers: (None, 'TTGCCAGTCAAATAAATGCA') have frequency: (None, 1) k = 19 commonest two kmers: (None, 'TTGCCAGTCAAATAAATGC') have frequency: (None, 1) k = 18 commonest two kmers: (None, 'TTGCCAGTCAAATAAATG') have frequency: (None, 2) k = 17 commonest two kmers: (None, 'TTGCCAGTCAAATAAAT') have frequency: (None, 2) k = 16 commonest two kmers: (None, 'TTGCCAGTCAAATAAA') have frequency: (None, 3) k = 15 commonest two kmers: (None, 'TTGCCAGTCAAATAA') have frequency: (None, 3) k = 14 commonest two kmers: (None, 'TTGCCAGTCAAATA') have frequency: (None, 4) k = 13 commonest two kmers: (None, 'TTGCCAGTCAAAT') have frequency: (None, 6) new left sequence: CCCCCCGTCACTTGAGTTGA new right sequence: TTGCCAGTCAAAT extend contig 1 new_length:957 added_left:20 added_right:13 map reads /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.8z5l6u6d/reads.0_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.8z5l6u6d/reads.0_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.3.2.map.map_index tmp.extend.1.3.2.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.3.2.map.map_index /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.8z5l6u6d/reads.0_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.8z5l6u6d/reads.0_2.fa | samtools view -bS -T tmp.extend.1.3.2.map.ref.fa - > tmp.extend.1.3.2.map.bam trying to extend left end ... all kmers: GTGAAAGAAGCCTTGCAGTATTTT GTGAAAGAAGCCTTGCAGTATT GTGAAAGAAGCCTTGC GTGAAAG GTGAAAGAAGCCTTGCAGTA GTGAAAGAAGCC GTGAAAGAAGCCTTGCAGTATT GTGAAAGAAGCCTTGCAGTATTT GTGAAAG GTGAAAGAAGCCTTGCAGTATT GTGAAAGAAGCCTTG GTGAAAGA GTGAAAGAAGCCTTGCAG GTGAAAGAAGCC GTGAAAGAAGCCTTGCAGTATTTT GTGAAAGAAGC GTGAAAGAA GTGA GTGAA GTGAAAGAAGCCTTG GTGAAAGAAGCCTTGCAGTATT k = 24 commonest two kmers: (None, 'GTGAAAGAAGCCTTGCAGTATTTT') have frequency: (None, 2) k = 23 commonest two kmers: (None, 'GTGAAAGAAGCCTTGCAGTATTT') have frequency: (None, 3) k = 22 commonest two kmers: (None, 'GTGAAAGAAGCCTTGCAGTATT') have frequency: (None, 7) trying to extend right end ... all kmers: AAATG AAA AAATGCAT k = 8 commonest two kmers: (None, 'AAATGCAT') have frequency: (None, 1) k = 7 commonest two kmers: (None, 'AAATGCA') have frequency: (None, 1) k = 6 commonest two kmers: (None, 'AAATGC') have frequency: (None, 1) k = 5 commonest two kmers: (None, 'AAATG') have frequency: (None, 2) k = 4 commonest two kmers: (None, 'AAAT') have frequency: (None, 2) k = 3 commonest two kmers: (None, 'AAA') have frequency: (None, 3) k = 2 commonest two kmers: (None, 'AA') have frequency: (None, 3) k = 1 commonest two kmers: (None, 'A') have frequency: (None, 3) new left sequence: TTATGACGTTCCGAAGAAAGTG new right sequence: extend contig 1 new_length:979 added_left:22 added_right:0 map reads /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.8z5l6u6d/reads.1_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.8z5l6u6d/reads.1_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.3.3.map.map_index tmp.extend.1.3.3.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.3.3.map.map_index /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.8z5l6u6d/reads.1_1.fa /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.extend.8z5l6u6d/reads.1_2.fa | samtools view -bS -T tmp.extend.1.3.3.map.ref.fa - > tmp.extend.1.3.3.map.bam trying to extend left end ... all kmers: TTAT TTATATAAG TTATATAAG k = 9 commonest two kmers: (None, 'TTATATAAG') have frequency: (None, 2) k = 8 commonest two kmers: (None, 'TTATATAA') have frequency: (None, 2) k = 7 commonest two kmers: (None, 'TTATATA') have frequency: (None, 2) k = 6 commonest two kmers: (None, 'TTATAT') have frequency: (None, 2) k = 5 commonest two kmers: (None, 'TTATA') have frequency: (None, 2) k = 4 commonest two kmers: (None, 'TTAT') have frequency: (None, 3) k = 3 commonest two kmers: (None, 'TTA') have frequency: (None, 3) k = 2 commonest two kmers: (None, 'TT') have frequency: (None, 3) k = 1 commonest two kmers: (None, 'T') have frequency: (None, 3) trying to extend right end ... all kmers: AAATG AAA AAATGCAT k = 8 commonest two kmers: (None, 'AAATGCAT') have frequency: (None, 1) k = 7 commonest two kmers: (None, 'AAATGCA') have frequency: (None, 1) k = 6 commonest two kmers: (None, 'AAATGC') have frequency: (None, 1) k = 5 commonest two kmers: (None, 'AAATG') have frequency: (None, 2) k = 4 commonest two kmers: (None, 'AAAT') have frequency: (None, 2) k = 3 commonest two kmers: (None, 'AAA') have frequency: (None, 3) k = 2 commonest two kmers: (None, 'AA') have frequency: (None, 3) k = 1 commonest two kmers: (None, 'A') have frequency: (None, 3) new left sequence: new right sequence: extend contig 1 new_length:979 added_left:0 added_right:0 --------------- tmp.extend.1 start extension subiteration 0004 ---------------- map reads /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_2.fa map reads. Index: smalt index -k 15 -s 3 tmp.extend.1.4.1.map.map_index tmp.extend.1.4.1.map.ref.fa map reads. Mapping: smalt map -i 800 -y 0.5 tmp.extend.1.4.1.map.map_index /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_2.fa | samtools view -bS -T tmp.extend.1.4.1.map.ref.fa - > tmp.extend.1.4.1.map.bam trying to extend left end ... all kmers: TTAT TTATATAAG TTATATAAG k = 9 commonest two kmers: (None, 'TTATATAAG') have frequency: (None, 2) k = 8 commonest two kmers: (None, 'TTATATAA') have frequency: (None, 2) k = 7 commonest two kmers: (None, 'TTATATA') have frequency: (None, 2) k = 6 commonest two kmers: (None, 'TTATAT') have frequency: (None, 2) k = 5 commonest two kmers: (None, 'TTATA') have frequency: (None, 2) k = 4 commonest two kmers: (None, 'TTAT') have frequency: (None, 3) k = 3 commonest two kmers: (None, 'TTA') have frequency: (None, 3) k = 2 commonest two kmers: (None, 'TT') have frequency: (None, 3) k = 1 commonest two kmers: (None, 'T') have frequency: (None, 3) trying to extend right end ... all kmers: AAATG AAA AAATGCAT k = 8 commonest two kmers: (None, 'AAATGCAT') have frequency: (None, 1) k = 7 commonest two kmers: (None, 'AAATGCA') have frequency: (None, 1) k = 6 commonest two kmers: (None, 'AAATGC') have frequency: (None, 1) k = 5 commonest two kmers: (None, 'AAATG') have frequency: (None, 2) k = 4 commonest two kmers: (None, 'AAAT') have frequency: (None, 2) k = 3 commonest two kmers: (None, 'AAA') have frequency: (None, 3) k = 2 commonest two kmers: (None, 'AA') have frequency: (None, 3) k = 1 commonest two kmers: (None, 'A') have frequency: (None, 3) new left sequence: new right sequence: extend contig 1 new_length:979 added_left:0 added_right:0 No bases added. Try trimming contigs map reads /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_2.fa map reads. Index: smalt index -k 15 -s 3 /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.trim_strand_biased_ends.ojf935y1/out.map_index /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.trim_strand_biased_ends.ojf935y1/out.ref.fa map reads. Mapping: smalt map -i 800 -y 0.9 /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.trim_strand_biased_ends.ojf935y1/out.map_index /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_1.fa /<>/iva-1.0.9+ds/iva/tests/data/assembly_test_read_pair_extend.ref.reads_2.fa | samtools view -bS -T /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.trim_strand_biased_ends.ojf935y1/out.ref.fa - > /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.trim_strand_biased_ends.ojf935y1/out.unsorted.bam map reads. sort: samtools sort -@1 -m 500M /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.trim_strand_biased_ends.ojf935y1/out.unsorted.bam /<>/iva-1.0.9+ds/tmp.run_kmc.90oy2grc/tmp.trim_strand_biased_ends.ojf935y1/out --------------------- >> end captured stdout << ---------------------- ====================================================================== ERROR: test_trim_ends (contig_trim_test.TestContigTrim) Test _trim_ends ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/iva-1.0.9+ds/iva/tests/contig_trim_test.py", line 82, in test_trim_ends contig_trim._trim_ends(before_trim, tmp_out, adapters, min_length=20, min_dist_to_end=5, window_length=10, min_pc=90) File "/<>/iva-1.0.9+ds/iva/contig_trim.py", line 79, in _trim_ends mapping.map_reads(to_trim, None, fasta_in, tmp_prefix, index_k=9, index_s=1, threads=1, minid=0.75, sort=True, extra_smalt_map_ops='-d -1 -m 10') File "/<>/iva-1.0.9+ds/iva/mapping.py", line 103, in map_reads common.syscall(sort_cmd) File "/<>/iva-1.0.9+ds/iva/common.py", line 44, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test_trim_primers_and_adapters (contig_trim_test.TestContigTrim) Test trim_primers_and_adapters ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/iva-1.0.9+ds/iva/tests/contig_trim_test.py", line 94, in test_trim_primers_and_adapters contig_trim.trim_primers_and_adapters(before_trim, tmp_out, adapters, primers, min_length=20, min_dist_to_end=5, window_length=10, min_pc=90) File "/<>/iva-1.0.9+ds/iva/contig_trim.py", line 111, in trim_primers_and_adapters _trim_ends(fasta_in, fasta_out, trim_query, min_length=min_length, min_dist_to_end=min_dist_to_end, window_length=window_length, min_pc=min_pc) File "/<>/iva-1.0.9+ds/iva/contig_trim.py", line 79, in _trim_ends mapping.map_reads(to_trim, None, fasta_in, tmp_prefix, index_k=9, index_s=1, threads=1, minid=0.75, sort=True, extra_smalt_map_ops='-d -1 -m 10') File "/<>/iva-1.0.9+ds/iva/mapping.py", line 103, in map_reads common.syscall(sort_cmd) File "/<>/iva-1.0.9+ds/iva/common.py", line 44, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test_get_most_common_kmers (kcount_test.TestKcount) Test get_most_common_kmers ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/iva-1.0.9+ds/iva/tests/kcount_test.py", line 88, in test_get_most_common_kmers counts = kcount.get_most_common_kmers(reads1, reads2, kmer_length=10, head=100000, min_count=2, max_count=4, most_common=100, method='kmc') File "/<>/iva-1.0.9+ds/iva/kcount.py", line 234, in get_most_common_kmers counts_file = _run_kmc(reads, os.path.join(tmpdir, 'out'), kmer_length, min_count, max_count, verbose=verbose, threads=kmc_threads) File "/<>/iva-1.0.9+ds/iva/kcount.py", line 113, in _run_kmc ran_ok = _run_kmc_with_script('run_kmc.sh', reads, kmer_counts_file, kmer, min_count, max_count, 4, verbose, False, threads=threads) File "/<>/iva-1.0.9+ds/iva/kcount.py", line 94, in _run_kmc_with_script return common.syscall('bash ' + script, allow_fail=allow_fail) File "/<>/iva-1.0.9+ds/iva/common.py", line 44, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test_run_kmc (kcount_test.TestKcount) Test test_run_kmc ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/iva-1.0.9+ds/iva/tests/kcount_test.py", line 54, in test_run_kmc counts_file = kcount._run_kmc(reads, 'tmp.run_kmc', 10, 2, 4) File "/<>/iva-1.0.9+ds/iva/kcount.py", line 113, in _run_kmc ran_ok = _run_kmc_with_script('run_kmc.sh', reads, kmer_counts_file, kmer, min_count, max_count, 4, verbose, False, threads=threads) File "/<>/iva-1.0.9+ds/iva/kcount.py", line 94, in _run_kmc_with_script return common.syscall('bash ' + script, allow_fail=allow_fail) File "/<>/iva-1.0.9+ds/iva/common.py", line 44, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test_run_kmc_two_threads (kcount_test.TestKcount) Test test_run_kmc with two threads ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/iva-1.0.9+ds/iva/tests/kcount_test.py", line 62, in test_run_kmc_two_threads counts_file = kcount._run_kmc(reads, 'tmp.run_kmc', 10, 2, 4, threads=2) File "/<>/iva-1.0.9+ds/iva/kcount.py", line 113, in _run_kmc ran_ok = _run_kmc_with_script('run_kmc.sh', reads, kmer_counts_file, kmer, min_count, max_count, 4, verbose, False, threads=threads) File "/<>/iva-1.0.9+ds/iva/kcount.py", line 94, in _run_kmc_with_script return common.syscall('bash ' + script, allow_fail=allow_fail) File "/<>/iva-1.0.9+ds/iva/common.py", line 44, in syscall sys.exit(1) SystemExit: 1 ====================================================================== ERROR: test_map_reads_and_sort (mapping_test.TestMapping) Test mapping reads and sort BAM ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/iva-1.0.9+ds/iva/tests/mapping_test.py", line 70, in test_map_reads_and_sort mapping.map_reads(reads_prefix + '_1.fastq', reads_prefix + '_2.fastq', ref, out_prefix, sort=True, verbose=3) File "/<>/iva-1.0.9+ds/iva/mapping.py", line 103, in map_reads common.syscall(sort_cmd) File "/<>/iva-1.0.9+ds/iva/common.py", line 44, in syscall sys.exit(1) SystemExit: 1 -------------------- >> begin captured stdout << --------------------- map reads. Index: smalt index -k 15 -s 3 tmp.out.map_index /<>/iva-1.0.9+ds/iva/tests/data/mapping_test.ref.trimmed.fa map reads. Mapping: smalt map -i 1000 -y 0.5 tmp.out.map_index /<>/iva-1.0.9+ds/iva/tests/data/mapping_test.reads_1.fastq /<>/iva-1.0.9+ds/iva/tests/data/mapping_test.reads_2.fastq | samtools view -bS -T /<>/iva-1.0.9+ds/iva/tests/data/mapping_test.ref.trimmed.fa - > tmp.out.unsorted.bam map reads. sort: samtools sort -@1 -m 500M tmp.out.unsorted.bam tmp.out --------------------- >> end captured stdout << ---------------------- ====================================================================== ERROR: test_calculate_ref_read_coverage (qc_test.TestQc) test _calculate_ref_read_coverage ---------------------------------------------------------------------- Traceback (most recent call last): File "/<>/iva-1.0.9+ds/iva/tests/qc_test.py", line 602, in test_calculate_ref_read_coverage self.qc._calculate_ref_read_coverage() File "/<>/iva-1.0.9+ds/iva/qc.py", line 581, in _calculate_ref_read_coverage self._map_reads_to_reference() File "/<>/iva-1.0.9+ds/iva/qc.py", line 575, in _map_reads_to_reference iva.mapping.map_reads(self.reads_fwd, self.reads_rev, self.ref_fasta, self.ref_bam[:-4], sort=True, threads=self.threads, index_k=self.smalt_k, index_s=self.smalt_s, minid=self.smalt_id, extra_smalt_map_ops='-x') File "/<>/iva-1.0.9+ds/iva/mapping.py", line 103, in map_reads common.syscall(sort_cmd) File "/<>/iva-1.0.9+ds/iva/common.py", line 44, in syscall sys.exit(1) SystemExit: 1 ---------------------------------------------------------------------- Ran 164 tests in 15.559s FAILED (errors=9) Test failed: error: Test failed: make[1]: *** [debian/rules:44: override_dh_auto_test] Error 1 make[1]: Leaving directory '/<>/iva-1.0.9+ds' make: *** [debian/rules:13: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200212-1831 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 20064 Build-Time: 27 Distribution: focal Fail-Stage: build Host Architecture: armhf Install-Time: 88 Job: iva_1.0.9+ds-6.dsc Machine Architecture: arm64 Package: iva Package-Time: 117 Source-Version: 1.0.9+ds-6 Space: 20064 Status: attempted Version: 1.0.9+ds-6 -------------------------------------------------------------------------------- Finished at 20200212-1831 Build needed 00:01:57, 20064k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-18309792 Scanning for processes to kill in build PACKAGEBUILD-18309792