Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/i/iva/iva_1.0.9+ds-11_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/iva-1.0.9+ds-1174m1cm1x/iva_1.0.9+ds-11_amd64.buildinfo Get source package info: iva=1.0.9+ds-11 Source URL: http://snapshot.notset.fr/mr/package/iva/1.0.9+ds-11/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-13 automake=1:1.16.3-1 autopoint=0.21-3 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1-1 binutils=2.35.1-5 binutils-common=2.35.1-5 binutils-x86-64-linux-gnu=2.35.1-5 bioperl=1.7.7-2 bsdextrautils=2.36.1-3 bsdutils=1:2.36.1-3 build-essential=12.8 bzip2=1.0.8-4 ca-certificates=20200601 ca-certificates-java=20190909 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.1-1 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3 debianutils=4.11.2 default-jdk-headless=2:1.11-72 default-jre-headless=2:1.11-72 dh-autoreconf=19 dh-python=4.20201102 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13+20201015-2 fastaq=3.17.0-3 file=1:5.39-3 findutils=4.7.0+git20201010-2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.0-1 g++-10=10.2.1-1 gawk=1:5.0.1+dfsg-1 gcc=4:10.2.0-1 gcc-10=10.2.1-1 gcc-10-base=10.2.1-1 gettext=0.21-3 gettext-base=0.21-3 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 help2man=1.47.16 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 java-common=0.72 kmc=3.1.1+dfsg-1 libacl1=2.2.53-8 libalgorithm-diff-perl=1.201-1 libarchive-zip-perl=1.68-1 libasan6=10.2.1-1 libasound2=1.2.4-1 libasound2-data=1.2.4-1 libatomic1=10.2.1-1 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1+b1 libavahi-client3=0.8-3 libavahi-common-data=0.8-3 libavahi-common3=0.8-3 libbambamc0=0.0.50-4 libbinutils=2.35.1-5 libbio-perl-perl=1.7.7-2 libblas3=3.9.0-3 libblkid1=2.36.1-3 libbrotli1=1.0.9-2+b2 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-6 libc-dev-bin=2.31-6 libc6=2.31-6 libc6-dev=2.31-6 libcap-ng0=0.7.9-2.2+b1 libcapture-tiny-perl=0.48-1 libcc1-0=10.2.1-1 libclass-data-inheritable-perl=0.08-3 libcom-err2=1.45.6-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-5 libctf0=2.35.1-5 libcups2=2.3.3op1-3 libcurl3-gnutls=7.72.0-1 libdata-stag-perl=0.14-2 libdb5.3=5.3.28+dfsg1-0.6 libdbus-1-3=1.12.20-1 libdebconfclient0=0.255 libdebhelper-perl=13.3 libdeflate0=1.6-1 libdevel-stacktrace-perl=2.0400-1 libdpkg-perl=1.20.5 libelf1=0.182-1 libexception-class-perl=1.44-1 libexpat1=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.4+dfsg-1 libgcc-10-dev=10.2.1-1 libgcc-s1=10.2.1-1 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran5=10.2.1-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.0-3 libgomp1=10.2.1-1 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhogweed6=3.6-2 libhts3=1.11-2 libicu67=67.1-5 libidn2-0=2.3.0-4 libio-string-perl=1.08-3.1 libisl23=0.23-1 libitm1=10.2.1-1 libjpeg62-turbo=1:2.0.5-1.1 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack3=3.9.0-3 liblcms2-2=2.9-4+b1 libldap-2.4-2=2.4.56+dfsg-1 liblocale-gettext-perl=1.07-4+b1 liblsan0=10.2.1-1 liblz4-1=1.9.3-1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-3 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses6=6.2+20201114-1 libncursesw6=6.2+20201114-1 libnettle8=3.6-2 libnghttp2-14=1.42.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnspr4=2:4.29-1 libnss3=2:3.60-1 libp11-kit0=0.23.22-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libpcsclite1=1.9.0-1 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libpng16-16=1.6.37-3 libpsl5=0.21.0-1.1 libpython3-stdlib=3.9.0-4 libpython3.9-minimal=3.9.1-1 libpython3.9-stdlib=3.9.1-1 libquadmath0=10.2.1-1 libreadline8=8.1-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.0-3+b1 libselinux1=3.1-2+b2 libsigsegv2=2.12-3 libsmartcols1=2.36.1-3 libsqlite3-0=3.34.0-1 libssh2-1=1.9.0-2 libssl-dev=1.1.1i-1 libssl1.1=1.1.1i-1 libstdc++-10-dev=10.2.1-1 libstdc++6=10.2.1-1 libsub-override-perl=0.09-2 libsub-uplevel-perl=0.2800-1 libsystemd0=247.1-4 libtasn1-6=4.16.0-2 libtest-deep-perl=1.130-1 libtest-differences-perl=0.67-1 libtest-exception-perl=0.43-1 libtest-most-perl=0.37-1 libtest-warn-perl=0.36-1 libtext-diff-perl=1.45-1 libtinfo6=6.2+20201114-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.1-1 libubsan1=10.2.1-1 libuchardet0=0.0.7-1 libudev1=247.1-4 libunistring2=0.9.10-4 libuuid1=2.36.1-3 libx11-6=2:1.6.12-1 libx11-data=2:1.6.12-1 libxau6=1:1.0.8-1+b2 libxcb1=1.14-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1.1 libxi6=2:1.7.10-1 libxml2=2.9.10+dfsg-6.3+b1 libxrender1=1:0.9.10-1 libxtst6=2:1.2.3-1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.15-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 mailcap=3.67 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=1.0.1 mime-support=3.66 mummer=3.23+dfsg-6 ncurses-base=6.2+20201114-1 ncurses-bin=6.2+20201114-1 openjdk-11-jdk-headless=11.0.9.1+1-1 openjdk-11-jre-headless=11.0.9.1+1-1 openssl=1.1.1i-1 patch=2.7.6-6 perl=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 po-debconf=1.0.21 python3=3.9.0-4 python3-decorator=4.4.2-2 python3-distutils=3.8.6-1 python3-lib2to3=3.8.6-1 python3-minimal=3.9.0-4 python3-networkx=2.5+ds-2 python3-nose=1.3.7-7 python3-numpy=1:1.19.4-1+b1 python3-packaging=20.4-1 python3-pkg-resources=50.3.0-1 python3-pyparsing=2.4.7-1 python3-pysam=0.15.4+ds-3+b2 python3-setuptools=50.3.0-1 python3-six=1.15.0-2 python3.9=3.9.1-1 python3.9-minimal=3.9.1-1 readline-common=8.1-1 samtools=1.11-1 sed=4.7-1 sensible-utils=0.0.12+nmu1 smalt=0.7.6-9 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 tzdata=2020d-1 ucf=3.0043 util-linux=2.36.1-3 x11-common=1:7.7+21 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211009T024746Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201220T203231Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d iva=1.0.9+ds-11 && mkdir -p /build/iva-y2my4p && dpkg-source --no-check -x /*.dsc /build/iva-y2my4p/iva-1.0.9+ds && chown -R builduser:builduser /build/iva-y2my4p" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/iva-y2my4p/iva-1.0.9+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1608624761" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/iva-y2my4p /tmp/iva-1.0.9+ds-1174m1cm1x bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201220T203231Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.EFMSyBO8BQ as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.EFMSyBO8BQ Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-3). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201220T203231Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201220T203231Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (712 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4621 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-6) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211009T024746Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201220T203231Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.EFMSyBO8BQ Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201220T203231Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211009T024746Z unstable/main amd64 Packages [11.9 MB] Fetched 34.6 MB in 30s (1136 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.EFMSyBO8BQ I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d iva=1.0.9+ds-11 && mkdir -p /build/iva-y2my4p && dpkg-source --no-check -x /*.dsc /build/iva-y2my4p/iva-1.0.9+ds && chown -R builduser:builduser /build/iva-y2my4p"' exec /tmp/mmdebstrap.EFMSyBO8BQ Reading package lists... NOTICE: 'iva' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/iva.git Please use: git clone https://salsa.debian.org/med-team/iva.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 8684 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main iva 1.0.9+ds-11 (dsc) [2292 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main iva 1.0.9+ds-11 (tar) [8675 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main iva 1.0.9+ds-11 (diff) [5864 B] Fetched 8684 kB in 7s (1230 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'iva_1.0.9+ds-11.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting iva in /build/iva-y2my4p/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-11.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 dpkg-source: info: applying samtools1.10 dpkg-source: info: applying disable-ram-test.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/iva-y2my4p/iva-1.0.9+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1608624761" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.EFMSyBO8BQ dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.9+ds-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/iva-y2my4p/iva-1.0.9+ds' rm -rf .pybuild rm -f iva/gage/*.class rm -rf /build/iva-y2my4p/iva-1.0.9+ds/debian/man find . -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/build/iva-y2my4p/iva-1.0.9+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-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:232: python3.9 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 '/build/iva-y2my4p/iva-1.0.9+ds' chmod a-x /build/iva-y2my4p/iva-1.0.9+ds/iva/read_trim/adapters.fasta chmod a+x /build/iva-y2my4p/iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh chmod a+x /build/iva-y2my4p/iva-1.0.9+ds/iva/ratt/main.ratt.pl chmod a+x scripts/* javac -verbose /build/iva-y2my4p/iva-1.0.9+ds/iva/gage/*.java [parsing started SimpleFileObject[/build/iva-y2my4p/iva-1.0.9+ds/iva/gage/GetFastaStats.java]] [parsing completed 234ms] [parsing started SimpleFileObject[/build/iva-y2my4p/iva-1.0.9+ds/iva/gage/SizeFasta.java]] [parsing completed 3ms] [parsing started SimpleFileObject[/build/iva-y2my4p/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 2ms] [parsing started SimpleFileObject[/build/iva-y2my4p/iva-1.0.9+ds/iva/gage/Utils.java]] [parsing completed 82ms] [parsing started SimpleFileObject[/build/iva-y2my4p/iva-1.0.9+ds/iva/gage/getScaffoldStats.java]] [parsing completed 182ms] [loading /modules/java.rmi/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/jdk.scripting.nashorn/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/java.management/module-info.class] [loading /modules/jdk.aot/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/jdk.jshell/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/java.transaction.xa/module-info.class] [loading /modules/java.scripting/module-info.class] [loading /modules/jdk.rmic/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [loading /modules/jdk.internal.jvmstat/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/java.base/module-info.class] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/jdk.sctp/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/java.security.sasl/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [loading 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/modules/jdk.jdi/module-info.class] [loading /modules/jdk.hotspot.agent/module-info.class] [loading /modules/java.xml/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/java.net.http/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/jdk.javadoc/module-info.class] [loading /modules/jdk.scripting.nashorn.shell/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/jdk.internal.vm.compiler.management/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/jdk.compiler/module-info.class] [loading /modules/jdk.naming.ldap/module-info.class] [loading /modules/java.instrument/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/jdk.internal.vm.ci/module-info.class] [loading /modules/jdk.security.auth/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/jdk.jstatd/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-11-openjdk-amd64/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 /build/iva-y2my4p/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$Lookup.class] [loading /modules/java.base/java/lang/invoke/MethodType.class] [loading /modules/java.base/java/io/InputStream.class] [loading /modules/java.base/java/lang/invoke/CallSite.class] [wrote /build/iva-y2my4p/iva-1.0.9+ds/iva/gage/GetFastaStats.class] [checking SizeFasta] [wrote /build/iva-y2my4p/iva-1.0.9+ds/iva/gage/SizeFasta.class] [checking SplitFastaByLetter] [wrote /build/iva-y2my4p/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.class] [checking Utils] [loading /modules/java.base/java/lang/CloneNotSupportedException.class] [loading /modules/java.base/java/lang/Class.class] [loading /modules/java.base/java/net/URI.class] [loading /modules/java.base/java/lang/Process.class] [loading /modules/java.base/java/lang/Runtime.class] [loading /modules/java.base/java/lang/StringBuilder.class] [loading /modules/java.base/java/lang/reflect/GenericDeclaration.class] [loading /modules/java.base/java/lang/reflect/AnnotatedElement.class] [loading /modules/java.base/java/lang/reflect/Type.class] [loading /modules/java.base/java/lang/AssertionError.class] [wrote /build/iva-y2my4p/iva-1.0.9+ds/iva/gage/Utils$Pair.class] [wrote /build/iva-y2my4p/iva-1.0.9+ds/iva/gage/Utils$Translate.class] [wrote /build/iva-y2my4p/iva-1.0.9+ds/iva/gage/Utils$ToProtein.class] [wrote /build/iva-y2my4p/iva-1.0.9+ds/iva/gage/Utils.class] [checking getScaffoldStats] [wrote /build/iva-y2my4p/iva-1.0.9+ds/iva/gage/getScaffoldStats$Scaffold.class] [wrote /build/iva-y2my4p/iva-1.0.9+ds/iva/gage/getScaffoldStats.class] [total 12351ms] dh_auto_build -- I: pybuild base:232: /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 /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/mapping.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/contig_trim.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/qc.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/__init__.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/assembly.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/test_data_runner.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/graph.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/edge.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/seed.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/common.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/kcount.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/external_progs.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/qc_external.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/contig.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/seed_processor.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/read_trim.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/mummer.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/kmers.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/kraken.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/egg_extract.py -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva creating /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils.class -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/SizeFasta.java -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/GetFastaStats.java -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/colsum.pl -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils.java -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/getScaffoldStats.java -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage creating /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/ratt.config -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt creating /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim creating /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/reads_1.fq.gz -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.9 copying and adjusting scripts/iva -> build/scripts-3.9 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.9 copying and adjusting scripts/iva_qc -> build/scripts-3.9 changing mode of build/scripts-3.9/iva from 644 to 755 changing mode of build/scripts-3.9/iva_qc_make_db from 644 to 755 changing mode of build/scripts-3.9/iva_qc from 644 to 755 make[1]: Leaving directory '/build/iva-y2my4p/iva-1.0.9+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/iva-y2my4p/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 /build/iva-y2my4p/iva-1.0.9+ds/iva/mapping.py:159: DeprecationWarning: invalid escape sequence \^ s = re.sub('\^.', '', s) /build/iva-y2my4p/iva-1.0.9+ds/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence \( 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), /build/iva-y2my4p/iva-1.0.9+ds/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence \( 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), /build/iva-y2my4p/iva-1.0.9+ds/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence \( 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), /build/iva-y2my4p/iva-1.0.9+ds/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence \( 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), /build/iva-y2my4p/iva-1.0.9+ds/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence \d 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), /build/iva-y2my4p/iva-1.0.9+ds/iva/kraken.py:360: DeprecationWarning: invalid escape sequence \. self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') /build/iva-y2my4p/iva-1.0.9+ds/iva/kraken.py:415: DeprecationWarning: invalid escape sequence \W return re.sub('\W', '_', s).strip('_') 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 '/build/iva-y2my4p/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 '/build/iva-y2my4p/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 '/build/iva-y2my4p/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 '/build/iva-y2my4p/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.1.4.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/iva-y2my4p/iva-1.0.9+ds/tmp.filter_reads.z7lzwvi5/out.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.5.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/iva-y2my4p/iva-1.0.9+ds/tmp.trim_strand_biased_ends.2p0es5dm/out.unsorted.bam' ok 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 ... ok test_trim_primers_and_adapters (contig_trim_test.TestContigTrim) Test trim_primers_and_adapters ... ok 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_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_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 '/build/iva-y2my4p/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 '/build/iva-y2my4p/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 '/build/iva-y2my4p/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 '/build/iva-y2my4p/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 '/build/iva-y2my4p/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 ... ok 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 '/build/iva-y2my4p/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 '/build/iva-y2my4p/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 '/build/iva-y2my4p/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 '/build/iva-y2my4p/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 ... ok 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 ---------------------------------------------------------------------- Ran 160 tests in 15.987s OK make[1]: Leaving directory '/build/iva-y2my4p/iva-1.0.9+ds' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/iva-y2my4p/iva-1.0.9+ds/debian/iva Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running install running build running build_py running build_scripts running install_lib creating /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr creating /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib creating /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9 creating /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages creating /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva creating /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reference.fasta -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reads_1.fq.gz -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reads_2.fq.gz -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/mapping.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/contig_trim.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/qc.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/__init__.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/assembly.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_data_runner.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/graph.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/edge.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/seed.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/common.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva creating /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt_correction.pm -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/start.ratt.sh -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/embl2gff.pl -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/main.ratt.pl -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt.config -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt.config.hiv -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/genbank2embl.pl -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kcount.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/external_progs.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva creating /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SplitFastaByLetter.java -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getMummerStats.sh -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$Pair.class -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils.class -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SplitFastaByLetter.class -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$Translate.class -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SizeFasta.java -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getCorrectnessStats.sh -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats.java -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats.class -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats.class -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/colsum.pl -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SizeFasta.class -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils.java -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$ToProtein.class -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats.java -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/qc_external.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/contig.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/seed_processor.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva creating /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim/adapters.fasta -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/mummer.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kmers.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kraken.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-y2my4p/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/egg_extract.py -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/mapping.py to mapping.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/contig_trim.py to contig_trim.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/qc.py to qc.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/__init__.py to __init__.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/assembly.py to assembly.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/graph.py to graph.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/edge.py to edge.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/seed.py to seed.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/common.py to common.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kcount.py to kcount.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/external_progs.py to external_progs.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/qc_external.py to qc_external.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/contig.py to contig.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/seed_processor.py to seed_processor.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim.py to read_trim.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/mummer.py to mummer.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kmers.py to kmers.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kraken.py to kraken.cpython-39.pyc byte-compiling /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/egg_extract.py to egg_extract.cpython-39.pyc running install_egg_info running 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 reading manifest file 'iva.egg-info/SOURCES.txt' writing manifest file 'iva.egg-info/SOURCES.txt' Copying iva.egg-info to /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva-1.0.9.egg-info Skipping SOURCES.txt running install_scripts creating /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.9/iva -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.9/iva_qc_make_db -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.9/iva_qc -> /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/bin changing mode of /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/bin/iva to 755 changing mode of /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc_make_db to 755 changing mode of /build/iva-y2my4p/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc to 755 dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/iva-y2my4p/iva-1.0.9+ds' mkdir -p /build/iva-y2my4p/iva-1.0.9+ds/debian/man PYTHONPATH=. help2man -N -o /build/iva-y2my4p/iva-1.0.9+ds/debian/man/iva.1 \ -n 'iterative virus assembler' \ --no-discard-stderr ./scripts/iva PYTHONPATH=. help2man -N -o /build/iva-y2my4p/iva-1.0.9+ds/debian/man/iva_qc.1 \ -n 'compare an assembly to a reference' \ --no-discard-stderr ./scripts/iva_qc PYTHONPATH=. help2man -N -o /build/iva-y2my4p/iva-1.0.9+ds/debian/man/iva_qc_make_db.1 \ -n 'make a database as input for iva_qc' \ --no-discard-stderr ./scripts/iva_qc_make_db dh_installman -- make[1]: Leaving directory '/build/iva-y2my4p/iva-1.0.9+ds' dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -a -O--buildsystem=pybuild dh_strip -a -a -O--buildsystem=pybuild dh_makeshlibs -a -a -O--buildsystem=pybuild dh_shlibdeps -a -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'iva' in '../iva_1.0.9+ds-11_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../iva_1.0.9+ds-11_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/iva-y2my4p /tmp/iva-1.0.9+ds-1174m1cm1x I: cleaning package lists and apt cache... W: deleting files in /tmp: hsperfdata_builduser W: deleting files in /tmp: hsperfdata_root I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.EFMSyBO8BQ... I: success in 860.4741 seconds md5: iva_1.0.9+ds-11_amd64.deb: OK sha1: iva_1.0.9+ds-11_amd64.deb: OK sha256: iva_1.0.9+ds-11_amd64.deb: OK Checksums: OK