Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/u/unicycler/unicycler_0.4.8+dfsg-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/unicycler-0.4.8+dfsg-27w67xlxr/unicycler_0.4.8+dfsg-2_amd64.buildinfo Get source package info: unicycler=0.4.8+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/unicycler/0.4.8+dfsg-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=ant=1.10.7-1 ant-optional=1.10.7-1 autoconf=2.69-11 automake=1:1.16.1-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 bamtools=2.5.1+dfsg-3 base-files=11 base-passwd=3.5.46 bash=5.0-5 bcftools=1.9-1 binutils=2.33.1-4 binutils-common=2.33.1-4 binutils-x86-64-linux-gnu=2.33.1-4 bowtie2=2.3.5.1-1 bsdmainutils=11.1.2+b1 bsdutils=1:2.34-0.1 build-essential=12.8 bwa=0.7.17-3 bzip2=1.0.8-2 ca-certificates=20190110 ca-certificates-java=20190909 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.2.1-21 dash=0.5.10.2-6 debconf=1.5.73 debhelper=12.7.1 debianutils=4.9 default-jdk=2:1.11-72 default-jdk-headless=2:1.11-72 default-jre=2:1.11-72 default-jre-headless=2:1.11-72 dh-autoreconf=19 dh-python=4.20191017 dh-strip-nondeterminism=1.6.3-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-4 fdisk=2.34-0.1 file=1:5.37-6 findutils=4.7.0-1 fontconfig-config=2.13.1-2 fonts-dejavu-core=2.37-1 g++=4:9.2.1-3.1 g++-9=9.2.1-21 gcc=4:9.2.1-3.1 gcc-9=9.2.1-21 gcc-9-base=9.2.1-21 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.3-1 groff-base=1.22.4-3 gzip=1.9-3+b1 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 java-common=0.72 java-wrappers=0.3 libacl1=2.2.53-5 libactivation-java=1.2.0-2 libaopalliance-java=20070526-6 libapache-pom-java=18-1 libarchive-zip-perl=1.67-1 libargs4j-java=2.33-1 libasan5=9.2.1-21 libasound2=1.1.9-1 libasound2-data=1.1.9-1 libatinject-jsr330-api-java=1.0+ds1-5 libatomic1=9.2.1-21 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-2 libaudit1=1:2.8.5-2+b1 libavahi-client3=0.7-4+b1 libavahi-common-data=0.7-4+b1 libavahi-common3=0.7-4+b1 libbamtools2.5.1=2.5.1+dfsg-3 libbinutils=2.33.1-4 libblkid1=2.34-0.1 libbrotli1=1.0.7-5+b1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.29-3 libc-dev-bin=2.29-3 libc6=2.29-3 libc6-dev=2.29-3 libcap-ng0=0.7.9-2.1+b1 libcc1-0=9.2.1-21 libcdi-api-java=1.2-2 libcodemodel-java=2.6+jaxb2.3.0.1-9 libcom-err2=1.45.4-1 libcommons-cli-java=1.4-1 libcommons-codec-java=1.11-1 libcommons-compress-java=1.18-3 libcommons-io-java=2.6-2 libcommons-jexl2-java=2.1.1-4 libcommons-lang-java=2.6-9 libcommons-lang3-java=3.8-2 libcommons-logging-java=1.2-2 libcommons-parent-java=43-1 libcroco3=0.6.13-1 libcups2=2.3.0-7 libcurl3-gnutls=7.67.0-2 libdb5.3=5.3.28+dfsg1-0.6 libdbus-1-3=1.12.16-2 libdebconfclient0=0.250 libdebhelper-perl=12.7.1 libdeflate0=1.3-3 libdom4j-java=2.1.1-2 libdpkg-perl=1.19.7 libdrm-amdgpu1=2.4.100-4 libdrm-common=2.4.100-4 libdrm-intel1=2.4.100-4 libdrm-nouveau2=2.4.100-4 libdrm-radeon1=2.4.100-4 libdrm2=2.4.100-4 libdtd-parser-java=1.2~svn20110404-1 libedit2=3.1-20191025-1 libedlib0=1.2.4-2+b1 libelf1=0.176-1.1 libexpat1=2.2.9-1 libfastinfoset-java=1.2.12-3 libfdisk1=2.34-0.1 libffi6=3.2.1-9 libfile-stripnondeterminism-perl=1.6.3-1 libfontconfig1=2.13.1-2+b1 libfreetype6=2.10.1-2 libgcc-9-dev=9.2.1-21 libgcc1=1:9.2.1-21 libgcrypt20=1.8.5-3 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libgeronimo-annotation-1.3-spec-java=1.0-1 libgeronimo-interceptor-3.0-spec-java=1.0.1-4 libgif7=5.1.4-3 libgl1=1.1.0-1+b1 libgl1-mesa-dri=19.2.6-1 libglapi-mesa=19.2.6-1 libglib2.0-0=2.62.3-2 libglvnd0=1.1.0-1+b1 libglx-mesa0=19.2.6-1 libglx0=1.1.0-1+b1 libgmp10=2:6.1.2+dfsg-4 libgnutls30=3.6.10-5 libgomp1=9.2.1-21 libgpg-error0=1.36-7 libgssapi-krb5-2=1.17-6 libguava-java=19.0-1 libguice-java=4.2.1-1 libhat-trie0=0.1.2-2 libhogweed5=3.5.1+really3.5.1-2 libhts2=1.9-11 libhtsjdk-java=2.18.2+dfsg-2 libhttpclient-java=4.5.10-2 libhttpcore-java=4.4.12-1 libicu63=63.2-2 libidn2-0=2.2.0-2 libisl22=0.22-2 libistack-commons-java=3.0.6-4 libitm1=9.2.1-21 libjaxb-api-java=2.3.1-1 libjaxb-java=2.3.0.1-9 libjaxen-java=1.1.6-4 libjpeg62-turbo=1:1.5.2-2+b1 libjsoncpp1=1.7.4-3+b1 libjsoup-java=1.10.2-2 libjsr305-java=0.1~+svn49-11 libk5crypto3=1.17-6 libkeyutils1=1.6-6 libkrb5-3=1.17-6 libkrb5support0=1.17-6 liblcms2-2=2.9-4 libldap-2.4-2=2.4.48+dfsg-1+b2 libldap-common=2.4.48+dfsg-1 libllvm9=1:9.0.0-4 liblmdb0=0.9.22-1 liblsan0=9.2.1-21 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.37-6 libmagic1=1:5.37-6 libmaven-file-management-java=3.0.0-1 libmaven-parent-java=31-2 libmaven-resolver-java=1.4.1-1 libmaven-shared-io-java=3.0.0-3 libmaven-shared-utils-java=3.3.0-1 libmaven3-core-java=3.6.2-1 libmbedcrypto3=2.16.3-1 libmbedtls12=2.16.3-1 libmbedx509-0=2.16.3-1 libmount1=2.34-0.1 libmpc3=1.1.0-1 libmpdec2=2.4.2-2 libmpfr6=4.0.2-1 libncurses6=6.1+20191019-1 libncursesw6=6.1+20191019-1 libnettle7=3.5.1+really3.5.1-2 libnghttp2-14=1.40.0-1 libngs-java=2.10.0-2 libngs-sdk-dev=2.10.0-2 libngs-sdk2=2.10.0-2 libnlopt0=2.6.1-7 libnspr4=2:4.23-1 libnss3=2:3.47.1-1 libp11-kit0=0.23.18.1-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpciaccess0=0.14-1 libpcre2-8-0=10.34-1 libpcre3=2:8.39-12+b1 libpcsclite1=1.8.25-3 libperl5.30=5.30.0-9 libpipeline1=1.5.1-2 libplexus-archiver-java=3.6.0-2 libplexus-cipher-java=1.7-3 libplexus-classworlds-java=2.6.0-1 libplexus-component-annotations-java=2.0.0-1 libplexus-interpolation-java=1.26-1 libplexus-io-java=3.1.1-1 libplexus-sec-dispatcher-java=1.4-4 libplexus-utils2-java=3.2.1-1 libpng16-16=1.6.37-1 libprocps7=2:3.3.15-2+b1 libpsl5=0.20.2-2 libpython3-stdlib=3.7.5-3 libpython3.7-minimal=3.7.5-2 libpython3.7-stdlib=3.7.5-2 libpython3.8-minimal=3.8.0-5 libpython3.8-stdlib=3.8.0-5 libquadmath0=9.2.1-21 libreadline8=8.0-3 librelaxng-datatype-java=1.0+ds1-3 librngom-java=2.3.0.1-9 librtmp1=2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2=2.1.27+dfsg-1 libsasl2-modules-db=2.1.27+dfsg-1 libseccomp2=2.4.2-2 libselinux1=2.9-3+b1 libsensors-config=1:3.6.0-2 libsensors5=1:3.6.0-2 libseqan2-dev=2.4.0+dfsg-11 libsigsegv2=2.12-2 libsisu-guice-java=4.2.0-1 libsisu-inject-java=0.3.3-1 libsisu-ioc-java=2.3.0-11 libsisu-plexus-java=0.3.3-3 libslf4j-java=1.7.25-3 libsmartcols1=2.34-0.1 libsnappy-java=1.1.7.2-1 libsnappy-jni=1.1.7.2-1 libsnappy1v5=1.1.7-1+b1 libspoa3=3.0.1-1 libsqlite3-0=3.30.1-1 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1d-2 libssw0=1.1-4 libstax-ex-java=1.7.8-3 libstdc++-9-dev=9.2.1-21 libstdc++6=9.2.1-21 libstreambuffer-java=1.5.4-1 libsub-override-perl=0.09-2 libsystemd0=243-9 libtasn1-6=4.15.0-2 libtbb2=2019~U9-2 libthread-pool0=2.0.1-4 libtinfo6=6.1+20191019-1 libtool=2.4.6-11 libtsan0=9.2.1-21 libtxw2-java=2.3.0.1-9 libubsan1=9.2.1-21 libuchardet0=0.0.6-3 libudev1=243-9 libunistring2=0.9.10-2 libuuid1=2.34-0.1 libwagon-http-java=3.3.3-1 libwagon-provider-api-java=3.3.3-1 libx11-6=2:1.6.8-1 libx11-data=2:1.6.8-1 libx11-xcb1=2:1.6.8-1 libxau6=1:1.0.8-1+b2 libxcb-dri2-0=1.13.1-2 libxcb-dri3-0=1.13.1-2 libxcb-glx0=1.13.1-2 libxcb-present0=1.13.1-2 libxcb-sync1=1.13.1-2 libxcb1=1.13.1-2 libxdamage1=1:1.1.5-1 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1+b2 libxfixes3=1:5.0.3-1 libxi6=2:1.7.9-1 libxml-commons-resolver1.1-java=1.2-9 libxml2=2.9.4+dfsg1-8 libxrender1=1:0.9.10-1 libxshmfence1=1.3-1 libxsom-java=2.3.0.1-9 libxtst6=2:1.2.3-1 libxxf86vm1=1:1.1.4-1+b2 libxz-java=1.8-2 libyaml-0-2=0.2.2-1 libz3-4=4.8.6-2+b2 linux-libc-dev=5.3.9-3 login=1:4.7-2 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-1.2 man-db=2.9.0-1 mawk=1.3.3-17+b3 mime-support=3.64 miniasm=0.3+dfsg-1 ncbi-blast+=2.9.0-2 ncbi-data=6.1.20170106+dfsg1-7 ncurses-base=6.1+20191019-1 ncurses-bin=6.1+20191019-1 openjdk-11-jdk=11.0.5+10-2 openjdk-11-jdk-headless=11.0.5+10-2 openjdk-11-jre=11.0.5+10-2 openjdk-11-jre-headless=11.0.5+10-2 openssl=1.1.1d-2 patch=2.7.6-6 perl=5.30.0-9 perl-base=5.30.0-9 perl-modules-5.30=5.30.0-9 pilon=1.23+dfsg-1 po-debconf=1.0.21 procps=2:3.3.15-2+b1 python3=3.7.5-3 python3-all=3.7.5-3 python3-distutils=3.8.0-1 python3-joblib=0.14.0-2 python3-lib2to3=3.8.0-1 python3-minimal=3.7.5-3 python3-pkg-resources=41.4.0-1 python3-setuptools=41.4.0-1 python3-yaml=5.1.2-1+b1 python3.7=3.7.5-2 python3.7-minimal=3.7.5-2 python3.8=3.8.0-5 python3.8-minimal=3.8.0-5 racon=1.4.10-1 readline-common=8.0-3 samtools=1.9-6 scala-library=2.11.12-4 sed=4.7-1 sensible-utils=0.0.12+nmu1 spades=3.13.1+dfsg-2 sysvinit-utils=2.96-1 tar=1.30+dfsg-6+b1 ucf=3.0038+nmu1 unzip=6.0-25 util-linux=2.34-0.1 x11-common=1:7.7+20 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-1+b1 zlib1g-dev=1:1.2.11.dfsg-1+b1 --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/20191208T210426Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20191202T160249Z/ 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 unicycler=0.4.8+dfsg-2 && mkdir -p /build/unicycler-17lkbA && dpkg-source --no-check -x /*.dsc /build/unicycler-17lkbA/unicycler-0.4.8+dfsg && chown -R builduser:builduser /build/unicycler-17lkbA" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/unicycler-17lkbA/unicycler-0.4.8+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1575447738" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/unicycler-17lkbA /tmp/unicycler-0.4.8+dfsg-27w67xlxr bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20191202T160249Z 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.MdeOfvp8d8 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.MdeOfvp8d8 Reading package lists... Building dependency tree... util-linux is already the newest version (2.34-0.1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20191202T160249Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20191202T160249Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (1122 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 ... 4507 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.29-3) ... 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/20191208T210426Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20191202T160249Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.MdeOfvp8d8 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20191208T210426Z unstable InRelease [142 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20191202T160249Z 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/20191208T210426Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20191208T210426Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20191208T210426Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20191208T210426Z unstable/main amd64 Packages [11.0 MB] Fetched 33.7 MB in 31s (1078 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.MdeOfvp8d8 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d unicycler=0.4.8+dfsg-2 && mkdir -p /build/unicycler-17lkbA && dpkg-source --no-check -x /*.dsc /build/unicycler-17lkbA/unicycler-0.4.8+dfsg && chown -R builduser:builduser /build/unicycler-17lkbA"' exec /tmp/mmdebstrap.MdeOfvp8d8 Reading package lists... NOTICE: 'unicycler' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/unicycler.git Please use: git clone https://salsa.debian.org/med-team/unicycler.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 14.7 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main unicycler 0.4.8+dfsg-2 (dsc) [2294 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main unicycler 0.4.8+dfsg-2 (tar) [14.6 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main unicycler 0.4.8+dfsg-2 (diff) [11.6 kB] Fetched 14.7 MB in 12s (1242 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'unicycler_0.4.8+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting unicycler in /build/unicycler-17lkbA/unicycler-0.4.8+dfsg dpkg-source: info: unpacking unicycler_0.4.8+dfsg.orig.tar.xz dpkg-source: info: unpacking unicycler_0.4.8+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spades.patch dpkg-source: info: applying install_wo_extra_steps.patch dpkg-source: info: applying append_flags I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/unicycler-17lkbA/unicycler-0.4.8+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1575447738" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.MdeOfvp8d8 dpkg-buildpackage: info: source package unicycler dpkg-buildpackage: info: source version 0.4.8+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' find . -name __pycache__ -type d | xargs rm -rf make distclean make[2]: Entering directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' Platform: Linux Compiler: g++ 9.2.1 rm -f unicycler/src/scoredalignment.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/asm.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/dotter.o unicycler/src/consensus_align.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/minimap_align.o unicycler/src/miniasm_assembly.o unicycler/src/start_end_align.o unicycler/src/string_functions.o unicycler/src/semi_global_align.o unicycler/src/random_alignments.o unicycler/src/global_align.o unicycler/src/overlap_align.o unicycler/src/scrub.o unicycler/src/ref_seqs.o unicycler/src/minimap/sdust.o unicycler/src/minimap/bseq.o unicycler/src/minimap/index.o unicycler/src/minimap/misc.o unicycler/src/minimap/kthread.o unicycler/src/minimap/sketch.o unicycler/src/minimap/map.o unicycler/src/kmers.o unicycler/src/path_align.o rm -f unicycler/cpp_functions.so make[2]: Leaving directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' make[1]: Leaving directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' 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: python3.8 setup.py config running config I: pybuild base:217: python3.7 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' make make[2]: Entering directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' Platform: Linux Compiler: g++ 9.2.1 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/scoredalignment.o unicycler/src/scoredalignment.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/asg.o unicycler/src/miniasm/asg.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/hit.o unicycler/src/miniasm/hit.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sdict.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/sys.o unicycler/src/miniasm/sys.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/asm.o unicycler/src/miniasm/asm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/paf.o unicycler/src/miniasm/paf.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm/dotter.o unicycler/src/miniasm/dotter.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/consensus_align.o unicycler/src/consensus_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/semi_global_align_exhaustive.o unicycler/src/semi_global_align_exhaustive.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap_align.o unicycler/src/minimap_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/miniasm_assembly.o unicycler/src/miniasm_assembly.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/start_end_align.o unicycler/src/start_end_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/string_functions.o unicycler/src/string_functions.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/semi_global_align.o unicycler/src/semi_global_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/random_alignments.o unicycler/src/random_alignments.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/global_align.o unicycler/src/global_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/overlap_align.o unicycler/src/overlap_align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/scrub.o unicycler/src/scrub.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/ref_seqs.o unicycler/src/ref_seqs.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/sdust.o unicycler/src/minimap/sdust.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/bseq.o unicycler/src/minimap/bseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/index.o unicycler/src/minimap/index.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/misc.o unicycler/src/minimap/misc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/kthread.o unicycler/src/minimap/kthread.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/sketch.o unicycler/src/minimap/sketch.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/minimap/map.o unicycler/src/minimap/map.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/kmers.o unicycler/src/kmers.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unicycler/src/path_align.o unicycler/src/path_align.cpp g++ -std=c++14 -Iunicycler/include -fPIC -lrt -lpthread -O3 -DNDEBUG -g -O2 -fdebug-prefix-map=/build/unicycler-17lkbA/unicycler-0.4.8+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-soname,unicycler/cpp_functions.so -o unicycler/cpp_functions.so unicycler/src/scoredalignment.o unicycler/src/miniasm/asg.o unicycler/src/miniasm/hit.o unicycler/src/miniasm/sdict.o unicycler/src/miniasm/sys.o unicycler/src/miniasm/asm.o unicycler/src/miniasm/paf.o unicycler/src/miniasm/dotter.o unicycler/src/consensus_align.o unicycler/src/semi_global_align_exhaustive.o unicycler/src/minimap_align.o unicycler/src/miniasm_assembly.o unicycler/src/start_end_align.o unicycler/src/string_functions.o unicycler/src/semi_global_align.o unicycler/src/random_alignments.o unicycler/src/global_align.o unicycler/src/overlap_align.o unicycler/src/scrub.o unicycler/src/ref_seqs.o unicycler/src/minimap/sdust.o unicycler/src/minimap/bseq.o unicycler/src/minimap/index.o unicycler/src/minimap/misc.o unicycler/src/minimap/kthread.o unicycler/src/minimap/sketch.o unicycler/src/minimap/map.o unicycler/src/kmers.o unicycler/src/path_align.o -Wl,-z,relro -Wl,-z,now -shared -lz make[2]: Leaving directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' dh_auto_build I: pybuild base:217: /usr/bin/python3.8 setup.py build running build running build_py creating /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/bridge_long_read_simple.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/blast_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/unicycler_scrub.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/bridge_long_read.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/log.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/unicycler_align.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/__init__.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/misc.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/assembly_graph_segment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/string_graph.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/bridge_spades_contig.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/path_finding.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/cpp_wrappers.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/alignment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/miniasm_assembly.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/unicycler_check.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/assembly_graph.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/vcf_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/settings.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/unicycler_polish.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/unicycler.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/minimap_alignment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/read_ref.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/bridge_miniasm.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/bridge_common.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/spades_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/bridge_loop_unroll.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/version.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/pilon_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler copying unicycler/assembly_graph_copy_depth.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_long_read_simple.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/blast_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/unicycler_scrub.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_long_read.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/log.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/unicycler_align.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/__init__.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/misc.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/assembly_graph_segment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/string_graph.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_spades_contig.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/path_finding.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/cpp_wrappers.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/alignment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/miniasm_assembly.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/unicycler_check.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/assembly_graph.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/vcf_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/settings.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/unicycler_polish.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/unicycler.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/minimap_alignment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/read_ref.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_miniasm.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_common.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/spades_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/bridge_loop_unroll.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/version.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/pilon_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler copying unicycler/assembly_graph_copy_depth.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler make[1]: Leaving directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' dh_auto_test -a -O--buildsystem=pybuild I: pybuild pybuild:272: cp -a unicycler-runner.py /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build; cp -a unicycler/cpp_functions.so /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler; cp -a sample_data /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build I: pybuild base:217: cd /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build; python3.8 -m unittest discover -v test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_filter_by_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_all_gfa_link_lines (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_estimated_sequence_len (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_n_segment_length (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_load_spades_paths (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_remove_all_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_remove_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_specific_segments_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_to_fasta_length (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_to_gfa (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_add_link_1 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_add_link_2 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_all_segments_below_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_bad_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_dead_end_change_if_deleted (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_dead_end_change_if_path_deleted (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_filter_homopolymer_loops (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_connected_components_and_remove_link (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_connected_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_exclusive_inputs (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_exclusive_outputs (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_mean_path_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_next_available_seg_number (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_path_sequence (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_simple_path (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_lead_exclusively_from (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_lead_exclusively_to (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_all_possible (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_simple_path_1 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_simple_path_2 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_simple_path_3 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_remove_small_dead_ends (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_seq_from_signed_seg_num (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_expand_repeats_1 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_2 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_3 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_4 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_5 (test.test_assembly_graph.TestExpandRepeats) ... ok test_graph (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_1 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_10 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_11 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_2 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_3 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_4 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_5 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_6 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_7 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_8 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_9 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_graph (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_1 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_2 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_3 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_4 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_5 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_6 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_merge_1 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_merge_split_1 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_merge_split_2 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_single_copy_segments_1 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_single_copy_segments_2 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_random_seq_no_start_gene (test.test_blast_func.TestBlastFunc) ... ok test_random_seq_with_exact_gene_forward_strand (test.test_blast_func.TestBlastFunc) ... ok test_random_seq_with_exact_gene_reverse_strand (test.test_blast_func.TestBlastFunc) ... ok test_1bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_1bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_2bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_2bp_insertion_and_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_long_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_one_mismatch (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_random_seqs (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_shift_big_band (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_shift_small_band (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_consensus_different_qualities (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_all (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_deletions_and_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_subs (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_start_end_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_start_end_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_start_end_insertions_and_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_two_way_consensus (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_bad_pilon (test.test_dependencies.TestDependencies) ... ok test_bowtie2_build_not_found (test.test_dependencies.TestDependencies) ... ok test_bowtie2_not_found (test.test_dependencies.TestDependencies) ... ok test_java_not_found (test.test_dependencies.TestDependencies) ... ok test_makeblastdb_not_found (test.test_dependencies.TestDependencies) ... ok test_no_pilon (test.test_dependencies.TestDependencies) ... ok test_no_rotate (test.test_dependencies.TestDependencies) ... ok test_pilon_not_found (test.test_dependencies.TestDependencies) ... ok test_samtools_not_found (test.test_dependencies.TestDependencies) ... ok test_spades_not_found (test.test_dependencies.TestDependencies) ... ok test_tblastn_not_found (test.test_dependencies.TestDependencies) ... ok test_verbosity_1 (test.test_dependencies.TestDependencies) ... ok test_verbosity_2 (test.test_dependencies.TestDependencies) ... ok test_basic_options (test.test_help_text.TestBasicHelpText) ... ok test_extended_options (test.test_help_text.TestBasicHelpText) ... ok test_output (test.test_help_text.TestBasicHelpText) ... ok test_return_code (test.test_help_text.TestBasicHelpText) ... ok test_title (test.test_help_text.TestBasicHelpText) ... ok test_error_message (test.test_help_text.TestEmptyCommand) ... ok test_output (test.test_help_text.TestEmptyCommand) ... ok test_return_code (test.test_help_text.TestEmptyCommand) ... ok test_basic_options (test.test_help_text.TestExtendedHelpText) ... ok test_extended_options (test.test_help_text.TestExtendedHelpText) ... ok test_output (test.test_help_text.TestExtendedHelpText) ... ok test_return_code (test.test_help_text.TestExtendedHelpText) ... ok test_title (test.test_help_text.TestExtendedHelpText) ... ok test_contig_placement_1 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_contig_placement_2 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_contig_placement_3 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_contig_placement_4 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_add_line_breaks_to_sequence (test.test_misc.TestMiscFunctions) ... ok test_colour (test.test_misc.TestMiscFunctions) ... ok test_convert_fastq_to_fasta (test.test_misc.TestMiscFunctions) ... ok test_flip_number_order (test.test_misc.TestMiscFunctions) ... ok test_float_to_str (test.test_misc.TestMiscFunctions) ... ok test_get_all_files_in_current_dir (test.test_misc.TestMiscFunctions) ... ok test_get_compression_type (test.test_misc.TestMiscFunctions) ... ok test_get_nice_header (test.test_misc.TestMiscFunctions) ... ok test_get_num_agreement (test.test_misc.TestMiscFunctions) ... ok test_get_percentile (test.test_misc.TestMiscFunctions) ... ok test_get_random_base (test.test_misc.TestMiscFunctions) ... ok test_get_random_sequence (test.test_misc.TestMiscFunctions) ... ok test_get_sequence_file_type (test.test_misc.TestMiscFunctions) ... ok test_int_to_str (test.test_misc.TestMiscFunctions) ... ok test_is_header_spades_format (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_1 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_2 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_3 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_4 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_5 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_6 (test.test_misc.TestMiscFunctions) ... ok test_len_without_format (test.test_misc.TestMiscFunctions) ... ok test_load_fasta (test.test_misc.TestMiscFunctions) ... ok test_load_fasta_with_full_header (test.test_misc.TestMiscFunctions) ... ok test_remove_formatting (test.test_misc.TestMiscFunctions) ... ok test_reverse_complement (test.test_misc.TestMiscFunctions) ... ok test_round_to_nearest_odd (test.test_misc.TestMiscFunctions) ... ok test_score_function (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_1 (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_2 (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_3 (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_4 (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_capitals (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fa (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fasta (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fastq (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fastq_extra_dots (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fna (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fq (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_other_fasta (test.test_misc.TestMiscFunctions) ... ok test_weighted_average (test.test_misc.TestMiscFunctions) ... ok test_weighted_average_list (test.test_misc.TestMiscFunctions) ... ok test_absolute_paths (test.test_options.TestUnicyclerOptions) ... ok test_defaults (test.test_options.TestUnicyclerOptions) ... ok test_modes (test.test_options.TestUnicyclerOptions) ... ok test_relative_paths (test.test_options.TestUnicyclerOptions) ... ok test_long_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments) ... ok test_medium_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments) ... ok test_short_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments) ... ok test_end_to_end (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_end_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_start_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_ref_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_ref_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_ref_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_tough_alignment_0 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_1 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_10 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_11 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_12 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_13 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_14 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_15 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_2 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_3 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_4 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_5 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_6 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_7 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_8 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_9 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_bad_fastq_1 (test.test_spades_func.TestSPAdesFunc) ... ok test_bad_fastq_2 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_count_1 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_count_2 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_lengths_1 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_lengths_2 (test.test_spades_func.TestSPAdesFunc) ... ok ---------------------------------------------------------------------- Ran 223 tests in 100.799s OK I: pybuild pybuild:298: rm /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler-runner.py; rm -r /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/sample_data; rm -r /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/__pycache__ I: pybuild pybuild:272: cp -a unicycler-runner.py /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build; cp -a unicycler/cpp_functions.so /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler; cp -a sample_data /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build I: pybuild base:217: cd /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build; python3.7 -m unittest discover -v test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_filter_by_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_all_gfa_link_lines (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_estimated_sequence_len (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_n_segment_length (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_load_spades_paths (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_remove_all_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_remove_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_specific_segments_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_to_fasta (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_to_fasta_length (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_save_to_gfa (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsFastg) ... ok test_add_link_1 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_add_link_2 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_all_segments_below_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_attributes (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_bad_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_dead_end_change_if_deleted (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_dead_end_change_if_path_deleted (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_filter_homopolymer_loops (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_forward_links (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_connected_components_and_remove_link (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_connected_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_exclusive_inputs (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_exclusive_outputs (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_mean_path_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_median_read_depth (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_next_available_seg_number (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_path_sequence (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_simple_path (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_total_length (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_get_total_length_no_overlaps (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_lead_exclusively_from (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_lead_exclusively_to (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_links_match (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_all_possible (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_simple_path_1 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_simple_path_2 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_merge_simple_path_3 (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_normalise_read_depths (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_remove_small_components (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_remove_small_dead_ends (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_reverse_links (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_segments (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_seq_from_signed_seg_num (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_sequence (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_total_dead_end_count (test.test_assembly_graph.TestAssemblyGraphFunctionsGfa) ... ok test_expand_repeats_1 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_2 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_3 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_4 (test.test_assembly_graph.TestExpandRepeats) ... ok test_expand_repeats_5 (test.test_assembly_graph.TestExpandRepeats) ... ok test_graph (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_1 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_10 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_11 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_2 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_3 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_4 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_5 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_6 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_7 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_8 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_remove_zero_length_segs_9 (test.test_assembly_graph.TestRemoveZeroLengthSegments) ... ok test_graph (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_1 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_2 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_3 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_4 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_5 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_repair_multi_way_junctions_6 (test.test_assembly_graph.TestRepairMultiwayJunction) ... ok test_merge_1 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_merge_split_1 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_merge_split_2 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_single_copy_segments_1 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_single_copy_segments_2 (test.test_assembly_graph_copy_depth.TestCopyDepth) ... ok test_random_seq_no_start_gene (test.test_blast_func.TestBlastFunc) ... ok test_random_seq_with_exact_gene_forward_strand (test.test_blast_func.TestBlastFunc) ... ok test_random_seq_with_exact_gene_reverse_strand (test.test_blast_func.TestBlastFunc) ... ok test_1bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_1bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_2bp_insertion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_2bp_insertion_and_2bp_deletion (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_long_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_one_mismatch (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_perfect_alignment (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_random_seqs (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_shift_big_band (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_shift_small_band (test.test_cpp_wrappers.TestFullyGlobalAlignment) ... ok test_consensus_different_qualities (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_all (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_deletions_and_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_consensus_with_subs (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_start_end_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_start_end_insertions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_start_end_insertions_and_deletions (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_two_way_consensus (test.test_cpp_wrappers.TestMultipleSequenceAlignment) ... ok test_bad_pilon (test.test_dependencies.TestDependencies) ... ok test_bowtie2_build_not_found (test.test_dependencies.TestDependencies) ... ok test_bowtie2_not_found (test.test_dependencies.TestDependencies) ... ok test_java_not_found (test.test_dependencies.TestDependencies) ... ok test_makeblastdb_not_found (test.test_dependencies.TestDependencies) ... ok test_no_pilon (test.test_dependencies.TestDependencies) ... ok test_no_rotate (test.test_dependencies.TestDependencies) ... ok test_pilon_not_found (test.test_dependencies.TestDependencies) ... ok test_samtools_not_found (test.test_dependencies.TestDependencies) ... ok test_spades_not_found (test.test_dependencies.TestDependencies) ... ok test_tblastn_not_found (test.test_dependencies.TestDependencies) ... ok test_verbosity_1 (test.test_dependencies.TestDependencies) ... ok test_verbosity_2 (test.test_dependencies.TestDependencies) ... ok test_basic_options (test.test_help_text.TestBasicHelpText) ... ok test_extended_options (test.test_help_text.TestBasicHelpText) ... ok test_output (test.test_help_text.TestBasicHelpText) ... ok test_return_code (test.test_help_text.TestBasicHelpText) ... ok test_title (test.test_help_text.TestBasicHelpText) ... ok test_error_message (test.test_help_text.TestEmptyCommand) ... ok test_output (test.test_help_text.TestEmptyCommand) ... ok test_return_code (test.test_help_text.TestEmptyCommand) ... ok test_basic_options (test.test_help_text.TestExtendedHelpText) ... ok test_extended_options (test.test_help_text.TestExtendedHelpText) ... ok test_output (test.test_help_text.TestExtendedHelpText) ... ok test_return_code (test.test_help_text.TestExtendedHelpText) ... ok test_title (test.test_help_text.TestExtendedHelpText) ... ok test_contig_placement_1 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_contig_placement_2 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_contig_placement_3 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_contig_placement_4 (test.test_miniasm_assembly.TestContigPlacement) ... ok test_add_line_breaks_to_sequence (test.test_misc.TestMiscFunctions) ... ok test_colour (test.test_misc.TestMiscFunctions) ... ok test_convert_fastq_to_fasta (test.test_misc.TestMiscFunctions) ... ok test_flip_number_order (test.test_misc.TestMiscFunctions) ... ok test_float_to_str (test.test_misc.TestMiscFunctions) ... ok test_get_all_files_in_current_dir (test.test_misc.TestMiscFunctions) ... ok test_get_compression_type (test.test_misc.TestMiscFunctions) ... ok test_get_nice_header (test.test_misc.TestMiscFunctions) ... ok test_get_num_agreement (test.test_misc.TestMiscFunctions) ... ok test_get_percentile (test.test_misc.TestMiscFunctions) ... ok test_get_random_base (test.test_misc.TestMiscFunctions) ... ok test_get_random_sequence (test.test_misc.TestMiscFunctions) ... ok test_get_sequence_file_type (test.test_misc.TestMiscFunctions) ... ok test_int_to_str (test.test_misc.TestMiscFunctions) ... ok test_is_header_spades_format (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_1 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_2 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_3 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_4 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_5 (test.test_misc.TestMiscFunctions) ... ok test_java_version_parsing_6 (test.test_misc.TestMiscFunctions) ... ok test_len_without_format (test.test_misc.TestMiscFunctions) ... ok test_load_fasta (test.test_misc.TestMiscFunctions) ... ok test_load_fasta_with_full_header (test.test_misc.TestMiscFunctions) ... ok test_remove_formatting (test.test_misc.TestMiscFunctions) ... ok test_reverse_complement (test.test_misc.TestMiscFunctions) ... ok test_round_to_nearest_odd (test.test_misc.TestMiscFunctions) ... ok test_score_function (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_1 (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_2 (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_3 (test.test_misc.TestMiscFunctions) ... ok test_spades_version_parsing_4 (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_capitals (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fa (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fasta (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fastq (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fastq_extra_dots (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fna (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_fq (test.test_misc.TestMiscFunctions) ... ok test_strip_read_extensions_other_fasta (test.test_misc.TestMiscFunctions) ... ok test_weighted_average (test.test_misc.TestMiscFunctions) ... ok test_weighted_average_list (test.test_misc.TestMiscFunctions) ... ok test_absolute_paths (test.test_options.TestUnicyclerOptions) ... ok test_defaults (test.test_options.TestUnicyclerOptions) ... ok test_modes (test.test_options.TestUnicyclerOptions) ... ok test_relative_paths (test.test_options.TestUnicyclerOptions) ... ok test_long_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments) ... ok test_medium_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments) ... ok test_short_contained_read (test.test_semi_global_alignment.TestContainedReadAlignments) ... ok test_end_to_end (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_end_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_read_start_overlap (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_ref_contained_1 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_ref_contained_2 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_ref_contained_3 (test.test_semi_global_alignment.TestPerfectMatchAlignments) ... ok test_tough_alignment_0 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_1 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_10 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_11 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_12 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_13 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_14 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_15 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_2 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_3 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_4 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_5 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_6 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_7 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_8 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_tough_alignment_9 (test.test_semi_global_alignment.TestToughAlignments) ... ok test_bad_fastq_1 (test.test_spades_func.TestSPAdesFunc) ... ok test_bad_fastq_2 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_count_1 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_count_2 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_lengths_1 (test.test_spades_func.TestSPAdesFunc) ... ok test_get_read_lengths_2 (test.test_spades_func.TestSPAdesFunc) ... ok ---------------------------------------------------------------------- Ran 223 tests in 113.744s OK I: pybuild pybuild:298: rm /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler-runner.py; rm -r /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/sample_data; rm -r /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/__pycache__ create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' dh_auto_install --destdir=debian/unicycler I: pybuild base:217: /usr/bin/python3.8 setup.py install --root /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler running install running build running build_py running install_lib creating /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr creating /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib creating /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8 creating /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages creating /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/bridge_long_read_simple.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/blast_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/unicycler_scrub.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/bridge_long_read.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/log.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/unicycler_align.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/__init__.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/misc.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/assembly_graph_segment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/string_graph.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/cpp_functions.so -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/bridge_spades_contig.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/path_finding.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/cpp_wrappers.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/alignment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/miniasm_assembly.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/unicycler_check.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/assembly_graph.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/vcf_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/settings.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/unicycler_polish.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/unicycler.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/minimap_alignment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/read_ref.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/bridge_miniasm.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/bridge_common.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/spades_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/bridge_loop_unroll.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/version.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/pilon_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.8_unicycler/build/unicycler/assembly_graph_copy_depth.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/bridge_long_read_simple.py to bridge_long_read_simple.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/blast_func.py to blast_func.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/unicycler_scrub.py to unicycler_scrub.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/bridge_long_read.py to bridge_long_read.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/log.py to log.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/unicycler_align.py to unicycler_align.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/__init__.py to __init__.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/misc.py to misc.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/assembly_graph_segment.py to assembly_graph_segment.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/string_graph.py to string_graph.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/bridge_spades_contig.py to bridge_spades_contig.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/path_finding.py to path_finding.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/cpp_wrappers.py to cpp_wrappers.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/alignment.py to alignment.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/miniasm_assembly.py to miniasm_assembly.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/unicycler_check.py to unicycler_check.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/assembly_graph.py to assembly_graph.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/vcf_func.py to vcf_func.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/settings.py to settings.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/unicycler_polish.py to unicycler_polish.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/unicycler.py to unicycler.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/minimap_alignment.py to minimap_alignment.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/read_ref.py to read_ref.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/bridge_miniasm.py to bridge_miniasm.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/bridge_common.py to bridge_common.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/spades_func.py to spades_func.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/bridge_loop_unroll.py to bridge_loop_unroll.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/version.py to version.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/pilon_func.py to pilon_func.cpython-38.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler/assembly_graph_copy_depth.py to assembly_graph_copy_depth.cpython-38.pyc running install_egg_info running egg_info creating unicycler.egg-info writing unicycler.egg-info/PKG-INFO writing dependency_links to unicycler.egg-info/dependency_links.txt writing entry points to unicycler.egg-info/entry_points.txt writing top-level names to unicycler.egg-info/top_level.txt writing manifest file 'unicycler.egg-info/SOURCES.txt' reading manifest file 'unicycler.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'unicycler.egg-info/SOURCES.txt' Copying unicycler.egg-info to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.8/dist-packages/unicycler-0.4.8.egg-info Skipping SOURCES.txt running install_scripts Installing unicycler script to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_align script to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_check script to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_polish script to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_scrub script to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin  __  \ \___  \ ___\  //  ____// _ _ _ _  //_ //\\ | | | | |_| | | // \// \\ | | | | _ __ _ ___ _ _ ___ | | ___ _ __ || (O) || | | | || '_ \ | | / __|| | | | / __|| | / _ \| '__| \\ \_ // | |__| || | | || || (__ | |_| || (__ | || __/| |  \\_____// \____/ |_| |_||_| \___| \__, | \___||_| \___||_|  __/ |  |___/ Unicycler is installed! Example commands: unicycler --help unicycler --help_all unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -o path/to/output_dir unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -l long_reads.fastq.gz -o path/to/output_dir All tools required by Unicycler were found. I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler running install running build running build_py running install_lib creating /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7 creating /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages creating /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_long_read_simple.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/blast_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/unicycler_scrub.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_long_read.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/log.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/unicycler_align.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/__init__.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/misc.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/assembly_graph_segment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/string_graph.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/cpp_functions.so -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_spades_contig.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/path_finding.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/cpp_wrappers.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/alignment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/miniasm_assembly.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/unicycler_check.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/assembly_graph.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/vcf_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/settings.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/unicycler_polish.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/unicycler.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/minimap_alignment.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/read_ref.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_miniasm.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_common.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/spades_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/bridge_loop_unroll.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/version.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/pilon_func.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler copying /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/.pybuild/cpython3_3.7_unicycler/build/unicycler/assembly_graph_copy_depth.py -> /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_long_read_simple.py to bridge_long_read_simple.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/blast_func.py to blast_func.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/unicycler_scrub.py to unicycler_scrub.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_long_read.py to bridge_long_read.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/log.py to log.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/unicycler_align.py to unicycler_align.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/__init__.py to __init__.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/misc.py to misc.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/assembly_graph_segment.py to assembly_graph_segment.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/string_graph.py to string_graph.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_spades_contig.py to bridge_spades_contig.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/path_finding.py to path_finding.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/cpp_wrappers.py to cpp_wrappers.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/alignment.py to alignment.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/miniasm_assembly.py to miniasm_assembly.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/unicycler_check.py to unicycler_check.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/assembly_graph.py to assembly_graph.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/vcf_func.py to vcf_func.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/settings.py to settings.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/unicycler_polish.py to unicycler_polish.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/unicycler.py to unicycler.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/minimap_alignment.py to minimap_alignment.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/read_ref.py to read_ref.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_miniasm.py to bridge_miniasm.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_common.py to bridge_common.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/spades_func.py to spades_func.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/bridge_loop_unroll.py to bridge_loop_unroll.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/version.py to version.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/pilon_func.py to pilon_func.cpython-37.pyc byte-compiling /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler/assembly_graph_copy_depth.py to assembly_graph_copy_depth.cpython-37.pyc running install_egg_info running egg_info writing unicycler.egg-info/PKG-INFO writing dependency_links to unicycler.egg-info/dependency_links.txt writing entry points to unicycler.egg-info/entry_points.txt writing top-level names to unicycler.egg-info/top_level.txt reading manifest file 'unicycler.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'unicycler.egg-info/SOURCES.txt' Copying unicycler.egg-info to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/lib/python3.7/dist-packages/unicycler-0.4.8.egg-info Skipping SOURCES.txt running install_scripts Installing unicycler script to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_align script to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_check script to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_polish script to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin Installing unicycler_scrub script to /build/unicycler-17lkbA/unicycler-0.4.8+dfsg/debian/unicycler/usr/bin  __  \ \___  \ ___\  //  ____// _ _ _ _  //_ //\\ | | | | |_| | | // \// \\ | | | | _ __ _ ___ _ _ ___ | | ___ _ __ || (O) || | | | || '_ \ | | / __|| | | | / __|| | / _ \| '__| \\ \_ // | |__| || | | || || (__ | |_| || (__ | || __/| |  \\_____// \____/ |_| |_||_| \___| \__, | \___||_| \___||_|  __/ |  |___/ Unicycler is installed! Example commands: unicycler --help unicycler --help_all unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -o path/to/output_dir unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -l long_reads.fastq.gz -o path/to/output_dir All tools required by Unicycler were found. make[1]: Leaving directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' dh_install -a -O--buildsystem=pybuild dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_installman -a -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' dh_python3 --no-ext-rename make[1]: Leaving directory '/build/unicycler-17lkbA/unicycler-0.4.8+dfsg' dh_installinit -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 -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: debian/unicycler/usr/lib/python3/dist-packages/unicycler/cpp_functions.so contains an unresolvable reference to symbol pthread_join: it's probably a plugin dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: package unicycler: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package unicycler: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'unicycler-dbgsym' in '../unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb'. dpkg-deb: building package 'unicycler' in '../unicycler_0.4.8+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../unicycler_0.4.8+dfsg-2_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/unicycler-17lkbA /tmp/unicycler-0.4.8+dfsg-27w67xlxr 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.MdeOfvp8d8... I: success in 1237.2746 seconds md5: Value of 'md5' differs for unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb md5: Size differs for unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb md5: Value of 'md5' differs for unicycler_0.4.8+dfsg-2_amd64.deb md5: Size differs for unicycler_0.4.8+dfsg-2_amd64.deb sha1: Value of 'sha1' differs for unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb sha1: Size differs for unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb sha1: Value of 'sha1' differs for unicycler_0.4.8+dfsg-2_amd64.deb sha1: Size differs for unicycler_0.4.8+dfsg-2_amd64.deb sha256: Value of 'sha256' differs for unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb sha256: Size differs for unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb sha256: Value of 'sha256' differs for unicycler_0.4.8+dfsg-2_amd64.deb sha256: Size differs for unicycler_0.4.8+dfsg-2_amd64.deb Checksums: FAIL Cannot generate diffoscope for unicycler-dbgsym_0.4.8+dfsg-2_amd64.deb: Cannot find URL: http://snapshot.notset.fr/mr/file/7b5b022ba08fbc2f523b89f94ca541d0e7e2c8dd852ef33c9d805baa3eac68e5/download diffoscope run passed