Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/t/tvc/tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/tvc-5.0.3+git20151221.80e144e+dfsg-4+b1987jkz50/tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.buildinfo Get source package info: tvc=5.0.3+git20151221.80e144e+dfsg-4 Source URL: http://snapshot.notset.fr/mr/package/tvc/5.0.3+git20151221.80e144e+dfsg-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-5 binutils=2.37-10 binutils-common=2.37-10 binutils-x86-64-linux-gnu=2.37-10 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-5 cmake=3.22.1-1+b1 cmake-data=3.22.1-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-elpa-helper=2.0.9 dh-strip-nondeterminism=1.12.1-1 diffutils=1:3.7-5 dpkg=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hdf5-helpers=1.10.7+repack-4 hostname=3.23 init-system-helpers=1.61 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libaec-dev=1.0.6-1 libaec0=1.0.6-1 libarchive-zip-perl=1.68-1 libarchive13=3.4.3-2+b1 libarmadillo-dev=1:10.7.4+dfsg-1+b1 libarmadillo10=1:10.7.4+dfsg-1+b1 libarpack2=3.8.0-1 libarpack2-dev=3.8.0-1 libasan6=11.2.0-12 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbamtools-dev=2.5.1+dfsg-10+b1 libbamtools2.5.1=2.5.1+dfsg-10+b1 libbinutils=2.37-10 libblas-dev=3.10.0-1 libblas3=3.10.0-1 libblkid1=2.37.2-4 libboost-math-dev=1.74.0.3 libboost-math1.74-dev=1.74.0-13 libboost-math1.74.0=1.74.0-13 libboost1.74-dev=1.74.0-13 libbrotli1=1.0.9-2+b3 libbz2-1.0=1.0.8-5 libc-bin=2.32-5 libc-dev-bin=2.32-5 libc6=2.32-5 libc6-dev=2.32-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-12 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-10 libctf0=2.37-10 libcurl4=7.79.1-2 libcurl4-openssl-dev=7.79.1-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdisorder-dev=0.0.2+git20130809.8062ee1-4 libdisorder0=0.0.2+git20130809.8062ee1-4 libdpkg-perl=1.21.1 libelf1=0.186-1 libexpat1=2.4.1-3 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.1-1 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-4 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran5=11.2.0-12 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.2-2 libgomp1=11.2.0-12 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libhdf5-103-1=1.10.7+repack-4 libhdf5-cpp-103-1=1.10.7+repack-4 libhdf5-dev=1.10.7+repack-4 libhdf5-fortran-102=1.10.7+repack-4 libhdf5-hl-100=1.10.7+repack-4 libhdf5-hl-cpp-100=1.10.7+repack-4 libhdf5-hl-fortran-100=1.10.7+repack-4 libhogweed6=3.7.3-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-12 libjpeg-dev=1:2.1.2-1 libjpeg62-turbo=1:2.1.2-1 libjpeg62-turbo-dev=1:2.1.2-1 libjsoncpp-dev=1.9.5-2 libjsoncpp25=1.9.5-2 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblapack-dev=3.10.0-1 liblapack3=3.10.0-1 libldap-2.4-2=2.4.59+dfsg-1 liblsan0=11.2.0-12 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 libncurses6=6.3-1 libncursesw6=6.3-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libprocps8=2:3.3.17-5 libpsl5=0.21.0-1.2 libquadmath0=11.2.0-12 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg2-2 libsasl2-modules-db=2.1.27+dfsg2-2 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libsmithwaterman-dev=0.0+git20160702.2610e25-12 libsmithwaterman0=0.0+git20160702.2610e25-12 libssh2-1=1.10.0-2 libssl-dev=1.1.1l-1 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-12 libstdc++6=11.2.0-12 libsub-override-perl=0.09-2 libsuperlu-dev=5.3.0+dfsg1-2 libsuperlu5=5.3.0+dfsg1-2 libsystemd0=249.7-1 libsz2=1.0.6-1 libtasn1-6=4.18.0-4 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-12 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.7-1 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libuv1=1.42.0-1 libxml2=2.9.12+dfsg-5+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.5-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.3-1 ncurses-bin=6.3-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 procps=2:3.3.17-5 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 util-linux=2.37.2-4 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211106T025313Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211106T025313Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211212T085436Z/ 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 tvc=5.0.3+git20151221.80e144e+dfsg-4 && mkdir -p /build/tvc-qhO5x0 && dpkg-source --no-check -x /*.dsc /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg && cd /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg && { printf '%s' 'tvc (5.0.3+git20151221.80e144e+dfsg-4+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libjsoncpp25 -- all / amd64 / i386 Build Daemon (x86-conova-01) Sun, 12 Dec 2021 10:47:22 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/tvc-qhO5x0" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1639306042" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/tvc-qhO5x0 /tmp/tvc-5.0.3+git20151221.80e144e+dfsg-4+b1987jkz50 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211212T085436Z 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.uYzipBfSo2 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.uYzipBfSo2 Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211212T085436Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211212T085436Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1052 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 ... 4679 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-5) ... 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/20211106T025313Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211106T025313Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211212T085436Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.uYzipBfSo2 Get:1 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm InRelease [128 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211212T085436Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm/main Sources [11.7 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.0 MB in 20s (1170 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.uYzipBfSo2 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d tvc=5.0.3+git20151221.80e144e+dfsg-4 && mkdir -p /build/tvc-qhO5x0 && dpkg-source --no-check -x /*.dsc /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg && cd /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg && { printf '%s' 'tvc (5.0.3+git20151221.80e144e+dfsg-4+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libjsoncpp25 -- all / amd64 / i386 Build Daemon (x86-conova-01) Sun, 12 Dec 2021 10:47:22 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/tvc-qhO5x0"' exec /tmp/mmdebstrap.uYzipBfSo2 Reading package lists... NOTICE: 'tvc' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tvc.git Please use: git clone https://salsa.debian.org/med-team/tvc.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 756 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm/main tvc 5.0.3+git20151221.80e144e+dfsg-4 (dsc) [2200 B] Get:2 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm/main tvc 5.0.3+git20151221.80e144e+dfsg-4 (tar) [745 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211106T025313Z bookworm/main tvc 5.0.3+git20151221.80e144e+dfsg-4 (diff) [9248 B] Fetched 756 kB in 1s (1022 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'tvc_5.0.3+git20151221.80e144e+dfsg-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting tvc in /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cmake.patch dpkg-source: info: applying bamtools.patch dpkg-source: info: applying help.patch dpkg-source: info: applying hurd.patch dpkg-source: info: applying sse.patch dpkg-source: info: applying use_debian_packaged_smithwaterman.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying gcc11.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1639306042" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.uYzipBfSo2 dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-4+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all / amd64 / i386 Build Daemon (x86-conova-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_CXX_FLAGS: '-g -O2 -ffile-prefix-map=/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3' -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu dh_auto_build -a cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory 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CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function ‘void TheSilenceOfTheArmadillos(std::ofstream&)’: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:9: warning: ‘void arma::set_stream_err1(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:357, from /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:92:1: note: declared here 92 | set_stream_err1(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: ‘void arma::set_stream_err1(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/armadillo:357, from /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:92:1: note: declared here 92 | set_stream_err1(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:9: warning: ‘void arma::set_stream_err2(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:357, from /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:103:1: note: declared here 103 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: ‘void arma::set_stream_err2(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/armadillo:357, from /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:103:1: note: declared here 103 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/realignment 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-I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp [ 13%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval 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CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/file-io 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CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp [ 35%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp [ 36%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function ‘ti_index_core’: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ [ 38%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller 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-D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/MetricsManager.cpp [ 40%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads 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/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function ‘_bgzf_check_EOF’: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 41%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping 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-DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function ‘ti_index_core’: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ [ 81%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function ‘_bgzf_check_EOF’: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter 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-I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/PIDloop.cpp [ 86%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval 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CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -c /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/DPTreephaser.cpp [ 87%] Building CXX object CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads 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CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o CMakeFiles/tvc.dir/file-io/ion_util.c.o CMakeFiles/tvc.dir/file-io/ion_error.c.o CMakeFiles/tvc.dir/IonVersion.cpp.o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -o tvc -lbamtools -lz -lpthread -lblas -llapack -larmadillo -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' dh_auto_test -a cd obj-x86_64-linux-gnu && make -j4 test ARGS\+=--verbose ARGS\+=-j4 make[1]: Entering directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j4 UpdateCTestConfiguration from :/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: tvc_call 1: Test command: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvc 1: Test timeout computed to be: 10000000 test 2 Start 2: tvc_test_1_thread_sse_on 2: Test command: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvc "--input-bam" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "on" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/test1" "--output-vcf" "small_variants.vcf" 2: Test timeout computed to be: 10000000 test 3 Start 3: tvc_test_1_thread_sse_off 3: Test command: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvc "--input-bam" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/test1" "--output-vcf" "small_variants.vcf" 3: Test timeout computed to be: 10000000 test 4 Start 4: tvc_test_4_threads_sse_on_with_parameter_file 4: Test command: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvc "--input-bam" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "on" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/test2" "--output-vcf" "small_variants.vcf" 4: Test timeout computed to be: 10000000 1: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 1: 1: Usage: tvc [options] 1: 1: General options: 1: -h,--help print this help message and exit 1: -v,--version print version and exit 1: -n,--num-threads INT number of worker threads [2] 1: -N,--num-variants-per-thread INT worker thread batch size [500] 1: --parameters-file FILE json file with algorithm control parameters [optional] 1: 1: Inputs: 1: -r,--reference FILE reference fasta file [required] 1: -b,--input-bam FILE bam file with mapped reads [required] 1: -g,--sample-name STRING sample for which variants are called (In case of input BAM files with multiple samples) [optional if there is only one sample] 1: --force-sample-name STRING force all read groups to have this sample name [off] 1: -t,--target-file FILE only process targets in this bed file [optional] 1: --trim-ampliseq-primers on/off match reads to targets and trim the ends that reach outside them [off] 1: -D,--downsample-to-coverage INT ?? [2000] 1: --model-file FILE HP recalibration model input file. 1: --recal-model-hp-thres INT Lower threshold for HP recalibration. 1: 1: Outputs: 1: -O,--output-dir DIRECTORY base directory for all output files [current dir] 1: -o,--output-vcf FILE vcf file with variant calling results [required] 1: --suppress-reference-genotypes on/off write reference calls into the filtered variants vcf [on] 1: --suppress-no-calls on/off write filtered variants into the filtered variants vcf [on] 1: --suppress-nocall-genotypes on/off do not report a genotype for filtered variants [on] 1: 1: Variant candidate generation (FreeBayes): 1: --allow-snps on/off allow generation of snp candidates [on] 1: --allow-indels on/off allow generation of indel candidates [on] 1: --allow-mnps on/off allow generation of mnp candidates [on] 1: --allow-complex on/off allow generation of block substitution candidates [off] 1: --max-complex-gap INT maximum number of reference alleles between two alternate alleles to allow merging of the alternate alleles [1] 1: -m,--use-best-n-alleles INT maximum number of snp alleles [2] 1: -M,--min-mapping-qv INT do not use reads with mapping quality below this [4] 1: -U,--read-snp-limit INT do not use reads with number of snps above this [10] 1: -z,--read-max-mismatch-fraction FLOAT do not use reads with fraction of mismatches above this [1.0] 1: --gen-min-alt-allele-freq FLOAT minimum required alt allele frequency to generate a candidate [0.2] 1: --gen-min-indel-alt-allele-freq FLOAT minimum required alt allele frequency to generate a homopolymer indel candidate [0.2] 1: --gen-min-coverage INT minimum required coverage to generate a candidate [6] 1: 1: External variant candidates: 1: -c,--input-vcf FILE vcf.gz file (+.tbi) with additional candidate variant locations and alleles [optional] 1: --process-input-positions-only on/off only generate candidates at locations from input-vcf [off] 1: --use-input-allele-only on/off only consider provided alleles for locations in input-vcf [off] 1: 1: Variant candidate scoring options: 1: --min-delta-for-flow FLOAT minimum prediction delta for scoring flows [0.1] 1: --max-flows-to-test INT maximum number of scoring flows [10] 1: --outlier-probability FLOAT probability for outlier reads [0.01] 1: --heavy-tailed INT degrees of freedom in t-dist modeling signal residual heavy tail [3] 1: --suppress-recalibration on/off Suppress homopolymer recalibration [on]. 1: --do-snp-realignment on/off Realign reads in the vicinity of candidate snp variants [on]. 1: --do-mnp-realignment on/off Realign reads in the vicinity of candidate mnp variants [do-snp-realignment]. 1: --realignment-threshold FLOAT Max. allowed fraction of reads where realignment causes an alignment change [1.0]. 1: 1: Advanced variant candidate scoring options: 1: --use-sse-basecaller on/off Switch to use the vectorized version of the basecaller [on]. 1: --resolve-clipped-bases on/off If 'true', the basecaller is used to solve soft clipped bases [off]. 1: --prediction-precision FLOAT prior weight in bias estimator [30.0] 1: --shift-likelihood-penalty FLOAT penalize log-likelihood for solutions involving large systematic bias [0.3] 1: --minimum-sigma-prior FLOAT prior variance per data point, constant [0.085] 1: --slope-sigma-prior FLOAT prior rate of increase of variance over minimum by signal [0.0084] 1: --sigma-prior-weight FLOAT weight of prior estimate of variance compared to observations [1.0] 1: --k-zero FLOAT variance increase for adding systematic bias [3.0] 1: --sse-relative-safety-level FLOAT dampen strand bias detection for SSE events for low coverage [0.025] 1: --tune-sbias FLOAT dampen strand bias detection for low coverage [0.01] 1: --max-detail-level INT number of evaluated frequencies for a given hypothesis, reduce for very high coverage, set to zero to disable this option [0] 1: 1: Variant filtering: 1: -k,--snp-min-coverage INT filter out snps with total coverage below this [6] 1: -C,--snp-min-cov-each-strand INT filter out snps with coverage on either strand below this [0] 1: -B,--snp-min-variant-score FLOAT filter out snps with QUAL score below this [10.0] 1: -s,--snp-strand-bias FLOAT filter out snps with strand bias above this [0.95] given pval < snp-strand-bias-pval 1: --snp-strand-bias-pval FLOAT filter out snps with pval below this [1.0] given strand bias > snp-strand-bias 1: -A,--snp-min-allele-freq FLOAT minimum required alt allele frequency for non-reference snp calls [0.2] 1: --mnp-min-coverage INT filter out mnps with total coverage below this [snp-min-coverage] 1: --mnp-min-cov-each-strand INT filter out mnps with coverage on either strand below this, [snp-min-cov-each-strand] 1: --mnp-min-variant-score FLOAT filter out mnps with QUAL score below this [snp-min-variant-score] 1: --mnp-strand-bias FLOAT filter out mnps with strand bias above this [snp-strand-bias] given pval < mnp-strand-bias-pval 1: --mnp-strand-bias-pval FLOAT filter out mnps with pval below this [snp-strand-bias-pval] given strand bias > mnp-strand-bias 1: --mnp-min-allele-freq FLOAT minimum required alt allele frequency for non-reference mnp calls [snp-min-allele-freq] 1: --indel-min-coverage INT filter out indels with total coverage below this [30] 1: --indel-min-cov-each-strand INT filter out indels with coverage on either strand below this [1] 1: --indel-min-variant-score FLOAT filter out indels with QUAL score below this [10.0] 1: -S,--indel-strand-bias FLOAT filter out indels with strand bias above this [0.95] given pval < indel-strand-bias-pval 1: --indel-strand-bias-pval FLOAT filter out indels with pval below this [1.0] given strand bias > indel-strand-bias 1: --indel-min-allele-freq FLOAT minimum required alt allele frequency for non-reference indel call [0.2] 1: --hotspot-min-coverage INT filter out hotspot variants with total coverage below this [6] 1: --hotspot-min-cov-each-strand INT filter out hotspot variants with coverage on either strand below this [snp-min-cov-each-strand] 1: --hotspot-min-variant-score FLOAT filter out hotspot variants with QUAL score below this [snp-min-variant-score] 1: --hotspot-strand-bias FLOAT filter out hotspot variants with strand bias above this [0.95] given pval < hotspot-strand-bias-pval 1: --hotspot-strand-bias-pval FLOAT filter out hotspot variants with pval below this [1.0] given strand bias > hotspot-strand-bias 1: -H,--hotspot-min-allele-freq FLOAT minimum required alt allele frequency for non-reference hotspot variant call [0.2] 1: -L,--hp-max-length INT filter out indels in homopolymers above this [8] 1: -e,--error-motifs FILE table of systematic error motifs and their error rates [optional] 1: --sse-prob-threshold FLOAT filter out variants in motifs with error rates above this [0.2] 1: --min-ratio-reads-non-sse-strand FLOAT minimum required alt allele frequency for variants with error motifs on opposite strand [0.2] 1: --indel-as-hpindel on/off apply indel filters to non HP indels [off] 1: 1: Position bias variant filtering: 1: --use-position-bias on/off enable the position bias filter [off] 1: --position-bias FLOAT filter out variants with position bias relative to soft clip ends in reads > position-bias [0.75] 1: --position-bias-pval FLOAT filter out if position bias above position-bias given pval < position-bias-pval [0.05] 1: --position-bias-ref-fraction FLOAT skip position bias filter if (reference read count)/(reference + alt allele read count) <= to this [0.05] 1: 1: Filters that depend on scoring across alleles: 1: --data-quality-stringency FLOAT minimum mean log-likelihood delta per read [4.0] 1: --read-rejection-threshold FLOAT filter variants where large numbers of reads are rejected as outliers [0.5] 1: --filter-unusual-predictions FLOAT posterior log likelihood threshold for accepting bias estimate [0.3] 1: --filter-deletion-predictions FLOAT check post-evaluation systematic bias in deletions; a high value like 100 effectively turns off this filter [100.0] 1: --filter-insertion-predictions FLOAT check post-evaluation systematic bias in insertions; a high value like 100 effectively turns off this filter [100.0] 1: 1: --heal-snps on/off suppress in/dels not participating in diploid variant genotypes if the genotype contains a SNP or MNP [on]. 1: 1: Debugging: 1: -d,--debug INT (0/1/2) display extra debug messages [0] 1: --do-json-diagnostic on/off (devel) dump internal state to json file (uses much more time/memory/disk) [off] 1: --postprocessed-bam FILE (devel) save tvc-processed reads to an (unsorted) BAM file [optional] 1: --do-minimal-diagnostic on/off (devel) provide minimal read information for called variants [off] 1: --override-limits on/off (devel) disable limit-check on input parameters [off]. 1: 1/10 Test #1: tvc_call ......................................... Passed 0.01 sec test 5 Start 5: tvc_test_4_threads_sse_off_with_parameter_file 5: Test command: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvc "--input-bam" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/test2" "--output-vcf" "small_variants.vcf" 5: Test timeout computed to be: 10000000 2: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 2: 2: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 2: hp-max-length = 8 (integer, builtin default) 2: sse-prob-threshold = 0.2 (double, builtin default) 2: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 2: sse-relative-safety-level = 0.025 (double, builtin default) 2: do-snp-realignment = true (boolean, builtin default) 2: do-mnp-realignment = true (boolean, builtin default) 2: realignment-threshold = 1 (double, builtin default) 2: indel-as-hpindel = false (boolean, builtin default) 2: data-quality-stringency = 4 (double, builtin default) 2: read-rejection-threshold = 0.5 (double, builtin default) 2: use-position-bias = false (boolean, builtin default) 2: position-bias-ref-fraction = 0.05 (double, builtin default) 2: position-bias = 0.75 (double, builtin default) 2: position-bias-pval = 0.05 (double, builtin default) 2: downsample-to-coverage = 2000 (integer, builtin default) 2: tune-sbias = 0.01 (double, builtin default) 2: suppress-reference-genotypes = true (boolean, builtin default) 2: suppress-nocall-genotypes = true (boolean, builtin default) 2: suppress-no-calls = true (boolean, builtin default) 2: heal-snps = true (boolean, builtin default) 2: snp-min-cov-each-strand = 0 (integer, builtin default) 2: snp-min-variant-score = 10 (double, builtin default) 2: snp-min-allele-freq = 0.2 (double, builtin default) 2: snp-min-coverage = 6 (integer, builtin default) 2: snp-strand-bias = 0.95 (double, builtin default) 2: snp-strand-bias-pval = 1 (double, builtin default) 2: mnp-min-cov-each-strand = 0 (integer, builtin default) 2: mnp-min-variant-score = 10 (double, builtin default) 2: mnp-min-allele-freq = 0.2 (double, builtin default) 2: mnp-min-coverage = 6 (integer, builtin default) 2: mnp-strand-bias = 0.95 (double, builtin default) 2: mnp-strand-bias-pval = 1 (double, builtin default) 2: indel-min-cov-each-strand = 1 (integer, builtin default) 2: indel-min-variant-score = 10 (double, builtin default) 2: indel-min-allele-freq = 0.2 (double, builtin default) 2: indel-min-coverage = 15 (integer, builtin default) 2: indel-strand-bias = 0.85 (double, builtin default) 2: indel-strand-bias-pval = 1 (double, builtin default) 2: hotspot-min-cov-each-strand = 0 (integer, builtin default) 2: hotspot-min-variant-score = 10 (double, builtin default) 2: hotspot-min-allele-freq = 0.2 (double, builtin default) 2: hotspot-min-coverage = 6 (integer, builtin default) 2: hotspot-strand-bias = 0.95 (double, builtin default) 2: hotspot-strand-bias-pval = 1 (double, builtin default) 2: max-flows-to-test = 10 (integer, builtin default) 2: min-delta-for-flow = 0.1 (double, builtin default) 2: prediction-precision = 30 (double, builtin default) 2: outlier-probability = 0.01 (double, builtin default) 2: germline-prior-strength = 0 (double, builtin default) 2: heavy-tailed = 3 (integer, builtin default) 2: filter-unusual-predictions = 0.3 (double, builtin default) 2: soft-clip-bias-checker = 0.1 (double, builtin default) 2: filter-deletion-predictions = 100 (double, builtin default) 2: filter-insertion-predictions = 100 (double, builtin default) 2: max-detail-level = 0 (integer, builtin default) 2: shift-likelihood-penalty = 0.3 (double, builtin default) 2: minimum-sigma-prior = 0.085 (double, builtin default) 2: slope-sigma-prior = 0.0084 (double, builtin default) 2: sigma-prior-weight = 1 (double, builtin default) 2: k-zero = 3 (double, builtin default) 2: num-threads = 1 (integer, command line option) 2: num-variants-per-thread = 250 (integer, builtin default) 2: use-sse-basecaller = true (boolean, command line option) 2: do-json-diagnostic = false (boolean, builtin default) 2: do-minimal-diagnostic = false (boolean, builtin default) 2: process-input-positions-only = false (boolean, builtin default) 2: suppress-recalibration = true (boolean, builtin default) 2: resolve-clipped-bases = false (boolean, builtin default) 2: prefix-exclude = 6 2: allow-indels = true (boolean, builtin default) 2: allow-snps = true (boolean, builtin default) 2: allow-mnps = true (boolean, builtin default) 2: allow-complex = false (boolean, builtin default) 2: left-align-indels = false (boolean, builtin default) 2: use-best-n-alleles = 2 (integer, builtin default) 2: use-input-allele-only = false (boolean, builtin default) 2: min-mapping-qv = 4 (integer, builtin default) 2: read-snp-limit = 10 (integer, builtin default) 2: read-max-mismatch-fraction = 1 (double, builtin default) 2: max-complex-gap = 1 (integer, builtin default) 2: gen-min-alt-allele-freq = 0.2 (double, builtin default) 2: gen-min-coverage = 6 (integer, builtin default) 2: gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) 2: override-limits = false (boolean, builtin default) 2: Limit check parameter hp-max-length: lim. 1 <= 8? OK! 2: Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 2: Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! 2: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 2: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 2: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 2: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 2: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 2: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 2: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! 2: Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! 2: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! 2: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 2: Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! 2: Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! 2: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! 2: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 2: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! 2: Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! 2: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! 2: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! 2: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! 2: Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! 2: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! 2: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 2: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 2: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 2: Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! 2: Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! 2: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 2: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 2: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! 2: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 2: Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! 2: Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! 2: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 2: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 2: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 2: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 2: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 2: Limit check parameter k-zero: lim. 0 <= 3? OK! 2: Limit check parameter num-threads: lim. 1 <= 1 <= lim. 128? OK! 2: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 2: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 2: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 2: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 2: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 2: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 2: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 2: TargetsManager: Loaded targets file /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 2: TargetsManager: 1 target(s) 2: TargetsManager: Trimming of AmpliSeq primers is enabled 3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 3: 3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 3: hp-max-length = 8 (integer, builtin default) 3: sse-prob-threshold = 0.2 (double, builtin default) 3: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 3: sse-relative-safety-level = 0.025 (double, builtin default) 3: do-snp-realignment = true (boolean, builtin default) 3: do-mnp-realignment = true (boolean, builtin default) 3: realignment-threshold = 1 (double, builtin default) 3: indel-as-hpindel = false (boolean, builtin default) 3: data-quality-stringency = 4 (double, builtin default) 3: read-rejection-threshold = 0.5 (double, builtin default) 3: use-position-bias = false (boolean, builtin default) 3: position-bias-ref-fraction = 0.05 (double, builtin default) 3: position-bias = 0.75 (double, builtin default) 3: position-bias-pval = 0.05 (double, builtin default) 3: downsample-to-coverage = 2000 (integer, builtin default) 3: tune-sbias = 0.01 (double, builtin default) 3: suppress-reference-genotypes = true (boolean, builtin default) 3: suppress-nocall-genotypes = true (boolean, builtin default) 3: suppress-no-calls = true (boolean, builtin default) 3: heal-snps = true (boolean, builtin default) 3: snp-min-cov-each-strand = 0 (integer, builtin default) 3: snp-min-variant-score = 10 (double, builtin default) 3: snp-min-allele-freq = 0.2 (double, builtin default) 3: snp-min-coverage = 6 (integer, builtin default) 3: snp-strand-bias = 0.95 (double, builtin default) 3: snp-strand-bias-pval = 1 (double, builtin default) 3: mnp-min-cov-each-strand = 0 (integer, builtin default) 3: mnp-min-variant-score = 10 (double, builtin default) 3: mnp-min-allele-freq = 0.2 (double, builtin default) 3: mnp-min-coverage = 6 (integer, builtin default) 3: mnp-strand-bias = 0.95 (double, builtin default) 3: mnp-strand-bias-pval = 1 (double, builtin default) 3: indel-min-cov-each-strand = 1 (integer, builtin default) 3: indel-min-variant-score = 10 (double, builtin default) 3: indel-min-allele-freq = 0.2 (double, builtin default) 3: indel-min-coverage = 15 (integer, builtin default) 3: indel-strand-bias = 0.85 (double, builtin default) 3: indel-strand-bias-pval = 1 (double, builtin default) 3: hotspot-min-cov-each-strand = 0 (integer, builtin default) 3: hotspot-min-variant-score = 10 (double, builtin default) 3: hotspot-min-allele-freq = 0.2 (double, builtin default) 3: hotspot-min-coverage = 6 (integer, builtin default) 3: hotspot-strand-bias = 0.95 (double, builtin default) 3: hotspot-strand-bias-pval = 1 (double, builtin default) 3: max-flows-to-test = 10 (integer, builtin default) 3: min-delta-for-flow = 0.1 (double, builtin default) 3: prediction-precision = 30 (double, builtin default) 3: outlier-probability = 0.01 (double, builtin default) 3: germline-prior-strength = 0 (double, builtin default) 3: heavy-tailed = 3 (integer, builtin default) 3: filter-unusual-predictions = 0.3 (double, builtin default) 3: soft-clip-bias-checker = 0.1 (double, builtin default) 3: filter-deletion-predictions = 100 (double, builtin default) 3: filter-insertion-predictions = 100 (double, builtin default) 3: max-detail-level = 0 (integer, builtin default) 3: shift-likelihood-penalty = 0.3 (double, builtin default) 3: minimum-sigma-prior = 0.085 (double, builtin default) 3: slope-sigma-prior = 0.0084 (double, builtin default) 3: sigma-prior-weight = 1 (double, builtin default) 3: k-zero = 3 (double, builtin default) 3: num-threads = 1 (integer, command line option) 3: num-variants-per-thread = 250 (integer, builtin default) 3: use-sse-basecaller = false (boolean, command line option) 3: do-json-diagnostic = false (boolean, builtin default) 3: do-minimal-diagnostic = false (boolean, builtin default) 3: process-input-positions-only = false (boolean, builtin default) 3: suppress-recalibration = true (boolean, builtin default) 3: resolve-clipped-bases = false (boolean, builtin default) 3: prefix-exclude = 6 3: allow-indels = true (boolean, builtin default) 3: allow-snps = true (boolean, builtin default) 3: allow-mnps = true (boolean, builtin default) 3: allow-complex = false (boolean, builtin default) 3: left-align-indels = false (boolean, builtin default) 3: use-best-n-alleles = 2 (integer, builtin default) 3: use-input-allele-only = false (boolean, builtin default) 3: min-mapping-qv = 4 (integer, builtin default) 3: read-snp-limit = 10 (integer, builtin default) 3: read-max-mismatch-fraction = 1 (double, builtin default) 3: max-complex-gap = 1 (integer, builtin default) 3: gen-min-alt-allele-freq = 0.2 (double, builtin default) 3: gen-min-coverage = 6 (integer, builtin default) 3: gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) 3: override-limits = false (boolean, builtin default) 3: Limit check parameter hp-max-length: lim. 1 <= 8? OK! 3: Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 3: Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! 3: Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! 3: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 3: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 3: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 3: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 3: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 3: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 3: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! 3: Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! 3: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! 3: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 3: Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 3: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! 3: Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! 3: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! 3: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 3: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 3: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! 3: Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! 3: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! 3: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! 3: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 3: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! 3: Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! 3: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! 3: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 3: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 3: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 3: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 3: Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! 3: Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! 3: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 3: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 3: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! 3: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 3: Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! 3: Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! 3: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 3: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 3: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 3: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 3: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 3: Limit check parameter k-zero: lim. 0 <= 3? OK! 3: Limit check parameter num-threads: lim. 1 <= 1 <= lim. 128? OK! 3: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 3: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 3: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 3: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 3: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 3: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 3: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 3: TargetsManager: Loaded targets file /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 3: TargetsManager: 1 target(s) 3: TargetsManager: Trimming of AmpliSeq primers is enabled 2: SampleManager: Found 1 read group(s) and 1 sample(s). 2: SampleManager: Primary sample "85" (default) present in 1 read group(s) 2: TVC found a total of 1 different flow orders of max flow lengths: 500 3: SampleManager: Found 1 read group(s) and 1 sample(s). 3: SampleManager: Primary sample "85" (default) present in 1 read group(s) 3: TVC found a total of 1 different flow orders of max flow lengths: 500 4: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 4: 4: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 4: hp-max-length = 8 (integer, parameters json file) 4: sse-prob-threshold = 1 (double, parameters json file) 4: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 4: sse-relative-safety-level = 0.025 (double, builtin default) 4: do-snp-realignment = false (boolean, parameters json file) 4: do-mnp-realignment = false (boolean, parameters json file) 4: realignment-threshold = 0 (double, parameters json file) 4: indel-as-hpindel = false (boolean, parameters json file) 4: data-quality-stringency = 10 (double, parameters json file) 4: read-rejection-threshold = 0.5 (double, builtin default) 4: use-position-bias = false (boolean, parameters json file) 4: position-bias-ref-fraction = 0.05 (double, parameters json file) 4: position-bias = 0.75 (double, parameters json file) 4: position-bias-pval = 0.05 (double, parameters json file) 4: downsample-to-coverage = 2000 (integer, parameters json file) 4: tune-sbias = 0.01 (double, builtin default) 4: suppress-reference-genotypes = true (boolean, builtin default) 4: suppress-nocall-genotypes = true (boolean, builtin default) 4: suppress-no-calls = true (boolean, builtin default) 4: heal-snps = true (boolean, builtin default) 4: snp-min-cov-each-strand = 4 (integer, parameters json file) 4: snp-min-variant-score = 6 (double, parameters json file) 4: snp-min-allele-freq = 0.02 (double, parameters json file) 4: snp-min-coverage = 100 (integer, parameters json file) 4: snp-strand-bias = 0.95 (double, parameters json file) 4: snp-strand-bias-pval = 0.01 (double, parameters json file) 4: mnp-min-cov-each-strand = 4 (integer, parameters json file) 4: mnp-min-variant-score = 6 (double, parameters json file) 4: mnp-min-allele-freq = 0.02 (double, parameters json file) 5: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 5: 5: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 4: mnp-min-coverage = 100 (integer, parameters json file) 4: mnp-strand-bias = 0.95 (double, parameters json file) 4: mnp-strand-bias-pval = 0.01 (double, parameters json file) 4: indel-min-cov-each-strand = 4 (integer, parameters json file) 4: indel-min-variant-score = 6 (double, parameters json file) 4: indel-min-allele-freq = 0.02 (double, parameters json file) 4: indel-min-coverage = 100 (integer, parameters json file) 4: indel-strand-bias = 0.9 (double, parameters json file) 4: indel-strand-bias-pval = 1 (double, parameters json file) 4: hotspot-min-cov-each-strand = 4 (integer, parameters json file) 4: hotspot-min-variant-score = 6 (double, parameters json file) 4: hotspot-min-allele-freq = 0.02 (double, parameters json file) 4: hotspot-min-coverage = 100 (integer, parameters json file) 4: hotspot-strand-bias = 0.95 (double, parameters json file) 4: hotspot-strand-bias-pval = 0.01 (double, parameters json file) 4: max-flows-to-test = 10 (integer, builtin default) 4: min-delta-for-flow = 0.1 (double, builtin default) 4: prediction-precision = 1 (double, parameters json file) 4: outlier-probability = 0.005 (double, parameters json file) 4: germline-prior-strength = 0 (double, builtin default) 4: heavy-tailed = 3 (integer, parameters json file) 4: filter-unusual-predictions = 0.12 (double, parameters json file) 5: hp-max-length = 8 (integer, parameters json file) 5: sse-prob-threshold = 1 (double, parameters json file) 5: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 5: sse-relative-safety-level = 0.025 (double, builtin default) 5: do-snp-realignment = false (boolean, parameters json file) 5: do-mnp-realignment = false (boolean, parameters json file) 5: realignment-threshold = 0 (double, parameters json file) 5: indel-as-hpindel = false (boolean, parameters json file) 5: data-quality-stringency = 10 (double, parameters json file) 5: read-rejection-threshold = 0.5 (double, builtin default) 5: use-position-bias = false (boolean, parameters json file) 5: position-bias-ref-fraction = 0.05 (double, parameters json file) 5: position-bias = 0.75 (double, parameters json file) 5: position-bias-pval = 0.05 (double, parameters json file) 5: downsample-to-coverage = 2000 (integer, parameters json file) 5: tune-sbias = 0.01 (double, builtin default) 5: suppress-reference-genotypes = true (boolean, builtin default) 5: suppress-nocall-genotypes = true (boolean, builtin default) 5: suppress-no-calls = true (boolean, builtin default) 5: heal-snps = true (boolean, builtin default) 5: snp-min-cov-each-strand = 4 (integer, parameters json file) 5: snp-min-variant-score = 6 (double, parameters json file) 5: snp-min-allele-freq = 0.02 (double, parameters json file) 5: snp-min-coverage = 100 (integer, parameters json file) 5: snp-strand-bias = 0.95 (double, parameters json file) 5: snp-strand-bias-pval = 0.01 (double, parameters json file) 5: mnp-min-cov-each-strand = 4 (integer, parameters json file) 5: mnp-min-variant-score = 6 (double, parameters json file) 4: soft-clip-bias-checker = 0.1 (double, builtin default) 4: filter-deletion-predictions = 0.2 (double, parameters json file) 4: filter-insertion-predictions = 0.2 (double, parameters json file) 5: mnp-min-allele-freq = 0.02 (double, parameters json file) 5: mnp-min-coverage = 100 (integer, parameters json file) 5: mnp-strand-bias = 0.95 (double, parameters json file) 5: mnp-strand-bias-pval = 0.01 (double, parameters json file) 5: indel-min-cov-each-strand = 4 (integer, parameters json file) 5: indel-min-variant-score = 6 (double, parameters json file) 5: indel-min-allele-freq = 0.02 (double, parameters json file) 5: indel-min-coverage = 100 (integer, parameters json file) 5: indel-strand-bias = 0.9 (double, parameters json file) 5: indel-strand-bias-pval = 1 (double, parameters json file) 5: hotspot-min-cov-each-strand = 4 (integer, parameters json file) 5: hotspot-min-variant-score = 6 (double, parameters json file) 5: hotspot-min-allele-freq = 0.02 (double, parameters json file) 5: hotspot-min-coverage = 100 (integer, parameters json file) 5: hotspot-strand-bias = 0.95 (double, parameters json file) 5: hotspot-strand-bias-pval = 0.01 (double, parameters json file) 5: max-flows-to-test = 10 (integer, builtin default) 5: min-delta-for-flow = 0.1 (double, builtin default) 5: prediction-precision = 1 (double, parameters json file) 5: outlier-probability = 0.005 (double, parameters json file) 5: germline-prior-strength = 0 (double, builtin default) 5: heavy-tailed = 3 (integer, parameters json file) 5: filter-unusual-predictions = 0.12 (double, parameters json file) 5: soft-clip-bias-checker = 0.1 (double, builtin default) 5: filter-deletion-predictions = 0.2 (double, parameters json file) 5: filter-insertion-predictions = 0.2 (double, parameters json file) 5: max-detail-level = 0 (integer, builtin default) 5: shift-likelihood-penalty = 0.3 (double, builtin default) 5: minimum-sigma-prior = 0.085 (double, builtin default) 5: slope-sigma-prior = 0.0084 (double, builtin default) 5: sigma-prior-weight = 1 (double, builtin default) 5: k-zero = 3 (double, builtin default) 4: max-detail-level = 0 (integer, builtin default) 4: shift-likelihood-penalty = 0.3 (double, builtin default) 4: minimum-sigma-prior = 0.085 (double, builtin default) 5: num-threads = 4 (integer, command line option) 5: num-variants-per-thread = 250 (integer, builtin default) 5: use-sse-basecaller = false (boolean, command line option) 5: do-json-diagnostic = false (boolean, builtin default) 5: do-minimal-diagnostic = false (boolean, builtin default) 5: process-input-positions-only = false (boolean, builtin default) 5: suppress-recalibration = false (boolean, parameters json file) 5: resolve-clipped-bases = false (boolean, builtin default) 5: prefix-exclude = 6 5: allow-indels = true (boolean, parameters json file) 5: allow-snps = true (boolean, parameters json file) 5: allow-mnps = true (boolean, parameters json file) 5: allow-complex = false (boolean, parameters json file) 5: left-align-indels = false (boolean, builtin default) 5: use-best-n-alleles = 2 (integer, builtin default) 5: use-input-allele-only = false (boolean, builtin default) 5: min-mapping-qv = 4 (integer, parameters json file) 5: read-snp-limit = 10 (integer, parameters json file) 5: read-max-mismatch-fraction = 1 (double, parameters json file) 5: max-complex-gap = 1 (integer, builtin default) 5: gen-min-alt-allele-freq = 0.01 (double, parameters json file) 5: gen-min-coverage = 6 (integer, parameters json file) 5: gen-min-indel-alt-allele-freq = 0.01 (double, parameters json file) 5: override-limits = false (boolean, builtin default) 5: Limit check parameter hp-max-length: lim. 1 <= 8? OK! 5: Limit check parameter sse-prob-threshold: lim. 0 <= 1 <= lim. 1? OK! 5: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 5: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 5: Limit check parameter realignment-threshold: lim. 0 <= 0 <= lim. 1? OK! 5: Limit check parameter data-quality-stringency: lim. 0 <= 10? OK! 5: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 5: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 5: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 5: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 5: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 5: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 5: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 4? OK! 5: Limit check parameter snp-min-variant-score: lim. 0 <= 6? OK! 5: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 5: Limit check parameter snp-min-coverage: lim. 0 <= 100? OK! 5: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 5: Limit check parameter snp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 5: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 4? OK! 4: slope-sigma-prior = 0.0084 (double, builtin default) 4: sigma-prior-weight = 1 (double, builtin default) 4: k-zero = 3 (double, builtin default) 4: num-threads = 4 (integer, command line option) 5: Limit check parameter mnp-min-variant-score: lim. 0 <= 6? OK! 5: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 5: Limit check parameter mnp-min-coverage: lim. 0 <= 100? OK! 5: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 5: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 5: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 4? OK! 5: Limit check parameter indel-min-variant-score: lim. 0 <= 6? OK! 5: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 5: Limit check parameter indel-min-coverage: lim. 0 <= 100? OK! 5: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.9 <= lim. 1? OK! 5: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 5: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 4? OK! 5: Limit check parameter hotspot-min-variant-score: lim. 0 <= 6? OK! 5: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 5: Limit check parameter hotspot-min-coverage: lim. 0 <= 100? OK! 5: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 5: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 5: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 5: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 5: Limit check parameter prediction-precision: lim. 0.1 <= 1? OK! 5: Limit check parameter outlier-probability: lim. 0 <= 0.005 <= lim. 1? OK! 5: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 5: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 5: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.12? OK! 5: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 5: Limit check parameter filter-deletion-predictions: lim. 0 <= 0.2? OK! 5: Limit check parameter filter-insertion-predictions: lim. 0 <= 0.2? OK! 5: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 5: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 5: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 5: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 5: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 5: Limit check parameter k-zero: lim. 0 <= 3? OK! 5: Limit check parameter num-threads: lim. 1 <= 4 <= lim. 128? OK! 5: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 5: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 5: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 5: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 5: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 5: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! 5: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 5: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! 4: num-variants-per-thread = 250 (integer, builtin default) 4: use-sse-basecaller = true (boolean, command line option) 4: do-json-diagnostic = false (boolean, builtin default) 4: do-minimal-diagnostic = false (boolean, builtin default) 4: process-input-positions-only = false (boolean, builtin default) 4: suppress-recalibration = false (boolean, parameters json file) 5: TargetsManager: Loaded targets file /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 5: TargetsManager: 1 target(s) 5: TargetsManager: Trimming of AmpliSeq primers is enabled 4: resolve-clipped-bases = false (boolean, builtin default) 4: prefix-exclude = 6 4: allow-indels = true (boolean, parameters json file) 4: allow-snps = true (boolean, parameters json file) 4: allow-mnps = true (boolean, parameters json file) 4: allow-complex = false (boolean, parameters json file) 4: left-align-indels = false (boolean, builtin default) 4: use-best-n-alleles = 2 (integer, builtin default) 4: use-input-allele-only = false (boolean, builtin default) 4: min-mapping-qv = 4 (integer, parameters json file) 4: read-snp-limit = 10 (integer, parameters json file) 4: read-max-mismatch-fraction = 1 (double, parameters json file) 4: max-complex-gap = 1 (integer, builtin default) 4: gen-min-alt-allele-freq = 0.01 (double, parameters json file) 4: gen-min-coverage = 6 (integer, parameters json file) 4: gen-min-indel-alt-allele-freq = 0.01 (double, parameters json file) 4: override-limits = false (boolean, builtin default) 4: Limit check parameter hp-max-length: lim. 1 <= 8? OK! 4: Limit check parameter sse-prob-threshold: lim. 0 <= 1 <= lim. 1? OK! 4: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 4: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 4: Limit check parameter realignment-threshold: lim. 0 <= 0 <= lim. 1? OK! 4: Limit check parameter data-quality-stringency: lim. 0 <= 10? OK! 4: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 4: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 4: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 4: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 4: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 4: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 4: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 4? OK! 4: Limit check parameter snp-min-variant-score: lim. 0 <= 6? OK! 4: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 4: Limit check parameter snp-min-coverage: lim. 0 <= 100? OK! 4: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 4: Limit check parameter snp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 4: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 4? OK! 4: Limit check parameter mnp-min-variant-score: lim. 0 <= 6? OK! 4: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 4: Limit check parameter mnp-min-coverage: lim. 0 <= 100? OK! 4: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 4: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 4: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 4? OK! 4: Limit check parameter indel-min-variant-score: lim. 0 <= 6? OK! 4: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 4: Limit check parameter indel-min-coverage: lim. 0 <= 100? OK! 4: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.9 <= lim. 1? OK! 4: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 4: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 4? OK! 4: Limit check parameter hotspot-min-variant-score: lim. 0 <= 6? OK! 4: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 4: Limit check parameter hotspot-min-coverage: lim. 0 <= 100? OK! 4: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 4: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 4: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 4: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 4: Limit check parameter prediction-precision: lim. 0.1 <= 1? OK! 4: Limit check parameter outlier-probability: lim. 0 <= 0.005 <= lim. 1? OK! 4: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 4: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 4: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.12? OK! 4: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 4: Limit check parameter filter-deletion-predictions: lim. 0 <= 0.2? OK! 4: Limit check parameter filter-insertion-predictions: lim. 0 <= 0.2? OK! 4: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 4: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 4: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 4: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 4: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 4: Limit check parameter k-zero: lim. 0 <= 3? OK! 4: Limit check parameter num-threads: lim. 1 <= 4 <= lim. 128? OK! 4: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 4: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 4: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 4: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 4: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 4: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! 4: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 4: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! 4: TargetsManager: Loaded targets file /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 4: TargetsManager: 1 target(s) 4: TargetsManager: Trimming of AmpliSeq primers is enabled 5: SampleManager: Found 1 read group(s) and 1 sample(s). 5: SampleManager: Primary sample "85" (default) present in 1 read group(s) 5: TVC found a total of 1 different flow orders of max flow lengths: 500 4: SampleManager: Found 1 read group(s) and 1 sample(s). 4: SampleManager: Primary sample "85" (default) present in 1 read group(s) 4: TVC found a total of 1 different flow orders of max flow lengths: 500 2: Recalibration was detected from comment lines in bam file(s): 2: 1 unique blocks of recalibration info detected. 2: Loading systematic error contexts. 3: Recalibration was detected from comment lines in bam file(s): 3: 1 unique blocks of recalibration info detected. 3: Loading systematic error contexts. 5: Recalibration was detected from comment lines in bam file(s): 5: 1 unique blocks of recalibration info detected. 5: Loading systematic error contexts. 4: Recalibration was detected from comment lines in bam file(s): 4: 1 unique blocks of recalibration info detected. 4: Loading systematic error contexts. 2: Loaded. 5: Loaded. 3: Loaded. 4: Loaded. 2: Recalibration model: suppressed 2: 2: 2: [tvc] Normal termination. Processing time: 1 seconds. 5: 5: 5: [tvc] Normal termination. Processing time: 1 seconds. 2/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 1.30 sec test 6 Start 6: tvcutils_call 6: Test command: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvcutils 6: Test timeout computed to be: 10000000 6: 6: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 6: 6: Usage: tvcutils [options] 6: 6: Commands: 6: prepare_hotspots Convert BED or VCF file into a valid hotspot file 6: validate_bed Validate targets or hotspots file 6: unify_vcf Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) 6: 3/10 Test #6: tvcutils_call .................................... Passed 0.01 sec test 7 Start 7: tvcutils_prepare_hotspots_call 7: Test command: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvcutils "prepare_hotspots" 7: Test timeout computed to be: 10000000 7: 7: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 7: 7: Usage: tvcutils prepare_hotspots [options] 7: 7: General options: 7: -b,--input-bed FILE input is a hotspots BED file (either -b or -v required) 7: -v,--input-vcf FILE input is a hotspots VCF file (either -b or -v required) 7: -d,--output-bed FILE output left-aligned hotspots in BED format [none] 7: -o,--output-vcf FILE output is a hotspots VCF file. To be used as input to --hotspot-vcf argument of variant_caller_pipeline.py (recommended) [none] 7: -r,--reference FILE FASTA file containing reference genome (required) 7: -a,--left-alignment on/off perform left-alignment of indels [off] 7: -s,--allow-block-substitutions on/off do not filter out block substitution hotspots [on] 7: -u,--unmerged-bed FILE input a target bed file to filter out hotspots that contain a junction of 2 amplicons (optional) 7: 4/10 Test #7: tvcutils_prepare_hotspots_call ................... Passed 0.01 sec test 8 Start 8: tvcutils_validate_bed_call 8: Test command: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvcutils "validate_bed" 8: Test timeout computed to be: 10000000 8: 8: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 8: 8: Usage: tvcutils validate_bed [options] 8: 8: Input selection options (must provide one): 8: --target-regions-bed FILE input is a target regions BED file (required) 8: --hotspots-bed FILE input is a hotspots BED file (required) 8: 8: General options: 8: --reference FILE FASTA file containing reference genome (required) 8: --validation-log FILE log file for user-readable warning/error messages [stdout] 8: --meta-json FILE save validation and file statistics to json file [none] 8: --unmerged-detail-bed FILE output a valid unmerged BED. To be used as input to --primer-trim-bed argument of variant_caller_pipeline.py (recommended) [none] 8: --unmerged-plain-bed FILE output a valid merged BED. To be used as input to --region-bed argument of variant_caller_pipeline.py (recommended) [none] 8: --merged-detail-bed FILE output an (almost) valid bedDetail merged BED [none] 8: --merged-plain-bed FILE output a valid plain merged BED [none] 8: --effective-bed FILE output a valid effective BED [none] 8: 5/10 Test #8: tvcutils_validate_bed_call ....................... Passed 0.00 sec test 9 Start 9: tvcutils_unify_vcf_call 9: Test command: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvcutils "unify_vcf" 9: Test timeout computed to be: 10000000 9: Parameter novel-tvc-vcf is required and empty. 9: 9: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 9: 9: Usage: tvcutils unify_vcf [options] 9: 9: General options: 9: -t,--novel-tvc-vcf FILE small variants VCF file produced by TVC (required) 9: -i,--novel-assembly-vcf FILE long indels VCF file produced by TVCASSEMBLY (optional) 9: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) 9: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) 9: -f,--reference-fasta FILE FASTA file containing reference genome (required) 9: -b,--target-file FILE target regions BED file (optional) 9: -o,--output-vcf FILE output merged and annotated VCF or VCF.GZ file (required) 9: -j,--tvc-metrics FILE JSON file with tvc metrics (optional) 9: -d,--input-depth FILE output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok) 9: -m,--min-depth INT minimum coverage depth in GVCF output (optional) 9: 6/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.00 sec test 10 Start 10: tvcassembly_call 10: Test command: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvcassembly 10: Test timeout computed to be: 10000000 10: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 10: 10: Usage: tvcassembly [options] 10: 10: General options: 10: -h,--help print this help message and exit 10: -v,--version print version and exit 10: -n,--num-threads INT number of worker threads [2] 10: --parameters-file FILE json file with algorithm control parameters [optional] 10: -r,--reference FILE reference fasta file [required] 10: -b,--input-bam FILE bam file with mapped reads [required] 10: -t,--target-file FILE only process targets in this bed file [optional] 10: -o,--output-vcf FILE vcf file with variant calling results [required] 10: -g,--sample-name STRING sample for which variants are called (In case of input BAM files with multiple samples) [optional if there is only one sample] 10: --force-sample-name STRING force all read groups to have this sample name [off] 10: 10: --kmer_len INT (klen) Size of the smallest k-mer used in assembly [19]. 10: --min_var_count INT (mincount) Minimum support for a variant to be evaluated [5]. 10: --short_suffix_match INT (ssm) Minimum sequence match on both sides of the variant [5]. 10: --min_indel_size INT (mis) Minimum size indel reported by assembly [4]. 10: --max_hp_length INT (maxhp) Variants containing HP larger than this are not reported [8]. 10: --min_var_freq FLOAT (minfreq) Minimum frequency of the variant to be reported [0.15]. 10: --min_var_score FLOAT (minscore) Minimum score of the variant to be reported [10]. 10: --relative_strand_bias FLOAT (stbias) Variants with strand bias above this are not reported [0.80]. 10: --output_mnv INT (mnv) Output multi-nucleotide variants assembled in a region with multiple adjacent variants [0]. 10: 7/10 Test #10: tvcassembly_call ................................. Passed 0.00 sec 8/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 1.33 sec 3: Recalibration model: suppressed 3: 3: 3: [tvc] Normal termination. Processing time: 1 seconds. 4: 4: 4: [tvc] Normal termination. Processing time: 1 seconds. 9/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 1.51 sec 10/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 1.54 sec 100% tests passed, 0 tests failed out of 10 Total Test time (real) = 1.55 sec make[1]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/tvc/ -a cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/build/tvc-qhO5x0/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target tvcassembly make[3]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'. make[3]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tvcutils make[3]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build [ 10%] Built target tvcassembly make[3]: Entering directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'. make[3]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [ 30%] Built target tvcutils Consolidate compiler generated dependencies of target tvc make[3]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'. make[3]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed -- Installing: /build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed make[1]: Leaving directory '/build/tvc-qhO5x0/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' dh_installdocs -a dh_installchangelogs -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc were not linked against libdisorder.so.0 (they use none of the library's symbols) dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.deb'. dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.deb'. dpkg-genbuildinfo --build=any -O../tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.buildinfo dpkg-genchanges --build=any -O../tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_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/tvc-qhO5x0 /tmp/tvc-5.0.3+git20151221.80e144e+dfsg-4+b1987jkz50 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.uYzipBfSo2... I: success in 1124.3963 seconds md5: tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.deb: OK md5: Value of 'md5' differs for tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.deb md5: Size differs for tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.deb sha1: tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.deb: OK sha1: Value of 'sha1' differs for tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.deb sha1: Size differs for tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.deb sha256: tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.deb: OK sha256: Value of 'sha256' differs for tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.deb sha256: Size differs for tvc_5.0.3+git20151221.80e144e+dfsg-4+b1_amd64.deb Checksums: FAIL diffoscope run passed