I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 3 03:18:34 -12 2025 I: pbuilder-time-stamp: 1738595914 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc] I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz] I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc: unsupported subcommand dpkg-source: info: extracting tvc in 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-5.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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/14613/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='819eca82d09b4079983c614fb4b58b89' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='14613' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ncHYB6gd/pbuilderrc_0FzR --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ncHYB6gd/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' SUDO_GID='112' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32b 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/14613/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19565 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libarmadillo-dev; however: Package libarmadillo-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-math-dev; however: Package libboost-math-dev is not installed. pbuilder-satisfydepends-dummy depends on libsmithwaterman-dev; however: Package libsmithwaterman-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libarmadillo-dev{a} libarmadillo14{a} libarpack2-dev{a} libarpack2t64{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas-dev{a} libblas3{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdisorder-dev{a} libdisorder0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-dev{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsuperlu-dev{a} libsuperlu7{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 126 newly installed, 0 to remove and 0 not upgraded. Need to get 66.8 MB of archives. After unpacking 369 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf libproc2-0 armhf 2:4.0.4-7 [56.3 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf procps armhf 2:4.0.4-7 [866 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.23.1-1 [238 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.4-2 [84.6 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-5 [272 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf automake all 1:1.17-3 [862 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf autopoint all 0.23.1-1 [770 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf cmake-data all 3.31.5-1 [2267 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-6 [9086 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libarchive13t64 armhf 3.7.4-1.1 [306 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-4 [30.3 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.2-1 [23.3 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-4 [75.8 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 27 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-4 [285 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-4 [116 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf libunistring5 armhf 1.3-1 [444 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libidn2-0 armhf 2.3.7-2+b1 [125 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8+b1 [18.6 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8+b1 [50.6 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf libldap2 armhf 2.6.9+dfsg-1 [167 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libffi8 armhf 3.4.6-1 [20.0 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libp11-kit0 armhf 0.25.5-3 [385 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf libtasn1-6 armhf 4.19.0-3+b3 [43.9 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf libgnutls30t64 armhf 3.8.8-2 [1370 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libcurl4t64 armhf 8.11.1-1+b1 [304 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf libjsoncpp26 armhf 1.9.6-3 [69.9 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf librhash1 armhf 1.4.5-1 [143 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libuv1t64 armhf 1.48.0-7 [134 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf cmake armhf 3.31.5-1 [5911 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf comerr-dev armhf 2.1-1.47.2-1 [55.1 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.24.1 [90.9 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf libtool all 2.5.4-3 [539 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 55 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.23.1-1 [1560 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf debhelper all 13.24.1 [920 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf hdf5-helpers armhf 1.14.5+repack-3 [26.6 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf libgssrpc4t64 armhf 1.21.3-4 [52.6 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libkadm5clnt-mit12 armhf 1.21.3-4 [37.5 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf libkdb5-10t64 armhf 1.21.3-4 [37.3 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libkadm5srv-mit12 armhf 1.21.3-4 [47.4 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf krb5-multidev armhf 1.21.3-4 [126 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libaec0 armhf 1.1.3-1+b1 [21.9 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf libsz2 armhf 1.1.3-1+b1 [8036 B] Get: 69 http://deb.debian.org/debian unstable/main armhf libaec-dev armhf 1.1.3-1+b1 [19.3 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libblas3 armhf 3.12.1-2 [116 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14.2.0-16 [263 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf liblapack3 armhf 3.12.1-2 [1835 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf libarpack2t64 armhf 3.9.1-4 [85.1 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf libarmadillo14 armhf 1:14.2.1+dfsg-1 [99.7 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf libblas-dev armhf 3.12.1-2 [127 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf liblapack-dev armhf 3.12.1-2 [1935 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf libarpack2-dev armhf 3.9.1-4 [103 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf libhdf5-310 armhf 1.14.5+repack-3 [1272 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libhdf5-fortran-310 armhf 1.14.5+repack-3 [102 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libhdf5-hl-310 armhf 1.14.5+repack-3 [67.3 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf libhdf5-hl-fortran-310 armhf 1.14.5+repack-3 [38.3 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf libhdf5-cpp-310 armhf 1.14.5+repack-3 [125 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf libhdf5-hl-cpp-310 armhf 1.14.5+repack-3 [24.1 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-3+b1 [263 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf libjpeg-dev armhf 1:2.1.5-3+b1 [72.2 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf libbrotli-dev armhf 1.1.0-2+b6 [293 kB] Get: 89 http://deb.debian.org/debian unstable/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB] Get: 90 http://deb.debian.org/debian unstable/main armhf libkrb5-dev armhf 1.21.3-4 [15.9 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf libldap-dev armhf 2.6.9+dfsg-1 [286 kB] Get: 92 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB] Get: 97 http://deb.debian.org/debian unstable/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-3 [328 kB] Get: 98 http://deb.debian.org/debian unstable/main armhf libgmp-dev armhf 2:6.3.0+dfsg-3 [592 kB] Get: 99 http://deb.debian.org/debian unstable/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB] Get: 100 http://deb.debian.org/debian unstable/main armhf libunbound8 armhf 1.22.0-1+b1 [539 kB] Get: 101 http://deb.debian.org/debian unstable/main armhf libgnutls-dane0t64 armhf 3.8.8-2 [440 kB] Get: 102 http://deb.debian.org/debian unstable/main armhf libgnutls-openssl27t64 armhf 3.8.8-2 [440 kB] Get: 103 http://deb.debian.org/debian unstable/main armhf libp11-kit-dev armhf 0.25.5-3 [208 kB] Get: 104 http://deb.debian.org/debian unstable/main armhf libtasn1-6-dev armhf 4.19.0-3+b3 [93.2 kB] Get: 105 http://deb.debian.org/debian unstable/main armhf nettle-dev armhf 3.10-1+b1 [1313 kB] Get: 106 http://deb.debian.org/debian unstable/main armhf libgnutls28-dev armhf 3.8.8-2 [1328 kB] Get: 107 http://deb.debian.org/debian unstable/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB] Get: 108 http://deb.debian.org/debian unstable/main armhf libssl-dev armhf 3.4.0-2 [2431 kB] Get: 109 http://deb.debian.org/debian unstable/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB] Get: 110 http://deb.debian.org/debian unstable/main armhf libzstd-dev armhf 1.5.6+dfsg-2 [326 kB] Get: 111 http://deb.debian.org/debian unstable/main armhf libcurl4-openssl-dev armhf 8.11.1-1+b1 [425 kB] Get: 112 http://deb.debian.org/debian unstable/main armhf libhdf5-dev armhf 1.14.5+repack-3 [3091 kB] Get: 113 http://deb.debian.org/debian unstable/main armhf libsuperlu7 armhf 7.0.0+dfsg1-2 [142 kB] Get: 114 http://deb.debian.org/debian unstable/main armhf libsuperlu-dev armhf 7.0.0+dfsg1-2 [21.9 kB] Get: 115 http://deb.debian.org/debian unstable/main armhf libarmadillo-dev armhf 1:14.2.1+dfsg-1 [414 kB] Get: 116 http://deb.debian.org/debian unstable/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-6+b1 [140 kB] Get: 117 http://deb.debian.org/debian unstable/main armhf libbamtools-dev armhf 2.5.2+dfsg-6+b1 [205 kB] Get: 118 http://deb.debian.org/debian unstable/main armhf libboost1.83-dev armhf 1.83.0-4 [10.6 MB] Get: 119 http://deb.debian.org/debian unstable/main armhf libboost-math1.83.0 armhf 1.83.0-4 [328 kB] Get: 120 http://deb.debian.org/debian unstable/main armhf libboost-math1.83-dev armhf 1.83.0-4 [346 kB] Get: 121 http://deb.debian.org/debian unstable/main armhf libboost-math-dev armhf 1.83.0.2+b2 [3788 B] Get: 122 http://deb.debian.org/debian unstable/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-4+b2 [5092 B] Get: 123 http://deb.debian.org/debian unstable/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-4+b2 [4688 B] Get: 124 http://deb.debian.org/debian unstable/main armhf libjsoncpp-dev armhf 1.9.6-3 [25.0 kB] Get: 125 http://deb.debian.org/debian unstable/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12+b2 [31.9 kB] Get: 126 http://deb.debian.org/debian unstable/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-12+b2 [37.2 kB] Fetched 66.8 MB in 3s (20.8 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:armhf. (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 ... 19565 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.4-7_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.4-7_armhf.deb ... Unpacking procps (2:4.0.4-7) ... Selecting previously unselected package sensible-utils. 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Setting up libelf1t64:armhf (0.192-4) ... Setting up libkrb5support0:armhf (1.21.3-4) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.12.1-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libunbound8:armhf (1.22.0-1+b1) ... Setting up libpkgconf3:armhf (1.8.1-4) ... Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-3+b1) ... Setting up libjpeg62-turbo-dev:armhf (1:2.1.5-3+b1) ... Setting up libjsoncpp26:armhf (1.9.6-3) ... Setting up libproc2-0:armhf (2:4.0.4-7) ... Setting up comerr-dev:armhf (2.1-1.47.2-1) ... Setting up libunistring5:armhf (1.3-1) ... Setting up libssl-dev:armhf (3.4.0-2) ... Setting up autopoint (0.23.1-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:armhf (1.21.3-4) ... Setting up libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-4+b2) ... Setting up libbamtools2.5.2:armhf (2.5.2+dfsg-6+b1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:armhf (14.2.0-16) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:armhf (3.4.6-1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up procps (2:4.0.4-7) ... Setting up libtasn1-6:armhf (4.19.0-3+b3) ... Setting up cmake-data (3.31.5-1) ... Setting up librhash1:armhf (1.4.5-1) ... Setting up libkrb5-3:armhf (1.21.3-4) ... Setting up libssh2-1t64:armhf (1.11.1-1) ... Setting up libboost-math1.83.0:armhf (1.83.0-4) ... Setting up libtasn1-6-dev:armhf (4.19.0-3+b3) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:armhf (2.6.9+dfsg-1) ... Setting up libbrotli-dev:armhf (1.1.0-2+b6) ... 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Processing triggers for libc-bin (2.40-6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Mohammed Bilal dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-arm-linux-gnueabihf && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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 -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf .. CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2' -- Configuring done (1.5s) -- Generating done (0.1s) CMake Warning: 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'/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/tvc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Leaving directory 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-ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp [ 6%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/prepare_hotspots.cpp /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/armadillo:412, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:83:1: note: declared here 83 | set_stream_err1(const std::ostream&) | ^~~~~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: 'void arma::set_stream_err2(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/armadillo_bits/debug.hpp:92:1: note: declared here 92 | set_stream_err2(const std::ostream&) | ^~~~~~~~~~~~~~~ [ 7%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/validate_bed.cpp [ 10%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE 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-ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -MF CMakeFiles/tvcassembly.dir/IonVersion.cpp.o.d -o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/IonVersion.cpp [ 23%] Linking CXX executable tvcassembly /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic -Wl,--dependency-file=CMakeFiles/tvcassembly.dir/link.d 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HandleVariant.cpp [ 26%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp [ 28%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HotspotReader.cpp In file included from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.h:64, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:19: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp: In instantiation of 'void markov_chain::optimal_path() [with T = unsigned int]': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:64:3: required from 'void markov_chain::initialize(_ForwardIterator, _ForwardIterator, T, T) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = unsigned int]' 64 | optimal_path(); | ^~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:38:13: required from 'markov_chain::markov_chain(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = unsigned int]' 38 | initialize(begin, end, *(m.first), *(m.second)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:550:69: required from here 550 | markov_chain ch(depth_values.begin(), depth_values.end()); | ^ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:114:13: warning: ignoring return value of 'constexpr bool std::operator!=(const reverse_iterator<_Iterator>&, const reverse_iterator<_Iterator>&) [with _Iterator = __gnu_cxx::__normal_iterator*, vector > >]', declared with attribute 'nodiscard' [-Wunused-result] 114 | for (; it != rend(), vit != values.rend(); it++, vit++) { | ~~~^~~~~~~~~ In file included from /usr/include/c++/14/string:48, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:7: /usr/include/c++/14/bits/stl_iterator.h:455:5: note: declared here 455 | operator!=(const reverse_iterator<_Iterator>& __x, | ^~~~~~~~ [ 29%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/MetricsManager.cpp [ 31%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/MiscUtil.cpp [ 32%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/ExtendParameters.cpp [ 34%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp [ 35%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 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/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp [ 56%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector&, std::vector&, bool)': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:191:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 191 | fprintf(stdout, "ref.size()=%lu; ", ref.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:192:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 192 | fprintf(stdout, "var.size()=%lu; ", var.size()); | ~~^ 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong 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CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o 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 -o tvc -lbamtools -lz -lpthread -lblas -llapack -larmadillo -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' [100%] Built target tvc make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' dh_auto_test cd obj-arm-linux-gnueabihf && make -j3 test ARGS\+=--verbose ARGS\+=-j3 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j3 UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl Test project /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 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 Connected to MAKE jobserver test 1 Start 1: tvc_call 1: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc 1: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 1: Test timeout computed to be: 10000000 test 2 Start 2: tvc_test_1_thread_sse_off 2: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/test1" "--output-vcf" "small_variants.vcf" 2: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 2: Test timeout computed to be: 10000000 test 3 Start 3: tvc_test_4_threads_sse_off_with_parameter_file 3: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/test2" "--output-vcf" "small_variants.vcf" 3: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 3: 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 [off]. 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: 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 = false (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/reproducible-path/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 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: 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, parameters json file) 3: sse-prob-threshold = 1 (double, parameters json file) 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 = false (boolean, parameters json file) 3: do-mnp-realignment = false (boolean, parameters json file) 3: realignment-threshold = 0 (double, parameters json file) 3: indel-as-hpindel = false (boolean, parameters json file) 3: data-quality-stringency = 10 (double, parameters json file) 3: read-rejection-threshold = 0.5 (double, builtin default) 3: use-position-bias = false (boolean, parameters json file) 3: position-bias-ref-fraction = 0.05 (double, parameters json file) 3: position-bias = 0.75 (double, parameters json file) 3: position-bias-pval = 0.05 (double, parameters json file) 3: downsample-to-coverage = 2000 (integer, parameters json file) 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 = 4 (integer, parameters json file) 3: snp-min-variant-score = 6 (double, parameters json file) 3: snp-min-allele-freq = 0.02 (double, parameters json file) 3: snp-min-coverage = 100 (integer, parameters json file) 3: snp-strand-bias = 0.95 (double, parameters json file) 3: snp-strand-bias-pval = 0.01 (double, parameters json file) 3: mnp-min-cov-each-strand = 4 (integer, parameters json file) 3: mnp-min-variant-score = 6 (double, parameters json file) 3: mnp-min-allele-freq = 0.02 (double, parameters json file) 3: mnp-min-coverage = 100 (integer, parameters json file) 3: mnp-strand-bias = 0.95 (double, parameters json file) 3: mnp-strand-bias-pval = 0.01 (double, parameters json file) 3: indel-min-cov-each-strand = 4 (integer, parameters json file) 3: indel-min-variant-score = 6 (double, parameters json file) 3: indel-min-allele-freq = 0.02 (double, parameters json file) 3: indel-min-coverage = 100 (integer, parameters json file) 3: indel-strand-bias = 0.9 (double, parameters json file) 3: indel-strand-bias-pval = 1 (double, parameters json file) 3: hotspot-min-cov-each-strand = 4 (integer, parameters json file) 3: hotspot-min-variant-score = 6 (double, parameters json file) 3: hotspot-min-allele-freq = 0.02 (double, parameters json file) 3: hotspot-min-coverage = 100 (integer, parameters json file) 3: hotspot-strand-bias = 0.95 (double, parameters json file) 3: hotspot-strand-bias-pval = 0.01 (double, parameters json file) 3: max-flows-to-test = 10 (integer, builtin default) 3: min-delta-for-flow = 0.1 (double, builtin default) 3: prediction-precision = 1 (double, parameters json file) 3: outlier-probability = 0.005 (double, parameters json file) 3: germline-prior-strength = 0 (double, builtin default) 3: heavy-tailed = 3 (integer, parameters json file) 3: filter-unusual-predictions = 0.12 (double, parameters json file) 3: soft-clip-bias-checker = 0.1 (double, builtin default) 3: filter-deletion-predictions = 0.2 (double, parameters json file) 3: filter-insertion-predictions = 0.2 (double, parameters json file) 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 = 4 (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 = false (boolean, parameters json file) 3: resolve-clipped-bases = false (boolean, builtin default) 3: prefix-exclude = 6 3: allow-indels = true (boolean, parameters json file) 3: allow-snps = true (boolean, parameters json file) 3: allow-mnps = true (boolean, parameters json file) 3: allow-complex = false (boolean, parameters json file) 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, parameters json file) 3: read-snp-limit = 10 (integer, parameters json file) 3: read-max-mismatch-fraction = 1 (double, parameters json file) 3: max-complex-gap = 1 (integer, builtin default) 3: gen-min-alt-allele-freq = 0.01 (double, parameters json file) 3: gen-min-coverage = 6 (integer, parameters json file) 3: gen-min-indel-alt-allele-freq = 0.01 (double, parameters json file) 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 <= 1 <= 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 <= 0 <= lim. 1? OK! 3: Limit check parameter data-quality-stringency: lim. 0 <= 10? 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 <= 4? OK! 3: Limit check parameter snp-min-variant-score: lim. 0 <= 6? OK! 3: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 3: Limit check parameter snp-min-coverage: lim. 0 <= 100? 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 <= 0.01 <= lim. 1? OK! 3: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 4? OK! 3: Limit check parameter mnp-min-variant-score: lim. 0 <= 6? OK! 3: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 3: Limit check parameter mnp-min-coverage: lim. 0 <= 100? 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 <= 0.01 <= lim. 1? OK! 3: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 4? OK! 3: Limit check parameter indel-min-variant-score: lim. 0 <= 6? OK! 3: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 3: Limit check parameter indel-min-coverage: lim. 0 <= 100? OK! 3: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.9 <= 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 <= 4? OK! 3: Limit check parameter hotspot-min-variant-score: lim. 0 <= 6? OK! 3: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 3: Limit check parameter hotspot-min-coverage: lim. 0 <= 100? 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 <= 0.01 <= 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 <= 1? OK! 3: Limit check parameter outlier-probability: lim. 0 <= 0.005 <= 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 <= 0.12? 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 <= 0.2? OK! 3: Limit check parameter filter-insertion-predictions: lim. 0 <= 0.2? 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 <= 4 <= 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 <= 0.01 <= 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 <= 0.01 <= lim. 1? OK! 3: TargetsManager: Loaded targets file /build/reproducible-path/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 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 1/8 Test #1: tvc_call ......................................... Passed 0.03 sec test 4 Start 4: tvcutils_call 4: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils 4: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 4: Test timeout computed to be: 10000000 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. 4: 4: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 4: 4: Usage: tvcutils [options] 4: 4: Commands: 4: prepare_hotspots Convert BED or VCF file into a valid hotspot file 4: validate_bed Validate targets or hotspots file 4: unify_vcf Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) 4: 2/8 Test #4: tvcutils_call .................................... Passed 0.01 sec test 5 Start 5: tvcutils_prepare_hotspots_call 5: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "prepare_hotspots" 5: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 5: Test timeout computed to be: 10000000 5: 5: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 5: 5: Usage: tvcutils prepare_hotspots [options] 5: 5: General options: 5: -b,--input-bed FILE input is a hotspots BED file (either -b or -v required) 5: -v,--input-vcf FILE input is a hotspots VCF file (either -b or -v required) 5: -d,--output-bed FILE output left-aligned hotspots in BED format [none] 5: -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] 5: -r,--reference FILE FASTA file containing reference genome (required) 5: -a,--left-alignment on/off perform left-alignment of indels [off] 5: -s,--allow-block-substitutions on/off do not filter out block substitution hotspots [on] 5: -u,--unmerged-bed FILE input a target bed file to filter out hotspots that contain a junction of 2 amplicons (optional) 5: 3/8 Test #5: tvcutils_prepare_hotspots_call ................... Passed 0.01 sec test 6 Start 6: tvcutils_validate_bed_call 6: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "validate_bed" 6: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 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 validate_bed [options] 6: 6: Input selection options (must provide one): 6: --target-regions-bed FILE input is a target regions BED file (required) 6: --hotspots-bed FILE input is a hotspots BED file (required) 6: 6: General options: 6: --reference FILE FASTA file containing reference genome (required) 6: --validation-log FILE log file for user-readable warning/error messages [stdout] 6: --meta-json FILE save validation and file statistics to json file [none] 6: --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] 6: --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] 6: --merged-detail-bed FILE output an (almost) valid bedDetail merged BED [none] 6: --merged-plain-bed FILE output a valid plain merged BED [none] 6: --effective-bed FILE output a valid effective BED [none] 6: 4/8 Test #6: tvcutils_validate_bed_call ....................... Passed 0.01 sec test 7 Start 7: tvcutils_unify_vcf_call 7: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcutils "unify_vcf" 7: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 7: Test timeout computed to be: 10000000 7: Parameter novel-tvc-vcf is required and empty. 7: 7: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 7: 7: Usage: tvcutils unify_vcf [options] 7: 7: General options: 7: -t,--novel-tvc-vcf FILE small variants VCF file produced by TVC (required) 7: -i,--novel-assembly-vcf FILE long indels VCF file produced by TVCASSEMBLY (optional) 7: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) 7: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) 7: -f,--reference-fasta FILE FASTA file containing reference genome (required) 7: -b,--target-file FILE target regions BED file (optional) 7: -o,--output-vcf FILE output merged and annotated VCF or VCF.GZ file (required) 7: -j,--tvc-metrics FILE JSON file with tvc metrics (optional) 7: -d,--input-depth FILE output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok) 7: -m,--min-depth INT minimum coverage depth in GVCF output (optional) 7: 5/8 Test #7: tvcutils_unify_vcf_call .......................... Passed 0.01 sec test 8 Start 8: tvcassembly_call 8: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf/tvcassembly 8: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf 8: Test timeout computed to be: 10000000 8: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 8: 8: Usage: tvcassembly [options] 8: 8: General options: 8: -h,--help print this help message and exit 8: -v,--version print version and exit 8: -n,--num-threads INT number of worker threads [2] 8: --parameters-file FILE json file with algorithm control parameters [optional] 8: -r,--reference FILE reference fasta file [required] 8: -b,--input-bam FILE bam file with mapped reads [required] 8: -t,--target-file FILE only process targets in this bed file [optional] 8: -o,--output-vcf FILE vcf file with variant calling results [required] 8: -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] 8: --force-sample-name STRING force all read groups to have this sample name [off] 8: 8: --kmer_len INT (klen) Size of the smallest k-mer used in assembly [19]. 8: --min_var_count INT (mincount) Minimum support for a variant to be evaluated [5]. 8: --short_suffix_match INT (ssm) Minimum sequence match on both sides of the variant [5]. 8: --min_indel_size INT (mis) Minimum size indel reported by assembly [4]. 8: --max_hp_length INT (maxhp) Variants containing HP larger than this are not reported [8]. 8: --min_var_freq FLOAT (minfreq) Minimum frequency of the variant to be reported [0.15]. 8: --min_var_score FLOAT (minscore) Minimum score of the variant to be reported [10]. 8: --relative_strand_bias FLOAT (stbias) Variants with strand bias above this are not reported [0.80]. 8: --output_mnv INT (mnv) Output multi-nucleotide variants assembled in a region with multiple adjacent variants [0]. 8: 6/8 Test #8: tvcassembly_call ................................. Passed 0.01 sec 3: Loaded. 2: Loaded. 2: Recalibration model: suppressed 2: 2: 2: [tvc] Normal termination. Processing time: 2 seconds. 3: 3: 3: [tvc] Normal termination. Processing time: 2 seconds. 7/8 Test #2: tvc_test_1_thread_sse_off ........................ Passed 2.02 sec 8/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 2.08 sec 100% tests passed, 0 tests failed out of 8 Total Test time (real) = 2.10 sec make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/tvc/ cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/reproducible-path/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-arm-linux-gnueabihf' dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged 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 dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb'. dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.deb'. dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.buildinfo dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/14613 and its subdirectories I: Current time: Mon Feb 3 03:25:17 -12 2025 I: pbuilder-time-stamp: 1738596317