Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/r/reapr/reapr_1.0.18+dfsg-5_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/reapr-1.0.18+dfsg-5329dbm3a/reapr_1.0.18+dfsg-5_amd64.buildinfo Get source package info: reapr=1.0.18+dfsg-5 Source URL: http://snapshot.notset.fr/mr/package/reapr/1.0.18+dfsg-5/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=asciidoctor=2.0.10-2 autoconf=2.69-11 automake=1:1.16.1-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 bamtools=2.5.1+dfsg-5 base-files=11 base-passwd=3.5.47 bash=5.0-5 binutils=2.33.1-6 binutils-common=2.33.1-6 binutils-x86-64-linux-gnu=2.33.1-6 bsdmainutils=11.1.2+b1 bsdutils=1:2.34-0.1 build-essential=12.8 bzip2=1.0.8-2 ca-certificates=20190110 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.2.1-21 dash=0.5.10.2-6 debconf=1.5.73 debhelper=12.7.2 debianutils=4.9.1 dh-autoreconf=19 dh-strip-nondeterminism=1.6.3-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-5 fdisk=2.34-0.1 file=1:5.37-6 findutils=4.7.0-1 fontconfig=2.13.1-2+b1 fontconfig-config=2.13.1-2 fonts-dejavu-core=2.37-1 g++=4:9.2.1-3.1 g++-9=9.2.1-21 gcc=4:9.2.1-3.1 gcc-9=9.2.1-21 gcc-9-base=9.2.1-21 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.3-1 groff-base=1.22.4-4 gzip=1.9-3+b1 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-5 libarchive-zip-perl=1.67-1 libasan5=9.2.1-21 libatomic1=9.2.1-21 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-2 libaudit1=1:2.8.5-2+b1 libbambamc0=0.0.50-3 libbamtools-dev=2.5.1+dfsg-5 libbamtools2.5.1=2.5.1+dfsg-5 libbinutils=2.33.1-6 libblas3=3.9.0-1 libblkid1=2.34-0.1 libbrotli1=1.0.7-5+b1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.29-6 libc-dev-bin=2.29-6 libc6=2.29-6 libc6-dev=2.29-6 libcairo2=1.16.0-4 libcap-ng0=0.7.9-2.1+b1 libcc1-0=9.2.1-21 libcom-err2=1.45.4-1 libcroco3=0.6.13-1 libcrypt1=1:4.4.10-7 libcrypt1-dev=1:4.4.10-7 libcurl3-gnutls=7.67.0-2 libcurl4=7.67.0-2 libdatrie1=0.2.12-3 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.250 libdebhelper-perl=12.7.2 libdeflate0=1.3-3 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libexpat1=2.2.9-1 libfdisk1=2.34-0.1 libffi6=3.2.1-9 libfile-copy-link-perl=0.140-2 libfile-stripnondeterminism-perl=1.6.3-1 libfontconfig1=2.13.1-2+b1 libfreetype6=2.10.1-2 libfribidi0=1.0.8-2 libgcc-9-dev=9.2.1-21 libgcc1=1:9.2.1-21 libgcrypt20=1.8.5-3 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libgfortran5=9.2.1-21 libglib2.0-0=2.62.3-2 libgmp10=2:6.1.2+dfsg-4 libgnutls30=3.6.11.1-2 libgomp1=9.2.1-21 libgpg-error0=1.36-7 libgraphite2-3=1.3.13-11 libgssapi-krb5-2=1.17-6 libharfbuzz0b=2.6.4-1 libhogweed5=3.5.1+really3.5.1-2 libhts-dev=1.10.2-2 libhts3=1.10.2-2 libice6=2:1.0.9-2 libicu63=63.2-2 libidn2-0=2.2.0-2 libisl22=0.22-2 libitm1=9.2.1-21 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:1.5.2-2+b1 libjsoncpp1=1.7.4-3+b1 libk5crypto3=1.17-6 libkeyutils1=1.6-6 libkrb5-3=1.17-6 libkrb5support0=1.17-6 liblapack3=3.9.0-1 libldap-2.4-2=2.4.48+dfsg-1+b2 libldap-common=2.4.48+dfsg-1 liblsan0=9.2.1-21 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.37-6 libmagic1=1:5.37-6 libmount1=2.34-0.1 libmpc3=1.1.0-1 libmpfr6=4.0.2-1 libncurses6=6.1+20191019-1 libncursesw6=6.1+20191019-1 libnettle7=3.5.1+really3.5.1-2 libnghttp2-14=1.40.0-1 libp11-kit0=0.23.18.1-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpango-1.0-0=1.42.4-8 libpangocairo-1.0-0=1.42.4-8 libpangoft2-1.0-0=1.42.4-8 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre2-8-0=10.34-7 libpcre3=2:8.39-12+b1 libperl5.30=5.30.0-9 libpipeline1=1.5.1-3 libpixman-1-0=0.36.0-1 libpng16-16=1.6.37-1 libpsl5=0.20.2-2 libquadmath0=9.2.1-21 libreadline8=8.0-3 librtmp1=2.4+20151223.gitfa8646d.1-2+b1 libruby2.5=2.5.7-1 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.4.2-2 libselinux1=3.0-1 libsigsegv2=2.12-2 libsm6=2:1.2.3-1 libsmartcols1=2.34-0.1 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1d-2 libstdc++-9-dev=9.2.1-21 libstdc++6=9.2.1-21 libsub-override-perl=0.09-2 libsystemd0=244-3 libtabixpp-dev=1.1.0-1 libtabixpp0=1.1.0-1 libtasn1-6=4.15.0-2 libtcl8.6=8.6.10+dfsg-1 libthai-data=0.1.28-3 libthai0=0.1.28-3 libtiff5=4.1.0+git191117-1 libtinfo6=6.1+20191019-1 libtk8.6=8.6.10-1 libtool=2.4.6-11 libtsan0=9.2.1-21 libubsan1=9.2.1-21 libuchardet0=0.0.6-3 libudev1=244-3 libunistring2=0.9.10-2 libuuid1=2.34-0.1 libwebp6=0.6.1-2+b1 libx11-6=2:1.6.8-1 libx11-data=2:1.6.8-1 libxau6=1:1.0.8-1+b2 libxcb-render0=1.13.1-2 libxcb-shm0=1.13.1-2 libxcb1=1.13.1-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1+b2 libxft2=2.3.2-2 libxml2=2.9.4+dfsg1-8 libxrender1=1:0.9.10-1 libxss1=1:1.2.3-1 libxt6=1:1.1.5-1+b3 libyaml-0-2=0.2.2-1 libzstd1=1.4.4+dfsg-1 linux-libc-dev=5.3.15-1 login=1:4.8-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-1.2 man-db=2.9.0-2 mawk=1.3.3-17+b3 ncurses-base=6.1+20191019-1 ncurses-bin=6.1+20191019-1 openssl=1.1.1d-2 patch=2.7.6-6 perl=5.30.0-9 perl-base=5.30.0-9 perl-modules-5.30=5.30.0-9 po-debconf=1.0.21 r-base=3.6.2-2 r-base-core=3.6.2-2 r-cran-boot=1.3-24-1 r-cran-class=7.3-15-1+b1 r-cran-cluster=2.1.0-2 r-cran-codetools=0.2-16-1 r-cran-foreign=0.8.74-1 r-cran-kernsmooth=2.23-16-1+1 r-cran-lattice=0.20-38-1+b1 r-cran-mass=7.3-51.5-1 r-cran-matrix=1.2-18-1 r-cran-mgcv=1.8-31-1 r-cran-nlme=3.1.143-1 r-cran-nnet=7.3-12-2+b2 r-cran-rpart=4.1-15-2 r-cran-spatial=7.3-11-2+b2 r-cran-survival=3.1-8-1 r-recommended=3.6.2-2 rake=12.3.3-1 readline-common=8.0-3 ruby=1:2.5.2 ruby-asciidoctor=2.0.10-2 ruby-did-you-mean=1.2.1-1 ruby-minitest=5.13.0-1 ruby-net-telnet=0.1.1-2 ruby-power-assert=1.1.1-1 ruby-test-unit=3.3.4-1 ruby-xmlrpc=0.3.0-2 ruby2.5=2.5.7-1 rubygems-integration=1.15 samtools=1.10-3 sed=4.7-1 sensible-utils=0.0.12+nmu1 smalt=0.7.6-8 snpomatic=1.0-4 sysvinit-utils=2.96-1 tabix=1.10.2-2 tar=1.30+dfsg-6+b1 tzdata=2019c-3 ucf=3.0038+nmu1 unzip=6.0-25 util-linux=2.34-0.1 x11-common=1:7.7+20 xdg-utils=1.1.3-1 xz-utils=5.2.4-1+b1 zip=3.0-11+b1 zlib1g=1:1.2.11.dfsg-1+b1 zlib1g-dev=1:1.2.11.dfsg-1+b1 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20191227T155055Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d reapr=1.0.18+dfsg-5 && mkdir -p /build/reapr-kayTD4 && dpkg-source --no-check -x /*.dsc /build/reapr-kayTD4/reapr-1.0.18+dfsg && chown -R builduser:builduser /build/reapr-kayTD4" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/reapr-kayTD4/reapr-1.0.18+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1577373722" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/reapr-kayTD4 /tmp/reapr-1.0.18+dfsg-5329dbm3a bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20191227T155055Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.bQNK4r3Yh_ as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.bQNK4r3Yh_ Reading package lists... Building dependency tree... util-linux is already the newest version (2.34-0.1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20191227T155055Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20191227T155055Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (769 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4508 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.29-6) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20191227T155055Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.bQNK4r3Yh_ Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20191227T155055Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1122 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.bQNK4r3Yh_ I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d reapr=1.0.18+dfsg-5 && mkdir -p /build/reapr-kayTD4 && dpkg-source --no-check -x /*.dsc /build/reapr-kayTD4/reapr-1.0.18+dfsg && chown -R builduser:builduser /build/reapr-kayTD4"' exec /tmp/mmdebstrap.bQNK4r3Yh_ Reading package lists... NOTICE: 'reapr' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/reapr.git Please use: git clone https://salsa.debian.org/med-team/reapr.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 396 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main reapr 1.0.18+dfsg-5 (dsc) [2178 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main reapr 1.0.18+dfsg-5 (tar) [74.6 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main reapr 1.0.18+dfsg-5 (diff) [320 kB] Fetched 396 kB in 0s (1182 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'reapr_1.0.18+dfsg-5.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting reapr in /build/reapr-kayTD4/reapr-1.0.18+dfsg dpkg-source: info: unpacking reapr_1.0.18+dfsg.orig.tar.gz dpkg-source: info: unpacking reapr_1.0.18+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying use_shared_libs dpkg-source: info: applying hardening dpkg-source: info: applying fix_sort_samtools13 dpkg-source: info: applying ld_as_needed I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/reapr-kayTD4/reapr-1.0.18+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1577373722" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.bQNK4r3Yh_ dpkg-buildpackage: info: source package reapr dpkg-buildpackage: info: source version 1.0.18+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' rm -rf /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/man_src/*.html /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/man_src/*.? rm -rf /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/man rm -rf /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/test dh_auto_clean -- make[1]: Leaving directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' cd src && /usr/bin/make make[2]: Entering directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c errorWindow.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c histogram.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_score.cpp task_score.cpp: In function ‘int main(int, char**)’: task_score.cpp:235:79: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 235 | map > >::iterator p = globalGaps.find(currentRefID); | ^ g++ -o task_score -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_score.o errorWindow.o utils.o histogram.o -lbamtools -ltabixpp -lhts -lz -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c trianglePlot.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c coveragePlot.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fasta.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_stats.cpp task_stats.cpp: In function ‘int main(int, char**)’: task_stats.cpp:441:16: warning: ‘ti_perfect’ may be used uninitialized in this function [-Wmaybe-uninitialized] 441 | delete ti_perfect; | ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_stats.o trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_stats -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_break.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_break.o -lbamtools fasta.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_break -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fragCov.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fragCov.o -lbamtools coveragePlot.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2fragCov -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2insert.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2insert.o -lbamtools histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2insert -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fcdEstimate.cpp bam2fcdEstimate.cpp: In function ‘int main(int, char**)’: bam2fcdEstimate.cpp:84:34: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 84 | while (bamAlign.Position > triplot.centreCoord()) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bam2fcdEstimate.cpp: In function ‘void initialiseFCDHists(std::vector&, CmdLineOptions&)’: bam2fcdEstimate.cpp:210:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 210 | for (unsigned long i = 0; i <= ops.maxInsert; i++) | ~~^~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fcdEstimate.o -lbamtools histogram.o utils.o trianglePlot.o -ltabixpp -lhts -lz -o bam2fcdEstimate -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c make_plots.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include make_plots.o -o make_plots -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gaps.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gaps.o fasta.o -o fa2gaps -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gc.o fasta.o -o fa2gc -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c scaff2contig.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include scaff2contig.o fasta.o -o scaff2contig -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c n50.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include n50.o fasta.o -o n50 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_gapresize.cpp task_gapresize.cpp: In function ‘int main(int, char**)’: task_gapresize.cpp:129:127: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~~~~~~~~~^~~~~~~~~ task_gapresize.cpp:129:148: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_gapresize.o -lbamtools utils.o trianglePlot.o fasta.o -ltabixpp -lhts -lz -o task_gapresize -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_fcdrate.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_fcdrate.o -ltabixpp -lhts -lz histogram.o utils.o -lbamtools -o task_fcdrate -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2perfect.cpp bam2perfect.cpp: In function ‘void writeAlignments(std::multimap&, BamTools::BamWriter&, long unsigned int)’: bam2perfect.cpp:213:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 213 | if (p->second.Position >= endPos) break; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reapr-kayTD4/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2perfect.o -lbamtools utils.o -lbamtools -ltabixpp -lhts -lz -o bam2perfect -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg/src' make[1]: Leaving directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' mkdir /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/test ln -s /build/reapr-kayTD4/reapr-1.0.18+dfsg/src/reapr.pl /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/test/reapr PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin:/build/reapr-kayTD4/reapr-1.0.18+dfsg/src:/build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/test /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/tests/test-example [wgsim] seed = 42 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 1 sequences, total length: 1000111 foo 1384 T K + foo 4961 T W + foo 5885 - T - foo 9598 A C - foo 10177 G R + foo 11305 G K + foo 11592 G R + foo 13931 T - - foo 15907 C A - foo 17264 G K + foo 17780 A - - foo 18711 A W + foo 19249 T W + foo 19522 C S + foo 23053 T K + foo 23681 A R + foo 23730 C S + foo 24075 G S + foo 24555 G C - foo 26775 G K + foo 26896 C M + foo 27253 G K + foo 28210 T Y + foo 28224 A W + foo 28377 - G + foo 29035 G K + foo 29898 C M + foo 30274 A R + foo 30542 G K + foo 31566 A C - foo 32252 - A - foo 33303 T K + foo 33390 - G + foo 34073 A R + foo 34171 G R + foo 34718 T Y + foo 34801 - C + foo 35204 T W + foo 35342 G S + foo 35489 G T - foo 36153 A M + foo 36273 C S + foo 37356 G T - foo 37596 C S + foo 39308 T - - foo 40333 C G - foo 42295 T K + foo 42372 T Y + foo 44433 C G - foo 44630 - AG + foo 44902 T C - foo 47156 C A - foo 48210 C M + foo 48390 A R + foo 49652 C M + foo 52739 T Y + foo 52858 A M + foo 54737 A G - foo 55306 C T - foo 55434 C T - foo 59204 A W + foo 59300 G C - foo 59335 T Y + foo 59444 T - - foo 59531 C S + foo 59766 C Y + foo 61950 C S + foo 62887 G S + foo 63390 A G - foo 64365 G K + foo 64703 C S + foo 64932 C Y + foo 68383 - CG + foo 68464 A W + foo 68727 A W + foo 69080 A M + foo 72071 T C - foo 72720 - G - foo 73354 C T - foo 73637 G T - foo 74741 A M + foo 75101 C T - foo 75207 T K + foo 76400 T Y + foo 76780 A C - foo 77172 A W + foo 78385 C Y + foo 80705 C M + foo 82440 A R + foo 83021 G K + foo 83116 A - - foo 83846 T K + foo 84633 G S + foo 85891 G S + foo 87759 A C - foo 87778 T W + foo 88581 T K + foo 88606 T Y + foo 88880 A G - foo 89945 G C - foo 90728 T K + foo 91798 G R + foo 95957 G C - foo 96173 T W + foo 96665 A M + foo 98019 - G + foo 98131 A M + foo 98669 A R + foo 98719 G T - foo 99062 A W + foo 99590 A T - foo 100532 - TC + foo 103015 A W + foo 103172 G S + foo 103609 G R + foo 106549 T Y + foo 108808 C Y + foo 109191 G C - foo 111686 C G - foo 113436 C A - foo 113763 A W + foo 115671 C T - foo 117460 - A - foo 118193 G - - foo 118585 T K + foo 121219 A M + foo 121876 T K + foo 122071 T A - foo 124918 C G - foo 125300 G S + foo 125967 C S + foo 127443 G S + foo 127565 C Y + foo 128700 C A - foo 129912 G A - foo 130847 T W + foo 131677 G S + foo 132189 T C - foo 135878 CGGC - - foo 136825 T K + foo 138881 TGT - - foo 139288 A W + foo 141054 A W + foo 141055 - T + foo 141101 C S + foo 141404 A R + foo 142698 T C - foo 143990 C A - foo 144167 T Y + foo 144814 C Y + foo 146381 T Y + foo 146393 C A - foo 146510 A C - foo 147182 A W + foo 148783 T C - foo 149068 G S + foo 150208 T K + foo 151554 T W + foo 151709 C G - foo 153072 G R + foo 153307 T Y + foo 154050 G S + foo 154415 C S + foo 154594 G R + foo 155839 G T - foo 156106 G A - foo 159356 T W + foo 159926 A W + foo 160303 T K + foo 161323 C Y + foo 161904 G S + foo 162533 - ACC - foo 164738 C G - foo 165413 A R + foo 166944 C M + foo 167464 T Y + foo 168420 T C - foo 168579 A M + foo 168787 T W + foo 168959 A T - foo 169884 G S + foo 170032 G T - foo 172058 G K + foo 174942 A R + foo 175014 G K + foo 178406 G A - foo 179028 - A + foo 182394 C M + foo 182735 T Y + foo 183384 T K + foo 183893 - AT - foo 185360 G A - foo 185538 - G - foo 187948 G S + foo 188120 T G - foo 188179 T W + foo 188316 T Y + foo 189963 - G + foo 190093 C Y + foo 192220 C M + foo 192368 A W + foo 192782 T K + foo 193307 A R + foo 193501 G K + foo 194276 G S + foo 194930 C S + foo 196728 A W + foo 197559 G C - foo 198467 T W + foo 199042 C Y + foo 199259 AA - - foo 199687 TT - - foo 200287 C A - foo 200678 A R + foo 201208 C T - foo 201882 A - - foo 204456 T K + foo 206327 G R + foo 207311 G T - foo 209184 G A - foo 209279 C Y + foo 211459 C Y + foo 213807 T Y + foo 213846 T Y + foo 214635 A G - foo 214884 C A - foo 216244 A M + foo 216652 A M + foo 216745 T - - foo 216909 A T - foo 217579 A G - foo 217895 C Y + foo 218870 G K + foo 223098 T A - foo 223283 - C + foo 223666 C A - foo 224011 - C + foo 225681 C S + foo 227345 T C - foo 228778 T G - foo 229926 C - - foo 230778 T K + foo 230939 CG - - foo 231988 CT - - foo 234593 T W + foo 235496 C S + foo 235705 G K + foo 235758 A G - foo 236852 T C - foo 238790 A M + foo 238865 T K + foo 239329 A M + foo 239576 - C + foo 243058 G S + foo 244147 T - - foo 244462 C G - foo 245443 - A + foo 246544 C Y + foo 246744 T W + foo 247473 C M + foo 248129 C T - foo 249060 A C - foo 249515 G T - foo 250138 G S + foo 250567 C A - foo 254381 G R + foo 257864 C M + foo 257879 C Y + foo 259859 A M + foo 260643 C S + foo 261681 C G - foo 262645 T Y + foo 263279 A R + foo 263575 A - - foo 264587 - TA + foo 264689 T K + foo 265758 G K + foo 266272 A M + foo 268550 C M + foo 269986 G S + foo 270321 AC - - foo 273346 C S + foo 275367 C A - foo 277334 C G - foo 277629 G T - foo 278431 C Y + foo 281456 T Y + foo 281556 T G - foo 281737 G K + foo 282290 AC - - foo 282851 - C - foo 284405 A C - foo 288751 A C - foo 290501 TAAA - - foo 291315 A W + foo 291368 C - - foo 292154 A C - foo 292385 C M + foo 292555 G K + foo 297709 G C - foo 298183 A W + foo 298228 T W + foo 299902 T G - foo 302575 A T - foo 304823 G R + foo 305308 T Y + foo 305487 G S + foo 305697 G T - foo 306098 C G - foo 306882 T Y + foo 308201 A M + foo 308833 A T - foo 312033 A - - foo 312895 C G - foo 313889 C - - foo 315109 A R + foo 316083 C - - foo 316466 A R + foo 318040 G C - foo 319446 T C - foo 320236 C S + foo 320652 A - - foo 320716 T K + foo 323644 A - - foo 325359 G T - foo 329476 - CA + foo 329706 T G - foo 330181 T Y + foo 330703 C Y + foo 331315 G S + foo 332351 C A - foo 333408 A R + foo 333468 C S + foo 336247 A G - foo 336586 A M + foo 337364 G K + foo 337686 A T - foo 338043 A - - foo 338292 C G - foo 338962 A C - foo 339353 G K + foo 340647 - A + foo 341705 G R + foo 344283 C M + foo 345898 - AG - foo 347959 T - - foo 349162 C M + foo 352072 T Y + foo 354614 C Y + foo 359304 T - - foo 359312 - G + foo 360972 C S + foo 363857 C Y + foo 366226 A C - foo 367259 C M + foo 372502 T Y + foo 372747 A M + foo 375140 C S + foo 376298 T W + foo 376313 C - - foo 376760 T W + foo 378494 A W + foo 381137 T G - foo 381186 A R + foo 381701 A G - foo 382614 A W + foo 382761 C T - foo 382854 T C - foo 383201 C T - foo 385104 G S + foo 385233 - A + foo 386138 C T - foo 386316 A W + foo 387072 A R + foo 387642 - A + foo 388232 T C - foo 388890 GGG - - foo 390508 C S + foo 390625 C M + foo 391921 C G - foo 395256 G T - foo 395542 G S + foo 397015 A - - foo 397516 C Y + foo 397528 GC - - foo 398152 C T - foo 399802 A W + foo 400972 T K + foo 401419 - T + foo 401477 T W + foo 402437 A M + foo 402722 G R + foo 403452 C M + foo 404234 - A + foo 405344 A W + foo 407040 G S + foo 408483 G R + foo 408586 A C - foo 408721 A R + foo 409494 A M + foo 410078 A G - foo 411170 C A - foo 415342 T Y + foo 416265 C G - foo 417740 C A - foo 418622 C S + foo 420232 A W + foo 420288 T Y + foo 420908 A W + foo 421109 T A - foo 421357 A R + foo 422799 G A - foo 424383 C S + foo 424871 - GCA + foo 427273 T A - foo 429822 C M + foo 429846 T W + foo 432015 A G - foo 432414 G K + foo 433606 C Y + foo 433831 T Y + foo 437721 - A - foo 438402 G - - foo 438799 A T - foo 439422 C M + foo 440734 C A - foo 441840 T G - foo 442021 - C + foo 445021 T A - foo 445591 G A - foo 446138 T W + foo 447757 A W + foo 449156 T - - foo 449161 G K + foo 450114 A W + foo 450688 A W + foo 454421 C G - foo 454718 T Y + foo 455675 TC - - foo 461721 G R + foo 462526 G S + foo 467296 G A - foo 467510 G K + foo 468267 T K + foo 469118 G R + foo 469830 C Y + foo 471073 G T - foo 472056 G A - foo 472773 - A + foo 473046 G R + foo 473188 G A - foo 473742 C - - foo 474789 T A - foo 477763 G R + foo 478246 T W + foo 478975 T G - foo 479038 A R + foo 480275 T Y + foo 480317 G A - foo 481512 T K + foo 482069 G S + foo 482534 A R + foo 483760 C Y + foo 485281 T W + foo 486255 T C - foo 487038 T K + foo 487225 T A - foo 488012 C Y + foo 488795 T C - foo 490241 A R + foo 492595 - CGG + foo 493224 C A - foo 494284 A T - foo 495990 - T - foo 497306 A R + foo 497403 T Y + foo 499569 C Y + foo 499651 T K + foo 503139 T C - foo 504660 A R + foo 508679 C - - foo 513643 G K + foo 515668 CC - - foo 515836 G R + foo 516488 C S + foo 517602 G R + foo 517962 G K + foo 517975 T K + foo 519144 A T - foo 520068 T K + foo 520926 A W + foo 521562 C S + foo 522076 CG - - foo 522838 T Y + foo 523513 - C + foo 523907 - TA + foo 526271 T A - foo 526533 AC - - foo 526767 C Y + foo 528217 C Y + foo 531924 G S + foo 532333 - TT + foo 533132 C M + foo 534689 A T - foo 534779 A W + foo 535594 C A - foo 535795 G R + foo 538368 A R + foo 540879 G K + foo 542530 A - - foo 543620 G R + foo 544733 - C - foo 546300 - TT + foo 548196 A T - foo 548878 C M + foo 548885 G R + foo 549459 T K + foo 550908 A G - foo 551170 A - - foo 553130 T Y + foo 555293 T G - foo 556198 G R + foo 556355 A T - foo 557688 G K + foo 558415 G C - foo 558461 - G + foo 559287 T Y + foo 559465 C M + foo 560184 T W + foo 560252 T W + foo 562579 A M + foo 562961 G A - foo 566986 C A - foo 568134 C A - foo 569698 T C - foo 570180 T K + foo 570451 TG - - foo 570832 - A - foo 571589 A W + foo 572208 C M + foo 572871 C S + foo 574334 G - - foo 575673 T Y + foo 576797 G S + foo 578486 - C - foo 578494 C S + foo 579257 G A - foo 580103 G T - foo 580872 A W + foo 580925 G S + foo 580950 G C - foo 581637 T Y + foo 581654 A G - foo 582538 A T - foo 582691 C M + foo 582938 A W + foo 583104 T K + foo 584763 T W + foo 585723 T W + foo 588253 T Y + foo 588972 T C - foo 589438 - C - foo 591131 C Y + foo 591950 G R + foo 592194 T G - foo 592310 G S + foo 593892 G A - foo 598556 A - - foo 601660 G S + foo 602112 G T - foo 602412 T Y + foo 607282 - C + foo 607394 A M + foo 608438 A T - foo 609255 A W + foo 609365 - T + foo 611161 G K + foo 612224 C G - foo 614493 G R + foo 614601 G A - foo 614607 C Y + foo 619507 C M + foo 619798 T C - foo 621872 C T - foo 622375 C Y + foo 623208 - G - foo 624366 C A - foo 625320 - ACA - foo 626664 - G + foo 627140 T C - foo 627353 G T - foo 628714 T Y + foo 628744 A - - foo 629152 A G - foo 630110 T G - foo 631744 G K + foo 632763 C S + foo 634419 G - - foo 634459 A G - foo 634571 G A - foo 635366 - A + foo 635604 G T - foo 637057 T C - foo 637525 A T - foo 638412 A R + foo 640547 A W + foo 641514 T K + foo 642219 A R + foo 642427 A G - foo 642612 A R + foo 643553 T W + foo 647316 - T + foo 647598 C - - foo 651093 G A - foo 651718 G R + foo 652235 A G - foo 652579 A C - foo 653355 A W + foo 655174 C M + foo 655487 A M + foo 656849 G S + foo 661081 T K + foo 661134 G C - foo 661935 A W + foo 662010 A M + foo 662040 G R + foo 663030 A W + foo 663268 - C + foo 664991 T - - foo 665489 T K + foo 665555 C M + foo 665965 C Y + foo 668725 A C - foo 668834 - G - foo 668873 C S + foo 669654 T W + foo 671041 G S + foo 671485 T W + foo 671690 C M + foo 673022 G R + foo 674137 - T + foo 674782 A C - foo 676373 G T - foo 676793 T C - foo 677409 G S + foo 677536 - AA - foo 677620 G K + foo 677686 C Y + foo 678327 G S + foo 678704 G S + foo 678771 A C - foo 678866 C T - foo 679960 A W + foo 680447 - C + foo 682102 C T - foo 685497 T A - foo 686884 G S + foo 687324 ACA - - foo 687684 - AC + foo 687823 T C - foo 688590 G K + foo 690802 C M + foo 691388 T C - foo 691403 T G - foo 691790 G A - foo 692973 C A - foo 694058 G S + foo 694550 G R + foo 694968 T W + foo 695898 A T - foo 696721 C S + foo 696787 C S + foo 696935 A M + foo 698024 - C + foo 699813 A - - foo 700179 G R + foo 701421 A M + foo 701989 T A - foo 702862 C A - foo 707020 G A - foo 708420 A - - foo 708669 C G - foo 710521 T W + foo 711801 G C - foo 711913 T G - foo 715830 C M + foo 717664 TC - - foo 718845 A W + foo 719069 T Y + foo 719565 A W + foo 721136 T K + foo 726116 T K + foo 727809 T K + foo 728864 G K + foo 728918 G A - foo 730296 - T + foo 731988 C Y + foo 734658 A M + foo 734715 A W + foo 736618 C G - foo 737257 T Y + foo 740864 C A - foo 741640 G - - foo 741859 - TA - foo 742011 T K + foo 742237 A R + foo 742960 G K + foo 743731 G R + foo 743971 A W + foo 744635 T K + foo 746430 C G - foo 746489 - GC - foo 746881 C M + foo 756997 TC - - foo 757776 A M + foo 759870 A T - foo 760224 G K + foo 760799 G C - foo 761692 T C - foo 762569 G S + foo 763140 A G - foo 763842 - T - foo 764192 A M + foo 764334 G A - foo 764889 - AAT + foo 766464 G S + foo 768226 G A - foo 770272 T G - foo 771145 C Y + foo 772209 T A - foo 773672 T K + foo 773932 G C - foo 774658 C S + foo 775969 A M + foo 776816 T G - foo 777591 C Y + foo 777891 A M + foo 778164 C M + foo 778219 T W + foo 779260 G T - foo 779465 A W + foo 779779 G S + foo 780033 G K + foo 783243 C M + foo 783860 A R + foo 788345 A M + foo 789554 G - - foo 790025 G K + foo 791454 T K + foo 792009 C A - foo 792872 C G - foo 794616 T W + foo 795031 G R + foo 796919 C M + foo 797020 G S + foo 797042 G C - foo 797149 G A - foo 797177 A C - foo 799076 G C - foo 799580 G S + foo 800356 A R + foo 802297 G T - foo 802309 T Y + foo 802343 - C + foo 802769 A W + foo 803104 C G - foo 805819 C Y + foo 805972 T Y + foo 807503 T K + foo 807950 C M + foo 807994 - A - foo 809167 A G - foo 809658 A W + foo 810152 A M + foo 811506 G R + foo 813494 A M + foo 814035 G T - foo 814476 A W + foo 819399 T K + foo 820171 T W + foo 820445 G C - foo 822178 C G - foo 822504 C T - foo 823378 C M + foo 823591 CG - - foo 824229 C M + foo 824579 C T - foo 824858 C M + foo 826101 T K + foo 827593 C G - foo 827794 T Y + foo 828228 A M + foo 828367 T K + foo 828788 C M + foo 829002 C Y + foo 830345 C M + foo 831018 C A - foo 831459 T K + foo 832413 A T - foo 832782 T Y + foo 832908 T Y + foo 833130 T - - foo 833142 G S + foo 833241 G A - foo 836727 A T - foo 836829 G S + foo 838452 T G - foo 838543 A T - foo 838605 C M + foo 838954 G C - foo 841829 G K + foo 842324 - TC + foo 842996 - C + foo 844390 C A - foo 844793 A C - foo 844925 C A - foo 845082 G C - foo 846202 G R + foo 846707 A G - foo 848713 G A - foo 849372 C S + foo 849742 G A - foo 850499 C - - foo 850927 GT - - foo 851084 - G + foo 852247 A R + foo 852972 C A - foo 854808 T W + foo 855956 G K + foo 856225 G A - foo 856582 T K + foo 857351 C M + foo 857504 AC - - foo 858324 A T - foo 858858 T C - foo 859488 T Y + foo 862441 T Y + foo 863827 C Y + foo 864165 C A - foo 865997 C M + foo 866370 G S + foo 867653 G S + foo 867722 C Y + foo 868696 C M + foo 869005 T W + foo 869791 T Y + foo 875339 C Y + foo 875347 C M + foo 875584 T G - foo 876780 C T - foo 878368 A C - foo 878916 - CAG + foo 879005 A R + foo 880112 G T - foo 881021 - T - foo 881175 T W + foo 882168 - GGG + foo 882223 - G - foo 883033 TG - - foo 883381 C G - foo 884378 C - - foo 885075 A M + foo 885190 A W + foo 885568 A W + foo 885827 T Y + foo 887610 TG - - foo 889139 G R + foo 890978 T - - foo 891500 C Y + foo 892257 G C - foo 892642 G R + foo 892644 T W + foo 892757 C A - foo 893222 T - - foo 893348 T W + foo 894161 - C - foo 894447 A G - foo 894614 A W + foo 897817 T W + foo 899408 C S + foo 902450 A T - foo 902970 AT - - foo 905836 G K + foo 906524 GA - - foo 907484 A W + foo 907537 C M + foo 908515 G R + foo 908642 C T - foo 911145 T C - foo 912220 T Y + foo 912682 C Y + foo 914260 C S + foo 914757 T Y + foo 916413 G C - foo 916783 T G - foo 917033 G C - foo 917218 A - - foo 918225 G - - foo 918459 A - - foo 918732 A M + foo 919640 TC - - foo 920824 T W + foo 920836 G C - foo 924560 G R + foo 924659 GA - - foo 925868 T A - foo 928254 T G - foo 928369 - A - foo 928641 - AG + foo 929857 C M + foo 930211 T W + foo 930935 C T - foo 931986 A M + foo 932852 G T - foo 933965 T A - foo 935564 A W + foo 936034 T Y + foo 936221 AC - - foo 936670 C S + foo 936704 T A - foo 936786 T W + foo 939218 C S + foo 939312 A W + foo 939467 A W + foo 939934 C S + foo 941603 C Y + foo 942910 A W + foo 944654 T Y + foo 945301 A C - foo 945770 C T - foo 946078 G S + foo 948833 G K + foo 948999 A W + foo 949193 A R + foo 950276 C M + foo 950414 A W + foo 951285 G C - foo 953158 G R + foo 953287 A W + foo 954150 C G - foo 954258 G - - foo 955396 CC - - foo 956490 - AC + foo 958129 A R + foo 959027 T A - foo 959964 A W + foo 962042 A G - foo 962742 C G - foo 963306 T W + foo 963422 G K + foo 964082 G S + foo 965561 C S + foo 966531 T K + foo 967324 T W + foo 968419 - C - foo 969054 G - - foo 969158 G S + foo 972658 C M + foo 974266 T W + foo 974629 G K + foo 975034 A R + foo 975636 T W + foo 977078 - A - foo 978321 G T - foo 978595 C G - foo 979090 C M + foo 983855 TA - - foo 985725 T A - foo 988497 C Y + foo 990171 C M + foo 990804 - CA - foo 990941 T W + foo 991797 A W + foo 992469 A M + foo 994610 C Y + foo 998107 - T + foo 999725 G R + [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.972415.smaltmap.smalt_index foo1.fasta # Command line: smalt index -k 13 -s 2 out.bam.tmp.972415.smaltmap.smalt_index foo1.fasta # Reading sequences ... # Writing sequence set ... # Setting up hash index with collisions ... # word length = 13 bases, skip step = 2 bases ... # number of bits for key = 18 with 0 perfect bits # Counting keys ... # Counting k-tuples ... # Allocating k-tuple arrays ... # Counting k-tuple occurrences ... # Setting the k-tuple positions in index ... # Hash table is set up. # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Writing table to file ... # smalt: Total elapsed wall clock time: 1 seconds [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.972415.smaltmap.smalt_sample out.bam.tmp.972415.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Command line: smalt sample -u 1000 -o out.bam.tmp.972415.smaltmap.smalt_sample out.bam.tmp.972415.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Opening read files ... # Reading reference sequences ... # Reading hash table ... # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Check of read pairs ok ... # Mate names match ... # Sampling insert size distribution ... # Processed 9999 read pairs. # smalt: Time spent setting up hash index:0 seconds # smalt: Time spent mapping reads:3 seconds # smalt: Total elapsed wall clock time: 3 seconds [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.972415.smaltmap.smalt_sample -f samsoft out.bam.tmp.972415.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.972415.smaltmap.raw.bam # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.972415.smaltmap.smalt_sample -f samsoft out.bam.tmp.972415.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Reading distribution of insert sizes from file ... # Sampled histogram # Smoothed histogram # Opening read files ... # Reading reference sequences ... # Reading hash table ... # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Processing query reads ... # Processed 10000 read pairs. # smalt: Time spent setting up hash index:0 seconds # smalt: Time spent mapping reads:25 seconds # smalt: Total elapsed wall clock time: 25 seconds [REAPR smaltmap] Running: samtools sort out.bam.tmp.972415.smaltmap.raw.bam -O bam -o out.bam.tmp.972415.smaltmap.raw.bam.sort.bam [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.972415.smaltmap.raw.bam.sort.bam out.bam.tmp.972415.smaltmap.rmdup.bam [bam_rmdup_core] processing reference foo... [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' [REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.972415.smaltmap.header [REAPR smaltmap] Running: samtools view -H out.bam.tmp.972415.smaltmap.rmdup.bam >> out.bam.tmp.972415.smaltmap.header [REAPR smaltmap] Running: samtools reheader out.bam.tmp.972415.smaltmap.header out.bam.tmp.972415.smaltmap.rmdup.bam > out.bam [REAPR smaltmap] Running: samtools index out.bam [REAPR smaltmap] Running: rm out.bam.tmp.972415.smaltmap.* Running reapr version 1.0.18 pipeline: reapr foo1.fasta out.bam result [REAPR pipeline] Running facheck [REAPR pipeline] Running preprocess [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases [REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases [REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases [REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339 bases [REAPR preprocess] Sampled 996854 bases for GC/coverage estimation [REAPR pipeline] Running stats [REAPR pipeline] Running fcdrate [REAPR pipeline] Running score [REAPR pipeline] Running break [REAPR pipeline] Running summary rm -rf /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/test make[1]: Leaving directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' mkdir -p debian/reapr/usr/lib/reapr install src/reapr.pl debian/reapr/usr/lib/reapr/reapr.pl chmod -x src/*.cpp find src -executable -exec install {} debian/reapr/usr/lib/reapr \; install: omitting directory 'src' dh_auto_install -- make[1]: Leaving directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' for pl in `grep -Rl '#!/usr/bin/env' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' mkdir -p /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/man_src/*.adoc cp /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/man_src/*.? /build/reapr-kayTD4/reapr-1.0.18+dfsg/debian/man dh_installman -- make[1]: Leaving directory '/build/reapr-kayTD4/reapr-1.0.18+dfsg' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'reapr-dbgsym' in '../reapr-dbgsym_1.0.18+dfsg-5_amd64.deb'. dpkg-deb: building package 'reapr' in '../reapr_1.0.18+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../reapr_1.0.18+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/reapr-kayTD4 /tmp/reapr-1.0.18+dfsg-5329dbm3a I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.bQNK4r3Yh_... I: success in 613.0274 seconds md5: reapr-dbgsym_1.0.18+dfsg-5_amd64.deb: OK md5: reapr_1.0.18+dfsg-5_amd64.deb: OK sha1: reapr-dbgsym_1.0.18+dfsg-5_amd64.deb: OK sha1: reapr_1.0.18+dfsg-5_amd64.deb: OK sha256: reapr-dbgsym_1.0.18+dfsg-5_amd64.deb: OK sha256: reapr_1.0.18+dfsg-5_amd64.deb: OK Checksums: OK